+ 255 23.2 1.2 6.8 chr15_MATERNAL_p_2-50000:. 1 88 (49911) C LTR60B LTR/ERV1 (419) 346 264 1
ANNOTATION EVIDENCE:
255 23.17 1.21 6.82 chr15_MATERNAL_p_2-50000:. 1 88 44800 C LTR60B LTR/ERV1 264 346 419
255 23.17 1.21 6.82 chr15_MATERNAL_p_2-50000:. 1 88 (44800) C LTR60B#LTR/ERV1 (419) 346 264 m_b1s502i0
chr15_MATERNA 1 ACCGTCACCCTAACCCAGGCAGGCTG-ACAGCGGTCAAGTTTCTGCCTAC 49
i ----- v ii - i i i v i i i
C LTR60B#LTR/ER 346 ACCGCCAC-----CCCAGGAAGGTCGTATAGCGGTCAAATCTGTACTTAT 302
chr15_MATERNA 50 AGCGCCTGCCTATCTCTTTTGAATGTCCTTCTCTACCCT 88
v v vv - i i i i
C LTR60B#LTR/ER 301 TGCGCCTGCGTATCTCTTAGGAAT-TTCTCCTTTGCCCT 264
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 26.92
Transitions / transversions = 2.17 (13/6)
Gap_init rate = 0.08 (7 / 87), avg. gap size = 1.00 (7 / 7)
+ 703 15.8 5.2 7.0 chr15_MATERNAL_p_2-50000:. 91 247 (49752) C LTR60B LTR/ERV1 (453) 312 159 1
ANNOTATION EVIDENCE:
703 15.75 5.20 7.01 chr15_MATERNAL_p_2-50000:. 91 247 44641 C LTR60B LTR/ERV1 159 312 453
703 15.75 5.20 7.01 chr15_MATERNAL_p_2-50000:. 91 247 (44641) C LTR60B#LTR/ERV1 (453) 312 159 m_b1s502i1
chr15_MATERNA 91 TCTGTACTTATGGTGCCAG-GTTTCTCTTAAGAATGTCCCCTTTG----- 134
v i v - v i v i -----
C LTR60B#LTR/ER 312 TCTGTACTTATTGCGCCTGCGTATCTCTTAGGAATTTCTCCTTTGCCCTC 263
chr15_MATERNA 135 --TCCTTCTTATCAGCATGTAGCCAGCAATATTGTGACATTTTTACTGCA 182
-- i i v i v vv v
C LTR60B#LTR/ER 262 TTTCCTCCTTATCAGCATGTAGCTAGCTACATTCTGACAGGTTAACTGCA 213
chr15_MATERNA 183 GAGTGAATGATGACTGGGGCATCTTAAATGGAGTTCTGGGGTGTTTCTTT 232
ii v - i ---------- i i
C LTR60B#LTR/ER 212 GAGTGAGCGATTACT-GGGCGTCTTAA----------GGGGCGTTCCTTT 174
chr15_MATERNA 233 CTGCATAGGTACCTC 247
ii
C LTR60B#LTR/ER 173 CTGCATAGGTATTTC 159
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 14.67
Transitions / transversions = 1.30 (13/10)
Gap_init rate = 0.09 (14 / 156), avg. gap size = 1.36 (19 / 14)
+ 1849 18.8 8.0 5.5 chr15_MATERNAL_p_2-50000:. 254 765 (49234) + MER31-int LTR/ERV1 1702 2227 (2705) 2
ANNOTATION EVIDENCE:
1849 18.80 7.98 5.47 chr15_MATERNAL_p_2-50000:. 254 765 44123 + MER31-int LTR/ERV1 1702 2227 2705
1849 18.80 7.98 5.47 chr15_MATERNAL_p_2-50000:. 254 765 (44123) MER31-int#LTR/ERV1 1702 2227 (2705) m_b1s701i0
chr15_MATERNA 254 AGTAGTTTCCAAAATACTTTTGGTAATTTTTAACCTTAAAGTTAACCTTA 303
i ---i? i v? i vv --
MER31-int#LTR 1702 AATAGTTTCCAAA---TNTTTGGTAACTTGNAACCTTAGAGTTATGCT-- 1746
chr15_MATERNA 304 AAGTTAAGCTAAGTAAAAGATTTGCATTAAATATCTAGACCATTTATAAA 353
ii v v v i v i
MER31-int#LTR 1747 AAGTTAAATTAAGTAATAGATATTCATTAAATATCTAGATCATTTCTAAG 1796
chr15_MATERNA 354 TAAGATACAATACTAAAACATTACTGAAGATAAATAATTCAAGTTTACAT 403
v v i i iv? i --- i i
MER31-int#LTR 1797 TAAGATAAACTACTGAAACATTACTAAGCNTAAGT---TTAAGTTTATAT 1843
chr15_MATERNA 404 ACTTTTGGCTACTTATTTTTA-------CAGAGAAACTAAAG-ATATTTT 445
? v ------- ii i- v
MER31-int#LTR 1844 ACTTTTGGNTTCTTATTTTTATATGGTACAGAGAGGCTAAAATATATTTG 1893
chr15_MATERNA 446 AGCCCATTAATAAACATGTTTTTGTCTACCACACTGTGAAATTGTACTAT 495
i i ii -------------- ----i
MER31-int#LTR 1894 GGTCTGTTAATAAACATG--------------A----AAAATTGTACTAT 1925
chr15_MATERNA 496 GAGGA--AACACATCCCTCTAGATGTTGGGAGATGGTATACTCATACA-T 542
i -- i i v ? i vi v i v -
MER31-int#LTR 1926 GAGAAGCAGCATATGCCTNTAAAAATTGTGAGATGGTATATTCATAAAAT 1975
chr15_MATERNA 543 TTTCTAACCTAC---TATAGAATGCTAACATATGACAG----TTTATAAC 585
v ii i --- i iii i ---- i i i
MER31-int#LTR 1976 TTGCTAGTCTGCGCGTACAGAATGCTGGTATGTGACAGACAGTTCACAAT 2025
chr15_MATERNA 586 TGTCTACTTCCTAGTTTTCT-CTGGAAAATAAAAGATTACTAAGTATTAA 634
- v -i i vvi
MER31-int#LTR 2026 TGTCTACTTCCTAGTTTTCTTCTGTAAAA-GAAAGGTTACTAATGGTTAA 2074
chr15_MATERNA 635 AA----TTAT-----AATCAATATGTGTAAATAAAACTACTGGAAATAAT 675
---- -----? i ? i
MER31-int#LTR 2075 AAANTATTATCNANNNATCAATATATGTAANTAAAACTACTAGAAATAAT 2124
chr15_MATERNA 676 A-GAATAACTAGAAACAACTCT--ATGCAAAGCATGCAAGAAAAGTAGTG 722
- i? i v-i i -- i i v?
MER31-int#LTR 2125 AAGGNTGAG-GGAAACAACTTTGTATGCAAAGTATGCAAGGAAAGTAGGN 2173
chr15_MATERNA 723 CATGTTTT-------GCAAGTAAAGTA----GGACGTATTTTTTATAAGG 761
ii ------- ? vi ---- i i ivv
MER31-int#LTR 2174 TGTGTTTTTAATAAAGNATATAAAGTATGAAGGATGTGTTTTCGTTAAGG 2223
chr15_MATERNA 762 AAAA 765
MER31-int#LTR 2224 AAAA 2227
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 19.58
Transitions / transversions = 2.24 (56/25)
Gap_init rate = 0.08 (41 / 511), avg. gap size = 1.71 (70 / 41)
+ 3119 19.6 4.5 6.9 chr15_MATERNAL_p_2-50000:. 780 949 (49050) + MER31-int LTR/ERV1 2935 3110 (1822) 2
ANNOTATION EVIDENCE:
3119 19.60 4.55 6.91 chr15_MATERNAL_p_2-50000:. 780 949 44242 + MER31-int LTR/ERV1 2935 3110 1822
3119 19.60 4.55 6.91 chr15_MATERNAL_p_2-50000:. 780 949 (44242) MER31-int#LTR/ERV1 2935 3110 (1822) m_b1s701i1
chr15_MATERNA 780 CAAATAAAAAGAGATACCTAGCCTTCCCTGTGTTATATTTGTATGGGTAA 829
i v i i i ii v ?
MER31-int#LTR 2935 CAAATAAGAAGTGATGCTTAACCTTCTTTGAGTTATATTTGTATGGGTAN 2984
chr15_MATERNA 830 AATGTCAT--------GT-TTTCAGAAATTATATAAAATTCCTGGAAATT 870
?- i -------- - i i i i
MER31-int#LTR 2985 N-TGTTATTAATATAAGTGTTCCAGAAATTGTATGAAATTCCTAGAAATT 3033
chr15_MATERNA 871 TGTCAATGTTCTCCTTATCCATGCTATGTGCCAGTATA--GA-GTTATGA 917
?i v? ? ? v - i --? - v
MER31-int#LTR 3034 TGTCAATGNCCTCGNTNTNCATGATATGT-CCGGTATAATNATGTTATCA 3082
chr15_MATERNA 918 GTCATAATTCCAATTATTATTTTAAATGTTGT 949
ii ? ----i
MER31-int#LTR 3083 GTCATAATTCCGGTTATTATNTTAAA----AT 3110
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 20.80
Transitions / transversions = 3.20 (16/5)
Gap_init rate = 0.06 (10 / 169), avg. gap size = 1.80 (18 / 10)
+ 2213 9.3 0.0 0.0 chr15_MATERNAL_p_2-50000:. 950 1254 (48745) + AluY SINE/Alu 2 311 (0) 3
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 chr15_MATERNAL_p_2-50000:. 1230 1254 48745 + (TAAA)n Simple_repeat 1 25 0
26 0.00 0.00 0.00 chr15_MATERNAL_p_2-50000:. 1230 1254 (48745) (TAAA)n#Simple_repeat 1 25 (0) c_b1s251i0
chr15_MATERNA 1230 TAAATAAATAAATAAATAAATAAAT 1254
(TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAAT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
2213 9.29 0.00 0.00 chr15_MATERNAL_p_2-50000:. 950 1229 48561 + AluY SINE/Alu 2 281 30
2213 9.29 0.00 0.00 chr15_MATERNAL_p_2-50000:. 950 1229 (48561) AluY#SINE/Alu 2 281 (30) c_b1s352i0
chr15_MATERNA 950 GCTGGGTGCAGTGGCTCACGTCTGTAATCCCAGCACCTTGGGAGGCCTAG 999
i i i i i v
AluY#SINE/Alu 2 GCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG 51
chr15_MATERNA 1000 GCAGGTGGATCACAAGGTCAGGAGATCGAGAACATCCTGGCTGACATGGT 1049
i i i v i i
AluY#SINE/Alu 52 GCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGT 101
chr15_MATERNA 1050 GAAACCCCATCTCTACTAAAAATACAAAAAATTAGCCAGGCGTGGTGGTG 1099
i i i
AluY#SINE/Alu 102 GAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCG 151
chr15_MATERNA 1100 GGCACCTGTACTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATGGCATG 1149
i v i i
AluY#SINE/Alu 152 GGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTG 201
chr15_MATERNA 1150 AACCAGGGAGGCAGAGCTTGCAGTGAGCCAAGATAGCGCCACTGCACTCC 1199
v i i v
AluY#SINE/Alu 202 AACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC 251
chr15_MATERNA 1200 AGCATGGGCAACAGAGCGAGACTCTGTCTC 1229
v i i
AluY#SINE/Alu 252 AGCCTGGGCGACAGAGCGAGACTCCGTCTC 281
Matrix = 14p41g.matrix
Kimura (with divCpGMod) = 3.92
Transitions / transversions = 3.33 (20/6)
Gap_init rate = 0.00 (0 / 279), avg. gap size = 0.0 (0 / 0)
+ 3119 19.6 4.5 6.9 chr15_MATERNAL_p_2-50000:. 1255 1893 (48106) + MER31-int LTR/ERV1 3111 3724 (1208) 2
ANNOTATION EVIDENCE:
3119 19.60 4.55 6.91 chr15_MATERNAL_p_2-50000:. 1255 1893 43298 + MER31-int LTR/ERV1 3111 3724 1208
3119 19.60 4.55 6.91 chr15_MATERNAL_p_2-50000:. 1255 1893 (43298) MER31-int#LTR/ERV1 3111 3724 (1208) m_b1s701i1
chr15_MATERNA 1255 XGTTGTATCCCACAGAAAAAATCGAATATCCTTGTCAGTTGTGGTATAAT 1304
- v v i i v ----------
MER31-int#LTR 3111 -GTTGTATGCCACAGAAATAACCAAATTTCCTTGTCA----------AAT 3149
chr15_MATERNA 1305 GAACTCTCATCAGATCTTTCATCACAGCCATTTCATATTCTTTATCATTT 1354
v i ii i vi ii i ii
MER31-int#LTR 3150 GAACTCTCATCAGATCTTTAACCATGGCCATTTTAAGTCTTTTGTCATCC 3199
chr15_MATERNA 1355 AGA------TATTATTTCCCCCTGATGCTTTCCTGAAAGC-TCCTGCAAT 1397
v ------ i iv i v ii - i
MER31-int#LTR 3200 ACAGACAGTTATTGTTTTACTCTGATTCTTCTCTGAAAGCATCTTGCAAT 3249
chr15_MATERNA 1398 CAGCTACAGGTCAGAATG-TTCATCTCCATCACGGGATTCCCTCTGAGAC 1446
?i i - i i -- v i ----------
MER31-int#LTR 3250 CAGCTACAGNCCAAAATGCTTCGTCTTCA--AGGAGATTC---------- 3287
chr15_MATERNA 1447 ACACAGAAAAGAGTATGCAAGATAGTCTGGT-TATAGGCTTCTGATGATA 1495
-- ii ----- - v v- i i ----
MER31-int#LTR 3288 --ATGGAAAAGA-----CAAG-TACTCTGGAATACAGGTTTCTGAT---- 3325
chr15_MATERNA 1496 TTGCTTAAATAACTTTA-AGACCATACACTTCG-CTCAGTGAAGATCTCC 1543
----------- - i vv v - vi i ii i
MER31-int#LTR 3326 -----------ACTTTANAGATCATACCATTGGACTGGGTAAGAATTTCC 3364
chr15_MATERNA 1544 AGAAGTCTGCTTCAGAAATTGATGGGTTCATGACACTGCTAACCCAAGAT 1593
-v iv vv i v
MER31-int#LTR 3365 AGA-CTCTAATGAAGAAACTGATGGGTTCATGAAACTGCTAACCCAAGAT 3413
chr15_MATERNA 1594 GCAACAAGACTGGAATTGATTACATGGTACTGAATGAACTGATGAAAATT 1643
vv i ii vi i v i v
MER31-int#LTR 3414 CAAGCAGAACAAGAATTAATTACATGGGACTGAATGAACTGATGAAGATG 3463
chr15_MATERNA 1644 GATTATAATTTTATA-GCTTTTTG----GAGCATTGCTGGTTCTTTAATG 1688
iv i v - ? ----i i
MER31-int#LTR 3464 ATTTATAGTTTTTTATGNTTTTTGTTTGAAACATTGCTGGTTCTTTAATG 3513
chr15_MATERNA 1689 TTCTAGTTTCTGGACTTAAGAAA----TCTCTTT-CTCTTAACCTAACTG 1733
i iv ii i i ---- i - v v i
MER31-int#LTR 3514 TTTTGTTTTCCAGATTTAAGGAAACTTTTTCTTTTCTCTTAAGCTATCTA 3563
chr15_MATERNA 1734 TAACATACA---ATTTAGTAGATTATACTTTTGAAAACAGAAGTGAAGCA 1780
i v --- i i v vi i i i
MER31-int#LTR 3564 TAGCTTACAGCAATTTGGTAAAGTATACTTTTGTGAACAAAAATGAAACA 3613
chr15_MATERNA 1781 TTTATCTTTTTTCCCCTGCCTGATTTTTCCAGAATTTTGAAATCCTTACT 1830
- i - i iii iv iiv ??
MER31-int#LTR 3614 TTTA-CTTTTCTCCC-TACCTGATCCCTCCAGAATTCGGAAACTATTNNT 3661
chr15_MATERNA 1831 GAACACTCTTATTTTCACGATGATATAGTTGTTAGCAAAAGTCCAATAAG 1880
ii i i iii i v v i
MER31-int#LTR 3662 GAGTATTCTTATTTTCATGGCAATATAGTTATTTGCATAAGTTCAATAAG 3711
chr15_MATERNA 1881 AATCTGTTCACCT 1893
v
MER31-int#LTR 3712 AATCTGTTCTCCT 3724
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 20.80
Transitions / transversions = 2.03 (77/38)
Gap_init rate = 0.09 (60 / 638), avg. gap size = 1.22 (73 / 60)
+ 7547 3.8 0.0 0.8 chr15_MATERNAL_p_2-50000:. 1894 3249 (46750) + L1PA4 LINE/L1 4811 6155 (0) 4
ANNOTATION EVIDENCE:
4871 4.22 0.00 0.00 chr15_MATERNAL_p_2-50000:. 1894 2486 42705 + L1P1_orf2 LINE/L1 2702 3294 0
4871 4.22 0.00 0.00 chr15_MATERNAL_p_2-50000:. 1894 2486 (42705) L1P1_orf2#LINE/L1 2702 3294 (0) m_b1s551i0
chr15_MATERNA 1894 GAACAGAGACCTCAGAAATAATGCCGCATATCTACAACCATCTGATCTTT 1943
v i i
L1P1_orf2#LIN 2702 GAACAGAGCCCTCAGAAATAACGCCGCATATCTACAACTATCTGATCTTT 2751
chr15_MATERNA 1944 GACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAA 1993
v
L1P1_orf2#LIN 2752 GACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAA 2801
chr15_MATERNA 1994 ATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATC 2043
L1P1_orf2#LIN 2802 ATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATC 2851
chr15_MATERNA 2044 CCTTCCTTACACATTATACAAAAATTAATTCAAGATGAATTAAAGACTTA 2093
v i
L1P1_orf2#LIN 2852 CCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTA 2901
chr15_MATERNA 2094 CATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTAC 2143
v i ?
L1P1_orf2#LIN 2902 AACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTAC 2951
chr15_MATERNA 2144 CATTCAGAACTTAGGCATGGGCAAGGACTTCATGTCCAAAACACCAAAAG 2193
i v i
L1P1_orf2#LIN 2952 CATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAG 3001
chr15_MATERNA 2194 CAATGGCAACAAAAGACAAAATTGATAGATGGGATCTAATTAAACTAAAG 2243
v i i
L1P1_orf2#LIN 3002 CAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAG 3051
chr15_MATERNA 2244 AGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTAC 2293
L1P1_orf2#LIN 3052 AGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTAC 3101
chr15_MATERNA 2294 AAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAGGGCTAATAT 2343
i i
L1P1_orf2#LIN 3102 AGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATAT 3151
chr15_MATERNA 2344 CCAGAATCTACAATGAACACAAAGAAATTTACAAGAAAAAAACAAACAAC 2393
v v
L1P1_orf2#LIN 3152 CCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAAC 3201
chr15_MATERNA 2394 CCCATCAAAAAGTGGGCGAAGGATGTGAACAGACACTTCTCAAAAGAAGA 2443
ii
L1P1_orf2#LIN 3202 CCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGA 3251
chr15_MATERNA 2444 CATTTATGCAGCCAAAAGACATGTGAAAGAATGCTCATCATCA 2486
i ii i
L1P1_orf2#LIN 3252 CATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCA 3294
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 3.70
Transitions / transversions = 2.00 (16/8)
Gap_init rate = 0.00 (0 / 592), avg. gap size = 0.0 (0 / 0)
7547 3.54 0.00 1.20 chr15_MATERNAL_p_2-50000:. 2337 3249 41942 + L1PA4_3end LINE/L1 1 902 0
7547 3.54 0.00 1.20 chr15_MATERNAL_p_2-50000:. 2337 3249 (41942) L1PA4_3end#LINE/L1 1 902 (0) m_b1s551i1
chr15_MATERNA 2337 CTAATATCCAGAATCTACAATGAACACAAAGAAATTTACAAGAAAAAAAC 2386
v v
L1PA4_3end#LI 1 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAAC 50
chr15_MATERNA 2387 AAACAACCCCATCAAAAAGTGGGCGAAGGATGTGAACAGACACTTCTCAA 2436
i
L1PA4_3end#LI 51 AAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTCAA 100
chr15_MATERNA 2437 AAGAAGACATTTATGCAGCCAAAAGACATGTGAAAGAATGCTCATCATCA 2486
ii i
L1PA4_3end#LI 101 AAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCATCA 150
chr15_MATERNA 2487 CTGGCCATCAGAGAAATGCAAATCAAAATCACAATGAGACACCATCTCAC 2536
i i
L1PA4_3end#LI 151 CTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCAC 200
chr15_MATERNA 2537 ACCAGTTAGAATGGCGATCAATAAAAAGTCAGGAAACAACAGGTGCTGGA 2586
v
L1PA4_3end#LI 201 ACCAGTTAGAATGGCGATCATTAAAAAGTCAGGAAACAACAGGTGCTGGA 250
chr15_MATERNA 2587 GAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAA 2636
L1PA4_3end#LI 251 GAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAA 300
chr15_MATERNA 2637 CTAGTTCAACCATTGTAGAAGATGGTGTGGCGATTCCTCAGGGATCTAGA 2686
i vii
L1PA4_3end#LI 301 CTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGA 350
chr15_MATERNA 2687 ACTAGAAATACCATTTGACCCAGCCATCCCATTACTTGGTATATACCCAA 2736
v
L1PA4_3end#LI 351 ACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAA 400
chr15_MATERNA 2737 AGGAGTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATT 2786
v
L1PA4_3end#LI 401 AGGATTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATT 450
chr15_MATERNA 2787 GCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATACCCAAC 2836
ii
L1PA4_3end#LI 451 GCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAAC 500
chr15_MATERNA 2837 AATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACT 2886
L1PA4_3end#LI 501 AATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACT 550
chr15_MATERNA 2887 ATGCAGCCATAAAAAATGAAGAGTTCATGTCCTTTGTAGGGACATGGATG 2936
v
L1PA4_3end#LI 551 ATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGATG 600
chr15_MATERNA 2937 AAACTGGAAACCATCATTCTCAGCAAACTATCACAAGGACAAAAAAACCA 2986
i i -
L1PA4_3end#LI 601 AAGCTGGAAACCATCATTCTCAGCAAACTATCGCAAGGACAAAAAA-CCA 649
chr15_MATERNA 2987 AACACTGCATGTTCTCACTCATAGGTGGGAATTGAACAATGAGAATACAT 3036
i i
L1PA4_3end#LI 650 AACACCGCATGTTCTCACTCATAGGTGGGAATTGAACAATGAGAACACAT 699
chr15_MATERNA 3037 GGACATGGGAAGGGGAACATCACACTCCAGGGACTGTTGTGGGGTGGGGG 3086
ii v i v
L1PA4_3end#LI 700 GGACACAGGAAGGGGAACATCACACACCGGGGCCTGTTGTGGGGTGGGGG 749
chr15_MATERNA 3087 GGGAGGGGGGAGGGATAGCATTAGGAGATATACCTAATGCTAAATGACAA 3136
-- i
L1PA4_3end#LI 750 G--AGGGGGGAGGGATAGCATTAGGAGATATACCTAATGCTAAATGACGA 797
chr15_MATERNA 3137 GTTAATGGGTGCAGCACACCAACATGGCACATGTGCACATGTATACATAT 3186
--------
L1PA4_3end#LI 798 GTTAATGGGTGCAGCACACCAACATGGCACATGT--------ATACATAT 839
chr15_MATERNA 3187 GTAACAAACCTGCACATTGTGCACATGTACCCTAAAACTTAAACTATAAT 3236
i v
L1PA4_3end#LI 840 GTAACAAACCTGCACGTTGTGCACATGTACCCTAAAACTTAAAGTATAAT 889
chr15_MATERNA 3237 AATAATAAAATAA 3249
v v
L1PA4_3end#LI 890 AATAAAAAAAAAA 902
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 3.12
Transitions / transversions = 1.67 (20/12)
Gap_init rate = 0.01 (11 / 912), avg. gap size = 1.00 (11 / 11)
+ 772 16.8 1.2 8.0 chr15_MATERNAL_p_2-50000:. 3346 3520 (46479) + MER31-int LTR/ERV1 3706 3868 (1064) 2
ANNOTATION EVIDENCE:
772 16.77 1.22 8.00 chr15_MATERNAL_p_2-50000:. 3346 3520 41671 + MER31-int LTR/ERV1 3706 3868 1064
772 16.77 1.22 8.00 chr15_MATERNAL_p_2-50000:. 3346 3520 (41671) MER31-int#LTR/ERV1 3706 3868 (1064) m_b1s701i2
chr15_MATERNA 3346 AAAAAAAATCTGTTTACCTTATAACAGGACATAATTGGAAATTTTTGTTA 3395
v i iv i i iv v
MER31-int#LTR 3706 AATAAGAATCTGTTCTCCTTGTAACAGGACACAATTGGAAACATTGGTTA 3755
chr15_MATERNA 3396 TATTATCAAGGTTTTTACTGGAATATCATATTTAGGAA--ATGTACCTAA 3443
i i v i ii -- ?i v i
MER31-int#LTR 3756 TATTACCAAGGCTTTGACTGGAATGTCATATTTGAGAATGATGNGCATAG 3805
chr15_MATERNA 3444 GATCACTTATGACCAGCAATTTTAAGGAAGTAAGGTTGACTTTTATGCAG 3493
i ---------- --- v - v
MER31-int#LTR 3806 AATCA----------GC---TTTAAGGAACTAAGGTTGACTTT-ATGGAG 3841
chr15_MATERNA 3494 ACAGTGCTTACAAAGCACTCTGAGAAA 3520
v i v vi
MER31-int#LTR 3842 CCAATGCTTACAAAGCCCTCTTGGAAA 3868
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 18.50
Transitions / transversions = 1.36 (15/11)
Gap_init rate = 0.09 (15 / 174), avg. gap size = 1.07 (16 / 15)
+ 38 0.0 0.0 0.0 chr15_MATERNAL_p_2-50000:. 3593 3625 (46374) + (TG)n Simple_repeat 1 33 (0) 5
ANNOTATION EVIDENCE:
38 0.00 0.00 0.00 chr15_MATERNAL_p_2-50000:. 3593 3625 46374 + (TG)n Simple_repeat 1 33 0
38 0.00 0.00 0.00 chr15_MATERNAL_p_2-50000:. 3593 3625 (46374) (TG)n#Simple_repeat 1 33 (0) c_b1s251i1
chr15_MATERNA 3593 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 3625
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 33
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 1317 26.3 4.5 0.8 chr15_MATERNAL_p_2-50000:. 3648 4008 (45991) + LTR10C LTR/ERV1 188 562 (29) 6
ANNOTATION EVIDENCE:
1317 26.26 4.53 0.83 chr15_MATERNAL_p_2-50000:. 3648 4008 41215 + LTR10C LTR/ERV1 188 562 29
1317 26.26 4.53 0.83 chr15_MATERNAL_p_2-50000:. 3648 4008 (41215) LTR10C#LTR/ERV1 188 562 (29) m_b1s502i2
chr15_MATERNA 3648 TTGCTCCAGCATGCCTGGACAGAACTAGACAAGCCCCAGCCCATAGTGCA 3697
i ii i iv v iv i ii vii vi ivii
LTR10C#LTR/ER 188 TTGCCCTGGCATGCTTATACTGGTCCAAGCAAGCATTAGGTCATAGCCTG 237
chr15_MATERNA 3698 TGCC-ATTCCTTATTTGGAGATG-------CTTCCTTAACTATCCCTGGG 3739
v -v i i ------- i i i vv viii
LTR10C#LTR/ER 238 TTCCTCTTCCTTATTTGAAGGTGTTTTTACCTTTCTCAGCATTCCACAAG 287
chr15_MATERNA 3740 CAACTTCCTGTTCTTTCTTTGTTCTATTC--CCCTTACCTAATTAATAAA 3787
iv --i i vi -- i i vv v v
LTR10C#LTR/ER 288 TTACTTCCT--CCTTCCTTTGTTCTCCTCTGCCTTTGCCTCTTTTAAAAA 335
chr15_MATERNA 3788 GTTTTAAACTAATAGCCAACTGGGTAAAGTGTAAAATGTGAGGTCTTATT 3837
i ii iv ii vv i ii i iii
LTR10C#LTR/ER 336 GTTCTAAGTTGCTAGCCAATCGGGACAAATACAGAATGTGAGGTCCCGTT 385
chr15_MATERNA 3838 CCAGCCAATGGAAACTGGACACAGCAGTAGGGTAGACACATAAGGTTATA 3887
i i i i v
LTR10C#LTR/ER 386 CCAGCCAATGGAAACCGGACACAGCAGTAGGGTGGACGCGTCAGGTTATA 435
chr15_MATERNA 3888 AGTAACTCTGTCTCCTTTGTTCGGTGTGTTCTTCTGGCTGGACAGCTATT 3937
i i i ii iv vii v ivi
LTR10C#LTR/ER 436 AATGACCCTGTCTCCTTTGTTCGGTGTACTCTCGTGGCAAAACTGCTGGC 485
chr15_MATERNA 3938 GAGTAGCACCCTTTCTGCAGAAAGTA--AAGCTCACCTTGCTAAG-AGAT 3984
- i -- iv vi i - i
LTR10C#LTR/ER 486 GAGT-GTACCCTTTCTGCAGAAAGTANAAAAATGGCCTTGCTGAGGAAAT 534
chr15_MATERNA 3985 CA--TTT--GTTCCCATGTTAATTCTTT 4008
i -- -- vvi i v
LTR10C#LTR/ER 535 TAAATTTATGTTCAAGTGCTATTTCTTT 562
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 30.59
Transitions / transversions = 2.13 (64/30)
Gap_init rate = 0.03 (10 / 360), avg. gap size = 2.00 (20 / 10)
+ 2060 17.6 2.5 0.8 chr15_MATERNAL_p_2-50000:. 4050 4439 (45560) + MER31-int LTR/ERV1 3803 4199 (1019) 2
ANNOTATION EVIDENCE:
2060 17.58 2.51 0.77 chr15_MATERNAL_p_2-50000:. 4050 4439 40784 + MER92-int LTR/ERV1 3803 4199 1019
2060 17.58 2.51 0.77 chr15_MATERNAL_p_2-50000:. 4050 4439 (40784) MER92-int#LTR/ERV1 3803 4199 (1019) m_b1s701i3
chr15_MATERNA 4050 AGCACTCTGAGAAAAGCCAGCCTGATA-CCTGGATTACAGGGTTCACAGC 4098
v vi i i i i - v v
MER92-int#LTR 3803 AGCCCTCTCGGGAAAACCGGCCTGGTANCCTGGCTTACAGGGTTCCCAGC 3852
chr15_MATERNA 4099 CTTACAGGTTAGTAAGGAAGGTCATTTCCTGGTAGGCCCAGGAATTTAGG 4148
v i i ii vi
MER92-int#LTR 3853 CTTACAGGTGAGTAAGGAAGGTCACTTCCTGGCAGGCCCAGGAACCTTAG 3902
chr15_MATERNA 4149 GATATTTTGGGGGCCTCAAGAAGAGAGAAATTCACACAAAGCTATAAGGA 4198
i i i v v i v
MER92-int#LTR 3903 GATATTTTGGGGACCTCGAGAAGAGAGGAATTCACCCAAATCTATAGGTA 3952
chr15_MATERNA 4199 CTGCAGCTGAAATTTGATAGTATGTTCTTAGCTTGGCTT-TTAGCCTGAA 4247
v i i i iiv i -i v
MER92-int#LTR 3953 CTGCAGGTGAAATCTGGTGGCGAGTTCTTGGCTTGGCTTCCTAGCCTCAA 4002
chr15_MATERNA 4248 TAAGGCCTTTAAAAGTCAAATCTGAGATTCTATATGAAAACTTCCAGCAA 4297
-i i v iv
MER92-int#LTR 4003 -GAGGCTTTTAAAAGTCCAATCTGAGATTCCTTATGAAAACTTCCAGCAA 4051
chr15_MATERNA 4298 AG-AAACTTGAAAGCACCTATGTGGT-CATCGCCTGTTCTTGCTGCAATT 4345
- i i ivi -v ii -i vi
MER92-int#LTR 4052 AGCAAACTTAAGAAGGCCTATGTGGTAAATTACC-ATTCTTGCTGCACCT 4100
chr15_MATERNA 4346 ACATAAATAATCAAGCAAAATCTAATAAAACAAGACTTATTTTTAAAACA 4395
ii i v i i v v vvi v
MER92-int#LTR 4101 ATGTAAATAATCAGGCCAAATCTAATGAGACCAGCCTTATTTTGTGATCA 4150
chr15_MATERNA 4396 AGAATAGTCTTACTTTGA--TTAT----GATAAAAAATGATGGTTACTAC 4439
i v -- ---- v iv i- v
MER92-int#LTR 4151 AGAATAATCTTTCTTTGAGATTATTTTTGATCAAAAGGGG-GGTGACTAC 4199
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 18.98
Transitions / transversions = 1.52 (41/27)
Gap_init rate = 0.02 (9 / 389), avg. gap size = 1.44 (13 / 9)
+ 267 24.5 0.0 11.3 chr15_MATERNAL_p_2-50000:. 4442 4478 (45521) + LTR37A LTR/ERV1 4 38 (388) 7
ANNOTATION EVIDENCE:
267 24.54 0.00 11.29 chr15_MATERNAL_p_2-50000:. 4442 4478 41009 + LTR37A LTR/ERV1 4 38 388
267 24.54 0.00 11.29 chr15_MATERNAL_p_2-50000:. 4442 4478 (41009) LTR37A#LTR/ERV1 4 38 (388) m_b1s502i3
chr15_MATERNA 4442 AGAGAAATTTTATATTTCAAAGGAAAACTATAACATA 4478
i vv i ii v i- -
LTR37A#LTR/ER 4 AGGGAAAAATTGTGCTTCAATGGAAAACTATG-CAT- 38
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 29.62
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2)
+ 1687 14.7 8.3 0.0 chr15_MATERNAL_p_2-50000:. 4479 4743 (45256) + AluJb SINE/Alu 2 290 (22) 8
ANNOTATION EVIDENCE:
1687 14.72 8.31 0.00 chr15_MATERNAL_p_2-50000:. 4479 4743 45103 + AluJb SINE/Alu 2 290 22
1687 14.72 8.31 0.00 chr15_MATERNAL_p_2-50000:. 4479 4743 (45103) AluJb#SINE/Alu 2 290 (22) c_b1s352i1
chr15_MATERNA 4479 GCCGGGCATGGTGGCACATGCCTATAATTCCAGCACTTTGGGAGGCC--- 4525
ii v i i i ---
AluJb#SINE/Al 2 GCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG 51
chr15_MATERNA 4526 ---------------------AGGAGTTCAAGACCAGCCTGGGCAACATG 4554
--------------------- i
AluJb#SINE/Al 52 GCGGGNGGATCGCTTGAGCCCAGGAGTTCGAGACCAGCCTGGGCAACATG 101
chr15_MATERNA 4555 GTAAAACCCTGTTTCTACCAAAAATACAAAAATTAGTTGGGTATGATGGC 4604
ii i i v ii ii i
AluJb#SINE/Al 102 GCGAAACCCCGTCTCTACAAAAAATACAAAAATTAGCCGGGCGTGGTGGC 151
chr15_MATERNA 4605 ATGTGCCTGTAGTCCCAGCTAATCAGGAAGCTGAGGAGGGAAGATCGTTT 4654
ii i v i i v i i
AluJb#SINE/Al 152 GCGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCGGGAGGATCGCTT 201
chr15_MATERNA 4655 GCACCCAGGAGGTAGAGGTTGCAGTGAGCTGAGATTGCACCTTTGCACTC 4704
vi i v i i v i i vi
AluJb#SINE/Al 202 GAGCCCGGGAGGTCGAGGCTGCAGTGAGCCGTGATCGCGCCACTGCACTC 251
chr15_MATERNA 4705 CAGCCTGGGTGACAGAGCCAGACCCTGTCTCAAAAAAAA 4743
i v
AluJb#SINE/Al 252 CAGCCTGGGCGACAGAGCGAGACCCTGTCTCAAAAAAAA 290
Matrix = 14p41g.matrix
Kimura (with divCpGMod) = 9.50
Transitions / transversions = 3.33 (30/9)
Gap_init rate = 0.01 (2 / 264), avg. gap size = 12.00 (24 / 2)
+ 267 24.5 0.0 11.3 chr15_MATERNAL_p_2-50000:. 4744 4829 (45170) + LTR37A LTR/ERV1 39 113 (313) 7
ANNOTATION EVIDENCE:
267 24.54 0.00 11.29 chr15_MATERNAL_p_2-50000:. 4744 4829 40658 + LTR37A LTR/ERV1 39 113 313
267 24.54 0.00 11.29 chr15_MATERNAL_p_2-50000:. 4744 4829 (40658) LTR37A#LTR/ERV1 39 113 (313) m_b1s502i3
chr15_MATERNA 4744 TGTTTTTAAAGGAAAACTACAGCCTTTGTGGGTTATCAGATTCTAGTCTT 4793
i ------- i i - v i-i v iii
LTR37A#LTR/ER 39 TGTCT-------AGAGC-ACACCCTTC-CGGGTTATCTGATTCTAGCTCT 79
chr15_MATERNA 4794 GTTTCTTGTTTCTGGGCTGTTTTTACCTCTTTGTAA 4829
i-v i i i i - vv i
LTR37A#LTR/ER 80 GTC-ATTGTCTTTGAGCTATTTT-ACAACTCTGTAA 113
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 29.62
Transitions / transversions = 2.80 (14/5)
Gap_init rate = 0.13 (11 / 85), avg. gap size = 1.00 (11 / 11)
+ 238 27.1 4.5 0.0 chr15_MATERNAL_p_2-50000:. 4897 4981 (45018) + MER34A LTR/ERV1 479 567 (4) 9
ANNOTATION EVIDENCE:
238 27.06 4.50 0.00 chr15_MATERNAL_p_2-50000:. 4897 4981 40506 + MER34A LTR/ERV1 479 567 4
238 27.06 4.50 0.00 chr15_MATERNAL_p_2-50000:. 4897 4981 (40506) MER34A#LTR/ERV1 479 567 (4) m_b1s502i4
chr15_MATERNA 4897 TCTCTCCTACTAATGTATCTATTGTCAGTT-AATTTGATGGTCACCAACC 4945
i ii v i v - i vv i v i?
MER34A#LTR/ER 479 TTTCTCCTGTTAATCTGTCTTTTGTCAGTTTAATTCGCAGGCCCCCAGNC 528
chr15_MATERNA 4946 -CTGGAACAAAGTTAGAAGAGGAA--GGTTTGGCTCCCC 4981
- i v v vvi v -- v vv
MER34A#LTR/ER 529 ACTGAACCTAAGAGGGTAGAGGAAAAGTTTTTCCTCCCC 567
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 30.62
Transitions / transversions = 0.69 (9/13)
Gap_init rate = 0.04 (3 / 84), avg. gap size = 1.33 (4 / 3)
+ 1895 24.4 2.5 1.3 chr15_MATERNAL_p_2-50000:. 4984 5392 (44607) + L1MC3 LINE/L1 5762 6227 (1558) 10
ANNOTATION EVIDENCE:
833 24.56 2.98 0.87 chr15_MATERNAL_p_2-50000:. 4984 5213 40274 + L1MC3_3end LINE/L1 509 743 1789
833 24.56 2.98 0.87 chr15_MATERNAL_p_2-50000:. 4984 5213 (40274) L1MC3_3end#LINE/L1 509 743 (1789) m_b1s551i2
chr15_MATERNA 4984 AATGCATAACCAAATTGTGGTACATTCATGCAATGGAATGCTACTTAGCC 5033
v v i i i ii i i v
L1MC3_3end#LI 509 AATGGATAAACAAACTGTGGTACATCCATACAATGGAATATTATTCAGCG 558
chr15_MATERNA 5034 ATAGAAAGGAACAAGCTATCAACTCACACAAAGACATGAGCGACTATTGC 5083
i i ii vi iv iii v v iv
L1MC3_3end#LI 559 ATAAAAAGAAATGAGCTATCAAGCCACGAAAAGACATGGATGAATCTTAA 608
chr15_MATERNA 5084 ATGCACATTGCTAAGTGGAAGAAGACAGTGTGAGGAGCATACACACAGTG 5133
i i v v ii vv i v i
L1MC3_3end#LI 609 ATGCATATTGCTAAGTGAAAGAAGCCAGTCTGAAAAGGCTACATACTGTA 658
chr15_MATERNA 5134 TGACCTCATTTA-ATGAGACACTGGAGAAGGCAAA-CTACACAGATGGGA 5181
iii v - v iv i - i v i v
L1MC3_3end#LI 659 TGATTCCAATTATATGACATTCTGGAAAAGGCAAAACTATAGAGACGGTA 708
chr15_MATERNA 5182 AGC----CATTGGCT-CCATGGGGTGGGGGTTAGAAG 5213
i?---- v i - v v v -- ?
L1MC3_3end#LI 709 AANAGATCAGTGGTTGCCAGGGGTTCGGGG--AGNAG 743
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 28.09
Transitions / transversions = 1.45 (32/22)
Gap_init rate = 0.03 (6 / 229), avg. gap size = 1.50 (9 / 6)
1895 24.26 1.95 1.76 chr15_MATERNAL_p_2-50000:. 5202 5392 40539 + L1MC3_3end LINE/L1 783 974 1558
1895 24.26 1.95 1.76 chr15_MATERNAL_p_2-50000:. 5202 5392 (40539) L1MC3_3end#LINE/L1 783 974 (1558) m_b1s551i3
chr15_MATERNA 5202 GGGGGTTAGAAGCATTCCATATTATACTTTAATAGTGGGATACCTGCCAC 5251
v v ii vi ii v v i - v v
L1MC3_3end#LI 783 GGGCGGTGAAACTATTCTGTATGATACTGTAATGGTGG-ATACATGACAC 831
chr15_MATERNA 5252 AATGCATTTGTCAAAATATGCAGAATTTTACAGC-CAAATGGTTAAAGAA 5300
v iviii i - vi v vvvv
L1MC3_3end#LI 832 TATGCATTTGTCAAAACCCATAGAACTTTACAGCACAAAGAGTGAACCTT 881
chr15_MATERNA 5301 AACTCTATTCAAATTAAATAAAATTACTCAGGATGT-GGAGTATCTCAGG 5349
- v v vv v i i i v - i v i
L1MC3_3end#LI 882 AA-TGTATGCAAATTTTAAAAAATCATTTAGGAGGTCGGGGGATCCCAGG 930
chr15_MATERNA 5350 ACAGAATACATCATGTGA-AAAAGAATTTAACTATGCTACAAAT 5392
ii i vv? - ? i i ii
L1MC3_3end#LI 931 ATGGAATGCAGANTGTGACAAAANAATCTAACTGTATTACAAAT 974
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 27.91
Transitions / transversions = 1.00 (24/24)
Gap_init rate = 0.03 (5 / 190), avg. gap size = 1.00 (5 / 5)
+ 2361 18.2 5.6 1.4 chr15_MATERNAL_p_2-50000:. 5393 5837 (44162) + MSTA1 LTR/ERVL-MaLR 1 465 (0) 11
ANNOTATION EVIDENCE:
2361 18.23 5.59 1.35 chr15_MATERNAL_p_2-50000:. 5393 5837 41952 + MSTA1 LTR/ERVL-MaLR 1 465 0
2361 18.23 5.59 1.35 chr15_MATERNAL_p_2-50000:. 5393 5837 (41952) MSTA1#LTR/ERVL-MaLR 1 465 (0) c_b1s401i0
chr15_MATERNA 5393 TACTATCTTTTGGATGTGGCTTGTCCCCGCAAAAACTCATATTGAAATTT 5442
i vv --- v i
MSTA1#LTR/ERV 1 TGCTATGGTTTGGATGT---TTGTCCCCGCCAAAACTCATGTTGAAATTT 47
chr15_MATERNA 5443 GACCCCCACTGTGTCAGTGTGGGGCGATGGGGCCTAGTGGAAGATGTTTG 5492
i v v v i- i i i
MSTA1#LTR/ERV 48 GATCCCCAATGTGGCAGTGTTGGA-GGTGGGGCCTAGTGGGAGGTGTTTG 96
chr15_MATERNA 5493 GGTCATGGTGATGGATCTCTCATGAATAGATTAATGTACTC-----TGAT 5537
v ii i iv -----? i
MSTA1#LTR/ERV 97 GGTCATGGGGGCGGATCCCTCATGAATAGATTAATGCCCTCCCTCGNGGT 146
chr15_MATERNA 5538 GGGGGTGAATGAGTTCT-GCTCT--CACAGGAATGGATTAATTCCTGCAG 5584
? i - -- i i i i ii
MSTA1#LTR/ERV 147 GGGNGTGAGTGAGTTCTCGCTCTNNCGCGGGAATGGATTAGTTCCCGCGA 196
chr15_MATERNA 5585 GAGTAGGTAGTTAAAAAGAGTCTGGC---TTCCTTGGCT-TCCCTCTTGC 5630
ii v --- i ivv - i
MSTA1#LTR/ERV 197 GAGCGGGTTGTTAAAAAGAGTCTGGCGNCTCCCTCCTCTCTCTCTCTTGC 246
chr15_MATERNA 5631 TT----TCACTTTTGCTATGTGATCTCTGGTGCACCCCTTGCTCCCCTTC 5676
----i v i i i -ii v i-
MSTA1#LTR/ERV 247 TTGCTTCCTCTCTCGCCATGTGATCTCTG-CACACGCCC-GCTCCCCTTC 294
chr15_MATERNA 5677 CACTT-----TCCACCATGAGGTGAAAAAGACTGAAGCCCCC--CAGATG 5719
? ----- i v? iv v i i --
MSTA1#LTR/ERV 295 CNCTTCGCTTTCCGCCATGAGTNGAAGCAGCCTGAGGCCCTCACCAGATG 344
chr15_MATERNA 5720 CAAGTGCCCAATCTCAGACATTC---CAGCCACAAATATTGTGAGCCAAA 5766
iv i?v i?v viv --- v iv i
MSTA1#LTR/ERV 345 CAGCTGCCCGNACCNTGCTTTTCGNCCAGCCACCAGAATCGTGAGCCAAA 394
chr15_MATERNA 5767 TGAACCTTTTTTACTTATAAATTACCCAGCCTCAGGTATTCTGTTACAGA 5816
i i vi i i v
MSTA1#LTR/ERV 395 TAAACCTCTTTTCTTTATAAATTACCCAGCCTCAGGTATTCCGTTATAGC 444
chr15_MATERNA 5817 AGCACGAAATGGACTAAGACA 5837
i i i
MSTA1#LTR/ERV 445 AACACAAAACGGACTAAGACA 465
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 16.11
Transitions / transversions = 1.96 (49/25)
Gap_init rate = 0.03 (15 / 444), avg. gap size = 2.13 (32 / 15)
+ 1895 24.3 1.9 1.8 chr15_MATERNAL_p_2-50000:. 5838 6157 (43842) + L1MC3 LINE/L1 6228 6548 (1237) 10
ANNOTATION EVIDENCE:
1895 24.26 1.95 1.76 chr15_MATERNAL_p_2-50000:. 5838 6157 39774 + L1MC3_3end LINE/L1 975 1295 1237
1895 24.26 1.95 1.76 chr15_MATERNAL_p_2-50000:. 5838 6157 (39774) L1MC3_3end#LINE/L1 975 1295 (1237) m_b1s551i3
chr15_MATERNA 5838 CAAATGTAGGTAAAAAC-TCACTGAAGG---TGTAGGGAAAATGATGTTG 5883
----- v v v - --- -i v i i
L1MC3_3end#LI 975 -----GTATGAAACAACCTCACTGAAGGGGGTG-GGGGAAAAAGGTGCTG 1018
chr15_MATERNA 5884 ACCTAACTCACTTTGAAAATGAATAGAATCTGTAGG-CTGAAGGCAAA-T 5931
v v i i i i i - i -v
L1MC3_3end#LI 1019 ACCTAAGTAACTTTGGAAATGAGTGGAGTCTGTAAGACTAAAGGCAAAAG 1068
chr15_MATERNA 5932 GAACTATACTTCATCATTGGATTCCATTTTATAAAGTTCTTTCCAACAGA 5981
i v v v i v i i v v v v i i
L1MC3_3end#LI 1069 GAACTGTACATAAGCACTGTACTCTAGTTGATAAAGTTGTTTCCCACGGG 1118
chr15_MATERNA 5982 AGCAATTGTTAACAGTTGTAAAACCACAGTATCTGTAT-CTGGAATAAAA 6030
i i vvv i v i ? i vi iv - vi
L1MC3_3end#LI 1119 GGTACGGGTTAACAATTCTGANACCGCTATACATGTATACTGGAATTGAA 1168
chr15_MATERNA 6031 CAATGACTTACATAAGTTGCAGATGGTAGGAACCAGATCTCTCACTGGTG 6080
v vv v iii v i i i i i v
L1MC3_3end#LI 1169 CAATTAAGTAAATGGATGGCGGATGGTGGGAGCCAGGTTTCTCACTGTTG 1218
chr15_MATERNA 6081 AAGTGGGAGGTTACAAATTAGCAAGGTGAGAAGGCTAGAATGATTCATGT 6130
i ? i v v i i
L1MC3_3end#LI 1219 GAGTGGGAGNTTACAGATAAGCAAGGGGAGGAGGCTAGAATGATCCATGT 1268
chr15_MATERNA 6131 GATAGTAGATCAGAGGTGGAGACATCA 6157
i i i i v
L1MC3_3end#LI 1269 GGTAATGGATTAGAGTTGGAGACATCA 1295
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 27.91
Transitions / transversions = 1.26 (39/31)
Gap_init rate = 0.03 (11 / 319), avg. gap size = 1.18 (13 / 11)
+ 7774 7.9 2.6 0.0 chr15_MATERNAL_p_2-50000:. 6166 7166 (42833) + LTR5A LTR/ERVK 6 1033 (0) 12
ANNOTATION EVIDENCE:
7774 7.89 2.63 0.00 chr15_MATERNAL_p_2-50000:. 6166 7166 38765 + LTR5A LTR/ERVK 6 1033 0
7774 7.89 2.63 0.00 chr15_MATERNAL_p_2-50000:. 6166 7166 (38765) LTR5A#LTR/ERVK 6 1033 (0) m_b1s502i5
chr15_MATERNA 6166 GGAAAAGAAAGAGAGATCAGACTGTTACTGTGTCCATGTAGAAAGGGAAG 6215
i i
LTR5A#LTR/ERV 6 GGAAAAGAAAGAGAGATCAGACTGTCACTGTGTCTATGTAGAAAGGGAAG 55
chr15_MATERNA 6216 ACATAAGAAATTCCATTTTGA------TCTGTACCTTGAAAAATTTCTTT 6259
i i ------i i i v v
LTR5A#LTR/ERV 56 ACATAAGAGACTCCATTTTGAAAAAGACCTGTACTTTAAACAATTGCTTT 105
chr15_MATERNA 6260 GC-TGAGATGCTGTTAATTTGTAACTTTGCCCCAGCCACTTTGCCCCA-- 6306
- i i --
LTR5A#LTR/ERV 106 GCNTGAGATGTTGTTAATTTGTAGCTTTGCCCCAGCCACTTTGCCCCAGC 155
chr15_MATERNA 6307 -ACTTTGA-----------GCTCACAAAAACATGTGTTATATGGAATCAA 6344
- ----------- i i
LTR5A#LTR/ERV 156 CACTTTGACCCAACCTGGAGCTCACAAAAACATGTGTTGTATGAAATCAA 205
chr15_MATERNA 6345 GGTTTAAGGGATCTAGGGCTGTGCAGGATGTGCCTTGTTAACAAAATATT 6394
i i
LTR5A#LTR/ERV 206 GGTTTAAGGGATCTAGGGCTGTGCAGGACGTGCCTTGTTAACAAAATGTT 255
chr15_MATERNA 6395 TACAAGCAGTATGCTTGGTAAAACTCATTGCCATTCTCTAGTCTCAATAA 6444
i v i
LTR5A#LTR/ERV 256 TACAAGCAGTATACTTGGTAAAAGTCATCGCCATTCTCTAGTCTCAATAA 305
chr15_MATERNA 6445 ACCAGAGGCACAATGCACTGCAAAAAGCCACAGGGACCTCTGCCCTGGAA 6494
i ii i v
LTR5A#LTR/ERV 306 ACCAGGGGCACAATGCACTGCGGAAAGCCGCAGGGACCTCTGCCCTTGAA 355
chr15_MATERNA 6495 AGCCGGGTATTGTCCAAGGTTTGTCCCCATGTGATAGTCTGAAATGTGGC 6544
v v i
LTR5A#LTR/ERV 356 AGCGGGGTATTGTCCAAGGTTTCTCCCCATGTGATAGTCTGAAATATGGC 405
chr15_MATERNA 6545 CTCATGGGATAAGAAAGACTTGACCATCCCCCAGCCTGACACCCATAAAG 6594
i i i i i i
LTR5A#LTR/ERV 406 CTCGTGGGATGAGAAAGACCTGACCGTCCCCCAGCCCGACACCCGTAAAG 455
chr15_MATERNA 6595 GGTCTGTGCTGAGGTGGATTAGTAAAAGAGGAAAGCCTCTTGCAGTTGAG 6644
LTR5A#LTR/ERV 456 GGTCTGTGCTGAGGTGGATTAGTAAAAGAGGAAAGCCTCTTGCAGTTGAG 505
chr15_MATERNA 6645 AT-AGAGGAAGGCCACCATTTCCTGCCTGCCCCTGGGAACTTGATGTCTC 6693
i- ii i vi
LTR5A#LTR/ERV 506 ACGAGAGGAAGGCCACTGTCTCCTGCCTGCCCCTGGGAACTGAATGTCTC 555
chr15_MATERNA 6694 GGTATAAAACCCGATTGTACACCTGTTCAATTCTGAGATAGGAGGAAAAC 6743
ii i
LTR5A#LTR/ERV 556 GGTATAAAACCCGATTGTACATTTGTTCAATTCTGAGATAGGAGAAAAAC 605
chr15_MATERNA 6744 CACCCTATGGTGGGAGGTGAGACATGTTGGCAGCAATGCTGTCTAGTTAT 6793
i i i v i v
LTR5A#LTR/ERV 606 CGCCCTATGGCGGGAGGCGAGACATGTTTGCAGCAATGCTGCCTTGTTAT 655
chr15_MATERNA 6794 TCTTTACTCCACTGAAATGTTTGGGTGGACAGTAACATAAATCTGGCCTA 6843
i i v v
LTR5A#LTR/ERV 656 TCTTTACTCCGCTGAGATGTTTGGGTGGAGAGAAACATAAATCTGGCCTA 705
chr15_MATERNA 6844 CATGCACATCCAGGCATAGTACCTACCCTTGAACTTAATTATGACATAGA 6893
i i ? v
LTR5A#LTR/ERV 706 CGTGCACGTCCAGNCATAGTACCTTCCCTTGAACTTAATTATGACATAGA 755
chr15_MATERNA 6894 TTCTTTTGCTCACATGTTTTTTTGCTGACCTCCTCCTTATTATCACCCTG 6943
? i
LTR5A#LTR/ERV 756 TTCTTTTGCTCACATGTTTTNTTGCTGACCTTCTCCTTATTATCACCCTG 805
chr15_MATERNA 6944 CTCTCCTACAGCATTCCTCTT-GCTGAGATAATGAAAATAATAAT----A 6988
vi i - i ----
LTR5A#LTR/ERV 806 CTCTCCTACTACATTCCTTTTTGCTGAAATAATGAAAATAATAATCAATA 855
chr15_MATERNA 6989 AAAACTGAGGGAACTTAGAGACCGGTGCTGGTGCATGTCCTTGGTATGCT 7038
i i i v i
LTR5A#LTR/ERV 856 AAAACTGAGGGAACTCAGAGGCCGGTGCCGGTGCAGGTCCTTGGTGTGCT 905
chr15_MATERNA 7039 GAGAGCCAGTCCCCTGGCCCCACTTTTCTTTCTCTATACTTTGTCTCTGA 7088
v i v v v v
LTR5A#LTR/ERV 906 GAGCGCCGGTCCCCTGGGCCCACTGTTGTTTCTCTATACTTTGTCTCTGT 955
chr15_MATERNA 7089 GTCTTATTTTTTTTCTCAGTCTCTCATCCCATCTGACGAGATATACCCAC 7138
i i i i v v
LTR5A#LTR/ERV 956 GTCTTATTTCTTTTCTCAGTCTCTCGTCCCACCCGACTAGAAATACCCAC 1005
chr15_MATERNA 7139 AGGTGTGGAGGAGCAGGCCACCCCTTCA 7166
i
LTR5A#LTR/ERV 1006 AGGTGTGGAGGGGCAGGCCACCCCTTCA 1033
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 6.28
Transitions / transversions = 2.67 (56/21)
Gap_init rate = 0.01 (8 / 1000), avg. gap size = 3.38 (27 / 8)
+ 2664 9.7 5.5 0.5 chr15_MATERNAL_p_2-50000:. 7167 7548 (42451) + HERVK-int LTR/ERVK 1 402 (7134) 12
ANNOTATION EVIDENCE:
2664 9.74 5.47 0.52 chr15_MATERNAL_p_2-50000:. 7167 7548 38383 + HERVK LTR/ERVK 1 402 7134
2664 9.74 5.47 0.52 chr15_MATERNAL_p_2-50000:. 7167 7548 (38383) HERVK#LTR/ERVK 1 402 (7134) m_b1s701i4
chr15_MATERNA 7167 TCTGCCACCCAATGTGGGTGCCTTTCTCTAGGATGAAGGTATGCTAAGAA 7216
v i i v i i i -v i
HERVK#LTR/ERV 1 TCTGGCGCCCAACGTGGGGGCTTTTCTCTAGGGTGAAGGTACGCT-CGAG 49
chr15_MATERNA 7217 TGTGAGCATTGAGGACA-GTCGA---GAGATTCCTAAGTACATCCACCAT 7262
i iv - --- i -i i i vi
HERVK#LTR/ERV 50 CGTGGTCATTGAGGACAAGTCGACGAGAGATCCC-GAGTACGTCTACGGT 98
chr15_MATERNA 7263 CAGCCTTGCGGTAAGCTTGTGCGCTCAGAGAAACCCAGGGTAACAATGGG 7312
i i v
HERVK#LTR/ERV 99 CAGCCTTGCGGTAAGCTTGTGCGCTCGGAGGAAGCCAGGGTAACAATGGG 148
chr15_MATERNA 7313 GCAAACTGAAAGTAAA------------TATGCCTCTTATCTCAGCTTCA 7350
------------ i
HERVK#LTR/ERV 149 GCAAACTGAAAGTAAAANTAAAAGTAAATATGCCTCTTATCTCAGCTTTA 198
chr15_MATERNA 7351 TCAAAATTCTCTTAAGAAGAGGGGGAGTTAAAGCTTCTACAGAAAATCTA 7400
i i i i i?
HERVK#LTR/ERV 199 TTAAAATTCTTTTAAAAAGAGGGGGAGTTAGAGTNTCTACAGAAAATCTA 248
chr15_MATERNA 7401 ATTACACTATTTCAAACAATAGAACGATTCTGCCCATGGTTTCCAGAACA 7450
i ?i i
HERVK#LTR/ERV 249 ATCANGCTATTTCAAACAATAGAACAATTCTGCCCATGGTTTCCAGAACA 298
chr15_MATERNA 7451 GGGAACTTTAGATTTAAAAGACTGGGAAAAA-TTGGCAAAGAATTAA--- 7496
i i - i ---
HERVK#LTR/ERV 299 GGGAACTTTAGATCTAAAAGATTGGGAAAAAATTGGCAAAGAACTAAAAC 348
chr15_MATERNA 7497 --GCAAGTAGGGAAGGTAAAACCATCCCACTTACAGTATGGAATGATTGG 7544
-- i i
HERVK#LTR/ERV 349 AAGCAAGTAGGGAGGGTAAAATCATCCCACTTACAGTATGGAATGATTGG 398
chr15_MATERNA 7545 GCCA 7548
HERVK#LTR/ERV 399 GCCA 402
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 8.11
Transitions / transversions = 4.83 (29/6)
Gap_init rate = 0.02 (8 / 381), avg. gap size = 3.00 (24 / 8)
+ 45 0.0 2.2 0.0 chr15_MATERNAL_p_2-50000:. 7549 7593 (42406) + (TTAT)n Simple_repeat 1 46 (0) 13
ANNOTATION EVIDENCE:
45 0.00 2.22 0.00 chr15_MATERNAL_p_2-50000:. 7549 7593 42406 + (TTAT)n Simple_repeat 1 46 0
45 0.00 2.22 0.00 chr15_MATERNAL_p_2-50000:. 7549 7593 (42406) (TTAT)n#Simple_repeat 1 46 (0) c_b1s251i2
chr15_MATERNA 7549 TTATTT-TTTATTTATTTATTTATTTATTTATTTATTTATTTATTT 7593
-
(TTAT)n#Simpl 1 TTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTT 46
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1)
+ 1143 8.2 0.0 0.0 chr15_MATERNAL_p_2-50000:. 7594 7740 (42259) C AluY SINE/Alu (29) 282 136 14
ANNOTATION EVIDENCE:
1143 8.16 0.00 0.00 chr15_MATERNAL_p_2-50000:. 7594 7740 38235 C AluY SINE/Alu 136 282 29
1143 8.16 0.00 0.00 chr15_MATERNAL_p_2-50000:. 7594 7740 (38235) C AluY#SINE/Alu (29) 282 136 m_b1s356i0
chr15_MATERNA 7594 TGAGACAGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGTAGTGGCGCGATC 7643
i i
C AluY#SINE/Alu 282 TGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATC 233
chr15_MATERNA 7644 TCAGCTCACTGCAAGCTCTGCCTCCTGGGCTCACGCCATTCTCCTGCCTC 7693
i i i i
C AluY#SINE/Alu 232 TCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTC 183
chr15_MATERNA 7694 AGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCTGCGATGCTGGGC 7740
ii v i iv
C AluY#SINE/Alu 182 AGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGC 136
Matrix = 14p41g.matrix
Kimura (with divCpGMod) = 5.32
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.00 (0 / 146), avg. gap size = 0.0 (0 / 0)
+ 1928 14.0 1.4 0.3 chr15_MATERNAL_p_2-50000:. 7741 8033 (41966) + HERVK-int LTR/ERVK 401 696 (6840) 12
ANNOTATION EVIDENCE:
1928 14.04 1.36 0.34 chr15_MATERNAL_p_2-50000:. 7741 8033 37942 + HERVK LTR/ERVK 401 696 6840
1928 14.04 1.36 0.34 chr15_MATERNAL_p_2-50000:. 7741 8033 (37942) HERVK#LTR/ERVK 401 696 (6840) m_b1s701i5
chr15_MATERNA 7741 CATTGTTAAAGCAACTTTAGAATGGTTTCAAGTAGAAGAAGACAGCATTT 7790
i i iv ii i i
HERVK#LTR/ERV 401 CATTATTAAAGCAGCTTTAGAACCGTTTCAAACAGAAGAAGATAGCGTTT 450
chr15_MATERNA 7791 CAGTTTCTGCTGCCTCTGAAAGCTGTGTAATAGATTGTGAAGA---GGCG 7837
v i i --- i
HERVK#LTR/ERV 451 CAGTTTCTGATGCCCCTGGAAGCTGTGTAATAGATTGTGAAGAAGAGGCA 500
chr15_MATERNA 7838 GGGACAAAATCCAGGAAATGAATGGAAAGTTCATATTGTAAATATGTAGC 7887
? i vi v i i ii
HERVK#LTR/ERV 501 GGGANAGAATCCCAGAAAGGAACGGAAAGTTCACATTGCGAATATGTAGC 550
chr15_MATERNA 7888 AGAGCCGGTAATGGCTCGGTCAATGCAAAATGTTGACTACAATCAATTAC 7937
i i
HERVK#LTR/ERV 551 AGAGCCGGTAATGGCTCGGTCAACGCAAAATGTTGACTATAATCAATTAC 600
chr15_MATERNA 7938 AGGAGGTAATATATCCTGAAACATTAAAATTAAAAGGAAAAAGTCCAGAA 7987
i i i i
HERVK#LTR/ERV 601 AGGAGGTGATATATCCTGAAACGTTAAAATTAGAAGGAAAAGGTCCAGAA 650
chr15_MATERNA 7988 CCATCAGGGCCATTGG-GTCTAAAAGCATGATGGCCACCTCCTCCTC 8033
ii vii ii - -v i v v v? i
HERVK#LTR/ERV 651 TTAGTGGGGCCATCAGAGTCTAAA-CCACGAGGCCCAANTCCTCTTC 696
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 12.76
Transitions / transversions = 3.33 (30/9)
Gap_init rate = 0.01 (3 / 292), avg. gap size = 1.67 (5 / 3)
+25427 9.3 1.6 0.1 chr15_MATERNAL_p_2-50000:. 8160 11531 (38468) + HERVK-int LTR/ERVK 3007 6429 (1107) 12
ANNOTATION EVIDENCE:
25427 9.32 1.61 0.12 chr15_MATERNAL_p_2-50000:. 8160 11531 34444 + HERVK LTR/ERVK 3007 6429 1107
25427 9.32 1.61 0.12 chr15_MATERNAL_p_2-50000:. 8160 11531 (34444) HERVK#LTR/ERVK 3007 6429 (1107) m_b1s701i6
chr15_MATERNA 8160 CCTGTATAGGTCAAACAGTGGCCGCTCCCTAAGGAAAAGTTGGGGGTGCT 8209
? i v v v v iv i i ivi
HERVK#LTR/ERV 3007 CCNGTATGGGTAAATCAGTGGCCGCTACCAAAACAAAAGCTGGAGGCTTT 3056
chr15_MATERNA 8210 ACATAAAATAGTTAAAAAGCTATTTTATAAAGGACATGTTTCACCCACTT 8259
vv v iv ?i i vi vv v i i vvi iv v
HERVK#LTR/ERV 3057 ACATTTATTAGCAAANGAACAGTTAGAAAAGGGACATATTGAGCCTTCGT 3106
chr15_MATERNA 8260 TCTGTCTTTAGAATTCTCCTGTTTTTGTAATTCAGAAAAAATCAGGCAGA 8309
vv i i v
HERVK#LTR/ERV 3107 TCTCGCCTTGGAATTCTCCTGTGTTTGTAATTCAGAAAAAATCAGGCAGA 3156
chr15_MATERNA 8310 TGGCGCATGCTAACTGACTTAAGAGCCATTAATGCAGTAATTCAACCTAT 8359
i i i ? i v i
HERVK#LTR/ERV 3157 TGGCGCATGTTAACTGACTTAAGGGCCGTNAACGCCGTAATTCAACCCAT 3206
chr15_MATERNA 8360 GAGGCCTCTCCAACCCGTGTTGCCCTCTCCAGCCACGATCTC-------- 8401
i v i i i --------
HERVK#LTR/ERV 3207 GGGGCCTCTCCAACCCGGGTTGCCCTCTCCGGCCATGATCCCNAAAGATT 3256
chr15_MATERNA 8402 ---CTTTAATTATAATTGATCTGAAGGATTGCTTTTTTACCATTTCTCTG 8448
--- i
HERVK#LTR/ERV 3257 GGCCTTTAATTATAATTGATCTGAAGGATTGCTTTTTTACCATTCCTCTG 3306
chr15_MATERNA 8449 GCAAAACAGGATTTTGAAAAATTTGCTTTTACTATACCAGCCATAAATAA 8498
i i ? i
HERVK#LTR/ERV 3307 GCAGAGCAGGATTNTGAAAAATTTGCCTTTACTATACCAGCCATAAATAA 3356
chr15_MATERNA 8499 TAAAGAACCAGCCACCAGATTTCAGTGGAAAGTGTTGCCTCAGGGAATGC 8548
i
HERVK#LTR/ERV 3357 TAAAGAACCAGCCACCAGGTTTCAGTGGAAAGTGTTGCCTCAGGGAATGC 3406
chr15_MATERNA 8549 TTAATAGTCCAATTATTTGTCAGACTTTTGTAGCTCAAGTTCTTCAACCA 8598
i i i
HERVK#LTR/ERV 3407 TTAATAGTCCAACTATTTGTCAGACTTTTGTAGCTCGAGCTCTTCAACCA 3456
chr15_MATERNA 8599 GTTAGAGACAAGTTTTCAGACTGTTATGTCATTCATTATGTTGAT---AT 8645
i ---
HERVK#LTR/ERV 3457 GTTAGAGACAAGTTTTCAGACTGTTATATCATTCATTATGTTGATGATAT 3506
chr15_MATERNA 8646 TTTGTGTGCTGCAGAAACAAGAGGCAAATTAATTGACTGTTACACATTTC 8695
i i
HERVK#LTR/ERV 3507 TTTGTGTGCTGCAGAAACGAGAGACAAATTAATTGACTGTTACACATTTC 3556
chr15_MATERNA 8696 TGCA----GAGGTTGCAAACGCAG-----------------------ATT 8718
---- v -----------------------
HERVK#LTR/ERV 3557 TGCAAGCAGAGGTTGCCAACGCAGGACTGGCAATAGCATCTGATAAGATT 3606
chr15_MATERNA 8719 CAGACCTCTACTCCTTTTCATTATTTGGGAATGCAAGTAGAGGAAAGAAA 8768
i i i i v
HERVK#LTR/ERV 3607 CAAACCTCTACTCCTTTTCATTATTTAGGGATGCAGGTAGAGGATAGAAA 3656
chr15_MATERNA 8769 AATTAAACCACAACAAATAGAAATAAGAAAAGACACATTAAGAACATTAA 8818
i v i
HERVK#LTR/ERV 3657 AATTAAGCCACAAAAAATAGAAATAAGAAAAGACACATTAAAAACATTAA 3706
chr15_MATERNA 8819 ATGACTTTCAAAAATTGCTAGGAGATATTAATTGGATTCGGCCAACTCTA 8868
HERVK#LTR/ERV 3707 ATGACTTTCAAAAATTGCTAGGAGATATTAATTGGATTCGGCCAACTCTA 3756
chr15_MATERNA 8869 GGCATCCCTACTTATGCCATGTCGAATTTGTTCTCTATCTTGAGAGGGTA 8918
i i i v
HERVK#LTR/ERV 3757 GGCATTCCTACTTATGCCATGTCAAATTTGTTCTCTATCTTAAGAGGGGA 3806
chr15_MATERNA 8919 TCCAGACTTGAATAGTAAAAGAACATTAACTCCAGAGGCAGCTAAGGAAA 8968
i i i i i ? i
HERVK#LTR/ERV 3807 CCCAGACTTAAATAGTAAAAGAACGTTAACCCCAGAGGCAACNAAAGAAA 3856
chr15_MATERNA 8969 TTGAATTAGTTGAAGAAAAAATTCCGTCAGCACAAGTAAATAGAATAGAT 9018
i ? v i
HERVK#LTR/ERV 3857 TTAAATTAGTNGAAGAAAAAATTCAGTCAGCGCAAGTAAATAGAATAGAT 3906
chr15_MATERNA 9019 CACTTAGCCCCACTCCAACTTTTGATTTTTGCTACTGTACATTCTCCAAC 9068
v i
HERVK#LTR/ERV 3907 CCCTTAGCCCCACTCCAACTTTTGATTTTTGCTACTGCACATTCTCCAAC 3956
chr15_MATERNA 9069 AGGCATTATTGTTCAAAATACAGATCTTGTGGAGTGGTCATTCTTTCCTC 9118
i ? i
HERVK#LTR/ERV 3957 AGGCATCATTGTTCAAAATACNGATCTTGTGGAGTGGTCATTCCTTCCTC 4006
chr15_MATERNA 9119 ACAGTACAATTAAGACTTTTACATTGTACTTAGATCAAATGGCTACATTA 9168
i i
HERVK#LTR/ERV 4007 ACAGTACAGTTAAGACTTTTACATTGTACTTGGATCAAATGGCTACATTA 4056
chr15_MATERNA 9169 ATTGGTCAGGGAAGACTACGAATAGTAAAATTGTGTGGAAGTGACCCAGA 9218
v i i i
HERVK#LTR/ERV 4057 ATTGGTCAGGCAAGATTACGAATAATAAAATTGTGTGGAAATGACCCAGA 4106
chr15_MATERNA 9219 TAAAATCATTGTTCCTTTAAACAAGGAACAGGTTAGACAAGCCTTTATCA 9268
i i
HERVK#LTR/ERV 4107 CAAAATCGTTGTTCCTTTAAACAAGGAACAGGTTAGACAAGCCTTTATCA 4156
chr15_MATERNA 9269 ATTCTGCTGCATGGCAGATTGGTCTTGCTGCTTTTGTGGGAATTGTTGAT 9318
v v i
HERVK#LTR/ERV 4157 ATTCTGGTGCATGGCAGATTGGTCTTGCTGATTTTGTGGGAATTATTGAT 4206
chr15_MATERNA 9319 CATCATTACCCAAGAACAAAAATCTTCCAGTTTTCAAAACTGACTACTTG 9368
v i i i
HERVK#LTR/ERV 4207 AATCATTACCCAAAAACAAAAATCTTCCAGTTTTTAAAATTGACTACTTG 4256
chr15_MATERNA 9369 GATTTTACCTAAAATTACCAGACATAAACCTTTAGAAAATGCTCTGATGG 9418
i i i
HERVK#LTR/ERV 4257 GATTTTACCTAAAATTACCAGACGTGAACCTTTAGAAAATGCTCTGACGG 4306
chr15_MATERNA 9419 TGTTTACTGATGGTTCCAGCAATGGAAAAATGGCTTACCCCAGGCCAAAA 9468
ii v ?i i
HERVK#LTR/ERV 4307 TGTTTACTGATGGTTCCAGCAATGGAAAAGCGGCTTACACNGGGCCGAAA 4356
chr15_MATERNA 9469 GAATGAATCATTGAAACTCAATATCACTCAGCTCAAAGAGCAGAATTGGT 9518
i i i ? i i
HERVK#LTR/ERV 4357 GAACGAGTCATCGAAACTCAATATCANTCGGCTCAAAGAGCAGAGTTGGT 4406
chr15_MATERNA 9519 TGCTGTTATTTCAGTGTTACAAGATTTTAATCAGCCTATTAACATTGTTT 9568
? i v i i v
HERVK#LTR/ERV 4407 TGCNGTCATTACAGTGTTACAAGATTTTGATCAGCCTATCAACATTGTAT 4456
chr15_MATERNA 9569 CAGATTCTGCATATGTAGTACAGGCTACAAAGGATGTTGAGACAGCCCTA 9618
i
HERVK#LTR/ERV 4457 CAGATTCTGCATATGTAGTACAGGCTACAAGGGATGTTGAGACAGCCCTA 4506
chr15_MATERNA 9619 ATCAAATGTAGTATGGATGATCAGTTGAATCAGCTGTTTAATTTTTTACA 9668
i i i i i v
HERVK#LTR/ERV 4507 ATCAAATATAGCATGGATGATCAGTTAAACCAGCTGTTCAATTTGTTACA 4556
chr15_MATERNA 9669 ATAAACTGTAAGAAAAAGAAATTTCCCATTTTATATTACTCATATTCAAG 9718
i i
HERVK#LTR/ERV 4557 ACAAACTGTAAGAAAAAGAAATTTCCCATTTTATATTACTCATATTCGAG 4606
chr15_MATERNA 9719 CACATACTAATTTACCAGGGCCTT-AACTAAGGGAAATGAACAAGCTGAC 9767
i - i v
HERVK#LTR/ERV 4607 CACACACTAATTTACCAGGGCCTTTAACTAAAGCAAATGAACAAGCTGAC 4656
chr15_MATERNA 9768 TTGCTAGTATCATCTGCCTTCATGGAAGCACAAGAACGTCATGCTCTGAC 9817
i v ii v i
HERVK#LTR/ERV 4657 TTGCTGGTATCATCTGCATTCATAAAAGCACAAGAACTTCATGCTTTGAC 4706
chr15_MATERNA 9818 TCATGTAAATGCAACAGGATTAAAAAATAAATTTGATATCACATGGAAAC 9867
i i i
HERVK#LTR/ERV 4707 TCATGTAAATGCAGCAGGATTAAAAAACAAATTTGATGTCACATGGAAAC 4756
chr15_MATERNA 9868 AGGCAAAAAATATTGTACAACATTGTACTGAGTGTCAAGTCCTACACCTG 9917
i iv
HERVK#LTR/ERV 4757 AGGCAAAAAATATTGTACAACATTGCACCCAGTGTCAAGTCCTACACCTG 4806
chr15_MATERNA 9918 CCCACTCAGGAGGCAGGACTTAATCCCAGAGGTTTATGTCCTAATGCATT 9967
i v i i i
HERVK#LTR/ERV 4807 CCCACTCAAGAGGCAGGAGTTAATCCCAGAGGTCTGTGTCCTAATGCGTT 4856
chr15_MATERNA 9968 ATGGCAAATGGATGTCACACATGTACCTTCATTTGGAAAATTGTCATTTG 10017
i i ?
HERVK#LTR/ERV 4857 ATGGCAAATGGATGTCACGCATGTACCTTCATTTGGAAGATTGTCATNTG 4906
chr15_MATERNA 10018 TCCATGTGATGGTTGATACTTGTTCACATTTCATATGGGCAACCTGCTAG 10067
ii i i
HERVK#LTR/ERV 4907 TCCATGTGACAGTTGATACTTATTCACATTTCATATGGGCAACCTGCCAG 4956
chr15_MATERNA 10068 ACAGAA-AATGTACTTCCCATGTTAAAAGACATTTATTATCTTGTTTTGC 10116
i - v i
HERVK#LTR/ERV 4957 ACAGGAGAAAGTACTTCCCATGTTAAAAAACATTTATTATCTTGTTTTGC 5006
chr15_MATERNA 10117 TGTCATGGGAGTTCCAGAAAAAATTAAAACAGATAATGGACCAGGCTACT 10166
v i i v
HERVK#LTR/ERV 5007 TGTCATGGGAGTTCCAGAAAAAATTAAAACTGACAATGGGCCAGGATACT 5056
chr15_MATERNA 10167 ATAGTAAAGCATTCCAAAAATTCTTAAATCAGTGGAAAATTACACATACA 10216
i ?
HERVK#LTR/ERV 5057 GTAGTAAAGCNTTCCAAAAATTCTTAAATCAGTGGAAAATTACACATACA 5106
chr15_MATERNA 10217 ACAGGAATCCCTTATAATTCCCAAGGACAGGCCATAATTGAAAGAAATAA 10266
i i v
HERVK#LTR/ERV 5107 ACAGGAATTCCTTATAATTCCCAAGGACAGGCCATAGTTGAAAGAACTAA 5156
chr15_MATERNA 10267 TAGGACACTCAAAGCTCAATTGGTTAAACAAAAA-AGGAAAAAGAGAGTA 10315
i - i iiii v
HERVK#LTR/ERV 5157 TAGAACACTCAAAGCTCAATTGGTTAAACAAAAAGAAGGGGGAGACAGTA 5206
chr15_MATERNA 10316 AGGAGTATAACACTCCCCAGATGCAACTTAATCTAGCACTCTATACTTTA 10365
i ?
HERVK#LTR/ERV 5207 AGGAGTGTANCACTCCCCAGATGCAACTTAATCTAGCACTCTATACTTTA 5256
chr15_MATERNA 10366 ATTTTTTTAAACATTTATAGAAATAAGACCACTACTTCTGCAGAACAACA 10415
v v
HERVK#LTR/ERV 5257 AATTTTTTAAACATTTATAGAAATCAGACCACTACTTCTGCAGAACAACA 5306
chr15_MATERNA 10416 TTTTACTGGTAAAAAGAACAGCCCACATGAGGGAAAACTGATTTGGTGGA 10465
i i
HERVK#LTR/ERV 5307 TCTTACTGGTAAAAAGAACAGCCCACATGAAGGAAAACTGATTTGGTGGA 5356
chr15_MATERNA 10466 AAGAT--CAAAAATAAGACATGAGAAATAGGTAAGATGATAACATGTGGG 10513
i-- i v i i v
HERVK#LTR/ERV 5357 AAGACAACAAAAATAAGACATGGGAAATAGGGAAGGTGATAACGTGGGGG 5406
chr15_MATERNA 10514 AGAGGTTTTGCTTGTGTTTCACCAGGAGAAAATCAGCTTCCTGTTTGGAT 10563
HERVK#LTR/ERV 5407 AGAGGTTTTGCTTGTGTTTCACCAGGAGAAAATCAGCTTCCTGTTTGGAT 5456
chr15_MATERNA 10564 ACCCACTAGACATTTGAAATTCTACAATGAACCCATCAGAGATGCAAAGA 10613
i i
HERVK#LTR/ERV 5457 ACCCACTAGACATTTGAAGTTCTACAATGAACCCATCGGAGATGCAAAGA 5506
chr15_MATERNA 10614 AAAGTGCCTCCGTGGAGATGGAAAACCCGCAATGGAGCACCATCGACTCG 10663
i i i vv v i
HERVK#LTR/ERV 5507 AAAGCGCCTCCGCGGAGACGGAAACACCGCAATCGAGCATCATCGACTCG 5556
chr15_MATERNA 10664 CCAGGTGAACAAAATGGTGATATCAGAAGAACAGATGAAGTTGCCATCCA 10713
vi
HERVK#LTR/ERV 5557 CAGGGTGAACAAAATGGTGATATCAGAAGAACAGATGAAGTTGCCATCCA 5606
chr15_MATERNA 10714 CCAAGAAAGTGGAGCTGCTGACCTGGGCCCAGCTAAAGAAGCTGACACAG 10763
i i i i
HERVK#LTR/ERV 5607 CCAAGAAAGCGGAGCCGCCGACCTGGGCCCAACTAAAGAAGCTGACACAG 5656
chr15_MATERNA 10764 TTAGCTGAAAAAAAGCCTGAAGAATACAAGGTTAACACAAACTCCAGAGA 10813
- i i v i
HERVK#LTR/ERV 5657 TTAGCTGAAAAAA-GCCTGGAGAACACAAGGGTGACACAAACTCCAGAGA 5705
chr15_MATERNA 10814 ATATGCTGCTTGCAGCTTTAATGATTGTACCAACGGTGGTAAGTCTCCCT 10863
i i
HERVK#LTR/ERV 5706 ATATGCTGCTTGCAGCTTTGATGATTGTATCAACGGTGGTAAGTCTCCCT 5755
chr15_MATERNA 10864 ATGTCTGCAGGAGCAGCTGCAGCTAATTATACTTACTTGGCCTATGTGCC 10913
i v
HERVK#LTR/ERV 5756 ATGTCTGCAGGAGCAGCTGCAGCTAACTATACTTACTGGGCCTATGTGCC 5805
chr15_MATERNA 10914 TTTCCCACCCTTAATTCGGACAGTCACTTGGATAGATAATCCTATTGAAG 10963
i i v i
HERVK#LTR/ERV 5806 TTTCCCGCCCTTAATTCGGGCAGTCACATGGATGGATAATCCTATTGAAG 5855
chr15_MATERNA 10964 TATATGTTAATAATAGTGCATGGGTACCAGGCCCCACAGATGACCGTGGC 11013
i v i iv
HERVK#LTR/ERV 5856 TATATGTTAATGATAGTGCATGGGTACCTGGCCCCACAGATGATCGCTGC 5905
chr15_MATERNA 11014 CCTGCCCAACCTGAAGAAGAAGGAATGATGATAAACATTTCCATTGGGTA 11063
v i i i
HERVK#LTR/ERV 5906 CCTGCCAAACCTGAGGAAGAAGGGATGATGATAAATATTTCCATTGGGTA 5955
chr15_MATERNA 11064 TCATTATCCTCCTATTTGCCTGGGGAAAGCACCAGGATGCTTAATACCTA 11113
i i i i i i
HERVK#LTR/ERV 5956 TCGTTATCCTCCTATTTGCCTAGGGAGAGCACCAGGATGTTTAATGCCTG 6005
chr15_MATERNA 11114 CAACCCAAAATTGGTTGGTAGAAGTACCTACTGTCAGTGCCATCAGCAGA 11163
ii ? i i
HERVK#LTR/ERV 6006 CAGTCCAAAATTGGTTGGTAGAAGTACCTACTGTCAGTNCCACCAGTAGA 6055
chr15_MATERNA 11164 TTTACTTATCACACGGTAAGTGGAATGTCACTCAGGCCACAGATAAATAA 11213
i i i i i i i v
HERVK#LTR/ERV 6056 TTCACTTATCACATGGTAAGCGGGATGTCACTCGGGCCACGGGTAAATTA 6105
chr15_MATERNA 11214 TTTACAGGATTTTTCTTATCAAAGATCATTACAATCTAGGCCTAAGGGGA 11263
i v i i
HERVK#LTR/ERV 6106 TTTACAGGACTTTTCTTATCAAAGATCATTAAAATTTAGGCCTAAAGGGA 6155
chr15_MATERNA 11264 AGCCTTGCCCCAAGGAAATTCCCAAAGAATCAAAAAGCCCAGAAGTCCTA 11313
i ii v ii
HERVK#LTR/ERV 6156 AACCTTGCCCCAAGGAAATTCCCAAAGAATCAAAAGACACAGAAGTTTTA 6205
chr15_MATERNA 11314 GTTTGGGAAGAATGTGTGGCTGATACTGCAGTGGTACTACAAAACAATGA 11363
i v i i i
HERVK#LTR/ERV 6206 GTTTGGGAAGAATGTGTGGCCGATAGTGCGGTGATATTACAAAACAATGA 6255
chr15_MATERNA 11364 ATTTGGAACTATTATAAACTGGGCTCCTTGAGGCCAATTATATCATAATT 11413
i i i v i i v i ii
HERVK#LTR/ERV 6256 ATTCGGAACTATTATAGATTGGGCACCTCGAGGTCAATTCTACCACGATT 6305
chr15_MATERNA 11414 GTGCAGGCCAGACTCAACCATGTTGACAGGTCC-CA--TCCATCTGGCCC 11460
ii i v i ii i i-- i v - -- vvi i -
HERVK#LTR/ERV 6306 GCACGGGACAAACTCAGTCGTGTC--CAAGTGCACAAGTGAGTCCGGCC- 6352
chr15_MATERNA 11461 ATTAAT-CTGGCCTAT--GAAAGGCTGGACCAGGTT---TATAGTAGGTT 11504
i i -vi i i v-- v i v ivv ---i iv ii
HERVK#LTR/ERV 6353 GTTGATAGCGACTTAACAGAAAGTCTAGACAAACATAAGCATAAAAAATT 6402
chr15_MATERNA 11505 AGAATCACTCTATCCATGGAAATGGGG 11531
v i v i v i
HERVK#LTR/ERV 6403 ACAGTCTCTCTACCCTTGGGAATGGGG 6429
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 8.35
Transitions / transversions = 2.70 (219/81)
Gap_init rate = 0.01 (18 / 3371), avg. gap size = 3.28 (59 / 18)
+ 6447 11.9 0.9 0.2 chr15_MATERNAL_p_2-50000:. 11532 12434 (37565) + HERVK-int LTR/ERVK 6626 7534 (2) 12
ANNOTATION EVIDENCE:
6447 11.88 0.88 0.22 chr15_MATERNAL_p_2-50000:. 11532 12434 33541 + HERVK LTR/ERVK 6626 7534 2
6447 11.88 0.88 0.22 chr15_MATERNAL_p_2-50000:. 11532 12434 (33541) HERVK#LTR/ERVK 6626 7534 (2) m_b1s701i7
chr15_MATERNA 11532 TGTGTAAAACCCCCTTATATGCTAGTTGTAGGAAACAGAGTTATTAAACC 11581
i i i v
HERVK#LTR/ERV 6626 TGCGTAAAGCCCCCTTATATGCTAGTTGTAGGAAATATAGTTATTAAACC 6675
chr15_MATERNA 11582 AGATTCCCAAACTATAACCTGTGAAAATTGTAGATTGTTTACTTGCATTG 11631
i
HERVK#LTR/ERV 6676 AGACTCCCAAACTATAACCTGTGAAAATTGTAGATTGTTTACTTGCATTG 6725
chr15_MATERNA 11632 ATTCAACTTTGGATTGGCAACACCGTATTCTGCTAGTGAGGGCAAGAGAG 11681
vi i i i
HERVK#LTR/ERV 6726 ATTCAACTTTTAATTGGCAGCACCGTATTCTGCTGGTGAGAGCAAGAGAG 6775
chr15_MATERNA 11682 GGCATGGGGATCCCTGTGTCCATGGACCAACAGTGGGAGGGTTCCCCATC 11731
i v i v vi v
HERVK#LTR/ERV 6776 GGCGTGTGGATCCCTGTGTCCATGGACCGACCGTGGGAGGCCTCGCCATC 6825
chr15_MATERNA 11732 CATCCATATTTTAACAGAAGTATTAAAAGGAGTTCTAACTAGATCCAAAA 11781
i i v v v
HERVK#LTR/ERV 6826 CGTCCATATTTTGACTGAAGTATTAAAAGGCGTTCTAAATAGATCCAAAA 6875
chr15_MATERNA 11782 GATTCATTTTTACTTTGATTGCAGTGATTATGGGTCTTA-------TCAC 11824
i -v -------
HERVK#LTR/ERV 6876 GATTCATTTTTACTTTAATTGCAGTGATTATGGG-ATTAATTGCAGTCAC 6924
chr15_MATERNA 11825 AGCTACTGCTGCGGCTGCTGGAATTGCTTTACACTCCTCTGTTCAAACTG 11874
v v i? v i ? i i i? ?
HERVK#LTR/ERV 6925 AGCTACGGCTGCTGTNGCAGGAGTTGCNTTGCACTCTTCTGTTCAGNCNG 6974
chr15_MATERNA 11875 CAGAATATGTGAATAATTGGCAAAAGAATTCCTCAAAATTGTGGAATTCT 11924
i i v v v i iv i v
HERVK#LTR/ERV 6975 TAAACTTTGTTAATGATTGGCAAAAGAATTCTACAAGATTGTGGAATTCA 7024
chr15_MATERNA 11925 CATACCCAA-ATAGATCAAAAATTGGCAAACCAAATTAATGATCTTAGAC 11973
- i i i- v i
HERVK#LTR/ERV 7025 CA-ATCTAGTATTGATCAAAAATTGGCAAATCAAATTAATGATCTTAGAC 7073
chr15_MATERNA 11974 AAACTGTAATTTGGATGGGAGATAGGCTCATGAGCTTGGAATACCTTTTT 12023
v i i i i v i
HERVK#LTR/ERV 7074 AAACTGTCATTTGGATGGGAGACAGGCTCATGAGCTTAGAACATCGTTTC 7123
chr15_MATERNA 12024 CAGTTACAGTGTGACTGGAATATATCAGATTTTTGTATTACACCTCGAGC 12073
ii i
HERVK#LTR/ERV 7124 CAGTTACAGTGTGACTGGAATACGTCAGATTTTTGTATTACACCCCGAGC 7173
chr15_MATERNA 12074 TTATAATGAATCTGAACATCACTAGGACATGGTGAGATGCCATCTACAAG 12123
i i i v i i
HERVK#LTR/ERV 7174 TTATAATGAGTCTGAGCATCACTGGGACATGGTTAGACGCCATCTACAGG 7223
chr15_MATERNA 12124 GAAGAGAAGATAATCTTACCTTAGAGATTTCAAAATTAAAAGAACAAATT 12173
i i v v
HERVK#LTR/ERV 7224 GAAGAGAAGATAATCTCACTTTAGACATTTCCAAATTAAAAGAACAAATT 7273
chr15_MATERNA 12174 TTTGAGGCATCAAAAGCCCAGTTAAATCTGGTACCAGAAACTGAGGCAAT 12223
i i v i i i
HERVK#LTR/ERV 7274 TTCGAAGCATCAAAAGCCCATTTAAATTTGGTGCCAGGAACTGAGGCAAT 7323
chr15_MATERNA 12224 CATGAAAGCTGTTGATAGCCTCACAAATCTTAACCCTGCCACTTGGGTTG 12273
iiiii i i i i i i
HERVK#LTR/ERV 7324 CGCAGGAGTTGCTGATGGCCTCGCAAATCTTAACCCTGTCACTTGGGTTA 7373
chr15_MATERNA 12274 AAAACATTGGAAGTTCCACCATTGAAATTTTTGTATTAATCCTTGTATGT 12323
i v i ? i v v i i i
HERVK#LTR/ERV 7374 AGACCATCGGAAGTNCCACTATTGTAAATTTCGTATTAATCCTTGTGTGC 7423
chr15_MATERNA 12324 CCGTTCTCTCTGTTGTTAGTCTACAGGTGTATCCAGCAGCTCTGGAGAGA 12373
i v i
HERVK#LTR/ERV 7424 CTGTTCTGTCTGTTGTTAGTCTACAGGTGTATCCAGCAGCTCCGGAGAGA 7473
chr15_MATERNA 12374 CAGTGACCAGTGAGAATGGACCATGATGACCATGGCAGTTTTGTCAAAAA 12423
i i i i v i
HERVK#LTR/ERV 7474 CAGCGACCAGCGAGAACGGGCCATGATGACGATGGCGGTTTTGTCAAAAA 7523
chr15_MATERNA 12424 GAAAAGGGGGA 12434
HERVK#LTR/ERV 7524 GAAAAGGGGGA 7534
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 10.56
Transitions / transversions = 2.40 (72/30)
Gap_init rate = 0.00 (4 / 902), avg. gap size = 2.50 (10 / 4)
+ 8173 7.7 2.7 0.0 chr15_MATERNAL_p_2-50000:. 12437 13441 (36558) + LTR5A LTR/ERVK 1 1033 (0) 12
ANNOTATION EVIDENCE:
8173 7.66 2.71 0.00 chr15_MATERNAL_p_2-50000:. 12437 13441 34392 + LTR5A LTR/ERVK 1 1033 0
8173 7.66 2.71 0.00 chr15_MATERNAL_p_2-50000:. 12437 13441 (34392) LTR5A#LTR/ERVK 1 1033 (0) c_b1s401i1
chr15_MATERNA 12437 TGTAGGGAAAAGA----GAGATCAGACTGTTACTGTGTCTATGTAGAAAG 12482
---- i
LTR5A#LTR/ERV 1 TGTAGGGAAAAGAAAGAGAGATCAGACTGTCACTGTGTCTATGTAGAAAG 50
chr15_MATERNA 12483 GGAAGACATAAGAAATTCCATTTTGA------TCTGTACCTTGAAAAATT 12526
i i ------i i i v
LTR5A#LTR/ERV 51 GGAAGACATAAGAGACTCCATTTTGAAAAAGACCTGTACTTTAAACAATT 100
chr15_MATERNA 12527 GTTTTGC-TGAGATGCTGTTAATTTGTAACTTTGCCCCAGCCACTTTGCC 12575
i - i i
LTR5A#LTR/ERV 101 GCTTTGCNTGAGATGTTGTTAATTTGTAGCTTTGCCCCAGCCACTTTGCC 150
chr15_MATERNA 12576 CCA---ACTTTGA-----------GCTCACAAAAACATGTGTTATATGGA 12611
--- ----------- i i
LTR5A#LTR/ERV 151 CCAGCCACTTTGACCCAACCTGGAGCTCACAAAAACATGTGTTGTATGAA 200
chr15_MATERNA 12612 ATCAAGGTTTAAGAGATCTAGGGCTGGGCAGGATGTGCCTTGCTAACAAA 12661
i v i i
LTR5A#LTR/ERV 201 ATCAAGGTTTAAGGGATCTAGGGCTGTGCAGGACGTGCCTTGTTAACAAA 250
chr15_MATERNA 12662 ATATTTACAAGCAGTATGCTTGGTAAAACTCATTGCCATTCTCTAGTCTC 12711
i i v i
LTR5A#LTR/ERV 251 ATGTTTACAAGCAGTATACTTGGTAAAAGTCATCGCCATTCTCTAGTCTC 300
chr15_MATERNA 12712 AATAAACCAGGGGCACAATGCACTGCAAAAAGCCACAGGGACCTCTGCCC 12761
ii i
LTR5A#LTR/ERV 301 AATAAACCAGGGGCACAATGCACTGCGGAAAGCCGCAGGGACCTCTGCCC 350
chr15_MATERNA 12762 TGGAAAGCCGGGTATTGTCCAAGGTTTGTCCCCATGTGATAGTCTGAAAT 12811
v v v
LTR5A#LTR/ERV 351 TTGAAAGCGGGGTATTGTCCAAGGTTTCTCCCCATGTGATAGTCTGAAAT 400
chr15_MATERNA 12812 GTGGCCACATGGGATGAGAAAGACAGGACTGTCCCCCAGCCTGACACCTG 12861
i v i vv i i i
LTR5A#LTR/ERV 401 ATGGCCTCGTGGGATGAGAAAGACCTGACCGTCCCCCAGCCCGACACCCG 450
chr15_MATERNA 12862 TAAAGGGTCTGTGCTGAGGTGGATTAGTAAAAGAGGAAAGCCTCTTGCAG 12911
LTR5A#LTR/ERV 451 TAAAGGGTCTGTGCTGAGGTGGATTAGTAAAAGAGGAAAGCCTCTTGCAG 500
chr15_MATERNA 12912 TTGAGAT-AGAGGAAGGCCACTGTTTCCTGCCTGCCCCTGGGAACTTGAT 12960
i- i vi
LTR5A#LTR/ERV 501 TTGAGACGAGAGGAAGGCCACTGTCTCCTGCCTGCCCCTGGGAACTGAAT 550
chr15_MATERNA 12961 GTCTCGGTATAAAACCCGATTGTACACCTGTTCAATTCTGAGATAAGAGG 13010
ii i i
LTR5A#LTR/ERV 551 GTCTCGGTATAAAACCCGATTGTACATTTGTTCAATTCTGAGATAGGAGA 600
chr15_MATERNA 13011 AAAACTGCCCTATGGTGGGAGGCAAGACATGTTGGCAGCAATGCTGCCTC 13060
i i i v i
LTR5A#LTR/ERV 601 AAAACCGCCCTATGGCGGGAGGCGAGACATGTTTGCAGCAATGCTGCCTT 650
chr15_MATERNA 13061 GTTATTCTTTACTCCACTGAGATGTTTGGGTGGGAAGAAACATAAATCTG 13110
i ii
LTR5A#LTR/ERV 651 GTTATTCTTTACTCCGCTGAGATGTTTGGGTGGAGAGAAACATAAATCTG 700
chr15_MATERNA 13111 GCCCACGTGTACATCCAGGCATAGTACCTCCCCTTGAACTTAATTATGAT 13160
i i i ? i i
LTR5A#LTR/ERV 701 GCCTACGTGCACGTCCAGNCATAGTACCTTCCCTTGAACTTAATTATGAC 750
chr15_MATERNA 13161 ATAGATTCTTTTGCTCACGTGTTTTTTTGCTGACCTTCTCCTTATTATCA 13210
i ?
LTR5A#LTR/ERV 751 ATAGATTCTTTTGCTCACATGTTTTNTTGCTGACCTTCTCCTTATTATCA 800
chr15_MATERNA 13211 CCCTGCTCTCCTACTGCATTCCTCTT-GCTGAGATAATGAAAATAATACT 13259
i i - i v
LTR5A#LTR/ERV 801 CCCTGCTCTCCTACTACATTCCTTTTTGCTGAAATAATGAAAATAATAAT 850
chr15_MATERNA 13260 CAATAAAAACTGAGGGAACTCAGAGACCGGTGCTGGTGCAGGTCCTTGGT 13309
i i
LTR5A#LTR/ERV 851 CAATAAAAACTGAGGGAACTCAGAGGCCGGTGCCGGTGCAGGTCCTTGGT 900
chr15_MATERNA 13310 ATGCTGAGTGCAGGTCCCCTGGGCCCACTATTCTTTCTCTATAGTTTGTC 13359
i i v i v v
LTR5A#LTR/ERV 901 GTGCTGAGCGCCGGTCCCCTGGGCCCACTGTTGTTTCTCTATACTTTGTC 950
chr15_MATERNA 13360 T-TGTATCTTATTTCTTTTCTCAGTCTCTCATCCCACCTGATGAGATATA 13408
- i i i iv v
LTR5A#LTR/ERV 951 TCTGTGTCTTATTTCTTTTCTCAGTCTCTCGTCCCACCCGACTAGAAATA 1000
chr15_MATERNA 13409 CCCACAGGTGTGGAGGGCCAGGCCACCCCTTCA 13441
v
LTR5A#LTR/ERV 1001 CCCACAGGTGTGGAGGGGCAGGCCACCCCTTCA 1033
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 6.14
Transitions / transversions = 3.17 (57/18)
Gap_init rate = 0.01 (8 / 1004), avg. gap size = 3.50 (28 / 8)
+ 1903 24.3 8.7 0.8 chr15_MATERNAL_p_2-50000:. 13445 14126 (35873) + L1MC3 LINE/L1 6585 7295 (490) 10
ANNOTATION EVIDENCE:
877 29.11 11.42 1.23 chr15_MATERNAL_p_2-50000:. 13445 13931 33048 + L1MC4a_3end LINE/L1 1332 1874 755
877 29.11 11.42 1.23 chr15_MATERNAL_p_2-50000:. 13445 13931 (33048) L1MC4a_3end#LINE/L1 1332 1874 (755) m_b1s551i4
chr15_MATERNA 13445 ATAAACTTATGTTTAGTTTAATATAGATACACACAGTTCTACATAGAAA- 13493
i i v -- i v v i v vv i i -
L1MC4a_3end#L 1332 ATGAACTCATGGTT--TTTAACATATATACAGATAGATAGATACAGAAAT 1379
chr15_MATERNA 13494 ACTTTATAATCAGCTGTGTATAGGTAGGTTAG-ACACACACATATACTTC 13542
vvv iviivv ivi i - i i i
L1MC4a_3end#L 1380 AAGATATAGATGTATGTGTATGCATGGGTTAGTATACATACATATATTTC 1429
chr15_MATERNA 13543 CTAGCATTG----CTAATGAGGGACAAGA----------------TA-CA 13571
vi ---- i - v v ---------------- -
L1MC4a_3end#L 1430 CTAGCTCTGTCCGCTGA-GAGGGCCTAGAAGCAATGACACCCCAGTAGCA 1478
chr15_MATERNA 13572 ATGTGCTAATTCAACAGCCAGATGTAAGTTTTCC--TACCATTCT----- 13614
v vv iii i iv v vi iiv-- -----
L1MC4a_3end#L 1479 ATGAGCACACCTAGCGCCCAGATCTTGGTTTCTAAATACCATTCTCCAAT 1528
chr15_MATERNA 13615 GAAAGGAATCAGG-CTCTTTGAAGAAATGTCTGATACTAGAACTGGGACA 13663
i i - i i v v i ii i
L1MC4a_3end#L 1529 AAAAGGAACCAGGGCTCCTTGGAGAAATGGCTGATTCCAGGGCTGGGGCA 1578
chr15_MATERNA 13664 GT--AAATATAGGA---GCCAGGATAATCTTGAAGTATCAGAAAGTAAG- 13707
v-- i i --- v vv vi ii -
L1MC4a_3end#L 1579 GGGAAAATACAAGATGAGCCTGGAACATCTTGTGGTGCCAGAAAGTAAGG 1628
chr15_MATERNA 13708 ---TACT--AAAAAAAATTAAAATATATCAAAGAAAAATAAGAGCCAA-- 13750
--- i -- ?i viiiii i i iii v i i --
L1MC4a_3end#L 1629 AAGTGCTCAAAAAANGATGGGGGCATGTCGAAAGGACACAGGAGCCAACC 1678
chr15_MATERNA 13751 TAATAACAGCTACCGAAGGCCAACACAGGAATGAATTGTGCAACA----- 13795
i - iv v i v v? v ii v v -----
L1MC4a_3end#L 1679 TGA-AGGAGCTCCCAATGGCCAAANCTGGAACAATTTGAGCAACAAAATA 1727
chr15_MATERNA 13796 --CAATGCTGCAGTGTTGAATAATAACTGA-AGCTTAAAGTAATTATCTA 13842
--i v -- i? i v iv - vv i v i
L1MC4a_3end#L 1728 AATAATGAT--AGTANTGGATTATAACCCATAGAATAAAATAAATATCCA 1775
chr15_MATERNA 13843 GGTGTCTGTATTTGTATACATAGGTGA--------ATAAGCTAATGGAGT 13884
v v ii i vi v ii i -------- iiv i v
L1MC4a_3end#L 1776 TGAGTCCATACTGATATAAATAAATAATTGAATAAATAAATAAATGGGGG 1825
chr15_MATERNA 13885 TGCATAGAAA--TCTCCTTTGCAAAAGAATTCCAAATAATTGATGTAGA 13931
v v vi v -- i i i i? v vi
L1MC4a_3end#L 1826 AGAAGGGACAGCTCTTCCTTACAGNAGAATTCCAATTAATAAATGTAGA 1874
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 36.10
Transitions / transversions = 1.39 (79/57)
Gap_init rate = 0.05 (24 / 486), avg. gap size = 2.83 (68 / 24)
1903 23.03 7.93 0.74 chr15_MATERNAL_p_2-50000:. 13589 14126 32853 + L1MC3_3end LINE/L1 1463 2042 490
1903 23.03 7.93 0.74 chr15_MATERNAL_p_2-50000:. 13589 14126 (32853) L1MC3_3end#LINE/L1 1463 2042 (490) m_b1s551i5
chr15_MATERNA 13589 CCAGATGTAAGTTT-TCCTACCATTCT-----GAAAGGAATCAGG-CTCT 13631
v vi - vv -----i i - i
L1MC3_3end#LI 1463 CCAGATCTTGGTTTCTAATACCATTCTCCAATAAAAGGAACCAGGGCTCC 1512
chr15_MATERNA 13632 TTGAAGAAATGTCTGATACTAGAACTGGGACAGTAAATATAG-----GAG 13676
i v v i i v v-----
L1MC3_3end#LI 1513 TTGGAGAAATGGCTGATTCTAGGACTGGGGCAGGAAATATACAAGATGAG 1562
chr15_MATERNA 13677 CCAGGATAATCTTGAAGTATCAGAAAGTAAG----TACTAAAAAAAATTA 13722
v vv v ii ---- i v iiv
L1MC3_3end#LI 1563 CCTGGAGCATCTTGTAGTGCCAGAAAGTAAGGAAGTGCTCAAAAAAACCC 1612
chr15_MATERNA 13723 AAA----------TATATCAAAGAAAAATAAGAGCCAATAATAACAGCTA 13762
v ---------- i ii v i i iviv v v
L1MC3_3end#LI 1613 ACAATGATGGGGGTATGTCAAAGGGACACAGGAGCCAACTGAAAGAGCTC 1662
chr15_MATERNA 13763 CCGAAGGCCAACACAGGAATGAATTGTGCAACACAATGC-T---GCAGTG 13808
i v vi v ii v v v iv- --- i i
L1MC3_3end#LI 1663 CCAATGGCCAAAGCTGGAACAATTTGAGCAACAAAATAAATAAAGTAGTA 1712
chr15_MATERNA 13809 TTGAATAATAACT-GAAGCTTAAAGTAATTATCTAGGTGTCTGTATTTGT 13857
i v i-i iv i v i v v ii i vi
L1MC3_3end#LI 1713 TTGGATTATAACCCAAAGTATAAAATAAATATCCATGAGTCCATACTGAT 1762
chr15_MATERNA 13858 ATACATAGGTGA--------ATAAGCTAATGGAGTTGCATAGA--AATCT 13897
v ii -------- iiv i vv v v --
L1MC3_3end#LI 1763 ATAAATAAATGATTGAATAAATAAATAAATGGGGGAGAAGAGACAAATCT 1812
chr15_MATERNA 13898 CCTTTGCAAAAGAATTCCAAATAATTGATGTAGACACTCAGCCATCAGGA 13947
iv i v i v v i i
L1MC3_3end#LI 1813 CCCGTGCAGAAGAATTCCAAATAATTTATGTAGATACTCCGCCCTCAAGG 1862
chr15_MATERNA 13948 AGGTGGAGC-CAACTCCTCACTCCATGAGTGTGGGCTCTGCATAGTGACT 13996
-i i v i vi
L1MC3_3end#LI 1863 AGGTGGAGCATAACTCCCCACTCCTTAAGTGTGGGCTGCGCATAGTGACT 1912
chr15_MATERNA 13997 TGCTCCAAAAGAACACATGCAGTATGGACAAGGAGGAAAAA----TAACT 14042
v i v ii ---- v i i ----
L1MC3_3end#LI 1913 TCCTTCCAAAGAGTACA----GTATGGAAAGGGGGGAAAAAAGAGTAACT 1958
chr15_MATERNA 14043 TCACAGTGGAGAAACCTGACAAACAGTAGCTCTGCCAAATGATCCAAGTG 14092
i v v v ii v i v
L1MC3_3end#LI 1959 TTACAGTGGAGAAACCTGACAAACACTACCTCAGCCAGGTGATCAAGGTC 2008
chr15_MATERNA 14093 AACATCAAAAATGACAGTTTACCTTGAGAACATG 14126
v i i iv i iv v ii
L1MC3_3end#LI 2009 AACATCAACAGTGATAAGTCATGTTGATAGTATG 2042
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 27.33
Transitions / transversions = 1.16 (66/57)
Gap_init rate = 0.03 (17 / 537), avg. gap size = 2.94 (50 / 17)
+ 1354 17.9 5.7 10.2 chr15_MATERNAL_p_2-50000:. 14133 14536 (35463) + L1MC3 LINE/L1 7400 7784 (1) 10
ANNOTATION EVIDENCE:
1354 17.91 5.72 10.15 chr15_MATERNAL_p_2-50000:. 14133 14536 32443 + L1MC3_3end LINE/L1 2147 2531 1
1354 17.91 5.72 10.15 chr15_MATERNAL_p_2-50000:. 14133 14536 (32443) L1MC3_3end#LINE/L1 2147 2531 (1) m_b1s551i6
chr15_MATERNA 14133 AAATGGGGGACATTCTACAAAATTCCTGACCAATCCTCCTCAGTACTGTC 14182
v i v i v iv
L1MC3_3end#LI 2147 AATTGAGGGACATTCTACAAAATACCTGACCAGTACTCCTCAAAACTGTC 2196
chr15_MATERNA 14183 AAGGTCATCATGAG-ATGGAAAGCCTGACACACTGTCACAGCCAGGAAGA 14231
vi i- v i v v i i
L1MC3_3end#LI 2197 AAGGTCATCAAAAACAAGGAAAGTCTGAGAAACTGTCACAGCCAAGAGGA 2246
chr15_MATERNA 14232 GCCTATG------TGATGACTACATGTCGTGCGGGATCCTGGATGGGATC 14275
v ------ i v vi i v
L1MC3_3end#LI 2247 GCCTAAGGAGACATGACGACTAAATGTAATGTGGTATCCTGGATGGGATC 2296
chr15_MATERNA 14276 CTGGGTCAGAGTAAG-ACA--------GAACTAAGGGAGTCCAAATGAAA 14316
iv iv - --------i i i ii i i
L1MC3_3end#LI 2297 CTGGAACAGAAAAAGGACATTAGGTAAAAACTAAGGAAATCTGAATAAAG 2346
chr15_MATERNA 14317 TGTGAACTTTAGTTAATAATAGTCTATCAGTATTGGTTCATTAACTGTGA 14366
i i i v i i
L1MC3_3end#LI 2347 TATGGACTTTAGTTAATAATAATGTATCAATATTGGTTCATTAATTGTGA 2396
chr15_MATERNA 14367 CAAATTATGTAAGATATTAATAAGCCATGTGAGACACACTGATAGAAGAT 14416
--- ------------- --------- i iv
L1MC3_3end#LI 2397 CAAAT---GTA-------------CCAT---------ACTAATGTAAGAT 2421
chr15_MATERNA 14417 GTTAATGA--GAGGAAACTAGGTTGTGGC-TACATGGGAAATCTCTGCTT 14463
i -- i i - v- i v ---
L1MC3_3end#LI 2422 GTTAATAATAGGGGAAACTGGGT-GTGGGGTATATGGGAACTCTCTG--- 2467
chr15_MATERNA 14464 TTTTTTTTTTTTTTTTTTTGGTAATTTCTGTGTAAGTAAAAAAAAAAGAT 14513
---------- vi v i v i i v i vv vv v--
L1MC3_3end#LI 2468 ----------TACTATCTTCGCAATTTTTCTGTAAATCTAAAACTAT--T 2505
chr15_MATERNA 14514 GTAAAATAAAA-CTTTATTT--AAAA 14536
v -v --
L1MC3_3end#LI 2506 CTAAAATAAAAAGTTTATTTTNAAAA 2531
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 20.31
Transitions / transversions = 1.24 (36/29)
Gap_init rate = 0.12 (49 / 403), avg. gap size = 1.29 (63 / 49)
+ 3210 11.3 5.9 0.0 chr15_MATERNAL_p_2-50000:. 15419 15862 (34137) + MER4A1 LTR/ERV1 1 472 (0) 15
ANNOTATION EVIDENCE:
3210 11.26 5.94 0.00 chr15_MATERNAL_p_2-50000:. 15419 15862 31971 + MER4A1 LTR/ERV1 1 472 0
3210 11.26 5.94 0.00 chr15_MATERNAL_p_2-50000:. 15419 15862 (31971) MER4A1#LTR/ERV1 1 472 (0) c_b1s401i2
chr15_MATERNA 15419 TGTGAAGGGAAAATAAATCTTGGGGACCCAAAATCGCTAAGCTAAAGGGA 15468
i v i
MER4A1#LTR/ER 1 TGTGAAAGGAAAATAAATCTTGGGGCCCCAAAATCACTAAGCTAAAGGGA 50
chr15_MATERNA 15469 AAAGTCAAGCTGGGAACTGCTTAGGGCAAATCTGCCTCCCATTCTATCCA 15518
i i
MER4A1#LTR/ER 51 AAAGTCAAGCTGGGAACTGCTTAGGGCAAACCTGCCTCCCATTCTATTCA 100
chr15_MATERNA 15519 AAGTCACCCATCTGCTCACCGAGACAAATGCATATCTGATTGCCTCATTT 15568
v i i v
MER4A1#LTR/ER 101 AAGTCACCCCTCTGCTCACTGAGATAAATGCATATCTGATTGCCTCCTTT 150
chr15_MATERNA 15569 GGAGAGGGTAATCAGCAAAGCAAAAGAATGAAACCATTTGTCTCTTACCT 15618
v v vv v i
MER4A1#LTR/ER 151 GGAGAGGCTAATCAGAAACTCAAAAGAATGCAACCATTTGTCTCTCACCT 200
chr15_MATERNA 15619 ACTTATGACCTGGAAGCCCCCT--------------GTCTGGCCTT---- 15650
i i --------------? iv ----
MER4A1#LTR/ER 201 ACCTGTGACCTGGAAGCCCCCTCCCCGCTTCGAGTCNTCCCGCCTTTGCT 250
chr15_MATERNA 15651 ---------CTCACCTTTCTGGACTGAACCAATGTACATCTTGCACATAT 15691
--------- i i i i ? i i i
MER4A1#LTR/ER 251 TCGAGTTGTCCCGCCTTTCCGGACCGAACCAATGTNCATCTTACATATGT 300
chr15_MATERNA 15692 TGATTGATGTCTCATGTCTCCCTAAAGTGTATAAAACCAAGCTGTGCCTC 15741
i i
MER4A1#LTR/ER 301 TGATTGATGTCTCATGTCTCCCTAAAATGTATAAAACCAAGCTGTGCCCC 350
chr15_MATERNA 15742 GACCACCTTGGGCCCATGTTGTCAGGACTTCCTGAGGAGGCATCATGGGG 15791
v i i vv ii i v
MER4A1#LTR/ER 351 GACCACCTTGGGCACATGTCGTCAGGACCTCCTGAGGCTGTGTCACGGGC 400
chr15_MATERNA 15792 GCGCATCCTCAAACTTGGCAAG-TAAACTTTCTAAAAAATCCGAGAGCTG 15840
i v i- vv v i v
MER4A1#LTR/ER 401 GCGCGTCCTCAACCTTGGCAAAATAAACTTTCTAAATTAACTGAGACCTG 450
chr15_MATERNA 15841 TTTCAGATTTTCAGGGTTCATA 15862
i i i
MER4A1#LTR/ER 451 TCTCAGATTTTCGGGGTTCACA 472
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 10.13
Transitions / transversions = 1.67 (30/18)
Gap_init rate = 0.01 (4 / 443), avg. gap size = 7.00 (28 / 4)
+ 47 33.9 0.5 2.1 chr15_MATERNAL_p_2-50000:. 16548 16739 (33260) + (CTAACC)n Simple_repeat 1 189 (0) 16
ANNOTATION EVIDENCE:
47 33.92 0.52 2.12 chr15_MATERNAL_p_2-50000:. 16548 16739 30683 + (CTAACC)n Simple_repeat 1 189 0
47 33.92 0.52 2.12 chr15_MATERNAL_p_2-50000:. 16548 16739 (30683) (CTAACC)n#Simple_repeat 1 189 (0) m_b1s252i0
chr15_MATERNA 16548 CTAATCCTAACCCTAACCCTGTCCCAAGACTTTGACCCTGAACCTAAACA 16597
i iv v - ii i - iv v
(CTAACC)n#Sim 1 CTAACCCTAACCCTAACCCTAACCCTA-ACCCTAACCCT-AACCCTAACC 48
chr15_MATERNA 16598 CTGATCCCT-ACCCTGGGCCCCAATTCTCACCCTTACTTTGACCCTGATT 16646
- v - -ii i ii v v ii i i ii
(CTAACC)n#Sim 49 CT-AACCCTAACCCT-AACCCTAACCCTAACCCTAACCCTAACCCTAACC 96
chr15_MATERNA 16647 TTGATCTTGACCCTGACCTTGACCCCACCTCTAACCATATTTCTGGCCCT 16696
i i i i i i i i i v i v vii ii
(CTAACC)n#Sim 97 CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT 146
chr15_MATERNA 16697 GACTCTGACCCAGATCCTAATCCTAACCCTAACCCTAACCCTA 16739
i i i vi i i
(CTAACC)n#Sim 147 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA 189
Matrix = Unknown
Transitions / transversions = 3.36 (37/11)
Gap_init rate = 0.03 (5 / 191), avg. gap size = 1.00 (5 / 5)
+ 11 25.3 3.2 4.9 chr15_MATERNAL_p_2-50000:. 16716 16777 (33222) + (ATCTCT)n Simple_repeat 1 61 (0) 17 *
ANNOTATION EVIDENCE:
11 25.33 3.23 4.92 chr15_MATERNAL_p_2-50000:. 16716 16777 30645 + (ATCTCT)n Simple_repeat 1 61 0
11 25.33 3.23 4.92 chr15_MATERNAL_p_2-50000:. 16716 16777 (30645) (ATCTCT)n#Simple_repeat 1 61 (0) m_b1s252i1
chr15_MATERNA 16716 ATC-CTAACCCTAACCCTAACCCTATTATTATCTTTATGATCTATCTCTA 16764
- v i v i v i ivi i -v -
(ATCTCT)n#Sim 1 ATCTCTATCTCTATCTCTATCTCTATCTCTATCTCTAT-CTCTATCTCT- 48
chr15_MATERNA 16765 ATCT-TACCCTCTA 16777
- -i
(ATCTCT)n#Sim 49 ATCTCTA-TCTCTA 61
Matrix = Unknown
Transitions / transversions = 1.40 (7/5)
Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.00 (5 / 5)
+ 858 33.6 4.6 5.3 chr15_MATERNAL_p_2-50000:. 16987 17398 (32601) + MLT1I LTR/ERVL-MaLR 3 411 (0) 18
ANNOTATION EVIDENCE:
858 33.59 4.64 5.34 chr15_MATERNAL_p_2-50000:. 16987 17398 30435 + MLT1I LTR/ERVL-MaLR 3 411 0
858 33.59 4.64 5.34 chr15_MATERNAL_p_2-50000:. 16987 17398 (30435) MLT1I#LTR/ERVL-MaLR 3 411 (0) c_b1s401i3
chr15_MATERNA 16987 TGATAGTCATTGGTGCTGTTCTCCAAATATTTTCAGTTCATTTGTTTGTG 17036
i i v i i i vi ?vi vi
MLT1I#LTR/ERV 3 TGGTAGTCATTAGTGCTGTTCACCAAATATTTCCGGCTCTCTNCCTTCCG 52
chr15_MATERNA 17037 AATGCATTCT--GACTGTTCCATCCCACCTACTTAAATTTTCCCATGGCC 17084
iiii vv -- i iv ivi i iv i v vvv i
MLT1I#LTR/ERV 53 GGCACATGGTAGGATTGCACTTCCCCGCCCCCTTGAAGTTAGGCGTGGCC 102
chr15_MATERNA 17085 ACATGACTT-TTTTGTTTGTTTGTTTGTTTTTTGCCAACGGAG-GTGAGA 17132
ii -i ------------------ i i i- v
MLT1I#LTR/ERV 103 ATGTGACTTGCTTTG------------------GCCAATGAAATGTGAGC 134
chr15_MATERNA 17133 AGAAATAACATGTGACTTTTTCAGAAGAAATCTCCAAGAAACAGAGTTCT 17182
i i i i v vi i i iv i v ii iv v iviv
MLT1I#LTR/ERV 135 GGAAGTGACGTGTGTCACTTCCGGGCGGAAGCTTTAAGAGCCAGTGCGTG 184
chr15_MATERNA 17183 ATTC--CGCATGCTTTTTTCTTTTTTCTATAGCAATGGGGA----TCTTA 17226
-- i i v iii ii i v i ii i iv v ---- ivi
MLT1I#LTR/ERV 185 ATTCGCCACGTTCCCCTTTCCCTCTGCCACGGCGACCGGCAATGTTCCAG 234
chr15_MATERNA 17227 TTGATGGTCCCTCCTTCCGTCTGGATTCCTGTGTTAGGATGACACAGCAC 17276
v i iiv v v i i i v v v i iii vi
MLT1I#LTR/ERV 235 ATGGTGGCTGCTCCGTCAGCCTGGGTCCCGGAGTGAGGACGACGTGGAGC 284
chr15_MATERNA 17277 AGAGCTACCTCACATCTGACCCATGATG-AGATGTAA-ATAAATGAGGAA 17324
iv ---- v i ii - v i-i i ii i
MLT1I#LTR/ERV 285 AGAGCCCCC----AGCCGACCCGCGATGGACATGTAGCGTGAGCGAGAAA 330
chr15_MATERNA 17325 -AAAGATTT------TTGAACCACTGAAATTTGGAGGTTGTTTGTCACCA 17367
- vv ------ i i i i i i
MLT1I#LTR/ERV 331 TAAACCTTTGTTGTTTTAAGCCACTGAGATTTGGGGGTTGTTTGTTACCG 380
chr15_MATERNA 17368 CAGTTTAACCTAGCCCCCATTGACTGATGCA 17398
iv ivivi i
MLT1I#LTR/ERV 381 CAGCATAACCTAGCCTATCCTGACTGATACA 411
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 37.93
Transitions / transversions = 2.02 (87/43)
Gap_init rate = 0.08 (31 / 411), avg. gap size = 1.32 (41 / 31)
+ 27 8.0 5.6 0.0 chr15_MATERNAL_p_2-50000:. 19019 19072 (30927) + (TATC)n Simple_repeat 1 57 (0) 19
ANNOTATION EVIDENCE:
27 8.02 5.56 0.00 chr15_MATERNAL_p_2-50000:. 19019 19072 30927 + (TATC)n Simple_repeat 1 57 0
27 8.02 5.56 0.00 chr15_MATERNAL_p_2-50000:. 19019 19072 (30927) (TATC)n#Simple_repeat 1 57 (0) c_b1s251i3
chr15_MATERNA 19019 TATCTATC-ATCTATCTACCTGCCTATC-ATCTATCTATCTATTTA-CTA 19065
- i ii - i -
(TATC)n#Simpl 1 TATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA 50
chr15_MATERNA 19066 TCTATCT 19072
(TATC)n#Simpl 51 TCTATCT 57
Matrix = Unknown
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3)
+ 909 28.1 1.3 0.0 chr15_MATERNAL_p_2-50000:. 19201 19421 (30578) + MER58A DNA/hAT-Charlie 1 224 (0) 20
ANNOTATION EVIDENCE:
909 28.05 1.34 0.00 chr15_MATERNAL_p_2-50000:. 19201 19421 28465 + MER58A DNA/hAT-Charlie 1 224 0
909 28.05 1.34 0.00 chr15_MATERNAL_p_2-50000:. 19201 19421 (28465) MER58A#DNA/hAT-Charlie 1 224 (0) m_b1s502i6
chr15_MATERNA 19201 CAGGGTGTGGCAAACTACCATTCATGGGCCATGTCTGAC--ATAGTCTGC 19248
vvi viii ii vi i i --iiv i i
MER58A#DNA/hA 1 CAGGGGTCGGCAAACTACGGCCCGCGGGCCAAATCCGGCCCGCCGCCTGT 50
chr15_MATERNA 19249 GTTTGTAAGAAAAGTTGTAATGGGACACAGCCACATACATGTGTT-ACAT 19297
v iv v v i iiv vi - i
MER58A#DNA/hA 51 TTTTGTAAATAAAGTTTTATTGGAACACAGCCACGCCCATTCGTTTACGT 100
chr15_MATERNA 19298 AATGTCTCTGGCTACTTTCATGGTATAACGGAAGAGCTGAGTCATTGAGA 19347
v v i ii v i v i vi v
MER58A#DNA/hA 101 ATTGTCTATGGCTGCTTTCGCGCTACAACGGCAGAGTTGAGTAGTTGCGA 150
chr15_MATERNA 19348 GAGGGACCACATGGCTTGGAAAACTTAAAATATTTAACATTTAGCCCTTC 19397
v i ii ii v i i vi i i i
MER58A#DNA/hA 151 CAGAGACCGTATGGCCCGCAAAGCCTAAAATATTTACTATCTGGCCCTTT 200
chr15_MATERNA 19398 GCAGAAAATATTTGCTGACTCTTG 19421
i vi i i i
MER58A#DNA/hA 201 ACAGAAAAAGTTTGCCGACCCCTG 224
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 27.60
Transitions / transversions = 1.95 (41/21)
Gap_init rate = 0.01 (2 / 220), avg. gap size = 1.50 (3 / 2)
+ 258 38.9 3.4 4.5 chr15_MATERNAL_p_2-50000:. 19505 19859 (30140) + L2b LINE/L2 2923 3273 (102) 21
ANNOTATION EVIDENCE:
258 38.94 3.42 4.51 chr15_MATERNAL_p_2-50000:. 19505 19859 28027 + L2b_3end LINE/L2 14 364 102
258 38.94 3.42 4.51 chr15_MATERNAL_p_2-50000:. 19505 19859 (28027) L2b_3end#LINE/L2 14 364 (102) m_b1s601i1
chr15_MATERNA 19505 CCCTGCTTCTATATCCAGCCTCATCTATTATTTCCGCTCCTCCTCCTTAT 19554
i v i- v i vi iiv i- i i v i i
L2b_3end#LINE 14 CCCCGCTACC-TCTCCGGCCTCATCTCCTACCACT-CTCCCCTTGCTCAC 61
chr15_MATERNA 19555 TTTCCTTCTGGCCATGCTGATGGATTGTCAGCTTCCCAGATGTGCAAGAA 19604
i v i -i ii iivvvi vv v i i i ii i i v ?iv
L2b_3end#LINE 62 TCTGCTCC-AGCCACACTGGCCTCCTTGCTGTTCCTCGAACGCGCCANGC 110
chr15_MATERNA 19605 TCTCTCCTCCCTTCCCGACATT--CTCATGCT-CTCCCTCTGCCTCTCAA 19651
? iv - vv i v -- v ? -i ----i
L2b_3end#LINE 111 TCNCTCCCGCCT-CAGGGCCTTTGCACNTGCTGTTCCCTCTGCCT----G 155
chr15_MATERNA 19652 GAACTTCCTGTACCATCTCT---CATGACGAATCTCTTCTTCATTCTTTA 19698
vi viv i --- v i v - i vi i i
L2b_3end#LINE 156 GAACGCCCTTCCCCACCTCTTCGCCTGGCCAA-CTCCTACTCATCCTTCA 204
chr15_MATERNA 19699 AGATGCAGCTCCTTTGCTCCTTCCTTAAAGATGTC-TGTCTGGCTCT--A 19745
i viv vvv iiv i ivii v i - vi i i i--
L2b_3end#LINE 205 GGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCA 254
chr15_MATERNA 19746 TTTTGGGTGACATGCTC-CTTCTGCATCTCCC-AGAGCCAGCCTGTGTGT 19793
vvii v vii i - i vii i - vv i v ivvv
L2b_3end#LINE 255 GGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTACCCTGCCACT 304
chr15_MATERNA 19794 GTCAGCTA-CAGCATTTATTTGCATCTCTGTGTCATATATCACCAAATCT 19842
v vi i -? vii i i? i v v vi---i i i -
L2b_3end#LINE 305 CTGGGTTATNATTGTCTGNTTACATGTCTGTCTCCC---CCACTAGA-CT 350
chr15_MATERNA 19843 GCCTAAGCTTGCGTGAG 19859
-- i i-
L2b_3end#LINE 351 G--TGAGCTC-CGTGAG 364
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 50.08
Transitions / transversions = 1.49 (76/51)
Gap_init rate = 0.07 (24 / 354), avg. gap size = 1.17 (28 / 24)
+ 330 31.9 5.1 0.0 chr15_MATERNAL_p_2-50000:. 20138 20335 (29664) + MIRc SINE/MIR 53 265 (3) 22
ANNOTATION EVIDENCE:
317 35.86 7.05 0.00 chr15_MATERNAL_p_2-50000:. 20138 20335 27551 + MIRb SINE/MIR 53 265 3
317 35.86 7.05 0.00 chr15_MATERNAL_p_2-50000:. 20138 20335 (27551) MIRb#SINE/MIR 53 265 (3) m_b1s601i2
chr15_MATERNA 20138 ACATGAATCTAAA-CACAACTCTGCT-CTTAGTAGCTGTGTGACCCTGGG 20185
v ii iii - v ii i- v i
MIRb#SINE/MIR 53 ACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 102
chr15_MATERNA 20186 AAAGTCACTCAATCTCCCTCAGC-TAAATTTTGTTGTGTGAGTAATGAGA 20234
v i i i i v - v i iv ii v viv i i
MIRb#SINE/MIR 103 CAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 152
chr15_MATERNA 20235 AGAG-AGT-TGTGATTTGTA----TTTAATGAGTAATAACAAACAAAAGG 20278
v i- i -iv ivi i i ---- v vi v v vvi v v v
MIRb#SINE/MIR 153 ATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATG 202
chr15_MATERNA 20279 CATTTA----GCTT--TCTGGAACCTGGTATGTAGTAGATCCTCATGAAA 20322
v ---- --ivii vi i ii iiiv vv
MIRb#SINE/MIR 203 CATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAA 252
chr15_MATERNA 20323 TACTAACTCTGTT 20335
iv i i
MIRb#SINE/MIR 253 TGGTAGCTCTATT 265
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 46.77
Transitions / transversions = 1.45 (42/29)
Gap_init rate = 0.04 (8 / 197), avg. gap size = 1.88 (15 / 8)
330 26.51 2.35 0.00 chr15_MATERNAL_p_2-50000:. 20153 20235 27651 + MIRc SINE/MIR 66 150 118
330 26.51 2.35 0.00 chr15_MATERNAL_p_2-50000:. 20153 20235 (27651) MIRc#SINE/MIR 66 150 (118) m_b1s601i3
chr15_MATERNA 20153 CAACTCTGCT-CTTAGTAGCTGTGTGACCCTGGGAAAGTCACTCAATCTC 20201
ii i- v i v i i
MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115
chr15_MATERNA 20202 CCTCAGC-TAAATTTTGTTGTGTGAGTAATGAGAA 20235
i v - v i iv ii v viv i i
MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 150
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 31.91
Transitions / transversions = 1.75 (14/8)
Gap_init rate = 0.02 (2 / 82), avg. gap size = 1.00 (2 / 2)
+ 17 13.2 0.0 2.9 chr15_MATERNAL_p_2-50000:. 20406 20440 (29559) + (GCT)n Simple_repeat 1 34 (0) 23
ANNOTATION EVIDENCE:
17 13.20 0.00 2.94 chr15_MATERNAL_p_2-50000:. 20406 20440 27446 + (GCT)n Simple_repeat 1 34 0
17 13.20 0.00 2.94 chr15_MATERNAL_p_2-50000:. 20406 20440 (27446) (GCT)n#Simple_repeat 1 34 (0) m_b1s252i2
chr15_MATERNA 20406 GCTGCTGCTGCTGCTGCTGCAGCCTACAGCTCCTG 20440
v - i v v
(GCT)n#Simple 1 GCTGCTGCTGCTGCTGCTGCTG-CTGCTGCTGCTG 34
Matrix = Unknown
Transitions / transversions = 0.33 (1/3)
Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1)
+ 21 17.0 2.2 0.0 chr15_MATERNAL_p_2-50000:. 21845 21890 (28109) + (TCTC)n Simple_repeat 1 47 (0) 24
ANNOTATION EVIDENCE:
21 17.03 2.17 0.00 chr15_MATERNAL_p_2-50000:. 21845 21890 25996 + (TCTC)n Simple_repeat 1 47 0
21 17.03 2.17 0.00 chr15_MATERNAL_p_2-50000:. 21845 21890 (25996) (TCTC)n#Simple_repeat 1 47 (0) m_b1s252i4
chr15_MATERNA 21845 TCTCTGTCTCTCTGTCTCTTTCTGTCCCTCTCTCTCTC-CTTTATCT 21890
v v i v i - i v
(TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 47
Matrix = Unknown
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1)
+ 9330 5.0 0.6 0.2 chr15_MATERNAL_p_2-50000:. 23372 25313 (24686) + L1PA5 LINE/L1 4207 6154 (0) 25
ANNOTATION EVIDENCE:
9330 5.97 0.42 0.17 chr15_MATERNAL_p_2-50000:. 23372 24562 23324 + L1P1_orf2 LINE/L1 2098 3291 3
9330 5.97 0.42 0.17 chr15_MATERNAL_p_2-50000:. 23372 24562 (23324) L1P1_orf2#LINE/L1 2098 3291 (3) m_b1s551i7
chr15_MATERNA 23372 TTTG-AGATGACATGATTATATATTTAGAAAACCTCATCATCTCTGCCCA 23420
- i i i i i v
L1P1_orf2#LIN 2098 TTTGCAGACGACATGATTGTATATCTAGAAAACCCCATCGTCTCAGCCCA 2147
chr15_MATERNA 23421 AAATCTCCTTACGCTGATAAGCAACTTCAGCAAAGTCTCAGGACACAAAA 23470
v i
L1P1_orf2#LIN 2148 AAATCTCCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAA 2197
chr15_MATERNA 23471 TCAATGTGCAAAAATCACAAGCATTCTTATACACCAATAACAGACAAACA 23520
L1P1_orf2#LIN 2198 TCAATGTGCAAAAATCACAAGCATTCTTATACACCAATAACAGACAAACA 2247
chr15_MATERNA 23521 GAGAGCCAAATCATGAGTGAACTCCCATTCACAATTGCTTCAAAGAGAAT 23570
L1P1_orf2#LIN 2248 GAGAGCCAAATCATGAGTGAACTCCCATTCACAATTGCTTCAAAGAGAAT 2297
chr15_MATERNA 23571 AAAATACCTAGGAATCAAACTTACAAGGGATGTGAAGGACTTCTTCAAGG 23620
v i
L1P1_orf2#LIN 2298 AAAATACCTAGGAATCCAACTTACAAGGGATGTGAAGGACCTCTTCAAGG 2347
chr15_MATERNA 23621 AGAACTACAAACCACTGCTCGATGAAATAAAAGAGGACACAAACAAATGG 23670
i ? i
L1P1_orf2#LIN 2348 AGAACTACAAACCACTGCTCAANGAAATAAAAGAGGATACAAACAAATGG 2397
chr15_MATERNA 23671 AACAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAATGGC 23720
v i i
L1P1_orf2#LIN 2398 AAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGC 2447
chr15_MATERNA 23721 CATACTGCCCAAGGTAATTTATAGATTCAATGCCATTTGCATCAAGCTAC 23770
iiv
L1P1_orf2#LIN 2448 CATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTAC 2497
chr15_MATERNA 23771 CAATGAATTTCTTTGCAGAATTGGAAAAAACTACTTTAAAGTTCATATGG 23820
v ii
L1P1_orf2#LIN 2498 CAATGACTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATATGG 2547
chr15_MATERNA 23821 AACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAGAACAA 23870
i i v
L1P1_orf2#LIN 2548 AACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAACAA 2597
chr15_MATERNA 23871 ACCTGGAGGCATCACACTACCTGAATTCGAACTATACTACAAGGCTACAG 23920
v i v i
L1P1_orf2#LIN 2598 AGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTACAG 2647
chr15_MATERNA 23921 TAACAAAAACAGATTGGTATTGGTACCAAAACAGAGATATACACCAATGG 23970
v vv i v i
L1P1_orf2#LIN 2648 TAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGG 2697
chr15_MATERNA 23971 AACAGAGCAGAGCCATCAGAAATAATACCACACATCTACAACCATCTGAT 24020
i v ii i i i
L1P1_orf2#LIN 2698 AACAGAACAGAGCCCTCAGAAATAACGCCGCATATCTACAACTATCTGAT 2747
chr15_MATERNA 24021 CTTTGAGAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTATTTA 24070
v v
L1P1_orf2#LIN 2748 CTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTA 2797
chr15_MATERNA 24071 ATAAATGGTGCTTGGAAAACTGGCTAGCCATACATAGAAAGCTGAAACTG 24120
v ii
L1P1_orf2#LIN 2798 ATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTG 2847
chr15_MATERNA 24121 GATCCCTTCCTTACACTTTATACAAAAATTAATTCAAGATGGATTAAAGA 24170
i
L1P1_orf2#LIN 2848 GATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGA 2897
chr15_MATERNA 24171 CTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA 24220
v i
L1P1_orf2#LIN 2898 CTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA 2947
chr15_MATERNA 24221 ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGCCTAAAACACCG 24270
? i i
L1P1_orf2#LIN 2948 NTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCA 2997
chr15_MATERNA 24271 AAAGCAATGGCAACAAAAGCCAAAATGCACAAATGGGATCTAATTAAACT 24320
vv
L1P1_orf2#LIN 2998 AAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACT 3047
chr15_MATERNA 24321 AAAGAGCTTCTGCACAGAAAAAGAAACTACCATCAGAGTGAACAGGCAAC 24370
v
L1P1_orf2#LIN 3048 AAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAAC 3097
chr15_MATERNA 24371 CTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAAGGACTA 24420
i i i i
L1P1_orf2#LIN 3098 CTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTA 3147
chr15_MATERNA 24421 ATATCCAGAATCTACAAAGAACTCAAA----TTTATAAGAAATAAAACAA 24466
v ---- i -
L1P1_orf2#LIN 3148 ATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA-AAAACAA 3196
chr15_MATERNA 24467 ACAACCTCATCAAGAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAA 24516
i i i i
L1P1_orf2#LIN 3197 ACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAA 3246
chr15_MATERNA 24517 GAAGGCATTTTGTGCAGCCAACAGACACGTGAAAAAATGCTCATCA 24562
i -i v i i
L1P1_orf2#LIN 3247 GAAGACATTT-ATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 3291
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 5.16
Transitions / transversions = 2.00 (46/23)
Gap_init rate = 0.00 (4 / 1190), avg. gap size = 1.75 (7 / 4)
7521 3.80 0.78 0.22 chr15_MATERNAL_p_2-50000:. 24418 25313 22573 + L1PA5_3end LINE/L1 1 901 0
7521 3.80 0.78 0.22 chr15_MATERNAL_p_2-50000:. 24418 25313 (22573) L1PA5_3end#LINE/L1 1 901 (0) m_b1s551i8
chr15_MATERNA 24418 CTAATATCCAGAATCTACAAAGAACTCAAA----TTTATAAGAAATAAAA 24463
---- i -
L1PA5_3end#LI 1 CTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA-AAAA 49
chr15_MATERNA 24464 CAAACAACCTCATCAAGAAGTGGGCAAAGGATATGAACAGACACTTCTCA 24513
i i i
L1PA5_3end#LI 50 CAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTCA 99
chr15_MATERNA 24514 AAAGAAGGCATTTTGTGCAGCCAACAGACACGTGAAAAAATGCTCATCA- 24562
i -i i -
L1PA5_3end#LI 100 AAAGAAGACATTT-ATGCAGCCAACAGACACATGAAAAAATGCTCATCAT 148
chr15_MATERNA 24563 --CTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTC 24610
--
L1PA5_3end#LI 149 CACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTC 198
chr15_MATERNA 24611 ACACCAGTTAGAATGGCGATCATTAAAAAGTCAGGAAACAACAAGTGCTG 24660
i
L1PA5_3end#LI 199 ACACCAGTTAGAATGGCGATCATTAAAAAGTCAGGAAACAACAGGTGCTG 248
chr15_MATERNA 24661 GAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTA 24710
L1PA5_3end#LI 249 GAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTA 298
chr15_MATERNA 24711 AACTAGTTCAACCATTGTAGAAGATGGTGTGGTGATTCCTCAAGGATCTA 24760
i ii i
L1PA5_3end#LI 299 AACTAGTTCAACCATTGTGGAAGACAGTGTGGCGATTCCTCAAGGATCTA 348
chr15_MATERNA 24761 GAACTAGAAATACCATTTGACCCAGCCATCCCATTACTTGGTATATACCC 24810
v
L1PA5_3end#LI 349 GAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCC 398
chr15_MATERNA 24811 AAAGGATTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTA 24860
L1PA5_3end#LI 399 AAAGGATTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTA 448
chr15_MATERNA 24861 TCGCAGTGCTATTCACAACAGCAAAGACTTGGAACCAACCCAAATGTCCA 24910
i i ii i
L1PA5_3end#LI 449 TTGCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCA 498
chr15_MATERNA 24911 TCAATGATAGACTGGATTAAGAAAATGTGGTACATATACACCGTGGAATA 24960
i i
L1PA5_3end#LI 499 TCAATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATA 548
chr15_MATERNA 24961 CTGTGCAGCCATAAAAAAGGATGAGTTCATTTCCTTTGTAGGGGCATGGA 25010
i v i
L1PA5_3end#LI 549 CTATGCAGCCATAAAAAAGGATGAGTTCATGTCCTTTGTAGGGACATGGA 598
chr15_MATERNA 25011 TGAAGCTGGAAACCATCATTCTCAGCAAACTATCACAAGCACAAGAAACC 25060
i v i
L1PA5_3end#LI 599 TGAAGCTGGAAACCATCATTCTCAGCAAACTATCGCAAGGACAAAAAACC 648
chr15_MATERNA 25061 AAACACTGCATGTTCTCACTCATAGGTGGGAATTGAACAATGAGAACACT 25110
i
L1PA5_3end#LI 649 AAACACCGCATGTTCTCACTCATAGGTGGGAATTGAACAATGAGAACACT 698
chr15_MATERNA 25111 TGGACACAGGAAGGGGAACATCACACACCGGGGCCTGTTGTGGGGTGGGG 25160
i
L1PA5_3end#LI 699 TGGACACAGGAAGGGGAACATCACACACCGGGGCCTGTCGTGGGGTGGGG 748
chr15_MATERNA 25161 GAAGGGGGGAGGGAAAGCATTAGGAGATATACCTAATGTAAATGACGAGG 25210
i v v
L1PA5_3end#LI 749 GGAGGGGGGAGGGATAGCATTAGGAGATATACCTAATGTAAATGACGAGT 798
chr15_MATERNA 25211 TAATGGGTGTAGCACACCAACATGGCACATGTATACATATGTAACAAACC 25260
i
L1PA5_3end#LI 799 TAATGGGTGCAGCACACCAACATGGCACATGTATACATATGTAACAAACC 848
chr15_MATERNA 25261 TGCACGTTGTGCACATGTACCCTAGAACTTAAAGTATAATAATAAAAAAA 25310
v
L1PA5_3end#LI 849 TGCACGTTGTGCACATGTACCCTAGAACTTAAAGTATAATAAAAAAAAAA 898
chr15_MATERNA 25311 AGA 25313
i
L1PA5_3end#LI 899 AAA 901
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 3.29
Transitions / transversions = 4.67 (28/6)
Gap_init rate = 0.01 (5 / 895), avg. gap size = 1.80 (9 / 5)
+ 230 24.8 7.3 0.0 chr15_MATERNAL_p_2-50000:. 26270 26370 (23629) C L1ME4a LINE/L1 (2) 6122 6014 26
ANNOTATION EVIDENCE:
230 24.75 7.34 0.00 chr15_MATERNAL_p_2-50000:. 26270 26370 21516 C L1ME4a_3end LINE/L1 761 869 2
230 24.75 7.34 0.00 chr15_MATERNAL_p_2-50000:. 26270 26370 (21516) C L1ME4a_3end#LINE/L1 (2) 869 761 m_b1s551i9
chr15_MATERNA 26270 TTTTTTTCTAATTATAAAAGT-GTATATTCTCTTTGGAGGATCTTTGGTA 26318
i -i i v v v i vv v
C L1ME4a_3end#L 869 TTTTTTTCTGATTATAAAAGTAATACATGCTCATTGTAGAAAATTTGGAA 820
chr15_MATERNA 26319 AATAT--AAAAT---GAGTTATAAGAAAAAGAAAA--ATTCATAATTTTA 26361
i-- ---i vv v vi -- ii iii
C L1ME4a_3end#L 819 AATACAGAAAATACAAAGAAAAAAGAAAATAAAAATCACCCATAATCCCA 770
chr15_MATERNA 26362 TCACTCAAA 26370
i i i
C L1ME4a_3end#L 769 CCACCCAGA 761
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 30.73
Transitions / transversions = 1.50 (15/10)
Gap_init rate = 0.04 (4 / 100), avg. gap size = 2.00 (8 / 4)
+ 210 25.3 10.8 8.1 chr15_MATERNAL_p_2-50000:. 27529 27627 (22372) C OldhAT1 DNA/hAT-Ac (2489) 353 252 27
ANNOTATION EVIDENCE:
210 25.27 10.78 8.08 chr15_MATERNAL_p_2-50000:. 27529 27627 20259 C OldhAT1 DNA/hAT-Ac 252 353 2489
210 25.27 10.78 8.08 chr15_MATERNAL_p_2-50000:. 27529 27627 (20259) C OldhAT1#DNA/hAT-Ac (2489) 353 252 m_b1s601i4
chr15_MATERNA 27529 CTGGTGTCCCTGGGTGTTCAGTTTCTTTCCACTCATGTGTTACTGAC--- 27575
ii ii i vii i i - i------ ---
C OldhAT1#DNA/h 353 CTGACGTCCCCAGGTGTCCACCCTCCTTTC-CTCG------ACTGACACT 311
chr15_MATERNA 27576 TGT---TCAGGTG--GCAAATGGCC---CATGACCTTTATGGGATTAAAA 27617
---v i -- --- - iv iiv i vi
C OldhAT1#DNA/h 310 TGTGCGGCAGATGGTGCAAATGGCCCGGCAT-ATATTTGCTGGATCAATG 262
chr15_MATERNA 27618 AGAAAAAAAA 27627
vi
C OldhAT1#DNA/h 261 TAAAAAAAAA 252
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 29.08
Transitions / transversions = 2.83 (17/6)
Gap_init rate = 0.12 (12 / 98), avg. gap size = 1.58 (19 / 12)
+ 6376 9.9 0.4 1.9 chr15_MATERNAL_p_2-50000:. 27644 28447 (21552) C L1PA14 LINE/L1 (0) 6161 5371 28
ANNOTATION EVIDENCE:
6376 9.95 0.44 1.85 chr15_MATERNAL_p_2-50000:. 27644 28447 19750 C L1PA14_3end LINE/L1 118 908 0
6376 9.95 0.44 1.85 chr15_MATERNAL_p_2-50000:. 27644 28447 (19750) C L1PA14_3end#LINE/L1 (0) 908 118 m_b1s551i10
chr15_MATERNA 27644 TTTTTTTTTAACTTTTATTTTAGGTTAGGGGGTACACGGGAGGGTTTGTT 27693
v i v i
C L1PA14_3end#L 908 TTTTTTTTTAACTTTTATTTTAGGTTCGGGGGTACATGTGAAGGTTTGTT 859
chr15_MATERNA 27694 ATACAGTTAAATATGTGTCACAGGGGTTTGTTGTACCTGTTATTTCATCA 27743
i i v i?i i vvi
C L1PA14_3end#L 858 ACATAGGTAAACNCGTGTCACGGGGGTTTGTTGTACAGATTATTTCATCA 809
chr15_MATERNA 27744 TCCAGGTATTAGGCCCAGTATCCAATAGTTATCTTTTCTGCTCCTCTCCC 27793
i i i
C L1PA14_3end#L 808 CCCAGGTATTAAGCCCAGTACCCAATAGTTATCTTTTCTGCTCCTCTCCC 759
chr15_MATERNA 27794 TCCTCCCACCCTCCCCCCATCAAGTAGACCCCAGTGTCTTTTGTTTCCTT 27843
? - v
C L1PA14_3end#L 758 TCCTCCCACCCTCCNCCC-TCAAGTAGACCCCAGTGTCTGTTGTTTCCTT 710
chr15_MATERNA 27844 CTTTGTGTTCACAAGTTCTTATCATTTAGCTCCCACTTATAAGTTAGAAC 27893
i i v
C L1PA14_3end#L 709 CTTTGTGTTCATAAGTTCTCATCATTTAGCTCCCACTTATAAGTGAGAAC 660
chr15_MATERNA 27894 ATGCTGTATTTGGTTTTCTATTCCTGCGTTAGTTTGCTAAGGATAATACC 27943
v i v
C L1PA14_3end#L 659 ATGCGGTATTTGGTTTTCTGTTCCTGCGTTAGTTTGCTAAGGATAATAGC 610
chr15_MATERNA 27944 CATCAGCTTCATCCATACTAATGCAAAAGACATAATCTCATTCTTTTTTA 27993
vi i ii vvi i i
C L1PA14_3end#L 609 CTCCAGCTCCATCCATGTTCCCGCAAAAGACATGATCTCGTTCTTTTTTA 560
chr15_MATERNA 27994 TGGCTGCATATTATTCCATGGTGTATATGTAGCACATTTTCTTTATCCAA 28043
v v
C L1PA14_3end#L 559 TGGCTGCATAGTATTCCATGGTGTATATGTACCACATTTTCTTTATCCAA 510
chr15_MATERNA 28044 TCCGTGACTGATGAGTATTTGGGTTGATTCTATGTCTTTGCTATTGTGAA 28093
i v i i i i i
C L1PA14_3end#L 509 TCTGTCATTGATGGGCATTTAGGTTGATTCCATGTCTTTGCTATTGTGAA 460
chr15_MATERNA 28094 TAGTGCTGCAATGAACATTTGCATGCATGTAACTTCATGGTAGAATGATT 28143
i i iv i
C L1PA14_3end#L 459 TAGTGCTGCAATGAACATTCGCGTGCATGTGTCTTTATGGTAGAATGATT 410
chr15_MATERNA 28144 TATATTCATCTGGGTATATAACCAGTAATGGGATTGCTAGGTCAAATGTT 28193
v v i i --
C L1PA14_3end#L 409 TATATTCCTCTGGGTATATACCCAGTAATGGGATTGCTGGGTCGAATG-- 362
chr15_MATERNA 28194 GTAGTTCTGCTTTTAGCTCTTTGAGGAATCACCATACTGCTTTCCACCAC 28243
i v i
C L1PA14_3end#L 361 GTAGTTCTGCTTTTAGCTCTTTGAGGAATCGCCATACTGCTTTCCACAAT 312
chr15_MATERNA 28244 AGTTGAATTAACTTACACTCCCACCAATGGTGTATACATGTTCACTTTTC 28293
i i i ii vi v
C L1PA14_3end#L 311 GGTTGAACTAATTTACACTCCCACCAACAGTGTATAAGTGTTCCCTTTTC 262
chr15_MATERNA 28294 CCTGCAACCTTGCCAACTTCTGTTAGTTTTTTACTTTTTAGTAATAGCCA 28343
i i i i v v v i
C L1PA14_3end#L 261 TCCGCAACCTCGCCAGCATCTGTTATTTTTTGACTTTTTAATAATAGCCA 212
chr15_MATERNA 28344 TTCTGACTGGTGTGAGATGGTGCCTCACTGTGGTTTTGATGAGCATTTCT 28393
ii i vv
C L1PA14_3end#L 211 TTCTGACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCT 162
chr15_MATERNA 28394 CTAGTGATCAGTGATCTAGAGCTTTTTTCCATATGCTTGTTTGCCACGTT 28443
i v v i v ------
C L1PA14_3end#L 161 CTAATGATCAGTGATATTGAGCTTTTTTTCATATGCTTGTTGGC------ 118
chr15_MATERNA 28444 TGCC 28447
----
C L1PA14_3end#L 118 ---- 119
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 9.24
Transitions / transversions = 1.76 (51/29)
Gap_init rate = 0.02 (13 / 803), avg. gap size = 1.00 (13 / 13)
+ 2139 11.2 0.0 0.0 chr15_MATERNAL_p_2-50000:. 28448 28761 (21238) C AluY SINE/Alu (0) 311 2 29
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 chr15_MATERNAL_p_2-50000:. 28448 28475 21524 + (T)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 chr15_MATERNAL_p_2-50000:. 28448 28475 (21524) (T)n#Simple_repeat 1 28 (0) c_b1s251i4
chr15_MATERNA 28448 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28475
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
2139 11.23 0.00 0.00 chr15_MATERNAL_p_2-50000:. 28477 28761 21209 C AluY SINE/Alu 2 286 25
2139 11.23 0.00 0.00 chr15_MATERNAL_p_2-50000:. 28477 28761 (21209) C AluY#SINE/Alu (25) 286 2 c_b1s352i2
chr15_MATERNA 28477 TTTCTTAGCCCGAGTCTCGATCTGTCACCCAGGCCAGAGTGCAGTGGTGT 28526
i v v v v i ii i i
C AluY#SINE/Alu 286 TTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGC 237
chr15_MATERNA 28527 GATCTCAGCTAACTGCAAGCTCTGCCTCCTTGGTTCACGCCATTCTCCTG 28576
i v i iv
C AluY#SINE/Alu 236 GATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTG 187
chr15_MATERNA 28577 CCTCAGCCTCCCAAGTAGCTGGGACTACAGGTGCCTGCCACCACACCCGG 28626
i i i i
C AluY#SINE/Alu 186 CCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGG 137
chr15_MATERNA 28627 CTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTAGTCAGG 28676
i i
C AluY#SINE/Alu 136 CTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGG 87
chr15_MATERNA 28677 ATGGTCTCAATCTCCTGACGTTGTGATCCACCCTCCTTGGCCTCCCAAAA 28726
i v i i v i i
C AluY#SINE/Alu 86 ATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAG 37
chr15_MATERNA 28727 TGCAGGAATTACAGGCGTGAGCCACCACGCCCAGC 28761
v i i i
C AluY#SINE/Alu 36 TGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p41g.matrix
Kimura (with divCpGMod) = 6.11
Transitions / transversions = 2.56 (23/9)
Gap_init rate = 0.00 (0 / 284), avg. gap size = 0.0 (0 / 0)
+ 6376 9.1 1.7 2.6 chr15_MATERNAL_p_2-50000:. 28762 29256 (20743) C L1PA14 LINE/L1 (776) 5370 4868 28
ANNOTATION EVIDENCE:
3565 9.11 1.68 2.59 chr15_MATERNAL_p_2-50000:. 28762 29256 18941 C L1PREC2_orf2 LINE/L1 2759 3261 33
3565 9.11 1.68 2.59 chr15_MATERNAL_p_2-50000:. 28762 29256 (18941) C L1PREC2_orf2#LINE/L1 (33) 3261 2759 m_b1s551i11
chr15_MATERNA 28762 ACACATGTTTGTCTCCTTTGGGGAAGTGTCTCTTTATGTCCTTGGCCCAC 28811
- i v i v ii v i v
C L1PREC2_orf2# 3261 -CGCATGTATGTCTTCTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCAC 3213
chr15_MATERNA 28812 TTTTTAATGGGG----TTGTTTTTCTCTTGTAAATTTGTTTAAGTTCCTT 28857
---- i
C L1PREC2_orf2# 3212 TTTTTAATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTT 3163
chr15_MATERNA 28858 ATAGATGCTGGATATTAGACCTTTGTCAGATGCATAGTTTGTAAATACTT 28907
i ? i
C L1PREC2_orf2# 3162 ATAGATGCTGGATATTAGACCTTTGTCAGATGCATAGTTTGCAAANATTT 3113
chr15_MATERNA 28908 TCTCCCAATCTGCAAGTTGCCTGTTTACTTTGTTGATAGTTTCTTTTGCA 28957
v i i i i v
C L1PREC2_orf2# 3112 TCTCCCATTCTGTAGGTTGTCTGTTTACTCTGTTGATAGTTTCTTTTGCT 3063
chr15_MATERNA 28958 GTGTAGAAGCTCTTTAGTTTAACTAGATCCCACTTGTCAATTTTTGCTTT 29007
i i i
C L1PREC2_orf2# 3062 GTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTTGCTTT 3013
chr15_MATERNA 29008 CATTGCTATTGCTTTTGTTGTCTTTGTCATGAAATCTTTGCCTGTTCTTA 29057
ii v vi i i i
C L1PREC2_orf2# 3012 TGTTGCAATTGCTTTTGGCGTCTTCGTCATGAAATCTTTGCCCGTTCCTA 2963
chr15_MATERNA 29058 TGTCCAGGATGGTATTGCCTAGGTTGTCTTCCAGGGTTTTTATATTTTTG 29107
i v
C L1PREC2_orf2# 2962 TGTCCAGAATGGTATTGCCTAGGTTGTCTTCCAGGGTTTTTATAGTTTTG 2913
chr15_MATERNA 29108 GGTTTTACACTTAAGTCTTTAATCCATCCTGAGTTCATTTTTGTGTATTG 29157
i i v i v
C L1PREC2_orf2# 2912 GGTTTTACATTTAAGTCTTTAATCCATCTTGAGTTGATTTTTGTATATGG 2863
chr15_MATERNA 29158 TGTAAGAAAGGGGCCCAG-CTCAATCTTCAGCATGTGGCTAGCCAGTTAT 29206
i i -i v i
C L1PREC2_orf2# 2862 TGTAAGGAAGGGGTCCAGTTTCAATCTTCTGCATATGGCTAGCCAGTTAT 2813
chr15_MATERNA 29207 CCCAGCACCATTTATTGAAC--GGAGTCTTTTCCCCATTGCTTG--TTTG 29252
i-- i --
C L1PREC2_orf2# 2812 CCCAGCACCATTTATTGAATAGGGAGTCCTTTCCCCATTGCTTGTTTTTG 2763
chr15_MATERNA 29253 TCAG 29256
C L1PREC2_orf2# 2762 TCAG 2759
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 8.81
Transitions / transversions = 2.58 (31/12)
Gap_init rate = 0.01 (5 / 494), avg. gap size = 2.00 (10 / 5)
6376 9.95 0.44 1.85 chr15_MATERNAL_p_2-50000:. 28762 28875 19322 C L1PA14_3end LINE/L1 1 117 791
6376 9.95 0.44 1.85 chr15_MATERNAL_p_2-50000:. 28762 28875 (19322) C L1PA14_3end#LINE/L1 (791) 117 1 m_b1s551i10
chr15_MATERNA 28762 ACACATGTTTGTCTCCTTTGGGGAAGTGTCTCTTTATGTCCTTGGCCCAC 28811
- i v i v i v i v
C L1PA14_3end#L 117 -CGCATGTATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTTGCCCAC 69
chr15_MATERNA 28812 TTTTTAATGGGG----TTGTTTTTCTCTTGTAAATTTGTTTAAGTTCCTT 28857
----
C L1PA14_3end#L 68 TTTTTAATGGGGTTGTTTGTTTTTCTCTTGTAAATTTGTTTAAGTTCCTT 19
chr15_MATERNA 28858 ATAGATGCTGGATATTAG 28875
C L1PA14_3end#L 18 ATAGATGCTGGATATTAG 1
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 9.24
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.02 (2 / 113), avg. gap size = 2.50 (5 / 2)
+ 203 30.1 0.0 9.7 chr15_MATERNAL_p_2-50000:. 30084 30186 (19813) C Tigger19b DNA/TcMar-Tigger (175) 375 283 30
ANNOTATION EVIDENCE:
203 30.10 0.00 9.71 chr15_MATERNAL_p_2-50000:. 30084 30186 18011 C Tigger19b DNA/TcMar-Tigger 283 375 175
203 30.10 0.00 9.71 chr15_MATERNAL_p_2-50000:. 30084 30186 (18011) C Tigger19b#DNA/TcMar-Tigger (175) 375 283 m_b1s601i5
chr15_MATERNA 30084 AAGTGAAAATGAAAGGAACTGACCCATGAAGGAACAGGTGTGAGCTATTT 30133
iv v v vi i v i - i i v - -i i ii
C Tigger19b#DNA 375 AAGCCACACTGTGAAGACCTGACTCA-GGAGGAGCTGG-G-AAGCTGTCC 329
chr15_MATERNA 30134 ACTTCATTCCTGCCCATCCTGGTTGATGTTGAGCTCTTGCCCTGCATCCC 30183
v --- --- vi vv iiv i i - ??
C Tigger19b#DNA 328 AGT---TTCCT---CATCCTGCCTCCTGCCCAACTCCT-CCCTGCNNCCC 286
chr15_MATERNA 30184 ACT 30186
C Tigger19b#DNA 285 ACT 283
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 36.86
Transitions / transversions = 1.36 (15/11)
Gap_init rate = 0.10 (10 / 102), avg. gap size = 1.00 (10 / 10)
+ 306 34.1 8.0 5.5 chr15_MATERNAL_p_2-50000:. 30332 30551 (19448) C MIRb SINE/MIR (12) 256 31 31
ANNOTATION EVIDENCE:
306 34.13 7.96 5.45 chr15_MATERNAL_p_2-50000:. 30332 30551 17646 C MIRb SINE/MIR 31 256 12
306 34.13 7.96 5.45 chr15_MATERNAL_p_2-50000:. 30332 30551 (17646) C MIRb#SINE/MIR (12) 256 31 m_b1s601i6
chr15_MATERNA 30332 ACCACTTATTCAGGGCTTTTTGGATGCCA-------TGCTAAGCATTTCA 30374
i v v vi ivi ------- ii i
C MIRb#SINE/MIR 256 ACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTA 207
chr15_MATERNA 30375 TAGTCATGAGCTCATTGTATAAACTACCCTTTATAACACTCCTATGA--- 30421
i vv v v --- -----i i i i vi ii ---
C MIRb#SINE/MIR 206 CATGCATTATCTCATT---TAA-----TCCTCACAACAACCCTGCGAGGT 165
chr15_MATERNA 30422 ----ATTCATATTCCCATATGAATTGGCCTGAGGAAGTGGCATGCT-GGA 30466
---- vv i v v --ii -v iiv - v -i
C MIRb#SINE/MIR 164 AGGTATTATTATCCCCATTTTA--CAG-ATGAGGAAACTG-AGGCTCAGA 119
chr15_MATERNA 30467 GAGATTAAGTAA-TTGAATGACAGCTTACAGTTAATTACTGAGGGGATTT 30515
i - vvii viv vi i i v v ivi iiiiv
C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 69
chr15_MATERNA 30516 GGGTTTGGACATAGATCTG--TGATTCAAACACTCATG 30551
i i i vi i -- i v vi i i
C MIRb#SINE/MIR 68 GGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTG 31
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 42.98
Transitions / transversions = 1.54 (43/28)
Gap_init rate = 0.08 (18 / 219), avg. gap size = 1.67 (30 / 18)
+15754 6.0 0.4 0.2 chr15_MATERNAL_p_2-50000:. 30826 33957 (16042) C L1P2 LINE/L1 (2054) 4267 1129 32
ANNOTATION EVIDENCE:
15754 5.51 0.20 0.10 chr15_MATERNAL_p_2-50000:. 30826 32806 15391 C L1P1_orf2 LINE/L1 1 1983 1311
15754 5.51 0.20 0.10 chr15_MATERNAL_p_2-50000:. 30826 32806 (15391) C L1P1_orf2#LINE/L1 (1311) 1983 1 m_b1s551i12
chr15_MATERNA 30826 GCATCCCTGTCTTGTGCCAGTTTTCAAAGTGAATGCTTCCTGTTTTTGCC 30875
v v
C L1P1_orf2#LIN 1983 GCATCCCTGTCTTGTGCCAGTTTTCAAAGGGAATGCTTCCAGTTTTTGCC 1934
chr15_MATERNA 30876 CATTCAGCATGATATTGGCTGTGGGTTTTTCATAAATAGCTCTTATTATT 30925
i v i
C L1P1_orf2#LIN 1933 CATTCAGTATGATATTGGCTGTGGGTTTGTCATAGATAGCTCTTATTATT 1884
chr15_MATERNA 30926 TTGAGATACATCCCATCAATACCTAGTTTATTGAGAGTTTTTAGCATGAA 30975
i i
C L1P1_orf2#LIN 1883 TTGAGATACGTCCCATCAATACCTAATTTATTGAGAGTTTTTAGCATGAA 1834
chr15_MATERNA 30976 GGGCTGTTGAATTTTGTCGAAGGCCTTTTCTGCATCTATTGAGATAATCA 31025
i i
C L1P1_orf2#LIN 1833 GGGTTGTTGAATTTTGTCAAAGGCCTTTTCTGCATCTATTGAGATAATCA 1784
chr15_MATERNA 31026 TGTGGTTTTTGTCTTTGGTTCTGTTTATATGATGGATTACATTTATTGAT 31075
v i
C L1P1_orf2#LIN 1783 TGTGGTTTTTGTCTTTGGTTCTGTTTATATGCTGGATTACGTTTATTGAT 1734
chr15_MATERNA 31076 TTGCATATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCAACTTGATC 31125
i v
C L1P1_orf2#LIN 1733 TTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCCACTTGATC 1684
chr15_MATERNA 31126 ATGGTAGATAAGCTTTTTGATGTGCTGCTGGATTTGGTTTGCCAGCATTT 31175
i i i
C L1P1_orf2#LIN 1683 ATGGTGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTATTT 1634
chr15_MATERNA 31176 TATTGAGGATTTTTGCATCGATGTTCATCAGGGATATTGGTCTAAAATTC 31225
i i
C L1P1_orf2#LIN 1633 TATTGAGGATTTTTGCATCAATGTTCATCAAGGATATTGGTCTAAAATTC 1584
chr15_MATERNA 31226 TCTTTTTTTTTGTTGTGCCTCTGCCAGGCTTTGGTATCAGGATAATGCTG 31275
-- v i ? i
C L1P1_orf2#LIN 1583 TC--TTTTTTGGTTGTGTCTCTGCCNGGCTTTGGTATCAGGATGATGCTG 1536
chr15_MATERNA 31276 GCCTCATAAAATTAGTTAGGGAGGATTCCCTCTTTTTCTATTGATTGGCA 31325
v v
C L1P1_orf2#LIN 1535 GCCTCATAAAATGAGTTAGGGAGGATTCCCTCTTTTTCTATTGATTGGAA 1486
chr15_MATERNA 31326 TAGTTTCAGAAGCAATGGCACCAGTTCCTCTTTGTACCTCCGGTAGAATT 31375
v i i i i
C L1P1_orf2#LIN 1485 TAGTTTCAGAAGGAATGGTACCAGCTCCTCCTTGTACCTCTGGTAGAATT 1436
chr15_MATERNA 31376 CAGCTGTGAATCCATCAGGTCCTGTACTTTTTTTGTTTGGGAGGCTATTA 31425
i v v i v v i i
C L1P1_orf2#LIN 1435 CGGCTGTGAATCCATCTGGTCCTGGACTCTTTTTGGTTGGTAAGCTATTG 1386
chr15_MATERNA 31426 ATTATTGCCTCAATTTCAGAGTCTGTTATTGGTCTTTTCAGGGATTCAAC 31475
? i v i
C L1P1_orf2#LIN 1385 ATTATTGCCNCAATTTCAGAGCCTGTTATTGGTCTATTCAGAGATTCAAC 1336
chr15_MATERNA 31476 TTCTTCCTGGTTTAGTCTTGGGAGGGTGTATGTGTCCAGGAATTTATCCA 31525
v
C L1P1_orf2#LIN 1335 TTCTTCCTGGTTTAGTCTTGGGAGGGTGTATGTGTCGAGGAATTTATCCA 1286
chr15_MATERNA 31526 TTTCTTCTAGATTTTCTACTTTATTTGTGTAGAGGTGTTTATAGTATTCT 31575
v i i
C L1P1_orf2#LIN 1285 TTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTGTAGTATTCT 1236
chr15_MATERNA 31576 CTGATGGTAGTTTGTATTTCCGTGGGATGGGTGGTGATATCCCTTTTATC 31625
i v i
C L1P1_orf2#LIN 1235 CTGATGGTAGTTTGTATTTCTGTGGGATCGGTGGTGATATCCCCTTTATC 1186
chr15_MATERNA 31626 ATTTTTTATTGCATCTATTTGATTCTTCTCTCTTTTCTTCTATATTAGTC 31675
i v
C L1P1_orf2#LIN 1185 ATTTTTTATTGCGTCTATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTC 1136
chr15_MATERNA 31676 TTGCTAGCAGTCTATCAATTATGTTGATCTTTTCAAAAAACCAGCTCCTG 31725
i v i
C L1P1_orf2#LIN 1135 TTGCTAGCGGTCTATCAATTTTGTTGATCCTTTCAAAAAACCAGCTCCTG 1086
chr15_MATERNA 31726 GATTCATTGCTTTTTTGAAGGGTTTTTTGTGTCTCTATCTCCTTCAGTTC 31775
v i
C L1P1_orf2#LIN 1085 GATTCATTGATTTTTTGAAGGGTTTTTTGTGTCTCTATTTCCTTCAGTTC 1036
chr15_MATERNA 31776 TGCTCTGATCTTAATTATTTCTTGCCTTCTGCTAGCTTTTGAA--TGTTT 31823
i --
C L1P1_orf2#LIN 1035 TGCTCTGATCTTAGTTATTTCTTGCCTTCTGCTAGCTTTTGAATGTGTTT 986
chr15_MATERNA 31824 GCTTTTGCTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGT-AATTTTA 31872
i i - i
C L1P1_orf2#LIN 985 GCTCTTGCTTTTCTAGTTCTTTTAATTGTGATGTTAGGGTGTCAATTTTG 936
chr15_MATERNA 31873 GATCTTTCCTGCTTTCTCTTGTGGGCATTTAGTGCCATAAATTTCCCTCT 31922
i
C L1P1_orf2#LIN 935 GATCTTTCCTGCTTTCTCTTGTGGGCATTTAGTGCTATAAATTTCCCTCT 886
chr15_MATERNA 31923 ACACACTGCTTTAAATGTGTCCCAGAGATTCTGGTATGTTGTGTCTTTGT 31972
i i
C L1P1_orf2#LIN 885 ACACACTGCTTTGAATGCGTCCCAGAGATTCTGGTATGTTGTGTCTTTGT 836
chr15_MATERNA 31973 TCTCACTGGTTTCAAAGAACATCTTTATTTCTGCCTTCATTCTGTTATGT 32022
ii ii
C L1P1_orf2#LIN 835 TCTCGTTGGTTTCAAAGAACATCTTTATTTCTGCCTTCATTTCGTTATGT 786
chr15_MATERNA 32023 ACCCAGTAGTCATTCAGGAGCAGGTTGCTCTGCTTCCATGTAGTTGAGTG 32072
i v i i
C L1P1_orf2#LIN 785 ACCCAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCATGTAGTTGAGCG 736
chr15_MATERNA 32073 GTTTTGAGTGAGTTTCTTAATCCTGAGTTATAGTTTGATTGCACTGTGGT 32122
v
C L1P1_orf2#LIN 735 GTTTTGAGTGAGTTTCTTAATCCTGAGTTCTAGTTTGATTGCACTGTGGT 686
chr15_MATERNA 32123 CTGAGAGAGAGTTTGTTACAATTTCTGTTCTTTTACATTTGCTGAGAAGT 32172
v i i ?
C L1P1_orf2#LIN 685 CTGAGAGACAGTTTGTTATAATTTCTGTTCTTTTACATTTGCTGAGGAGN 636
chr15_MATERNA 32173 GCTTTACTTCCAAATATGTGGTCAATTTTGGAATAAGTGCGATGTGGTTC 32222
v i i i v
C L1P1_orf2#LIN 635 GCTTTACTTCCAACTATGTGGTCAATTTTGGAATAGGTGTGGTGTGGTGC 586
chr15_MATERNA 32223 TGAGAAGAATGTATATTCTGTTGATTTGGGGTAGAGAGTTCTGTAGATAT 32272
i i i
C L1P1_orf2#LIN 585 TGAAAAGAATGTATATTCTGTTGATTTGGGGTGGAGAGTTCTGTAGATGT 536
chr15_MATERNA 32273 CTATTAGGGCCGCTTGGTGCAGAGCTGAGTTCAATTCCTGGATATCCTTG 32322
v i
C L1P1_orf2#LIN 535 CTATTAGGTCCGCTTGGTGCAGAGCTGAGTTCAATTCCTGGGTATCCTTG 486
chr15_MATERNA 32323 TTAACTTTCTGTTTCGTTGATCTGTCTAATGTTGATAGTGAGGTGTTAAA 32372
i i i
C L1P1_orf2#LIN 485 TTAACTTTCTGTCTCGTTGATCTGTCTAATGTTGACAGTGGGGTGTTAAA 436
chr15_MATERNA 32373 GTCTCCCGTTATTTTTGTGTGGGAGTCTAAGTCTCTTTGTAGGTCTCTAA 32422
i v? v v
C L1P1_orf2#LIN 435 GTCTCCCATTATTANTGTGTGGGAGTCTAAGTCTCTTTGTAGGTCACTCA 386
chr15_MATERNA 32423 GGACTTGCTTTATGAATCTGGGTGTTCCTGTATTGGGTGCATATATATTT 32472
i
C L1P1_orf2#LIN 385 GGACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGGTGCATATATATTT 336
chr15_MATERNA 32473 AGGATAGTTAGCTCTTCTTGTGGAATTGATCCCTTTACCATTATGTAATG 32522
v
C L1P1_orf2#LIN 335 AGGATAGTTAGCTCTTCTTGTTGAATTGATCCCTTTACCATTATGTAATG 286
chr15_MATERNA 32523 GCTTTCTTTGTCTCTTCTGATCTTTGTTGGTTTAAAGTCTGTTTTATCAC 32572
i i v
C L1P1_orf2#LIN 285 GCCTTCTTTGTCTCTTTTGATCTTTGTTGGTTTAAAGTCTGTTTTATCAG 236
chr15_MATERNA 32573 AGACTAGGATTATAACCCCTG-CTTTTTTTGCTTTCCATTTGCTTGACAG 32621
ii - i ii
C L1P1_orf2#LIN 235 AGACTAGGATTGCAACCCCTGCCTTTTTTTGTTTTCCATTTGCTTGGTAG 186
chr15_MATERNA 32622 ATCTTCCTCCACCCCTTTATTTTGAGCCTATGTGTGTCTCTGCACATGAG 32671
i i
C L1P1_orf2#LIN 185 ATCTTCCTCCATCCCTTTATTTTGAGCCTATGTGTGTCTCTGCACGTGAG 136
chr15_MATERNA 32672 ATGGGTCTCCTGAATACAGCACACTGATGGGTCTTGACTCTTTATCCAAT 32721
i
C L1P1_orf2#LIN 135 ATGGGTTTCCTGAATACAGCACACTGATGGGTCTTGACTCTTTATCCAAT 86
chr15_MATERNA 32722 TTGCCAGTCTGTGTCTTTTAATTGGAGCATTTATCCCATTTACATTTAAG 32771
vi i
C L1P1_orf2#LIN 85 TTGCCAGTCTGTGTCTTTTAATTGGAGCATTTAGTCCATTTACATTTAAA 36
chr15_MATERNA 32772 GTTAATATTGTTATGTGTGAATTTGATCCTGTCAT 32806
C L1P1_orf2#LIN 35 GTTAATATTGTTATGTGTGAATTTGATCCTGTCAT 1
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 4.90
Transitions / transversions = 2.28 (73/32)
Gap_init rate = 0.00 (5 / 1980), avg. gap size = 1.20 (6 / 5)
716 30.00 0.00 0.00 chr15_MATERNAL_p_2-50000:. 32610 32839 15358 C L1MEc_5end LINE/L1 2252 2481 46
716 30.00 0.00 0.00 chr15_MATERNAL_p_2-50000:. 32610 32839 (15358) C L1MEc_5end#LINE/L1 (46) 2481 2252 m_b1s551i13
chr15_MATERNA 32610 TTTGCTTGACAGATCTTCCTCCACCCCTTTATTTTGAGCCTATGTGTGTC 32659
v ii v ii i i i v i v
C L1MEc_5end#LI 2481 TTTGCATGGTATATCTTTTTCCATCCTTTTACTTTTAACCTATTTGTGTC 2432
chr15_MATERNA 32660 TCTGCACATGAGATGGGTCTCCTGAATACAGCACACTGATGGGTCTTGAC 32709
i ii iv i ii ? i i v vi i iv v vi
C L1MEc_5end#LI 2431 TTTATATTTAAAGTGNGTTTCTTGTAGGCAGCATATAGTTGGGTCTTGCT 2382
chr15_MATERNA 32710 TCTTTATCCAATTTGCCAGTCTGTGTCTTTTAATTGGAGCATTTATCCCA 32759
i i v i v i i ii vv
C L1MEc_5end#LI 2381 TTTTTATCCAATCTGACAATCTCTGCCTTTTAATTGGGGTGTTTAGACCA 2332
chr15_MATERNA 32760 TTTACATTTAAGGTTAATATTGTTATGTGTGAATTTGATCCTGTCATTAT 32809
v v v v vv ii i vi ii iv
C L1MEc_5end#LI 2331 TTTACATTTAATGTGATTATTGATATGGTTGGGTTTAAATCTACCATCTT 2282
chr15_MATERNA 32810 GATGTTAGCTGGTTATTTTGCTCATCAGTT 32839
v i v i vvi vv i v
C L1MEc_5end#LI 2281 GCTATTTGTTTTCTATTTGTCCCATCTGTT 2252
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 38.79
Transitions / transversions = 1.34 (39/29)
Gap_init rate = 0.00 (0 / 229), avg. gap size = 0.0 (0 / 0)
10271 6.03 0.85 0.46 chr15_MATERNAL_p_2-50000:. 32657 33957 14240 C L1P2_5end LINE/L1 970 2275 0
10271 6.03 0.85 0.46 chr15_MATERNAL_p_2-50000:. 32657 33957 (14240) C L1P2_5end#LINE/L1 (0) 2275 970 m_b1s551i14
chr15_MATERNA 32657 GTCTCTGCACATGAGATGGGTCTCCTGAATACAGCACACTGATGGGTCTT 32706
i
C L1P2_5end#LIN 2275 GTCTCTGCACGTGAGATGGGTCTCCTGAATACAGCACACTGATGGGTCTT 2226
chr15_MATERNA 32707 GACTCTTTATCCAATTTGCCAGTCTGTGTCTTTTAATTGGAGCATTTATC 32756
i v
C L1P2_5end#LIN 2225 GACTCTTTATCCAATTTGCCAGTCTGTGTCTTTTAATTGGGGCATTTAGC 2176
chr15_MATERNA 32757 CCATTTACATTTAAGGTTAATATTGTTATGTGTGAATTTGATCCTGTCAT 32806
C L1P2_5end#LIN 2175 CCATTTACATTTAAGGTTAATATTGTTATGTGTGAATTTGATCCTGTCAT 2126
chr15_MATERNA 32807 TATGATGTTAGCTGGTTATTTTGCTCATCAGTTGATGCAGTTTCTTCCTC 32856
i i i v
C L1P2_5end#LIN 2125 TATGATGTTAGCTGGTTATTTTGCCCGTTAGTTGATGCAGTTTCTTCCTA 2076
chr15_MATERNA 32857 GCATCAATGGTCTTTACAATTTGGCATGTTTTTGCAGTGGCTAGTACCGG 32906
i i
C L1P2_5end#LIN 2075 GCATCGATGGTCTTTACAATTTGGCATGTTTTTGCAGTGGCTGGTACCGG 2026
chr15_MATERNA 32907 TTGTTCCTTTCCATGTTTAGTGCTTCCTTCAGAAGCTCTTGTAAGGCAGG 32956
i --
C L1P2_5end#LIN 2025 TTGTTCCTTTCCATGTTTAGTGCTTCCTTCAGGAGCTCTTGTAAGGCA-- 1978
chr15_MATERNA 32957 CCTGGCCTGGTGGTGACAAAATCTCTCAGCATTTGCTTGTCTGTAAAGGA 33006
---
C L1P2_5end#LIN 1977 ---GGCCTGGTGGTGACAAAATCTCTCAGCATTTGCTTGTCTGTAAAGGA 1931
chr15_MATERNA 33007 TTTTATTTCTCCTTCACTTATGAAGCTTAGTTTGGCTGGATATGAAATTC 33056
C L1P2_5end#LIN 1930 TTTTATTTCTCCTTCACTTATGAAGCTTAGTTTGGCTGGATATGAAATTC 1881
chr15_MATERNA 33057 TGGGCTGAAAATTATTTTCTTTAAGAATGTTGAATATTGGCCCCCACACT 33106
i v v
C L1P2_5end#LIN 1880 TGGGTTGAAAATTCTTTTCTTTAAGAATGTTGAATATTGGCCCCCACTCT 1831
chr15_MATERNA 33107 CTTCTGGCATGTAGAGTTTCTGCTGAGAGATCCGCTGTTAGTCTGACAGG 33156
v i i ii
C L1P2_5end#LIN 1830 CTTCTGGCTTGTAGGGTTTCTGCCGAGAGATCCGCTGTTAGTCTGATGGG 1781
chr15_MATERNA 33157 CTTTCCTTTGT-GGTAACCCAACCTTTCTCTCTGGCTGCCCTTAACATTT 33205
i - i
C L1P2_5end#LIN 1780 CTTCCCTTTGTGGGTAACCCGACCTTTCTCTCTGGCTGCCCTTAACATTT 1731
chr15_MATERNA 33206 TTTCCTTCATTTC----------AATCTGACAATTATGTGTCTTGGAGTT 33245
---------- i
C L1P2_5end#LIN 1730 TTTCCTTCATTTCAACCTTGGTGAATCTGACAATTATGTGTCTTGGGGTT 1681
chr15_MATERNA 33246 GCTCTTCTCGAGGAGTATCTTTGTGGCATTCTCTGTATTTCCTGAATTTG 33295
i
C L1P2_5end#LIN 1680 GCTCTTCTCGAGGAGTATCTTTGTGGCGTTCTCTGTATTTCCTGAATTTG 1631
chr15_MATERNA 33296 AATGTTGGCCTGCCTTGCTAGGTTGGGAAAGTTCTCCTGGATAATATCCT 33345
i
C L1P2_5end#LIN 1630 AATGTTGGCCTGCCTTGCTAGGTTGGGGAAGTTCTCCTGGATAATATCCT 1581
chr15_MATERNA 33346 GAAGAGTGTTTTCAAACTCGTTTCCATTCTCCCTGTCACTTTCAGGTACA 33395
v i v i
C L1P2_5end#LIN 1580 GAAGAGTGTTTTCCAACTTGGTTCCATTCTCCCCGTCACTTTCAGGTACA 1531
chr15_MATERNA 33396 CCAATCAGATGTAGATTTGGTCTTTTCACATAGTCCCATATTTCTTGGAG 33445
i i
C L1P2_5end#LIN 1530 CCAATCAAACGTAGATTTGGTCTTTTCACATAGTCCCATATTTCTTGGAG 1481
chr15_MATERNA 33446 GATTTGTTGGTTTCTTTTTACTCTTTTTTCTCTAAACTTCTCTTCTCATT 33495
v v ? ? ii
C L1P2_5end#LIN 1480 GCTTTGTTCGTTTCTTTTTACTCTTTTTTCTCTAANCTTNTCTTCTCGCT 1431
chr15_MATERNA 33496 TCATTTCATTCATTAGATCTTCAATGACTGATACCCTTTCTTCCACTTGA 33545
i v v v
C L1P2_5end#LIN 1430 TTATTTCATTAATTTGATCTTCAATCACTGATACCCTTTCTTCCACTTGA 1381
chr15_MATERNA 33546 TTGAATTGGCTAAAGAAGCTAGTGCATGCATCATGTAGTTCTCGTGCCGC 33595
i i vv v i i ? i
C L1P2_5end#LIN 1380 TCGAATCGGCTACTGAAGCTTGTGCATGCGTCACGNAGTTCTCGTGCCGT 1331
chr15_MATERNA 33596 GGTTTTCAGCTCCATTAGGTCATTTAAGGTCTTCTCTACACTGTTTATTC 33645
i
C L1P2_5end#LIN 1330 GGTTTTCAGCTCCATCAGGTCATTTAAGGTCTTCTCTACACTGTTTATTC 1281
chr15_MATERNA 33646 TAGTTAGCTATTTGACTAATCTTTTTTCAAGGTTTTTAGCTTCTTTGTGA 33695
i i v i i
C L1P2_5end#LIN 1280 TAGTTAGCCATTCGTCTAATCTTTTTTCAAGGTTTTTAGCTTCCTTGCGA 1231
chr15_MATERNA 33696 TGGGTTCAAACATCCTCCATTAGCTCGGAGAAGGTTGTTATTACTGATCG 33745
i v v i i v
C L1P2_5end#LIN 1230 TGGGTTCGAACATCCTCCTTTAGCTCGGAGAAGTTTGTTATTACCGACCT 1181
chr15_MATERNA 33746 TCCGAAGCCTTCTTCTCCCAACTTGTCAAAGTCATTCTCCATTCAGCTTT 33795
i v vi i i i
C L1P2_5end#LIN 1180 TCTGAAGCCTACTTCTGTCAACTCGTCAAAGTCATTCTCCGTCCAGCTTT 1131
chr15_MATERNA 33796 GTTCTGTTGCTGGTGAGGAGCTGTGTTCCTTTGGAGGAGAAGAGATGCTC 33845
i i i v ii
C L1P2_5end#LIN 1130 GTTCCGTTGCTGGCGAGGAGCTGCGATCCTTTGGAGGAGAAGAGGCGCTC 1081
chr15_MATERNA 33846 TGATTTTTAGAATTTTCAGCTTTTCTGCTCTGGTTTCTCCCCATCTTTGT 33895
i
C L1P2_5end#LIN 1080 TGGTTTTTAGAATTTTCAGCTTTTCTGCTCTGGTTTCTCCCCATCTTTGT 1031
chr15_MATERNA 33896 GGTTTTTACCTACCTTTGGTCTTTGATGATGGTGATGTACAGATGGGGTT 33945
- i ? iv
C L1P2_5end#LIN 1030 GG-TTTTATCTACCTTTGGTCTTTGATGNTGGTGACCTACAGATGGGGTT 982
chr15_MATERNA 33946 TTGGTGTGGATG 33957
C L1P2_5end#LIN 981 TTGGTGTGGATG 970
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 4.25
Transitions / transversions = 2.22 (51/23)
Gap_init rate = 0.01 (8 / 1300), avg. gap size = 2.12 (17 / 8)
+ 6665 11.4 3.9 0.3 chr15_MATERNAL_p_2-50000:. 33958 34911 (15088) C LTR5B LTR/ERVK (0) 1002 13 33
ANNOTATION EVIDENCE:
6665 11.36 3.94 0.31 chr15_MATERNAL_p_2-50000:. 33958 34911 13286 C LTR5B LTR/ERVK 13 1002 0
6665 11.36 3.94 0.31 chr15_MATERNAL_p_2-50000:. 33958 34911 (13286) C LTR5B#LTR/ERVK (0) 1002 13 m_b1s502i7
chr15_MATERNA 33958 TGAAGGG--GTCCAGCCCCTCCACACCTGTGGGTGTTTCTCATCAGGTGG 34005
-- v ? i i
C LTR5B#LTR/ERV 1002 TGAAGGGNCGGCCNGCCCCTCCACACCTGTGGGTATTTCTCGTCAGGTGG 953
chr15_MATERNA 34006 GATGAGAGACTGAGAAAATAAATAAGAGACACAGACAAAGTATAGAGAAA 34055
i v v v
C LTR5B#LTR/ERV 952 GACGAGAGACTGAGAAAAGAAATAAGACACAGAGACAAAGTATAGAGAAA 903
chr15_MATERNA 34056 GAACAGTGGGCCCAGGGGACCAGCACTCAGCATACAGAGGACCCGCGCTG 34105
i i i i i
C LTR5B#LTR/ERV 902 GAACAGTGGGCCCAGGGGACCGGCGCTCAGCATACGGAGGACCCGCACCG 853
chr15_MATERNA 34106 GCCCTGGTCTCTGAGTTCCCTCAGTATTTATTGATCACTATCTCTACCAT 34155
v i i ii i
C LTR5B#LTR/ERV 852 GCACCGGTCTCTGAGTTCCCTCAGTATTTATTGATCACTATTTTCACTAT 803
chr15_MATERNA 34156 CTCGGAGAGGAGGATGTGGCCGGACAATAGGGTAATAGTGGGGAGAGGGT 34205
v i i i v v i i i
C LTR5B#LTR/ERV 802 CTCGGCGAGGGGAATGCGGCAGGAGAACAGGGTGATAGTGGGGAGAAGGT 753
chr15_MATERNA 34206 CAGCAGGAAAACATGTGAACAAAGATCTCTGTGTCATAAATAAGTTTAAG 34255
i ivv i
C LTR5B#LTR/ERV 752 CAGCAGGAAAACATGTGAGCAAAGGAATCTGTGTCATAAATAAGTTCAAG 703
chr15_MATERNA 34256 GAAAGGTGCTGTGCTTTGATGTGCACGT---------------------- 34283
i i i v ----------------------
C LTR5B#LTR/ERV 702 GGAAGGTACTGTGCCTGGATGTGCACGTAGGCCAGATTTATGTTTCTCTC 653
chr15_MATERNA 34284 -ACACAAACATCTCAGTTCATTAA--------AGAGCAGTATTGCCGCCA 34324
- v v? v -------- i
C LTR5B#LTR/ERV 652 CACCCAAACATCTCAGTGNAGTAAAGAGTAACAGAGCAGCATTGCCGCCA 603
chr15_MATERNA 34325 GCATGTCTCACCTCCAGCCCTAAGGTGG-TTTTCTCCTATCTCAG---TA 34370
i vi i i - ---?i
C LTR5B#LTR/ERV 602 GCATGTCTCGCCTCCAGCCACAGGGCGGNTTTTCTCCTATCTCAGAATNG 553
chr15_MATERNA 34371 AACAGAACATACAATCAGGTTTTACACCAAGACATTCCATTACCAGGGAC 34420
- ii i i i i v
C LTR5B#LTR/ERV 552 AAC-GAATGTACGATCGGGTTTTACACCGAGACATTCCGTTCCCAGGGAC 504
chr15_MATERNA 34421 GAGCAGGAGACAGATGCCTTCCTCTTATCTCAACTGCAAAGAGGCCTTCC 34470
i v -
C LTR5B#LTR/ERV 503 GGGCAGGAGACAGAGGCCTTCCTCTTATCTCAACTGC-AAGAGGCCTTCC 455
chr15_MATERNA 34471 TCTTTCACTAATCCTCCTCAGCACAGACCATTTATGGGTGTTGGGCTAGG 34520
v i i i
C LTR5B#LTR/ERV 454 TCTTTCACTAATCCTCCTCAGCACAGACCCTTTACGGGTGTCGGGCTGGG 405
chr15_MATERNA 34521 -GGATGGTCAGGTCTTTCCGTTCCCACAAGGCCATCTCTCAGGCTATTAC 34569
- i v i v i iv
C LTR5B#LTR/ERV 404 NGGACGGTCAGGTCTTTCCCTTCCCACGAGGCCATATCTCAGGCTGTCTC 355
chr15_MATERNA 34570 ATGGGGAGAAACCTTGGACAATACCTGGCTTTCCTGGGCAGAGGTCCCTG 34619
i
C LTR5B#LTR/ERV 354 ATGGGGAGAAACCTTGGACAATACCCGGCTTTCCTGGGCAGAGGTCCCTG 305
chr15_MATERNA 34620 TAGCCTTCCACAGTGTATTGTGTCCCTGGGTACTTGAGATTAGAGAATGG 34669
ii i i i i v v i ? i
C LTR5B#LTR/ERV 304 CGGCTTTCCGCAGTGCATTGTGCCCCTGGTTAATCGAGANTGGAGAATGG 255
chr15_MATERNA 34670 TGATAACTTTTACCAAGCATACTGCCTTCAAGCACTTTTTTAACAAAGCA 34719
i i v i i? v i
C LTR5B#LTR/ERV 254 CGATGACTTTTACCAAGCATACTGCCTGCAAACATNTTGTTAACAAGGCA 205
chr15_MATERNA 34720 CATCCTGCACAGCCCTAAATCCATTAAACCTTGAGTCAACACAGCACATG 34769
i v v ? i
C LTR5B#LTR/ERV 204 CATCCTGCACAGCCCTAGATCCCTTAAACCTTGATTCNATACAGCACATG 155
chr15_MATERNA 34770 TCTCTGCAAACACAGGGTTGGGGCTAGCATTACAGATTAACAGCATCTCA 34819
i ii i ivi
C LTR5B#LTR/ERV 154 TTTCTGTGAGCACAGGGTTGGGGCTAAAGTTACAGATTAACAGCATCTCA 105
chr15_MATERNA 34820 AGGCAGAA-TAATTTATCTTAGTACAGAACAAAATGGAGTTTCTTATGTC 34868
-i v ? i v
C LTR5B#LTR/ERV 104 AGGCAGAAGCAATTTTTCNTGGTACAGATCAAAATGGAGTTTCTTATGTC 55
chr15_MATERNA 34869 TACTTCTTTCTACATAGACACAGTAACAGTCTGATCTCTCTTT 34911
v i -
C LTR5B#LTR/ERV 54 TTCCT-TTTCTACATAGACACAGTAACAGTCTGATCTCTCTTT 13
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 9.07
Transitions / transversions = 2.26 (70/31)
Gap_init rate = 0.01 (11 / 953), avg. gap size = 3.82 (42 / 11)
+ 8508 10.8 3.6 0.1 chr15_MATERNAL_p_2-50000:. 34912 36099 (13900) C L1P2 LINE/L1 (4950) 1234 4 34
ANNOTATION EVIDENCE:
8508 10.78 3.57 0.08 chr15_MATERNAL_p_2-50000:. 34912 36099 12098 C L1P2_5end LINE/L1 4 1234 1041
8508 10.78 3.57 0.08 chr15_MATERNAL_p_2-50000:. 34912 36099 (12098) C L1P2_5end#LINE/L1 (1041) 1234 4 m_b1s551i15
chr15_MATERNA 34912 GCTATGGGTTCAAACATCCTCCATTAGCTTGGAGAAGGTTGTTATTACTG 34961
v i v i v i
C L1P2_5end#LIN 1234 GCGATGGGTTCGAACATCCTCCTTTAGCTCGGAGAAGTTTGTTATTACCG 1185
chr15_MATERNA 34962 ACCGTCTGAAGACTTCTTCTCTCAACTCATCAAAGTCATTCACCATCCAG 35011
v v v v i v i
C L1P2_5end#LIN 1184 ACCTTCTGAAGCCTACTTCTGTCAACTCGTCAAAGTCATTCTCCGTCCAG 1135
chr15_MATERNA 35012 CTTTGTTCCATTGCTGGTGAGGAGCTGCATTCCTTTGGAGGAGAAGAGGC 35061
i i iv
C L1P2_5end#LIN 1134 CTTTGTTCCGTTGCTGGCGAGGAGCTGCGATCCTTTGGAGGAGAAGAGGC 1085
chr15_MATERNA 35062 ACTCTGATTTTTAGACTTTTCAGCTTTTCTGCTCTGGTTTCTCCCCATCT 35111
i i v
C L1P2_5end#LIN 1084 GCTCTGGTTTTTAGAATTTTCAGCTTTTCTGCTCTGGTTTCTCCCCATCT 1035
chr15_MATERNA 35112 TTGTGGTTTTATTTACCTTTGGTCTTTGGTGATGGTGACGTACAGATGGG 35161
i i ? v
C L1P2_5end#LIN 1034 TTGTGGTTTTATCTACCTTTGGTCTTTGATGNTGGTGACCTACAGATGGG 985
chr15_MATERNA 35162 GTTTTGGTGTGGATG-------------------------TCCTTTCTGT 35186
-------------------------
C L1P2_5end#LIN 984 GTTTTGGTGTGGATGTCCTTTTTGTTGATGTTGATGCTATTCCTTTCTGT 935
chr15_MATERNA 35187 TTGTTAGTTTTTCTTCTAACGGTCAGGACCCTCAGCTGCAGGTCTGTTGG 35236
i i ?
C L1P2_5end#LIN 934 TTGTTAGTTTTCCTTCTAACAGTCAGGNCCCTCAGCTGCAGGTCTGTTGG 885
chr15_MATERNA 35237 AGTTTGCTGGAGGTCCACTCCAGACCCTATTTACATGGGTGTCACCAGCG 35286
i i v i
C L1P2_5end#LIN 884 AGTTTGCTGGAGGTCCACTCCAGACCCTGTTTGCCTGGGTATCACCAGCG 835
chr15_MATERNA 35287 GAGGC-----------------TGCAGAACAGCAAATGTTGCTGCCTGAG 35319
----------------- i v
C L1P2_5end#LIN 834 GAGGCTGCAGAACAGCAAATATTGCAGAACAGCAAATATTGCTGCCTGAT 785
chr15_MATERNA 35320 TGTTCCTCTGGAAACTTTGTCTCAGAGGGGCACCTGGCCATAAGAGGTGT 35369
iv i i i i v ii v
C L1P2_5end#LIN 784 CCTTCCTCTGGAAGCTTCGTCCCAGAGGGGCACCCGCCTGTATGAGGTGT 735
chr15_MATERNA 35370 CAGTCAGCCTCTACTGGGAGGTGCCTCCAAGTTAGGCTACTCGGGGGTCA 35419
? i i i v v
C L1P2_5end#LIN 734 CNGTCGGCCCCTACTGGGAGGTGTCTCCCAGTTAGGCTACACGGGGGTCA 685
chr15_MATERNA 35420 GGGACCCACTTTAGGAGGCAGTCTGTCCACTCTCAGATCTCAAACTCCGT 35469
v ii v v
C L1P2_5end#LIN 684 GGGACCCACTTGAGGAGGCAGTCTGTCCGTTCTCAGAGCTCAAACGCCGT 635
chr15_MATERNA 35470 GCTAGGAGAACCACTACTCTCTTCAAAGCTGTCACACAGGGATGTTTAAG 35519
i i i v i
C L1P2_5end#LIN 634 GCTGGGAGAACCACTGCTCTCTTCAGAGCTGTCAGACAGGGACGTTTAAG 585
chr15_MATERNA 35520 TTTGCAGAAGTT-TCTGCTGCCTTTTGTTCAGCTATGCCCTTTCCCCAGA 35568
i - vi
C L1P2_5end#LIN 584 TCTGCAGAAGTTGTCTGCTGCCTTTTGTTCAGCTATGCCCTGCCCCCAGA 535
chr15_MATERNA 35569 GGTGGAGTCCACAGAGGCAGGCAGGCCTCCTTGAGCTGTGGTGGGCTCCA 35618
i - vi i i
C L1P2_5end#LIN 534 GGTGGAGTCTACAGAGGCA-GCAGGCCTCGCTGAGCTGCGGTGGGCTCCG 486
chr15_MATERNA 35619 CACAGTTCGAGCTTCCTGGCCGCTTTGTTTACCTACTCAAGCCTCAGCAA 35668
v i
C L1P2_5end#LIN 485 CCCAGTTCGAGCTTCCCGGCCGCTTTGTTTACCTACTCAAGCCTCAGCAA 436
chr15_MATERNA 35669 TGACAGACACCACTCCCCCAGCCTTGCTGCTGCCTTGCAGTTCAATCTCA 35718
i i i v vv i i ? i
C L1P2_5end#LIN 435 TGGCGGACGCCCCTCCCCCAGCCAGGCTGCCGCCTCGCAGNTCGATCTCA 386
chr15_MATERNA 35719 GACTGCTGTGCTAGCAGTGAGCGAGGTTCTGTGGTCATAGGACCCTCCAA 35768
i i i i v i i v i
C L1P2_5end#LIN 385 GACTGCTGCGCTAGCAGTGAGCAAGGCTCCGTGGGCGTGGGACCCGCCGA 336
chr15_MATERNA 35769 GCCATGCACAGGATATAATCTCCTGGTGTGCCATTTGCTAAGACCACTGG 35818
v i i ? i ii
C L1P2_5end#LIN 335 GCCAGGCGCGGGATANAATCTCCTGGTGTGCCGTTTGCTAAGACCGTTGG 286
chr15_MATERNA 35819 AAAAGCACAGTATTAGGGTGGGAGTGTCCCGATTTTCCAGGTACCATCTG 35868
i v i ? vi
C L1P2_5end#LIN 285 AAAAGCGCAGTATTTGGGCGGGAGTGTCCCGNTTTTCCAGGTACAGTCTG 236
chr15_MATERNA 35869 TCACAGCTTCCCTTGGCTAGGAAAGGG-AATTCCCCAGCCCCTTGTGCTT 35917
i - i ii i
C L1P2_5end#LIN 235 TCACGGCTTCCCTTGGCTAGGAAAGGGAAATCCCCCGACCCCTTGCGCTT 186
chr15_MATERNA 35918 CCCAGGTGAGGTGATGCCCCACCCTGCTTCAGCTCACACTCTGTGGTCTG 35967
i i i i i v i v
C L1P2_5end#LIN 185 CCCGGGTGAGGCGATGCCCCGCCCTGCTTCGGCTCGCCCTCCGTGGGCTG 136
chr15_MATERNA 35968 CACCCACTGTCTGACAAGCCCCAGTGAGATGAACCCAGTACCTCAGTTGG 36017
ii v i vi
C L1P2_5end#LIN 135 CACCCACTGTCCAACCAGTCCCAGTGAGATGAACCAGGTACCTCAGTTGG 86
chr15_MATERNA 36018 AAATGCAGAAATCACCTGTCTTCTACGTCACTCATGCTGGGAGCTGTAGA 36067
i i iv i i
C L1P2_5end#LIN 85 AAATGCAGAAATCACCCGTCTTCTGCGTCGATCACGCTGGGAGCTGCAGA 36
chr15_MATERNA 36068 CTGGAGCTGTTCCTATTCAGCCATCTTGGAAC 36099
i i
C L1P2_5end#LIN 35 CCGGAGCTGTTCCTATTCGGCCATCTTGGAAC 4
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 7.17
Transitions / transversions = 2.21 (84/38)
Gap_init rate = 0.00 (5 / 1187), avg. gap size = 9.00 (45 / 5)
+ 237 33.6 15.3 3.6 chr15_MATERNAL_p_2-50000:. 36285 36503 (13496) C L2a LINE/L2 (175) 3251 3003 35
ANNOTATION EVIDENCE:
237 33.65 15.26 3.65 chr15_MATERNAL_p_2-50000:. 36285 36503 11694 C L2a_3end LINE/L2 94 342 175
237 33.65 15.26 3.65 chr15_MATERNAL_p_2-50000:. 36285 36503 (11694) C L2a_3end#LINE/L2 (175) 342 94 m_b1s601i7
chr15_MATERNA 36285 AAATGGTGATAACAGT--TGATAAAAAAGCAAGCATGACATTGATTTAGA 36332
i vv i-- ivi vv v ii ------- i
C L2a_3end#LINE 342 AGATGGTGATAAGTGCTATGGAGAAAAATAAAGCAGGGTA-------AGG 300
chr15_MATERNA 36333 CAAAT-GTGGTTGTTGAGAGTGATTGTGGACCACTCTCCATTAGGGTGTT 36381
vii - v iv ? i i ? vv vi ? i i vv - v
C L2a_3end#LINE 299 GGGATAGGGAGTGNTGGGGGNGAGGGTGTGCNATTTTAAA-TAGGGTGGT 251
chr15_MATERNA 36382 CAGGAAAGGCCTTTTTT---AAGTGACCT----GTAA----CTCATATCA 36420
i i?i v--- i v ---- i ---- v vivvi
C L2a_3end#LINE 250 CAGGGAAGGCCTCNCTGAGAAGGTGACATTTGAGCAAAGACCTGAAGGAG 201
chr15_MATERNA 36421 GTGAAAAAG---AACATGC---TAT------AAAAAG-ATTCCACAAAGT 36457
iii ---iv --- ------i i -i viv v
C L2a_3end#LINE 200 GTGAGGGAGCGAGCCATGCGGATATCTGGGGGAAGAGCGTTCCAGGCAGA 151
chr15_MATERNA 36458 GAGAGCATTAAGCTCAAAGGTCCTGAGGTA-----------GGTGTGTTT 36496
i i vi iv i ii----------- i i
C L2a_3end#LINE 150 GGGAACAGCAAGTGCAAAGGCCCTGAGGCGGGAGCGTGCCTGGCGTGTTC 101
chr15_MATERNA 36497 GAGGAGC 36503
i
C L2a_3end#LINE 100 GAGGAAC 94
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 40.36
Transitions / transversions = 1.48 (40/27)
Gap_init rate = 0.08 (18 / 218), avg. gap size = 2.56 (46 / 18)
+ 442 32.3 4.8 2.6 chr15_MATERNAL_p_2-50000:. 36516 36741 (13258) + MARNA DNA/TcMar-Mariner 200 430 (156) 36
ANNOTATION EVIDENCE:
442 32.28 4.76 2.65 chr15_MATERNAL_p_2-50000:. 36516 36741 11456 + MARNA DNA/TcMar-Mariner 200 430 156
442 32.28 4.76 2.65 chr15_MATERNAL_p_2-50000:. 36516 36741 (11456) MARNA#DNA/TcMar-Mariner 200 430 (156) m_b1s502i8
chr15_MATERNA 36516 GCTGTATAAGAAG-TCAACCTCCTTATTTT-CAGGTACATTTATTATTAT 36563
iii i i- ii v i -i vi ii --i --
MARNA#DNA/TcM 200 GCCACACAAGAAAATCAGTCTCATTACTTTATAGTCACACCT--CATT-- 245
chr15_MATERNA 36564 TTTAACCCCAAGCAGAATTGCCTAGCTGGGTCCCTCACCTT-TACACAAT 36612
i ?v ii v i i v i v i - v v v
MARNA#DNA/TcM 246 TTTGACCNAAAATAGTATTACCCAGCTTGATCACCCACCTTATTCACCAG 295
chr15_MATERNA 36613 AGT------CATAGGA--TTTGACTGTTATCAAAAAGTAAATCCACTCTC 36654
v ------ iv v -- i vi vi i
MARNA#DNA/TcM 296 ACTTGGCTCCGAATGACTTTTGGCTGTTTCCAAAAATCAAATCCACCCTC 345
chr15_MATERNA 36655 AGAGACCATAGATTTCCTATTACTGAGGTTCTTCAAAAGAATATGTAATC 36704
i iv iv v i ii i v v i iviiv
MARNA#DNA/TcM 346 AAAGGACGAAGATTTGCCACCATTGAGGATATTCAAAAGAATGTGCCGCA 395
chr15_MATERNA 36705 AATTTATATAGTAATTCCTAAAAATGAGATTCTAAAA 36741
iii ivv vi i - i - ii i
MARNA#DNA/TcM 396 GGCTCTGAAGGCAATTCC-AAAGA-GAAGTTCCAAAA 430
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 41.35
Transitions / transversions = 1.92 (46/24)
Gap_init rate = 0.05 (11 / 225), avg. gap size = 1.55 (17 / 11)
+ 32 0.0 0.0 0.0 chr15_MATERNAL_p_2-50000:. 37574 37603 (12396) + (GTTTT)n Simple_repeat 1 30 (0) 37
ANNOTATION EVIDENCE:
32 0.00 0.00 0.00 chr15_MATERNAL_p_2-50000:. 37574 37603 12396 + (GTTTT)n Simple_repeat 1 30 0
32 0.00 0.00 0.00 chr15_MATERNAL_p_2-50000:. 37574 37603 (12396) (GTTTT)n#Simple_repeat 1 30 (0) c_b1s251i5
chr15_MATERNA 37574 GTTTTGTTTTGTTTTGTTTTGTTTTGTTTT 37603
(GTTTT)n#Simp 1 GTTTTGTTTTGTTTTGTTTTGTTTTGTTTT 30
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 2060 11.1 0.4 0.4 chr15_MATERNAL_p_2-50000:. 37604 37884 (12115) C AluSx SINE/Alu (29) 283 3 38
ANNOTATION EVIDENCE:
2060 11.07 0.36 0.36 chr15_MATERNAL_p_2-50000:. 37604 37884 12115 C AluSx SINE/Alu 3 283 29
2060 11.07 0.36 0.36 chr15_MATERNAL_p_2-50000:. 37604 37884 (12115) C AluSx#SINE/Alu (29) 283 3 c_b1s352i3
chr15_MATERNA 37604 TGAGATGGAGTTTCACTCTTGTTGCCCAGGCTGGAGTGCAATGGCGCCAT 37653
i i i - i i v
C AluSx#SINE/Al 283 TGAGACGGAGTCTCGCTC-TGTCGCCCAGGCTGGAGTGCAGTGGCGCGAT 235
chr15_MATERNA 37654 CTCAGCTCACTGCAACCTCTGCCTCCCAGGTTCAAGCGATTCTCCTGCTT 37703
i i i i
C AluSx#SINE/Al 234 CTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCT 185
chr15_MATERNA 37704 CAGCCTCCCAAGCAGCTGGGATTACAGGCATGCACCACCATGACCAGCCA 37753
i i ii i i v i i
C AluSx#SINE/Al 184 CAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTA 135
chr15_MATERNA 37754 A-TTTTGTGTTGTTAGTAGAGATGGGGTTTCTCCATGTTGGTCAGGTTGG 37802
- i v i v i i
C AluSx#SINE/Al 134 ATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGG 85
chr15_MATERNA 37803 TCTCGAACGCCCGACCTCAGGTGATCCGCCTGCCTCGGCTTCCCAAAGTG 37852
v i i i
C AluSx#SINE/Al 84 TCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTG 35
chr15_MATERNA 37853 CTGGGATTACAGGCGTGAGCCACTGCGCCTGG 37884
i i
C AluSx#SINE/Al 34 CTGGGATTACAGGCGTGAGCCACCGCGCCCGG 3
Matrix = 14p41g.matrix
Kimura (with divCpGMod) = 6.22
Transitions / transversions = 5.20 (26/5)
Gap_init rate = 0.01 (2 / 280), avg. gap size = 1.00 (2 / 2)
+ 387 21.1 20.0 2.8 chr15_MATERNAL_p_2-50000:. 38064 38208 (11791) C MIRb SINE/MIR (55) 207 41 39
ANNOTATION EVIDENCE:
347 21.09 20.00 3.03 chr15_MATERNAL_p_2-50000:. 38064 38195 10311 C MIR SINE/MIR 48 207 55
347 21.09 20.00 3.03 chr15_MATERNAL_p_2-50000:. 38064 38195 (10311) C MIR#SINE/MIR (55) 207 48 m_b1s601i8
chr15_MATERNA 38064 CTTTATGTGAATGCTCAACTATATTTAA--AACACATCAATTCTATGAGG 38111
ii v --- i -i --vv v ii
C MIR#SINE/MIR 207 CTTTACATGTA---TTAACT-CATTTAATCCTCACAACAACCCTATGAGG 162
chr15_MATERNA 38112 TAGG------TATTAACCCTTTCTTACAGAAGAAGGAACTGAACCCCA-- 38153
------ v iv i v i i iv v --
C MIR#SINE/MIR 161 TAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGA 112
chr15_MATERNA 38154 --------------TG---AAGGCTACACA-----TAAGTGGCAGAGGTG 38181
-------------- --- ii ----- vi
C MIR#SINE/MIR 111 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 62
chr15_MATERNA 38182 AAATTTGAACCCAG 38195
ii i
C MIR#SINE/MIR 61 GGATTCGAACCCAG 48
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 23.21
Transitions / transversions = 1.70 (17/10)
Gap_init rate = 0.08 (10 / 131), avg. gap size = 3.60 (36 / 10)
387 21.74 19.58 0.00 chr15_MATERNAL_p_2-50000:. 38094 38208 10298 C MIRb SINE/MIR 41 183 85
387 21.74 19.58 0.00 chr15_MATERNAL_p_2-50000:. 38094 38208 (10298) C MIRb#SINE/MIR (85) 183 41 m_b1s601i9
chr15_MATERNA 38094 CACATCAATTCTATGAGGTAGGTATTA--A-CCCTTTCTTACAGAAGAAG 38140
v ii ii -- - iv i v i
C MIRb#SINE/MIR 183 CACAACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGG 134
chr15_MATERNA 38141 GAACTGAACCCCA----------------TG---AAGGCTACACA----- 38166
i iv i ---------------- --- ii -----
C MIRb#SINE/MIR 133 AAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG 84
chr15_MATERNA 38167 TAAGTGGCAGAGGTGAAATTTGAACCCAGATCTA-CCAACTCC 38208
vi ii i i i- ii
C MIRb#SINE/MIR 83 TAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCC 41
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 23.38
Transitions / transversions = 4.00 (20/5)
Gap_init rate = 0.05 (6 / 114), avg. gap size = 4.67 (28 / 6)
+ 234 22.8 12.2 0.0 chr15_MATERNAL_p_2-50000:. 38209 38287 (11712) C Charlie6 DNA/hAT-Charlie (2581) 938 849 40
ANNOTATION EVIDENCE:
234 22.78 12.22 0.00 chr15_MATERNAL_p_2-50000:. 38209 38287 10219 C Charlie6 DNA/hAT-Charlie 849 938 2581
234 22.78 12.22 0.00 chr15_MATERNAL_p_2-50000:. 38209 38287 (10219) C Charlie6#DNA/hAT-Charlie (2581) 938 849 m_b1s502i9
chr15_MATERNA 38209 AAGTTTCTTTTCAATTT-----GA-CTATAACTGCATTTGTGA-TTGCTT 38251
v ----- - i vi i - i
C Charlie6#DNA/ 938 AAGTGTCTTTTCAATTTTGCTGGAGCCATTGCTGCATTTGTAAGTTGTTT 889
chr15_MATERNA 38252 GTGACATAAGACATACGAGAGAGTAG----ATTTGAATTA 38287
iv v v ii i vi i ---- i i
C Charlie6#DNA/ 888 GCCACAGACGACGCACAATGGAATAGGACAACTTGGATTA 849
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 26.20
Transitions / transversions = 2.00 (12/6)
Gap_init rate = 0.05 (4 / 78), avg. gap size = 2.75 (11 / 4)
+ 1807 13.5 0.4 2.8 chr15_MATERNAL_p_2-50000:. 38919 39200 (10799) C AluSx SINE/Alu (10) 302 28 41
ANNOTATION EVIDENCE:
1807 13.50 0.36 2.84 chr15_MATERNAL_p_2-50000:. 38919 39200 10799 C AluSx SINE/Alu 28 302 10
1807 13.50 0.36 2.84 chr15_MATERNAL_p_2-50000:. 38919 39200 (10799) C AluSx#SINE/Alu (10) 302 28 c_b1s352i4
chr15_MATERNA 38919 TTTTACTTTTTTTTTTTTTTGAGACAAAGTTTTGTTCTTGTTGCCCAGGC 38968
vi ii i i i - i
C AluSx#SINE/Al 302 TTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTC-TGTCGCCCAGGC 254
chr15_MATERNA 38969 TGGAATGCAATGGCATGATCTCAGCTCACTGCAACCTCTGCCTCCCAGGT 39018
i i ii i i i
C AluSx#SINE/Al 253 TGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGT 204
chr15_MATERNA 39019 TTAAGCAATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACCAGAGT 39068
i i i vi v i
C AluSx#SINE/Al 203 TCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGC 154
chr15_MATERNA 39069 ACACCACCAGGCCCGGCTAA-TTTTGTACTTCTTTAGTAGAGACAGGGTT 39117
i i v - -- i i
C AluSx#SINE/Al 153 GCGCCACCACGCCCGGCTAATTTTTGTA--TTTTTAGTAGAGACGGGGTT 106
chr15_MATERNA 39118 TCACCATGTTGGTCAGGCTGGTCTTGAATCCCTGAACTCAAGTGATCCAC 39167
i i ii v i i
C AluSx#SINE/Al 105 TCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGC 56
chr15_MATERNA 39168 CCCTGCACACTCGGCCTCCCAAAATGTTGGAAT 39200
-- --- i i i
C AluSx#SINE/Al 55 CC--GC---CTCGGCCTCCCAAAGTGCTGGGAT 28
Matrix = 14p41g.matrix
Kimura (with divCpGMod) = 9.21
Transitions / transversions = 6.40 (32/5)
Gap_init rate = 0.03 (9 / 281), avg. gap size = 1.00 (9 / 9)
+ 2218 11.9 0.0 0.7 chr15_MATERNAL_p_2-50000:. 39501 39805 (10194) + AluSx SINE/Alu 1 303 (9) 42
ANNOTATION EVIDENCE:
2218 11.88 0.00 0.66 chr15_MATERNAL_p_2-50000:. 39501 39805 10194 + AluSx SINE/Alu 1 303 9
2218 11.88 0.00 0.66 chr15_MATERNAL_p_2-50000:. 39501 39805 (10194) AluSx#SINE/Alu 1 303 (9) c_b1s352i5
chr15_MATERNA 39501 GGCTGGGAGTGGTGGCTCACGCCTGTAATCCCAACACTTTGGGAGGCCGA 39550
i v i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
chr15_MATERNA 39551 GGCAGGTGGATCACCTGAGGTCAGGAGTTTGAGACTAGTGTGGCCAACAT 39600
i i i i iv
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
chr15_MATERNA 39601 GGTGAAACACCTTCTCTACTAAAAATACCAAAAATTAGCCAGGTGTAGTG 39650
v v - i i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATAC-AAAAATTAGCCGGGCGTGGTG 149
chr15_MATERNA 39651 GCGGACACCTGTAATCCCAGCTACTCAGGAGGCTGAAACAGGAGAATCAC 39700
vi i i ii i
AluSx#SINE/Al 150 GCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGC 199
chr15_MATERNA 39701 TTGAACCTGGGAGGGAGAGGTTGCAGTGAGCTGAGATTGCGCCATTACAC 39750
i vi i i i i
AluSx#SINE/Al 200 TTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAC 249
chr15_MATERNA 39751 TCTGGCCTGGGCAACAAGAGTGAAACTCTGTCTCAAAAAAAAAAAAAAAA 39800
ii i - i i i
AluSx#SINE/Al 250 TCCAGCCTGGGCGACA-GAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 298
chr15_MATERNA 39801 AGAAA 39805
i
AluSx#SINE/Al 299 AAAAA 303
Matrix = 14p41g.matrix
Kimura (with divCpGMod) = 6.89
Transitions / transversions = 5.00 (30/6)
Gap_init rate = 0.01 (2 / 304), avg. gap size = 1.00 (2 / 2)
+ 922 27.0 7.4 0.8 chr15_MATERNAL_p_2-50000:. 40225 40534 (9465) + MER21C LTR/ERVL 447 841 (97) 43
ANNOTATION EVIDENCE:
233 31.72 4.60 8.23 chr15_MATERNAL_p_2-50000:. 40225 40382 8709 + MER77 LTR/ERVL 447 598 6
233 31.72 4.60 8.23 chr15_MATERNAL_p_2-50000:. 40225 40382 (8709) MER77#LTR/ERVL 447 598 (6) m_b1s502i10
chr15_MATERNA 40225 CCCAGGCTCTGTAGCTTCTATACACCTGTTCCATTTCCAACTGTTCCTGT 40274
ii i i----i i i v - ---i v ii iv
MER77#LTR/ERV 447 CCTGGACTCTGC----CCTATGCGCCTTTTCC-TTT---GCTGATTTTAA 488
chr15_MATERNA 40275 GTTGTATATTTT----ATAACAAACTGTTATACACAAGTA---CAGTGTT 40317
vi vi ----i i i v i- iii --- iv
MER77#LTR/ERV 489 TCTGTATCCTTTCGCTGTAATAAACCGTAAC-CGTGAGTATAACAGCTTT 537
chr15_MATERNA 40318 TGGCTGAGTTCTGTGAGTATTTTAATCAAATTCTCAAACTTGAGAAAGGG 40367
-- vi iv v i iv i i i-- v
MER77#LTR/ERV 538 T--CTGAGTTCTGTGAGTCCTTCTAGCGAATCATCGAACCTGAGG--GTG 583
chr15_MATERNA 40368 GTTATGGGAGTCCTC 40382
iv iii i
MER77#LTR/ERV 584 GTCTTGGGGACCCCC 598
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 37.90
Transitions / transversions = 2.54 (33/13)
Gap_init rate = 0.10 (15 / 157), avg. gap size = 1.33 (20 / 15)
922 26.71 7.59 0.34 chr15_MATERNAL_p_2-50000:. 40242 40534 8557 + MER21C LTR/ERVL 526 841 97
922 26.71 7.59 0.34 chr15_MATERNAL_p_2-50000:. 40242 40534 (8557) MER21C#LTR/ERVL 526 841 (97) m_b1s502i11
chr15_MATERNA 40242 CTATACACCTGTTCCATTT------CCAACTGT-TCCTGTGTTGTATATT 40284
i i v i ------i v - v vi vi
MER21C#LTR/ER 526 CTATGCATCTCTTCCATCTGGCTGTTCATCTGTATCCTTTGTAATATCCT 575
chr15_MATERNA 40285 TTATAACAAACTGTTATACACAAGTACAGTGTTTGGCTGAGTTCTGTGAG 40334
i i v v ii v vv
MER21C#LTR/ER 576 TTATAATAAACCGGTAAACGTAAGTAAAGTGTTTCCCTGAGTTCTGTGAG 625
chr15_MATERNA 40335 -TATTTTAATCAAATTCTCAAACTTGAGAAAGGGGTTATGGGAGTCCTCA 40383
-ii i i- v i ii i i ii ii i i
MER21C#LTR/ER 626 CCGTTCTAG-CAAATTATCGAACCCGAGGAGGGGGTCGTGGGAACCCCCG 674
chr15_MATERNA 40384 CTTCTTAG----TAGCTCAGAAGTACGTATGGGTACCTGTGGTTTCTGAC 40429
v iv ---- v v vi ?ivv v ii vi
MER21C#LTR/ER 675 ATTTATAGCCGGTCGGTCAGAAGTACGGGTNACAACCTGGGACTTGCGAC 724
chr15_MATERNA 40430 TGGCATCTGCAGTAAGAGCAGTGTTGTGGGACTAAGCTCTGGA-CTCTAG 40478
i v ii i v i i vi - v i
MER21C#LTR/ER 725 TGGCGTCTGAAGTGGGGGCAGTCTTGTGGGACTGAGCCCTTAACCTGTGG 774
chr15_MATERNA 40479 GGCCTG-TGCTGACT-----TTGGTGGTGTGAGATTTAAA----A-TGTT 40517
i -i i ----- v ? i v v i ---- - v
MER21C#LTR/ER 775 GGTCTGACGCTAACTCCAGGTAGNTAGTGTCAGAATTGAATTGAATTGTA 824
chr15_MATERNA 40518 AAACAACTAGTTGGTGT 40534
ii v i
MER21C#LTR/ER 825 GGACACCCAGTTGGTGT 841
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 27.95
Transitions / transversions = 1.62 (47/29)
Gap_init rate = 0.03 (10 / 292), avg. gap size = 2.50 (25 / 10)
+ 2207 12.9 0.7 0.0 chr15_MATERNAL_p_2-50000:. 40593 40902 (9097) + AluSx SINE/Alu 1 312 (0) 44
ANNOTATION EVIDENCE:
2207 12.90 0.65 0.00 chr15_MATERNAL_p_2-50000:. 40593 40902 9097 + AluSx SINE/Alu 1 312 0
2207 12.90 0.65 0.00 chr15_MATERNAL_p_2-50000:. 40593 40902 (9097) AluSx#SINE/Alu 1 312 (0) c_b1s352i6
chr15_MATERNA 40593 GGCCAGGCATGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCTGA 40642
i ii i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
chr15_MATERNA 40643 GGTGGGCAGACCA--TGAGGTCAGGAGTTTGAGACCAGCCTGACCAACAC 40690
i i i -- i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
chr15_MATERNA 40691 GGTGAAACCCCATCTCTACTAAAAATACAAAAATTAGCTGGGCATGTTGG 40740
i i i v
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGG 150
chr15_MATERNA 40741 CAGGTGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCACT 40790
iv i i i i
AluSx#SINE/Al 151 CGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCT 200
chr15_MATERNA 40791 TGAACCCAGGAGGCAGAGGTTGCAGTGAGCTGAGATAGTGCCACTGCACT 40840
i i i v i
AluSx#SINE/Al 201 TGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACT 250
chr15_MATERNA 40841 CCAGCCTAAGTGACAGAGTGAGACTCCATCTCAAAAAAGAAGAAGAAGAA 40890
ii i i i i i i i
AluSx#SINE/Al 251 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 300
chr15_MATERNA 40891 GAAGGAGAAGAA 40902
i ii i i
AluSx#SINE/Al 301 AAAAAAAAAAAA 312
Matrix = 14p41g.matrix
Kimura (with divCpGMod) = 6.92
Transitions / transversions = 12.33 (37/3)
Gap_init rate = 0.00 (1 / 309), avg. gap size = 2.00 (2 / 1)
+ 149 6.7 0.5 1.4 chr15_MATERNAL_p_2-50000:. 40905 41114 (8885) + (AAG)n Simple_repeat 1 208 (0) 45
ANNOTATION EVIDENCE:
149 6.66 0.48 1.44 chr15_MATERNAL_p_2-50000:. 40905 41114 8286 + (AAG)n Simple_repeat 1 208 0
149 6.66 0.48 1.44 chr15_MATERNAL_p_2-50000:. 40905 41114 (8286) (AAG)n#Simple_repeat 1 208 (0) m_b1s252i5
chr15_MATERNA 40905 AAGAAGAAGAAGAAGAAGAAGAACAAGAACAAGAATAAGAACAAGAAGAA 40954
v v v v
(AAG)n#Simple 1 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA 50
chr15_MATERNA 40955 CAAGAACAAGAAGAAGAAGAAGAAAGAA-AAGAAGAAGAAGAAAGAAGAA 41003
v v - - -
(AAG)n#Simple 51 GAAGAAGAAGAAGAAGAAGAAG-AAGAAGAAGAAGAAGAAG-AAGAAGAA 98
chr15_MATERNA 41004 GGAAGAGGAAGAGGAAGAAGAACAAGAGGAAGAAGAAGAAGAAGAAGAAG 41053
- i i v i
(AAG)n#Simple 99 -GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 147
chr15_MATERNA 41054 AAAAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA 41103
i
(AAG)n#Simple 148 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA 197
chr15_MATERNA 41104 GAAGACGACGA 41114
v v
(AAG)n#Simple 198 GAAGAAGAAGA 208
Matrix = Unknown
Transitions / transversions = 0.44 (4/9)
Gap_init rate = 0.02 (4 / 209), avg. gap size = 1.00 (4 / 4)
+ 317 24.3 7.7 10.6 chr15_MATERNAL_p_2-50000:. 41771 41931 (8068) + MER67C LTR/ERV1 80 235 (476) 46
ANNOTATION EVIDENCE:
317 24.31 7.69 10.56 chr15_MATERNAL_p_2-50000:. 41771 41931 7469 + MER67C LTR/ERV1 80 235 476
317 24.31 7.69 10.56 chr15_MATERNAL_p_2-50000:. 41771 41931 (7469) MER67C#LTR/ERV1 80 235 (476) m_b1s502i12
chr15_MATERNA 41771 CTTTTCTTTAAAAAGCATTTAGCCTACA-----------TGTACATT-TT 41808
--- i vii v ----------- v -
MER67C#LTR/ER 80 CTTTTCTT---AGAGCATTTACTTTAGAAAACTTGTAATTGTAAATTCTT 126
chr15_MATERNA 41809 TGTTTGCTTTTTTGAAATACACACATATATATAAATTATTTTAACAGCTA 41858
v i ii i i-------- i iv v
MER67C#LTR/ER 127 TCTCTGTCTCTTTGAAATG--------TATGTAAATCTTTTTAAAAGCTA 168
chr15_MATERNA 41859 AATAAAACTTACCTTTTTTTCCTTTTTTTGACTCAGGATTCTCTTTATCT 41908
i------ i i vi vvi vi i v v v v
MER67C#LTR/ER 169 AATAAG------CCTCTTGCCAGCTTTACGACCCAGGAATGTCTTTCTCA 212
chr15_MATERNA 41909 AGGACCTGAGAACCACCACTTTG 41931
i i i v
MER67C#LTR/ER 213 AGGACCTGGGAGCCATCTCTTTG 235
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 28.90
Transitions / transversions = 1.33 (20/15)
Gap_init rate = 0.12 (19 / 160), avg. gap size = 1.53 (29 / 19)
+ 2526 6.3 0.0 0.3 chr15_MATERNAL_p_2-50000:. 43638 43940 (6059) + AluY SINE/Alu 1 302 (9) 47
ANNOTATION EVIDENCE:
2526 6.29 0.00 0.33 chr15_MATERNAL_p_2-50000:. 43638 43940 6059 + AluY SINE/Alu 1 302 9
2526 6.29 0.00 0.33 chr15_MATERNAL_p_2-50000:. 43638 43940 (6059) AluY#SINE/Alu 1 302 (9) c_b1s352i7
chr15_MATERNA 43638 GGCCGGGCGCGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCAA 43687
i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
chr15_MATERNA 43688 GGCGGGCAGATCACAAGGTCAGGAGATCGAGACCATCCTGGCTAACACAG 43737
i i i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
chr15_MATERNA 43738 TGAAATCCCGTCTCTACTAAAAATACAAAAAAATTAGCCAGGTGTGGTGG 43787
i - i i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAA-TTAGCCGGGCGTGGTGG 149
chr15_MATERNA 43788 CGGGCACCTGTAGTCCCAGCTACTAGGGAGGCTGAGTCAGGAGAATGGCG 43837
i v v
AluY#SINE/Alu 150 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 199
chr15_MATERNA 43838 TGAACCCGGGAGGCAGAGCTTGCAGTAAGCCAAGATCGCACCACTGCACT 43887
i i i i
AluY#SINE/Alu 200 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACT 249
chr15_MATERNA 43888 CCAGCCTGGGCGACAGAGCAAGACTCTGTCTCAAAAAAAGAAAAAAAAAG 43937
i i i i
AluY#SINE/Alu 250 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 299
chr15_MATERNA 43938 AAA 43940
AluY#SINE/Alu 300 AAA 302
Matrix = 14p41g.matrix
Kimura (with divCpGMod) = 2.46
Transitions / transversions = 8.50 (17/2)
Gap_init rate = 0.00 (1 / 302), avg. gap size = 1.00 (1 / 1)
+ 960 14.5 2.5 1.2 chr15_MATERNAL_p_2-50000:. 44041 44201 (5798) + LTR70 LTR/ERV1 16 178 (1108) 48
ANNOTATION EVIDENCE:
960 14.47 2.45 1.24 chr15_MATERNAL_p_2-50000:. 44041 44201 5501 + LTR70 LTR/ERV1 16 178 1108
960 14.47 2.45 1.24 chr15_MATERNAL_p_2-50000:. 44041 44201 (5501) LTR70#LTR/ERV1 16 178 (1108) m_b1s502i13
chr15_MATERNA 44041 GCTTACCTGCAACAGGCACCTGGCTCTAAGTTGCAAAACTGCCTCCTATC 44090
i v i ii i i
LTR70#LTR/ERV 16 GCCTACCTTCAGCAGGCACCTGGCTTCAAGTTGCAAAACTACCTCCTGTC 65
chr15_MATERNA 44091 ATGA---TGTTGGAAGTTTATTTTTTCTTTGCATATAACCAACCAGCATA 44137
--- vii v v v ii
LTR70#LTR/ERV 66 ATGAAGATGTGAAAAGTTTATTTTGTCATTGAATATAACCAATTAGCATA 115
chr15_MATERNA 44138 CACAGAAGGAGTCCCCAATTACCAGGTGAGTTTAAGATGAACTATGTATA 44187
i v vv i i i
LTR70#LTR/ERV 116 CACGGATGGCCTCCCCAATTACCAGGTGAATTTAGGATGAACTATGTATG 165
chr15_MATERNA 44188 ACAAATGGT-TTGTA 44201
-- -i
LTR70#LTR/ERV 166 ACA--TGGTGCTGTA 178
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 15.57
Transitions / transversions = 1.88 (15/8)
Gap_init rate = 0.03 (4 / 160), avg. gap size = 1.50 (6 / 4)
+ 3406 14.8 4.5 0.5 chr15_MATERNAL_p_2-50000:. 44209 44781 (5218) + MER51C LTR/ERV1 2 640 (0) 49
ANNOTATION EVIDENCE:
428 14.29 0.00 0.00 chr15_MATERNAL_p_2-50000:. 44209 44271 5431 + MER51A LTR/ERV1 2 64 570
428 14.29 0.00 0.00 chr15_MATERNAL_p_2-50000:. 44209 44271 (5431) MER51A#LTR/ERV1 2 64 (570) m_b1s502i14
chr15_MATERNA 44209 GAGGCAGGAGAATGGGGTATGGAGGCAGAGAACTTAAGGCCAATTTGTGC 44258
i v i i i iii
MER51A#LTR/ER 2 GAGGCAGGAGAATAGGGTCTGGAGGCAGGGAACCTAAGGCCGATTCACGC 51
chr15_MATERNA 44259 TGACTTCCTAAAA 44271
i
MER51A#LTR/ER 52 TGACTTCCTAGAA 64
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 12.76
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)
3406 14.88 5.00 0.54 chr15_MATERNAL_p_2-50000:. 44228 44781 4921 + MER51C LTR/ERV1 61 640 0
3406 14.88 5.00 0.54 chr15_MATERNAL_p_2-50000:. 44228 44781 (4921) MER51C#LTR/ERV1 61 640 (0) m_b1s502i15
chr15_MATERNA 44228 TGGAGGCAGAGAACTTAAGGCCAATTTGTGCTGACTTCCTAAA------- 44270
i i ii i i -------
MER51C#LTR/ER 61 TGGGGGCAGGGAATCTAAGGCCAATTCGTGCTGACTTCCCAAAGCTGGAT 110
chr15_MATERNA 44271 -AGAA--AAAACACCAAGGTCTGGAGGCAGGAAACCTAAGGCCAATTAAG 44317
- i -- vi i i v
MER51C#LTR/ER 111 CAAAAGGAAAACACCTGGGTCTGGGGGCAGGGAACCTAAGGCCAATTAAC 160
chr15_MATERNA 44318 ACAAACTTCCAACAGCTAAACCAAAAG-AAAAAGTCCCATCTCCCCACAC 44366
i vi v v - ?i i
MER51C#LTR/ER 161 GCCGACTTCCTAAAGCTAAACCAAAAGGAAAAANCCCCATCTCCCCACGC 210
chr15_MATERNA 44367 CTGAATAGCAAAGGATCAAAGGCTACTGTCCCTACAACCCTCCCCTTTCT 44416
i i i v i i
MER51C#LTR/ER 211 CCGAGTAACAAAGGATCAAAGGCTACTCTCCCTACAACCCTCCCCCTTCC 260
chr15_MATERNA 44417 ACCACTTCTCAGGTAGAAAGGGAAAGTGCCTTGGAGTGGCTGCAGGCCAA 44466
i v i i i i v i i
MER51C#LTR/ER 261 ACCGCGTCTCAGATGGAAAGGGAGAGTGCCTCGGATTGGCCGCGGGCCAA 310
chr15_MATERNA 44467 GCA----CCTGCATTCCTTCATCCGCATAGCGTGCCAATTCTCCTAAGCC 44512
---- --- i i v i v v
MER51C#LTR/ER 311 GCAGGGACC---ATCCCTTCATCTGCATAGGGCGCCAATTCACCTCAGCC 357
chr15_MATERNA 44513 TTTAATTAGCCACAGACCAAATCCTTAATCCATATCAGTGGTAGCTGATA 44562
i v v v v i
MER51C#LTR/ER 358 TTTAATTAGCCACGGACCAAATCCTTCATCCAGATAAGGGGTAGCCGATA 407
chr15_MATERNA 44563 GGGACCTCAAAAGGAGTACTAAAAACCCAGAAAACTTCGTAACTGGGTCC 44612
i v ? i i i
MER51C#LTR/ER 408 GGAACCTCAAAAGGAGTACTTAAANCCCAGAAAACTTTGTAACCGGGCCC 457
chr15_MATERNA 44613 TTGAGCCACTTGCTCAAGCCCATACCCACCCTAT--------TTCTTACC 44654
i ii iiv i -------- ii i
MER51C#LTR/ER 458 TTGAGCCGCTTGCTCGGGCCCGCTCCCACCCTGTGGAGTGCTTTCTCGCT 507
chr15_MATERNA 44655 TTAATAAATTTCCGCTTTTGATGCTTCCTCCCTCTGTTTTGTTCCTTTGT 44704
ii i i v v i v i
MER51C#LTR/ER 508 TTAATAAATCCCTGCTTTCGCTGCTTCGTTCCTGTGTTTCGTTCCTTTGT 557
chr15_MATERNA 44705 TACTTTGTGCATTTTGTTCAATTCTTTGTT------GCCAAGGACCTGGA 44748
i i ------ i
MER51C#LTR/ER 558 TACTTTGTGCGTTTTGTCCAATTCTTTGTTCAAAACGCCAAGAACCTGGA 607
chr15_MATERNA 44749 CAACTCACACTCACGGCCTTCGTTCTGGGAACA 44781
i v v i v i v
MER51C#LTR/ER 608 CAACTCGCAGTCAAGGCCCTCCTTCCGGTAACA 640
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 11.92
Transitions / transversions = 2.33 (56/24)
Gap_init rate = 0.02 (10 / 553), avg. gap size = 3.20 (32 / 10)
+ 4157 9.7 3.3 1.4 chr15_MATERNAL_p_2-50000:. 45062 45654 (4345) + LTR77 LTR/ERV1 1 605 (17) 50
ANNOTATION EVIDENCE:
4157 9.74 3.30 1.35 chr15_MATERNAL_p_2-50000:. 45062 45654 4048 + LTR77 LTR/ERV1 1 605 17
4157 9.74 3.30 1.35 chr15_MATERNAL_p_2-50000:. 45062 45654 (4048) LTR77#LTR/ERV1 1 605 (17) m_b1s502i16
chr15_MATERNA 45062 TGATAGAGGAGGCAGTCGGACGCTGGTTATGCAGATAGAGAG--AGGGCC 45109
v ii v v -- i
LTR77#LTR/ERV 1 TGAGAGAGGAGGCAGTTAGAGGCTGGTTAGGCAGATAGAGAGGGAGGGTC 50
chr15_MATERNA 45110 TGGGGAGAGGAA------------AAACACGTGTGCGACCGCACCTGCAC 45147
v ------------i vi i v
LTR77#LTR/ERV 51 TCGGGAGAGGAACAATGNNCGCGNGAACACCCGCGGGACCGCACCTGCAC 100
chr15_MATERNA 45148 CACATCTGTAGCTAGCAGGAAGAAATGTGGTTAAGAACTTCCTCTTATGC 45197
i vi i
LTR77#LTR/ERV 101 CGCCCCTGTAGCTAGCGGGAAGAAATGTGGTTAAGAACTTCCTCTTATGC 150
chr15_MATERNA 45198 CAGGATGTT-GCTCCAAAGGGACTGTCCCAACTTAG-CACAGGCGCAATA 45245
- vi - i
LTR77#LTR/ERV 151 CAGGATGTTTGCTCAGAAGGGACTGTCCCAACTTAGGCGCAGGCGCAATA 200
chr15_MATERNA 45246 AATCAACCCAAATGTCCTTAACTTGACCCAGCTCATTATAAGGTCATTAA 45295
i ---
LTR77#LTR/ERV 201 AATCAACCTAAATGTCCTTAACTTGACCCAGCTCATTATA---TCATTAA 247
chr15_MATERNA 45296 CATGACATTAGCATTGTGGTTTTGGCTCTCCTCGTGTAAGTTTCGCTTAG 45345
i --- i --i
LTR77#LTR/ERV 248 CATGACATTAGCATTGTGGTTTTAGC---CCCCGTG--GGTTTCGCTTAG 292
chr15_MATERNA 45346 GCACTCATGGGTAATAACCAAAATGGAGTCACTGTGGCCAATCCCAGGCA 45395
i ? i
LTR77#LTR/ERV 293 GCACTCATGGGTAATAACCAAGATGGAGTCACTNTGGCCAACCCCAGGCA 342
chr15_MATERNA 45396 TGCGCAGATGCAACACCCTTAGTGAGGAACTTTACCCCTCCCATTTGGGC 45445
i vii
LTR77#LTR/ERV 343 TGCGCAGATGCAACACCCCTAGGAGGGAACTTTACCCCTCCCATTTGGGC 392
chr15_MATERNA 45446 AGAACCCACAGAAGACATACTTGTTCTTGCCACATAAAAGAC----CCAG 45491
v v i ii ----
LTR77#LTR/ERV 393 AGAACCCACAGAAGACTTCCTTGCTTCTGCCACATAAAAGACGCGCCCAG 442
chr15_MATERNA 45492 ACCTCAGCCTCATTTCTGGCAACCTGCTTTCAGGTCCCCTCTTGCTTCTG 45541
v i i i?i v
LTR77#LTR/ERV 443 AACTCAGCCCCATTTCTGGCAACCCGCTTTCAGGTCCCCTCTCNTTGCTG 492
chr15_MATERNA 45542 AGAGCTTTCCTTTTGCTTAATAAATCCTACTCTGCCTTGCTCACTCTCTG 45591
i i
LTR77#LTR/ERV 493 AGAGCTTTCCTTTTGCTTAATAAATCCTACTCTGCCTTACTCACTCTCCG 542
chr15_MATERNA 45592 GTATCCGTGTGCTTCATTCTTTTTGGTCGTGGCACAAGAGTCCCGACCTG 45641
i i i i i v iii v i
LTR77#LTR/ERV 543 GTGTCCGCGTGCCTTATTCTTCTTGGTCGTGGGACAAGAACTCGGACCTA 592
chr15_MATERNA 45642 GCTGAACCGAGGA 45654
ii
LTR77#LTR/ERV 593 GCTGAACTAAGGA 605
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 8.76
Transitions / transversions = 2.67 (40/15)
Gap_init rate = 0.02 (13 / 592), avg. gap size = 2.15 (28 / 13)
+ 285 31.5 4.2 1.6 chr15_MATERNAL_p_2-50000:. 47129 47315 (2684) C MER57E3 LTR/ERV1 (0) 487 296 51
ANNOTATION EVIDENCE:
285 31.52 4.17 1.60 chr15_MATERNAL_p_2-50000:. 47129 47315 2387 C MER57E3 LTR/ERV1 296 487 0
285 31.52 4.17 1.60 chr15_MATERNAL_p_2-50000:. 47129 47315 (2387) C MER57E3#LTR/ERV1 (0) 487 296 m_b1s502i17
chr15_MATERNA 47129 TGGTCCG-GGGGT--CCGGTCCCTACTTTACCCTGTTCGGAATGAGATCG 47175
- -- i v vi vii v-v v
C MER57E3#LTR/E 487 TGGTCCGTGGGGTCCCCAGTCCCTCCTTTCTCCTGTTAAAAATT-TATGG 439
chr15_MATERNA 47176 AGGCCCCATCGAAACAAAGTT----CATGTGAGCAAACGGGGTCTCATTA 47221
ii --i i v v vi ----v v i v vi v vi ?v
C MER57E3#LTR/E 438 GAG--TCACCGCAAAAATATTAAAGAATTTAATCAAAGAGTGATTCANGA 391
chr15_MATERNA 47222 ATGGGACAGCG-TCGGCCGCGGCTCCTGGTTTGGGGACTGCCAGCGGGTC 47270
v v v i-i i iii i iv i v v ii vi v v
C MER57E3#LTR/E 390 ATCGTAGAGCACCCAGCTATGGTTTGTAGTTTGTGGTCCACGGGAGGGGC 341
chr15_MATERNA 47271 TTGAAGGAAAGGCTTTTGTGAGGTGTGTGAGCAAGCGAAGCAAAT 47315
i i ii ?v i v
C MER57E3#LTR/E 340 TTGAAGGAAAGGCTTTTATAAGGTGCATGANGAAGCAAACCAAAT 296
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 40.26
Transitions / transversions = 1.07 (29/27)
Gap_init rate = 0.04 (7 / 186), avg. gap size = 1.57 (11 / 7)
+ 750 24.9 10.6 1.2 chr15_MATERNAL_p_2-50000:. 47347 47688 (2311) + MER21C LTR/ERVL 519 896 (42) 52
ANNOTATION EVIDENCE:
750 24.85 10.59 1.17 chr15_MATERNAL_p_2-50000:. 47347 47688 2014 + MER21C LTR/ERVL 519 896 42
750 24.85 10.59 1.17 chr15_MATERNAL_p_2-50000:. 47347 47688 (2014) MER21C#LTR/ERVL 519 896 (42) m_b1s502i18
chr15_MATERNA 47347 CTTTGCCCTGTGCACCTCCTCCGCGTGGCTGTTC--CTG-A------GTA 47387
i i i i iiv -- - ------
MER21C#LTR/ER 519 CCTTGCCCTATGCATCTCTTCCATCTGGCTGTTCATCTGTATCCTTTGTA 568
chr15_MATERNA 47388 ACATCTTTTAGAATACGCTGGTGTCGGTGCGCACGGCGCTTCTC--AGTT 47435
i i v vi i ivvv iv i vi i i i --
MER21C#LTR/ER 569 ATATCCTTTATAATAAACCGGTAAACGTAAGTAAAGTGTTTCCCTGAGTT 618
chr15_MATERNA 47436 CTGTGAGTAGTTCTGCCACATTGCTGAACTTGAGG-----GT-GTGGGCG 47479
iv iv v iii ii ----- - vi
MER21C#LTR/ER 619 CTGTGAGCCGTTCTAGCAAATTATCGAACCCGAGGAGGGGGTCGTGGGAA 668
chr15_MATERNA 47480 CCCCTGGTTTGTAGACAGGCGTTCAGAAATGAAGACGGGTGTCCA---GA 47526
i i i v i v v i ---- ?v v --- i
MER21C#LTR/ER 669 CCCCCGATTTATAGCCGGTCGGTCAGAAGT----ACGGGTNACAACCTGG 714
chr15_MATERNA 47527 GGCA-GGGACTGGCGTCTGCAGCGGGAGCAGT--TGTGGGAA-GAGCGCT 47572
i v- v v i i -- v- v
MER21C#LTR/ER 715 GACTTGCGACTGGCGTCTGAAGTGGGGGCAGTCTTGTGGGACTGAGCCCT 764
chr15_MATERNA 47573 GAGCTTGTGGGGTCTG-CGCTGACTCTGGGT-GGTGTCGTTAG------- 47613
v i i - i ii - ? ivi i -------
MER21C#LTR/ER 765 TAACCTGTGGGGTCTGACGCTAACTCCAGGTAGNTAGTGTCAGAATTGAA 814
chr15_MATERNA 47614 -TGAGTTGCTGGACACCGCGTTGGGGT----TGGAGCATTGACTGGTGT- 47657
- i iv vv v ---- v ?i -
MER21C#LTR/ER 815 TTGAATTGTAGGACACCCAGTTGGTGTCCGCTGGAGAATTGNTTGGTGTG 864
chr15_MATERNA 47658 TGAGGAAA-CTCCGCACGTTTTCTGTCAGAAG 47688
i i - i i i vv
MER21C#LTR/ER 865 TGGGAAAAACCCCACACATTTGGTGTCAGAAG 896
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 27.76
Transitions / transversions = 1.61 (50/31)
Gap_init rate = 0.06 (20 / 341), avg. gap size = 2.20 (44 / 20)
+ 2290 6.5 0.3 2.4 chr15_MATERNAL_p_2-50000:. 48225 48522 (1477) C AluY SINE/Alu (19) 292 1 53
ANNOTATION EVIDENCE:
2290 6.53 0.35 2.35 chr15_MATERNAL_p_2-50000:. 48225 48522 1477 C AluY SINE/Alu 1 292 19
2290 6.53 0.35 2.35 chr15_MATERNAL_p_2-50000:. 48225 48522 (1477) C AluY#SINE/Alu (19) 292 1 c_b1s352i8
chr15_MATERNA 48225 TTTTTTTTTTTGAGATGGCGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAG 48274
i v i i
C AluY#SINE/Alu 292 TTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAG 243
chr15_MATERNA 48275 TGGCGTGATCTCGGCTTACTGCAAGCTCCGCCTCCCAGGTTCACGCCATT 48324
i i i
C AluY#SINE/Alu 242 TGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATT 193
chr15_MATERNA 48325 CTCCTAACTCAGTCTCCCGAGTAGCTGGGATTACAGGCGCCCGCCACCAT 48374
iv i i i
C AluY#SINE/Alu 192 CTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCAC 143
chr15_MATERNA 48375 GCCTGGCTAATTTTTTTTTTTTTGTATTTTTAGTAGAGACGGGGTTTCAC 48424
i -------
C AluY#SINE/Alu 142 GCCCGGCTAA-------TTTTTTGTATTTTTAGTAGAGACGGGGTTTCAC 100
chr15_MATERNA 48425 CGTGTTAGCCAGGATGGTCTGGATCTCCTGACCTTGAG-CCCTCCCGCCT 48473
v i v -i v
C AluY#SINE/Alu 99 CGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCT 50
chr15_MATERNA 48474 CGGCCTGCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 48522
v
C AluY#SINE/Alu 49 CGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p41g.matrix
Kimura (with divCpGMod) = 4.17
Transitions / transversions = 2.17 (13/6)
Gap_init rate = 0.03 (8 / 297), avg. gap size = 1.00 (8 / 8)
+ 4366 20.9 5.1 3.2 chr15_MATERNAL_p_2-50000:. 48680 49999 (0) + LTR70 LTR/ERV1 1 1072 (214) 54
ANNOTATION EVIDENCE:
1873 22.83 3.28 1.66 chr15_MATERNAL_p_2-50000:. 48680 49160 839 + MER67C LTR/ERV1 1 489 222
1873 22.83 3.28 1.66 chr15_MATERNAL_p_2-50000:. 48680 49160 (839) MER67C#LTR/ERV1 1 489 (222) m_b1s502i19
chr15_MATERNA 48680 TGTAGGAGCAAACACAAATTAGAA----GAGGCTTAATGCTTTCTCTTTA 48725
i i i i ---- v ii v v
MER67C#LTR/ER 1 TGTAAGGGCAAATACAAATTAAAAATAAGAGGCTTAATTCTCCCTGTTGA 50
chr15_MATERNA 48726 GAACGAGGGAA-GAATTTTTGCTCTTCTCCTTTTTCTTAAAGCATTTAGT 48774
i ii - ivi iv i- i i v
MER67C#LTR/ER 51 AAATAAGGGAAAGAGACTTCCCTCC-CTCCCTTTTCTTAGAGCATTTACT 99
chr15_MATERNA 48775 TT-GAGAACTTTTATATT-TAAATATTTTCTCTGCTTCTTTCAAATATAT 48822
- i v - - vi ii v i
MER67C#LTR/ER 100 TTAGAAAACTTGTA-ATTGTAAATTCTTTCTCTGTCTCTTTGAAATGTAT 148
chr15_MATERNA 48823 GTAAATCATTTTTATCAGTTAAATAGGTCATTTGTC--TTTTTTGGCTCA 48870
- vv i i i vi i --i vi i i
MER67C#LTR/ER 149 GTAAATC-TTTTTAAAAGCTAAATAAGCCTCTTGCCAGCTTTACGACCCA 197
chr15_MATERNA 48871 AAATTGTCTTCATCTGGGACCTGGGAACTATTGCTTTGAAATGTAAATAG 48920
ii v iv vi i i iv ?i v
MER67C#LTR/ER 198 GGAATGTCTTTCTCAAGGACCTGGGAGCCATCTCTTTGAAATGTAANCAT 247
chr15_MATERNA 48921 CAAG-AATATA-CACCC-TATTTCACAGTTTCTGTAGGGGACTAGGAGGC 48967
- v - i - i v i i iv v
MER67C#LTR/ER 248 CAAGGAAGATAGCGCCCCTATCTCCCAGTTTCTGTGGGAGGGTAGGAGCC 297
chr15_MATERNA 48968 TGCCTTCAGCAGGTACCTAGCTCCACATTGCAAATCTACATCCTGTCACG 49017
iv i ii ii v vi v v ii
MER67C#LTR/ER 298 TAACTTCGGTGGGCGCCTTGCTCCAAGTTGCAAAACTACCTCCTGTCATA 347
chr15_MATERNA 49018 AAGATGTG-GATGTTTATTTTTTCTTTAATGATTAGAAAA--AATTAGAA 49064
i - v i i-- --- i-- v?
MER67C#LTR/ER 348 AAGATATGAGAAGTTTATTTTTCCTTTG--GAT---AAAGCCAATTAGCN 392
chr15_MATERNA 49065 AACCCAGATGACCTCTCAAATTACATGATGAAATTATAATAAATTGTGTA 49114
v ii v i v vv i v vi i i i i
MER67C#LTR/ER 393 AACACAGATGGTCACCCCAATTACCAGGTGAATTTAGGATGAACTATGTG 442
chr15_MATERNA 49115 TGACAAATGGTGCTTTCAAGGCTTCT-ACTTGAGAACTAATTATGGT 49160
v v i - i i v
MER67C#LTR/ER 443 TGACAAATGGTGCTGTCAAGTCCTCTTACTTGAGGACTAGTTATTGT 489
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 26.19
Transitions / transversions = 1.72 (67/39)
Gap_init rate = 0.04 (19 / 480), avg. gap size = 1.26 (24 / 19)
4366 20.36 5.59 3.62 chr15_MATERNAL_p_2-50000:. 48950 49999 0 + LTR70 LTR/ERV1 1 1072 214
4366 20.36 5.59 3.62 chr15_MATERNAL_p_2-50000:. 48950 49999 (0) LTR70#LTR/ERV1 1 1072 (214) m_b1s502i20
chr15_MATERNA 48950 TGTAGGGGACTAGGAGGCTGCCTTCAGCAGGTACCTAGCTCCACATTGCA 48999
?i v ii v i i i i vi
LTR70#LTR/ERV 1 TGTAGNAGAGTGAGAGCCTACCTTCAGCAGGCACCTGGCTTCAAGTTGCA 50
chr15_MATERNA 49000 AATCTACATCCTGTCACGAAGATGTGGAT-GTTTATTTTTTCTTTAATGA 49048
v v i i v- v v ---
LTR70#LTR/ERV 51 AAACTACCTCCTGTCATGAAGATGTGAAAAGTTTATTTTGTCATT---GA 97
chr15_MATERNA 49049 TTAGAAAAAATTAGAAAACCCAGATGACCTCTCAAATTACATGATGAAAT 49098
v v vv v v v i i i v vv i v
LTR70#LTR/ERV 98 ATATAACCAATTAGCATACACGGATGGCCTCCCCAATTACCAGGTGAATT 147
chr15_MATERNA 49099 TATAATAAATTGTGTATGACAAATGGTGCTTTCAAGGCTTCTACTTGAGA 49148
vi i i i -- v v vv v i
LTR70#LTR/ERV 148 TAGGATGAACTATGTATGACA--TGGTGCTGTAAATTCTTCTACTTGTGG 195
chr15_MATERNA 49149 ACTAATTATGGTGAC----TTTCTGTGTTTGCATTTTCTTA----GATTG 49190
---- v v i ----
LTR70#LTR/ERV 196 ACTAATTATGGTGACCGTCTTTCTGTCTTTGCAATCTCTTAAGCAGATTG 245
chr15_MATERNA 49191 CTTGTGATGCACATCATATTTTGGTTTAATTATACAACAAAACA-TTTTC 49239
vi ii i i? i ii i -
LTR70#LTR/ERV 246 ACTGTGATGCATGTCACATTCNGGTTTAATTGTGTAATAAAACAGTTTTC 295
chr15_MATERNA 49240 TTGCAGTTCTGTTACTGTGGAGACTTTTTTAGGATTGCAGATGATTTTGC 49289
v v i i -i i i i ii v ?i v
LTR70#LTR/ERV 296 TTTCTGTTCTATTATTGTGGAG-TTTCTCTGGGGCTGGAGANAATTTTTC 344
chr15_MATERNA 49290 TTTTAGTTATATTTTCCACACACTGTCCAGAATTACCAGA--TGTTATA- 49336
i v -- v -
LTR70#LTR/ERV 345 TTTTAATTATATTTTCCAAACACTGTCCAGAATTACCAGACATGATATAA 394
chr15_MATERNA 49337 ---CACAAAATGTCGAGCAGACTTCACTT--GAGAAAACATTCTTTCTCA 49381
--- i ii i i v i i i-- iii v ii
LTR70#LTR/ERV 395 ACACATAAGGTGCCAACCAGGCTTTACTCTAGAGGGGACTTTCCCTCTCA 444
chr15_MATERNA 49382 GGATTCCAGTCACAACCTGCAATTGTGCGGCAAAGTGCA-GCAAAGTATT 49430
v -- iii i ? - ---- i i
LTR70#LTR/ERV 445 GGCTTCCAGTCA--ACTCACAGTTGTGCNGCAAAGTGCACGC----TGTC 488
chr15_MATERNA 49431 TCCTAAATCTGCAAACAGAATGGTCTCTCT-----CTTGGCATCTACAGT 49475
i v ii v v -----i i i
LTR70#LTR/ERV 489 CCCTAAATATGCAGGCAGAATTGTGTCTCTGCCTATTTGGTATCTATAGT 538
chr15_MATERNA 49476 CCT----------TTCTAGAGCAGTTAAA-----TTTCTACAAAAATAAC 49510
---------- vi i i ----- -----
LTR70#LTR/ERV 539 CCTCTACAGTCACTTCTAGAGAGGCTAGACCAGATTTCTACAAA-----C 583
chr15_MATERNA 49511 TTTTCAGGACAGCAGTCAGTTATTTCACCGCCTTCAGTGCTCCTGGCATC 49560
iv i i ii v i vii v i
LTR70#LTR/ERV 584 TTCACAGGGCAGCAATCAGCCATTTCACCTCTTTCAGTGACTCTTGTATC 633
chr15_MATERNA 49561 TTCCGTTCTGACACTGATTTCAGAGAT-ATGGGGCCCATAAACCTAACCA 49609
v vi v - i- v i i
LTR70#LTR/ERV 634 TTCAGACCTGAAACTGATT-CAGAGACCATGGGGCCCAGAAACCCAATCA 682
chr15_MATERNA 49610 GATTCACACATACGCATCGATTAAACCTG--------AGAAATTCTGCTC 49651
v v i ii i v i v -------- vi ii i
LTR70#LTR/ERV 683 GAGTAACACGTGTGCATTGAGTAGACATGTAGACATGAGAATCTCCACTT 732
chr15_MATERNA 49652 CCTCCCACCTCCCCTTGCCCACATGCCCACAAACATTTGGCATGGGCCAC 49701
i i iv i v v ii --- -- iv
LTR70#LTR/ERV 733 TCCCCTTCCTCCTCTTGCCAAAATGCCCACAAATGT---GCA--GGTAAC 777
chr15_MATERNA 49702 ATTGTGGCCCACAAACATAGCTCACCAGCCCTCCAAGACCTAAATGTGCA 49751
ii- -- i ----- - -- ? v i v
LTR70#LTR/ERV 778 ACC-TG--CCGC-----TA-CTC--CANCCATCCAGGACCTAAATCTGCA 816
chr15_MATERNA 49752 GTTCCAAATTCTGAATTTATGTCCTGAGATTTG----ATAAAA--GAACT 49795
i i v i ---- --?
LTR70#LTR/ERV 817 GCTCCAAATTCTGAATCTAGGTCTTGAGATTTGGGAAATAAAAAANAACT 866
chr15_MATERNA 49796 TTTATTTGAGAAATACAAGT--TTTTAGATTTATCAGACCCAGAGATGTG 49843
i i i -- -- i viii
LTR70#LTR/ERV 867 TTTATCTGAGGAATGCAAGTCCTTTTAG--TTATCAGACTCAGAGAGACA 914
chr15_MATERNA 49844 TTAAAATGAGACCACACTCACATACTGTTCTCCTCCTTGAACTAT----T 49889
v i v i ii vi vi i i i ----
LTR70#LTR/ERV 915 TTAAAATGAGAGCGCAGTTATGTCTTTCTCCCCCCTTTGAACTATGTATT 964
chr15_MATERNA 49890 TGTCTTTTGAAATTGCTTGCTATTGCCACAAGTGGCTGTAAATTAACCTA 49939
ii i i i i i i v
LTR70#LTR/ERV 965 CATCTCTTGAAACTGTTCGCTATTGCCACAAGTAGCTATAAATTAAACTA 1014
chr15_MATERNA 49940 ATAATGCCACACTGGACACTATGACCCATACCCTATAGCTTAACTATGTA 49989
i? v v v i
LTR70#LTR/ERV 1015 ATAATGCCACACTGGACACTATANCCCATACCCTAAACCTTAACGATATA 1064
chr15_MATERNA 49990 TATGGCCAAT 49999
--
LTR70#LTR/ERV 1065 TAT--CCAAT 1072
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 22.84
Transitions / transversions = 1.84 (129/70)
Gap_init rate = 0.05 (56 / 1049), avg. gap size = 1.75 (98 / 56)