position in query- -position in repeat-
% % % query C matching repeat (left) end begin linkage
+ score div. del. ins. sequence begin end (left) + repeat class/family begin end (left) id/graphic
+ 287 25.8 0.0 0.0 chr1:56519862-56521862 240 305 (1695) C MIR3 SINE/MIR (43) 165 100 1 *
ANNOTATION EVIDENCE: 287 25.76 0.00 0.00 chr1:56519862-56521862 240 305 1083 C MIR3 SINE/MIR 100 165 43 287 25.76 0.00 0.00 chr1:56519862-56521862 240 305 (1083) C MIR3#SINE/MIR (43) 165 100 m_b1s601i0 chr1:56519862 240 AGGCCATCTCATCCCACTCTTTCATCTGACAGATGGGGAAAGTGGGGTCC 289 ii vi v i ii i v i v i i C MIR3#SINE/MIR 165 AGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCC 116 chr1:56519862 290 AGAGAGGAAAAGTGGC 305 vi i C MIR3#SINE/MIR 115 AGAGAGGTGAAGTGAC 100 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.04 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)
+ 423 33.1 2.1 0.0 chr1:56519862-56521862 305 446 (1554) C MIRb SINE/MIR (87) 181 37 2
ANNOTATION EVIDENCE: 423 33.10 2.11 0.00 chr1:56519862-56521862 305 446 942 C MIRb SINE/MIR 37 181 87 423 33.10 2.11 0.00 chr1:56519862-56521862 305 446 (942) C MIRb#SINE/MIR (87) 181 37 m_b1s601i1 chr1:56519862 305 CAACAACTCTGCAAAATAGACATGATCACTTCCACTTTCCAGATGAGTAT 354 i i ii ii v i iii i v v v C MIRb#SINE/MIR 181 CAACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAA 132 chr1:56519862 355 GCTGAGGCTC--TAAAGCTATGTAACCCACTCATGGCTTCAGAGCTGGTC 402 i --vi i i v iii i v iiv v i v C MIRb#SINE/MIR 131 ACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTA 82 chr1:56519862 403 ATGGATACAGCC-AGATTTGATTCCACATCTGCTTGATTCTAAAG 446 vv ii v -i i vi vi ii i i C MIRb#SINE/MIR 81 AGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAG 37 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 43.79 Transitions / transversions = 2.13 (32/15) Gap_init rate = 0.01 (2 / 141), avg. gap size = 1.50 (3 / 2)
+ 246 29.6 0.0 0.0 chr1:56519862-56521862 721 774 (1226) + 7SLRNA srpRNA 1 54 (266) 3
ANNOTATION EVIDENCE: 246 29.63 0.00 0.00 chr1:56519862-56521862 721 774 614 + 7SLRNA SINE/Alu 1 54 266 246 29.63 0.00 0.00 chr1:56519862-56521862 721 774 (614) 7SLRNA#SINE/Alu 1 54 (266) m_b1s502i0 chr1:56519862 721 GCCAAACCTAGTGGCTCATGCCTGTAATCCCAACACTTTGGGAGGCTGAG 770 iii vii v ii i i vvi i 7SLRNA#SINE/A 1 GCCGGGCGCGGTGGCGCGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAG 50 chr1:56519862 771 GTGG 774 i 7SLRNA#SINE/A 51 GCGG 54 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.91 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 2450 9.6 0.0 0.0 chr1:56519862-56521862 775 1077 (923) + AluSx SINE/Alu 9 311 (1) 4
ANNOTATION EVIDENCE: 2450 9.57 0.00 0.00 chr1:56519862-56521862 775 1077 923 + AluSx SINE/Alu 9 311 1 2450 9.57 0.00 0.00 chr1:56519862-56521862 775 1077 (923) AluSx#SINE/Alu 9 311 (1) c_b1s352i0 chr1:56519862 775 GTGGTGGCTCATGCCTGTAATCCCAACACTTTGGGAGGCTGAGGTGGGTG 824 i i i i i i AluSx#SINE/Al 9 GCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCG 58 chr1:56519862 825 GATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAAC 874 i AluSx#SINE/Al 59 GATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAAC 108 chr1:56519862 875 CCTGTCTCTATTAAAAATACAAAAATTTGCTGGGTGTGGTGCCACACACC 924 i i v i i v i i i AluSx#SINE/Al 109 CCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCC 158 chr1:56519862 925 TGTAATCCCAGCTACTTGGGAGTCTAAGGCAGGAGAATTGCTTGAATCTG 974 i v i i i i AluSx#SINE/Al 159 TGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCG 208 chr1:56519862 975 GGAGGCAGAGGTTGCAGTGAGCCGAGATTGCACCACTGCACTCCAGCCTG 1024 i i i AluSx#SINE/Al 209 GGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG 258 chr1:56519862 1025 TGCAACAGAGCGAGACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAAAAG 1074 v i i i AluSx#SINE/Al 259 GGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAA 308 chr1:56519862 1075 AAA 1077 AluSx#SINE/Al 309 AAA 311 Matrix = 14p43g.matrix Kimura (with divCpGMod) = 3.73 Transitions / transversions = 6.25 (25/4) Gap_init rate = 0.00 (0 / 302), avg. gap size = 0.0 (0 / 0)
+ 2054 15.8 0.0 0.3 chr1:56519862-56521862 1090 1400 (600) + AluJb SINE/Alu 1 310 (2) 5
ANNOTATION EVIDENCE: 2054 15.81 0.00 0.32 chr1:56519862-56521862 1090 1400 600 + AluJb SINE/Alu 1 310 2 2054 15.81 0.00 0.32 chr1:56519862-56521862 1090 1400 (600) AluJb#SINE/Alu 1 310 (2) c_b1s352i1 chr1:56519862 1090 GGCCTAGCACGGAGGCTCACATCTGTAGTCCCAGCACTTTGGGAGGCCAA 1139 vi i v ii i i AluJb#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50 chr1:56519862 1140 GGTGGTTGGATTGCTTGAGCCCAGGAGTTCAAAACCAGCCTGGCCAACAT 1189 i v? i i i v AluJb#SINE/Al 51 GGCGGGNGGATCGCTTGAGCCCAGGAGTTCGAGACCAGCCTGGGCAACAT 100 chr1:56519862 1190 GGCAAAGCCTCGTCTCTACAAAAAAATACAAAAATTAGCTGGGTGTGGTG 1239 i i i - i i AluJb#SINE/Al 101 GGCGAAACCCCGTCTCTACAAAA-AATACAAAAATTAGCCGGGCGTGGTG 149 chr1:56519862 1240 GCATGTGCCTGTGGTCCCAGCTACTCAGGTGGCTGAGGTGGAAGGATCAC 1289 ii i i i v i i i AluJb#SINE/Al 150 GCGCGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCGGGAGGATCGC 199 chr1:56519862 1290 CTGAGTCCAAGAGGCAGAGGTTGCAGTGAGCCAAGATGGTGCCACTGTGC 1339 i i ii iv i iv v i ii AluJb#SINE/Al 200 TTGAGCCCGGGAGGTCGAGGCTGCAGTGAGCCGTGATCGCGCCACTGCAC 249 chr1:56519862 1340 TCCATCCTGAGTGACAGAATGAGACTCTGTCTCAAAAAAAAAAAAAAAAA 1389 v i i ii i AluJb#SINE/Al 250 TCCAGCCTGGGCGACAGAGCGAGACCCTGTCTCAAAAAAAAAAAAAAAAA 299 chr1:56519862 1390 AAAAAGAAGAA 1400 i i AluJb#SINE/Al 300 AAAAAAAAAAA 310 Matrix = 14p43g.matrix Kimura (with divCpGMod) = 10.91 Transitions / transversions = 4.44 (40/9) Gap_init rate = 0.00 (1 / 310), avg. gap size = 1.00 (1 / 1)
+ 16 24.8 5.7 0.0 chr1:56519862-56521862 1563 1615 (385) + (TG)n Simple_repeat 1 56 (0) 6
ANNOTATION EVIDENCE: 16 24.84 5.66 0.00 chr1:56519862-56521862 1563 1615 385 + (TG)n Simple_repeat 1 56 0 16 24.84 5.66 0.00 chr1:56519862-56521862 1563 1615 (385) (TG)n#Simple_repeat 1 56 (0) m_b1s252i0 chr1:56519862 1563 TGTGTATATATATGT-TGTATATGTGAGT-TGTGAGTGT-TGAATGTGTG 1609 i i i i - i i v - v - vi (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr1:56519862 1610 TTTGTG 1615 v (TG)n#Simple_ 51 TGTGTG 56 Matrix = Unknown Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3)
+ 479 25.9 1.9 0.0 chr1:56519862-56521862 1710 1817 (183) + SVA_A Retroposon/SVA 203 312 (1075) 7
ANNOTATION EVIDENCE: 479 25.93 1.85 0.00 chr1:56519862-56521862 1710 1817 183 + SVA_A Retroposon/SVA 203 312 1075 479 25.93 1.85 0.00 chr1:56519862-56521862 1710 1817 (183) SVA_A#Retroposon/SVA 203 312 (1075) m_b1s502i1 chr1:56519862 1710 TTTTATTTTTTTAA-AGAGACAGGGTCTCCCTGTGCTGTCCAGACTTGTC 1758 i v ii-i i v i i ? i i v SVA_A#Retropo 203 TTTTGTATTTTTGGTGGAGACGGGGTCTCGCCGTGTTGNCCGGGCTGGTC 252 chr1:56519862 1759 TCAAACTGCTGGCCTCAAGGGATCCTCTTATCTTGGCCTCTT-AAGTGCC 1807 ? i v i v v iiii i ii- i i SVA_A#Retropo 253 TCNAGCTCCTGGCCTCGAGCGATCCGCCCGCCTCGGCCTCCCGAGGTGCT 302 chr1:56519862 1808 GAGATTACAG 1817 i i SVA_A#Retropo 303 GGGATTGCAG 312 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 24.62 Transitions / transversions = 3.67 (22/6) Gap_init rate = 0.02 (2 / 107), avg. gap size = 1.00 (2 / 2)
+ 18 28.2 2.7 2.7 chr1:56519862-56521862 1846 1918 (82) + (CTCC)n Simple_repeat 1 73 (0) 8
ANNOTATION EVIDENCE: 18 28.23 2.74 2.74 chr1:56519862-56521862 1846 1918 82 + (CTCC)n Simple_repeat 1 73 0 18 28.23 2.74 2.74 chr1:56519862-56521862 1846 1918 (82) (CTCC)n#Simple_repeat 1 73 (0) m_b1s252i2 chr1:56519862 1846 CTCTCCTCCCTCCCTCTCT-CTTCCTTTCCTCTCTCCCT-TTTCTCTTCC 1893 - i - i i i i -ii - i (CTCC)n#Simpl 1 CTC-CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC-CCTCC 48 chr1:56519862 1894 TTCCCTCTTTCTCTTCCTTCCTTCC 1918 i ii i i i i (CTCC)n#Simpl 49 CTCCCTCCCTCCCTCCCTCCCTCCC 73 Matrix = Unknown Transitions / transversions = 1.00 (15/0) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.00 (4 / 4)