Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014940.1 Corchorus olitorius cultivar O-4 contig14973, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 132910
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:667 original size:331 final size:328
Alignment explanation
Indices: 1--2881 Score: 2803
Period size: 331 Copynumber: 8.7 Consensus size: 328
* * * * * * *
1 ATCAAGCAAAATTGAGCCGGGGGTTCCGAAAGGCGTTTTTAGTCCAAAAACCGTAGAT-GTAACA
1 ATCAAGCAAAACTGAGCC-GGGGCTCCGGAACGCGTTTTTAG-CAAAAAACAGT-GATGGTTA-A
* * *
65 TACACGATTTCGTCTAAAATTTT-TCAAAAACTGACCC-AAAAACTTTTTCCTAAATTTTTTGCC
62 TACACGATTTCGGCTAAAATTTTGT-AAAAACTGACCCGAAAAA-TATTTCCTAAA-TTTTTGGC
* * * * *
128 ACAGTATTCAGAAAAACTATATTATTCAAC-CCCAAAAATTAAAATGGTTTTTCACGCTTCCAAT
124 AAAATACTCAGAAAAACTATATTATTCAACGCCAAAAAATTAAAAGGGTTTTTCACGCTTCCAAT
*
192 ATCGTTTTTCCATTTTTTTCGAATTTATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
189 ATCGTTTTTCCATTTTTTTCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* *
257 AAACAAATCCTT-AAATCCATTGTGGCTAAGATTTGGTTAGATGAATATAGATATTTGAAGGAGT
254 AAACAAAT--TTAAAATCCATTGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGT
321 CTTTCGGC-CAAAA
317 CTTT--GCACAAAA
* *
334 ATCAAGCAAAATTGAGCCGGGGCTCCGGAACGCGATTTTAGCAAAAAACAGTGATGGTTAATACA
1 ATCAAGCAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTAGCAAAAAACAGTGATGGTTAATACA
* * * *
399 CGATTTCGGCTAAAATTTT-TCAAAAACTGACCCGAAAAGTTTTTCCTCAACTTTTTGGCACAAT
66 CGATTTCGGCTAAAATTTTGT-AAAAACTGACCCGAAAAATATTTCCT-AAATTTTTGGCAAAAT
* ** * *
463 ACTCAGAAAAACTATATTATTCAACACTGAAAAATTAAAATGGTTTTTCACGCATCCAATATCGT
129 ACTCAGAAAAACTATATTATTCAACGCCAAAAAATTAAAAGGGTTTTTCACGCTTCCAATATCGT
* * *
528 TTTTCCATTTTTTTCGAATTTATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACC
194 TTTTCCATTTTTTTCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
*
593 AATTTATAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGC
259 AATTTA-AAATCCATTGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTGC
658 ACTAAAA
323 AC-AAAA
* * * * * * *
665 ATCAAGCAAAATTGAGTCGGGGCTCCGAAAGGCGTTTTTAGCCAAAAACCGTGAT-GTAACATAC
1 ATCAAGCAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTAGCAAAAAACAGTGATGGTTA-ATAC
* * * * * * *
729 ACGATTTCGTCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTGCCACAATA
65 ACGATTTCGGCTAAAATTTTGTAAAAACTGACCCGAAAAATATTTCCTAAATTTTTGGCAAAATA
** * * *
794 CTCAGAAGTACTATATTATTCAACCCCAAAAAATTAAAATGGTTTTTCACGCTTGCAATATCGTT
130 CTCAGAAAAACTATATTATTCAACGCCAAAAAATTAAAAGGGTTTTTCACGCTTCCAATATCGTT
* * *
859 TTTCCATTTTTTTTCGAATTTATTTTTAATTAATTCGAAACAAGATTTAGATGCTCGTAAAAACA
195 TTTCCA-TTTTTTTCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* * *
924 AATCCTT-AAATTCATTGTGGCTAAGATTTGGTTAGATGAATATAGATATTTGAAGGAGTCTTTC
259 AAT--TTAAAATCCATTGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTT-
988 GGC-CAAAA
321 -GCACAAAA
* *
996 ATCAAGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCAAAAAACAGTGATGGTTAATACA
1 ATCAAGCAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTAGCAAAAAACAGTGATGGTTAATACA
* * * * * ** *
1061 CGATTTCGGCTAAAATATTT-CAAAAACGGACCCGAAAAGTTTTTCCTCAATTTTTTCCACAATA
66 CGATTTCGGCTAAAAT-TTTGTAAAAACTGACCCGAAAAATATTTCCTAAATTTTTGGCAAAATA
** *
1125 CTCAGAAAAACTATATTATTCAA-GCCCAAAAAATTAAATTGGTTTTTCACGCTTCCAATACCGT
130 CTCAGAAAAACTATATTATTCAACG-CCAAAAAATTAAAAGGGTTTTTCACGCTTCCAATATCGT
* * *
1189 TATTCC-TTTTTTTCGAATTTATTTTTAATTAAATCGAAACAAGATTCAGATACTCGT-AAAACA
194 TTTTCCATTTTTTTCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* * * * *
1252 AATCTTTAAATCCATTGTGGCTAAGATTTGGTTAAACGTATATAGATATTTCAAGGAGTCTTTGC
259 AAT-TTAAAATCCATTGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTGC
*
1317 GCCAAAA
323 -ACAAAA
* * * *
1324 ATCAAGAAAAACTGAGCTGGGGCTTCGGAACACGTTTTTAGCCAAAAAACAGTGATGGTTAATAC
1 ATCAAGCAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTAG-CAAAAAACAGTGATGGTTAATAC
* * * * * *
1389 ACGATTTTGGCTAAAATTTTGAAAAAAAGTGATCCGAAAAATATTTCTTCAATTTTTTGAG-AAA
65 ACGATTTCGGCTAAAATTTTG-TAAAAACTGACCCGAAAAATATTTCCT-AAATTTTTG-GCAAA
* * * * * ** * **
1453 ATACTCATGAAATA-TTTA-CAATCTAACACCAAAAATATT--GGGGGACTTTTCACGCTTTTAA
127 ATACTCA-GAAAAACTATATTATTC-AACGCCAAAAA-ATTAAAAGGG-TTTTTCACGCTTCCAA
* ** *
1514 TATTGTTTTT-CATATTTTTAAAGAATTAATTTTTAATTAAATGGAAACAAGATTCAGATGCTCG
188 TATCGTTTTTCCAT-TTTTT-TCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCG
* * * * * *
1578 TAAAAAGAAATTCTAAAATCTATAGTGGCTGAGATTTGATTAGATGAATATGGATATATCAAGGA
251 TAAAAACAAATT-TAAAATCCATTGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGA
1643 GTCTTTGTGCA-AAAA
315 GTC-TT-TGCACAAAA
* * * * * * * *
1658 ATCATGCAAAACTGAGCCGGTGCCCCGGAACGCTTTTTTTAGCCAAAATCTA-TGATGTTTATTA
1 ATCAAGCAAAACTGAGCCGGGGCTCCGGAACGC-GTTTTTAGCAAAAAAC-AGTGATGGTTAATA
* * * *
1722 CACGATTTCGGCTAAAATTTTGTGAAAATTGACCTGAAAAATATTTCCTAAATTTTTGGGTTAAA
64 CACGATTTCGGCTAAAATTTTGTAAAAACTGACCCGAAAAATATTTCCTAAATTTTT-GG-CAAA
* * * * * * * * * ** *
1787 ATCCTCATAAAAAATATATAATT-AGATGCCAAAAAGATT-AGAGGGCTTTTGACGATTTGAATT
127 ATACTCAGAAAAACTATATTATTCA-ACGCCAAAAA-ATTAAAAGGGTTTTTCACGCTTCCAATA
* * * * * * *
1850 TTGTTTTTCC-TATTTTTCCGAATTAATTTCTAATTAAATCGAAAGAATATTCAAATACTCGTAA
190 TCGTTTTTCCAT-TTTTTTCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* * * * *
1914 AAACAAATTCTAAAATCTATTGTGGCTGAGATTTGATTTGATGAA-AAAGGATATCTCAAGGAGT
254 AAACAAATT-TAAAATCCATTGTGGCTAAGATTTGATTAGATGAATATA-GATATTTCAAGGAGT
1978 CTTTGTGCA-AAAA
317 C-TT-TGCACAAAA
* * * * *
1991 ATCAAGCAAAACTGAGCCGGTGC-CCTGGAACGCTTTTTTAGCTAAAAACTGTGATGGTTATTAC
1 ATCAAGCAAAACTGAGCCGGGGCTCC-GGAACGCGTTTTTAGCAAAAAACAGTGATGGTTAATAC
* *
2055 ACGATTTCGGCTAAAATTTTGTGAAAATTGACCCGAAAAATATTTCCTAAATTTTTGGGCTAAAA
65 ACGATTTCGGCTAAAATTTTGTAAAAACTGACCCGAAAAATATTTCCTAAATTTTT-GGC-AAAA
* * * * * * *
2120 TACT-TGTAAAAAATATATAATT-AGACGCCAAAAAGATT-GAAGGGTTTTTGACGTTTCTAATA
128 TACTCAG-AAAAACTATATTATTCA-ACGCCAAAAA-ATTAAAAGGGTTTTTCACGCTTCCAATA
* * * *
2182 TCGTTTTTCCAATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAAAAATATTCAAATGCTCGT
190 TCGTTTTTCC-A-TTTTTTT-CGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * *
2247 AAAAACAAATTCTAAAATCTATTGTGGCTGAGATTTGATTAGATGAATATGGATATCTCAAGGAG
252 AAAAACAAATT-TAAAATCCATTGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAG
2312 TCTTGGTGCA-AAAA
316 TCTT--TGCACAAAA
* * ** * * *
2326 ATCAAGCAAAACTGAGCCGGTGC-CACGGAATGTTTTTTTAAGCCAAAAACTGTGATGGTTATTA
1 ATCAAGCAAAACTGAGCCGGGGCTC-CGGAACGCGTTTTT-AGCAAAAAACAGTGATGGTTAATA
* * *
2390 CACGATTTCGGCTAAAATTTTGTGAAAATTGACCTGAAAAATATTTCCTAAATTTTTGGGCTAAA
64 CACGATTTCGGCTAAAATTTTGTAAAAACTGACCCGAAAAATATTTCCTAAATTTTT-GGC-AAA
* * * * * * * *
2455 ATACT-TGTAAAAAATATATAATT-AGACGCCAAAAAGATT-GAAGGGCTTTTGACGTTTCTAAT
127 ATACTCAG-AAAAACTATATTATTCA-ACGCCAAAAA-ATTAAAAGGGTTTTTCACGCTTCCAAT
* * * * *
2517 ATCGTTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAAAAATATTCAAATGCTCGTA
189 ATCGTTTTTCC-ATTTTTTTCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * * * *
2582 AAAAAAAATTTAAAATCTATTGTGGGTGAGATTTGATTAGATGAATATGGATATTTCAAGGAGTC
253 AAAACAAATTTAAAATCCATTGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC
2647 TTGGTGCA-AAAA
318 TT--TGCACAAAA
* * **
2659 ATCAAGCAAAACTGAGCCGGTGCCCCGGAACGTTTTTTTAGCCAAAAAAACTA-TGATGG----T
1 ATCAAGCAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTAG-C-AAAAAAC-AGTGATGGTTAAT
* *
2719 ACACGAATTTTCGGCTAAAATTTTGTGAAAATTGACCCGAAAAATATTTCCTAAATTTTTGGGCT
63 ACACG-A-TTTCGGCTAAAATTTTGTAAAAACTGACCCGAAAAATATTTCCTAAATTTTT-GGC-
* * * * **
2784 AAAATACTC-GTAAAAA-TATATAATT-AGACGCCAAAAATATT-AAAGGGCTTTTAACGTTTAT
124 AAAATACTCAG-AAAAACTATATTATTCA-ACGCCAAAAA-ATTAAAAGGGTTTTTCACGCTTCC
2845 AATATCGTTTTTCCAATTTTTTTTTCCGAATTAATTT
186 AATATCGTTTTTCC-A--TTTTTTT-CGAATTAATTT
2882 CTAACTAAGT
Statistics
Matches: 2269, Mismatches: 208, Indels: 141
0.87 0.08 0.05
Matches are distributed among these distances:
326 2 0.00
327 3 0.00
328 103 0.05
329 91 0.04
330 197 0.09
331 673 0.30
332 270 0.12
333 335 0.15
334 257 0.11
335 172 0.08
336 166 0.07
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (328 bp):
ATCAAGCAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTAGCAAAAAACAGTGATGGTTAATACA
CGATTTCGGCTAAAATTTTGTAAAAACTGACCCGAAAAATATTTCCTAAATTTTTGGCAAAATAC
TCAGAAAAACTATATTATTCAACGCCAAAAAATTAAAAGGGTTTTTCACGCTTCCAATATCGTTT
TTCCATTTTTTTCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
TTTAAAATCCATTGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTGCACA
AAA
Found at i:2302 original size:668 final size:661
Alignment explanation
Indices: 33--2881 Score: 2890
Period size: 668 Copynumber: 4.3 Consensus size: 661
23 GTTCCGAAAG
* * *
33 GCGTTTTTAGTCC-AAAAACCGTAGAT-GTAACATACACGATTTCGTCTAAAATTTT-TCAAAAA
1 GCGTTTTTAG-CCAAAAAACTGT-GATGGTTA-ATACACGATTTCGGCTAAAATTTTGT-AAAAA
* * * * * * * * *
95 CTGACCC-AAAAACTTTTTCCTAAATTTTT-TGCCACAGTATTCAG-AAAAACTATATTATTCAA
62 TTGACCCGAAAAA-TATTTCCTAAATTTTTGGGCTAAAATACTC-GTAAAAAATATATAATT-AA
* * * * * *
157 CCCCAAAAAT-TAAAATGGTTTTTCACGCTTCCAATATCGTTTTTCCA-TTTTTTTCGAATTTAT
124 CGCCAAAAATATTAAAGGGTTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTTTCGAATTAAT
* *
220 TTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTA
189 TTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTAAAATCTATTGTGGCTA
* * * *
285 AGATTTGGTTAGATGAATATAGATATTTGAAGGAGTCTTTCGGCCAAAAATCAAGCAAAATTGAG
254 AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTCGGCAAAAAATCAAGCAAAACTGAG
* *
350 CCGGGGCTCCGGAACGCGATTTTAGCAAAAAACAGTGATGGTTAATACACGATTTCGGCTAAAAT
319 CCGGGGCCCCGGAACGCGTTTTTAGCAAAAAACAGTGATGGTTAATACACGATTTCGGCTAAAAT
* * * * *
415 TTTTCAAAAACTGACCCGAAAAGTTTTTCCTCAACTTTTTGG-CACAATACTCAGAAAAACTATA
384 TTTT-AAAAACTGACCCGAAAAATATTTCCT-AAATTTTTGGTCAAAATACTCAGAAAAAATATA
* * ** * * *
479 TTATTCAACACTGAAAAATTAAAATGGTTTTTCACGCA-TCCAATATCGTTTTTCC-ATTTTTTT
447 TAATTCAACGCCAAAAAATT-AAAGGGCTTTTCACG-ATTCCAATATCGTTTTTCCTATTTTTTC
* * * * * *
542 CGAATTTATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACCAATTTATAAATCCA
510 CGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATTTA-AAATCCA
* * * *
607 TTGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCACTAAAAATCAAGC
574 TTGTGGCTAAGATTTGATTAGATGAA-AAAGATATTTCAAGGAGTCTTTGCGCAAAAAATCAAGC
* * * * *
672 AAAATTGAGTCGGGGCTCC-GAAAG
638 AAAACTGAGCCGGTGC-CCTGGAAC
* * * * *
696 GCGTTTTTAGCC-AAAAACCGTGAT-GTAACATACACGATTTCGTCTAAAATTTTGCAAAAACTG
1 GCGTTTTTAGCCAAAAAACTGTGATGGTTA-ATACACGATTTCGGCTAAAATTTTGTAAAAATTG
* * * * * ** * * *
759 ACCCGAAAAGTTTTTCCTCAATTTTT--GCCACAATACTCAG-AAGTACTATATTATTCAACCCC
65 ACCCGAAAAATATTTCCTAAATTTTTGGGCTAAAATACTC-GTAAAAAATATATAATT-AACGCC
* * *
821 AAAAA-ATTAAAATGGTTTTTCACGCTTGC-AATATCGTTTTTCCATTTTTTTTCGAATTTATTT
128 AAAAATATT-AAAGGGTTTTTCACG-TTTCTAATATCGTTTTTCCATTTTTTTTCGAATTAATTT
* * *
884 TTAATTAATTCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAAT-TCATTGTGGCTAA
191 TTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTAAAATCT-ATTGTGGCTAA
* * * * *
948 GATTTGGTTAGATGAATATAGATATTTGAAGGAGTCTTTCGGCCAAAAATCAAGCAAAATTGAGT
255 GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTCGGCAAAAAATCAAGCAAAACTGAGC
*
1013 CGGGGCTCCGGAACGCGTTTTTAGCAAAAAACAGTGATGGTTAATACACGATTTCGGCTAAAATA
320 CGGGGCCCCGGAACGCGTTTTTAGCAAAAAACAGTGATGGTTAATACACGATTTCGGCTAAAAT-
* * * * * * *
1078 TTTCAAAAACGGACCCGAAAAGTTTTTCCTCAATTTTT--TCCACAATACTCAGAAAAACTATAT
384 TTTTAAAAACTGACCCGAAAAATATTTCCTAAATTTTTGGT-CAAAATACTCAGAAAAAATATAT
* * * * * *
1141 TATTCAA-GCCCAAAAAATTAAATTGGTTTTTCACGCTTCCAATACCGTTATTCCT-TTTTTT-C
448 AATTCAACG-CCAAAAAATTAAA-GGGCTTTTCACGATTCCAATATCGTTTTTCCTATTTTTTCC
* * * *
1203 GAATTTATTTTTAATTAAATCGAAACAAGATTCAGATACTCGT-AAAACAAATCTTTAAATCCAT
511 GAATTAATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAAT-TTAAAATCCAT
* * * * * * *
1267 TGTGGCTAAGATTTGGTTAAACGTATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCAAGAA
575 TGTGGCTAAGATTTGATTAGATG-AAAAAGATATTTCAAGGAGTCTTTGCGCAAAAAATCAAGCA
* * *
1332 AAACTGAGCTGG-GGCTTCGGAAC
639 AAACTGAGCCGGTGCCCT-GGAAC
* * * * *
1355 ACGTTTTTAGCCAAAAAACAGTGATGGTTAATACACGATTTTGGCTAAAATTTTGAAAAAAAGTG
1 GCGTTTTTAGCCAAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTG-TAAAAATTG
* * * * * * * * * *
1420 ATCCGAAAAATATTTCTTCAATTTTTTGAG--AAAATACTCATGAAATATTTACAATCTAACACC
65 ACCCGAAAAATATTTCCT-AAATTTTTGGGCTAAAATACTCGTAAAAAATATATAAT-TAACGCC
** * * ***
1483 AAAAATATT-GGGGGACTTTTCACGCTTT-TAATATTGTTTTT-CATATTTTTAAAGAATTAATT
128 AAAAATATTAAAGGG-TTTTTCACG-TTTCTAATATCGTTTTTCCAT-TTTTTTTCGAATTAATT
* * * * *
1545 TTTAATTAAATGGAAACAAGATTCAGATGCTCGTAAAAAGAAATTCTAAAATCTATAGTGGCTGA
190 TTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTAAAATCTATTGTGGCTAA
* * *
1610 GATTTGATTAGATGAATATGGATATATCAAGGAGTCTTT-GTGCAAAAAATCATGCAAAACTGAG
255 GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTCG-GCAAAAAATCAAGCAAAACTGAG
* * * * * *
1674 CCGGTGCCCCGGAACGCTTTTTTTAGCCAAAATCTA-TGATGTTTATTACACGATTTCGGCTAAA
319 CCGGGGCCCCGGAACGC-GTTTTTAGCAAAAAAC-AGTGATGGTTAATACACGATTTCGGCTAAA
* * * * * *
1738 ATTTTGTGAAAATTGACCTGAAAAATATTTCCTAAATTTTTGGGTTAAAATCCTCATAAAAAATA
382 ATTTT-TAAAAACTGACCCGAAAAATATTTCCTAAATTTTT-GGTCAAAATACTCAGAAAAAATA
* * * ** * *
1803 TATAATT-AGATGCCAAAAAGATTAGAGGGCTTTTGACGATTTGAATTTTGTTTTTCCTA-TTTT
445 TATAATTCA-ACGCCAAAAA-ATTAAAGGGCTTTTCACGATTCCAATATCGTTTTTCCTATTTTT
* *
1866 TCCGAATTAATTTCTAATTAAATCGAAAGAATATTCAAATACTCGTAAAAACAAATTCTAAAATC
508 TCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATT-TAAAATC
* * * * *
1931 TATTGTGGCTGAGATTTGATTTGATGAAAAAGGATATCTCAAGGAGTCTTTGTGCAAAAAATCAA
572 CATTGTGGCTAAGATTTGATTAGATGAAAAA-GATATTTCAAGGAGTCTTTGCGCAAAAAATCAA
1996 GCAAAACTGAGCCGGTGCCCTGGAAC
636 GCAAAACTGAGCCGGTGCCCTGGAAC
* * * *
2022 GCTTTTTTAG-CTAAAAACTGTGATGGTTATTACACGATTTCGGCTAAAATTTTGTGAAAATTGA
1 GCGTTTTTAGCCAAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGTAAAAATTGA
*
2086 CCCGAAAAATATTTCCTAAATTTTTGGGCTAAAATACTTGTAAAAAATATATAATTAGACGCCAA
66 CCCGAAAAATATTTCCTAAATTTTTGGGCTAAAATACTCGTAAAAAATATATAATTA-ACGCCAA
* * * *
2151 AAAGATTGAAGGGTTTTTGACGTTTCTAATATCGTTTTTCCAATTTTTTTTCCGAATTAATTTCT
130 AAATATTAAAGGGTTTTTCACGTTTCTAATATCGTTTTTCC-ATTTTTTTT-CGAATTAATTTTT
* * * * *
2216 AATTAAATCGAAAAAATATTCAAATGCTCGTAAAAACAAATTCTAAAATCTATTGTGGCTGAGAT
193 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTAAAATCTATTGTGGCTAAGAT
* * *
2281 TTGATTAGATGAATATGGATATCTCAAGGAGTC-TTGGTGCAAAAAATCAAGCAAAACTGAGCCG
258 TTGATTAGATGAATATAGATATTTCAAGGAGTCTTTCG-GCAAAAAATCAAGCAAAACTGAGCCG
* * * ** * * *
2345 GTGCCACGGAATGTTTTTTTAAGCCAAAAACTGTGATGGTTATTACACGATTTCGGCTAAAATTT
322 GGGCCCCGGAACGCGTTTTT-AGCAAAAAACAGTGATGGTTAATACACGATTTCGGCTAAAATTT
* * * * *
2410 TGTGAAAATTGACCTGAAAAATATTTCCTAAATTTTTGGGCTAAAATACT-TGTAAAAAATATAT
386 T-TAAAAACTGACCCGAAAAATATTTCCTAAATTTTTGGTC-AAAATACTCAG-AAAAAATATAT
* * * * *
2474 AATT-AGACGCCAAAAAGATTGAAGGGCTTTTGACGTTTCTAATATCGTTTTTCCAATTTTTTCC
448 AATTCA-ACGCCAAAAA-ATTAAAGGGCTTTTCACGATTCCAATATCGTTTTTCCTATTTTTTCC
* * * * *
2538 GAATTAATTTCTAATTAAATCGAAAAAATATTCAAATGCTCGTAAAAAAAAATTTAAAATCTATT
511 GAATTAATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATTTAAAATCCATT
* * ** * *
2603 GTGGGTGAGATTTGATTAGATGAATATGGATATTTCAAGGAGTCTTGGTGCAAAAAATCAAGCAA
576 GTGGCTAAGATTTGATTAGATGAA-AAAGATATTTCAAGGAGTCTTTGCGCAAAAAATCAAGCAA
*
2668 AACTGAGCCGGTGCCCCGGAAC
640 AACTGAGCCGGTGCCCTGGAAC
** * *
2690 GTTTTTTTAGCCAAAAAAACTATGATGG----TACACGAATTTTCGGCTAAAATTTTGTGAAAAT
1 GCGTTTTTAGCC-AAAAAACTGTGATGGTTAATACACG-A-TTTCGGCTAAAATTTTGTAAAAAT
2751 TGACCCGAAAAATATTTCCTAAATTTTTGGGCTAAAATACTCGT-AAAAATATATAATTAGACGC
63 TGACCCGAAAAATATTTCCTAAATTTTTGGGCTAAAATACTCGTAAAAAATATATAATTA-ACGC
* * *
2815 CAAAAATATTAAAGGGCTTTTAACGTTTATAATATCGTTTTTCCAATTTTTTTTTCCGAATTAAT
127 CAAAAATATTAAAGGGTTTTTCACGTTTCTAATATCGTTTTTCC-A-TTTTTTTT-CGAATTAAT
2880 TT
189 TT
2882 CTAACTAAGT
Statistics
Matches: 1897, Mismatches: 222, Indels: 129
0.84 0.10 0.06
Matches are distributed among these distances:
657 1 0.00
658 1 0.00
659 96 0.05
660 120 0.06
661 196 0.10
662 439 0.23
663 86 0.05
664 12 0.01
665 83 0.04
666 146 0.08
667 172 0.09
668 472 0.25
669 60 0.03
670 13 0.01
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (661 bp):
GCGTTTTTAGCCAAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGTAAAAATTGA
CCCGAAAAATATTTCCTAAATTTTTGGGCTAAAATACTCGTAAAAAATATATAATTAACGCCAAA
AATATTAAAGGGTTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTTTCGAATTAATTTTTAAT
TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTAAAATCTATTGTGGCTAAGATTTG
ATTAGATGAATATAGATATTTCAAGGAGTCTTTCGGCAAAAAATCAAGCAAAACTGAGCCGGGGC
CCCGGAACGCGTTTTTAGCAAAAAACAGTGATGGTTAATACACGATTTCGGCTAAAATTTTTAAA
AACTGACCCGAAAAATATTTCCTAAATTTTTGGTCAAAATACTCAGAAAAAATATATAATTCAAC
GCCAAAAAATTAAAGGGCTTTTCACGATTCCAATATCGTTTTTCCTATTTTTTCCGAATTAATTT
CTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATTTAAAATCCATTGTGGCTAAGA
TTTGATTAGATGAAAAAGATATTTCAAGGAGTCTTTGCGCAAAAAATCAAGCAAAACTGAGCCGG
TGCCCTGGAAC
Found at i:3112 original size:96 final size:96
Alignment explanation
Indices: 3004--3207 Score: 268
Period size: 96 Copynumber: 2.1 Consensus size: 96
2994 TATACTAATT
* **
3004 TGTAAAATTCCACGACTGGTCATTACTCT-ACCTTAATTATAATATTTTTCGTATAACACACAAA
1 TGTAAAAATCCACGACACGTCATTACT-TGACCTTAATTATAATATTTTTCGTATAACACACAAA
3068 ATATTGATTAAACTCGA-TCTTTCACACTTATC
65 ATATTGATTAAACTCGATTCTTT-ACACTTATC
* * **
3100 TGTAAAAATCCACGACACGTCATTGCTTGACCTTAATTGTAATATTTTTCGTATGTCACACAAAA
1 TGTAAAAATCCACGACACGTCATTACTTGACCTTAATTATAATATTTTTCGTATAACACACAAAA
*** * *
3165 TATTGATTATTTTGGATTCTTTACTCTTATC
66 TATTGATTAAACTCGATTCTTTACACTTATC
3196 TGTAAAAATCCA
1 TGTAAAAATCCA
3208 ATCTGCCTTA
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
95 1 0.01
96 88 0.94
97 5 0.05
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (96 bp):
TGTAAAAATCCACGACACGTCATTACTTGACCTTAATTATAATATTTTTCGTATAACACACAAAA
TATTGATTAAACTCGATTCTTTACACTTATC
Found at i:3926 original size:60 final size:59
Alignment explanation
Indices: 3774--3951 Score: 304
Period size: 60 Copynumber: 3.0 Consensus size: 59
3764 TATGCCAGCA
* *
3774 GACACGAAGGTACACGAGAAGACAGAGGCTCTCCGCAATGAGGCGAGGCCAGTAGACAC
1 GACACGAAGGTACACGAGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGCAGACAC
*
3833 -ACACAAAGGTACACGAGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGCAGACAC
1 GACACGAAGGTACACGAGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGCAGACAC
*
3891 GAACACGAAGGTACACGAGAAGACAGAGGCTCTCCGCAGTGAAGCGAGGCCAGCAGACAC
1 G-ACACGAAGGTACACGAGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGCAGACAC
3951 G
1 G
3952 TCGAGTCCCC
Statistics
Matches: 112, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
58 55 0.49
60 57 0.51
ACGTcount: A:0.34, C:0.26, G:0.32, T:0.07
Consensus pattern (59 bp):
GACACGAAGGTACACGAGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGCAGACAC
Found at i:4892 original size:326 final size:326
Alignment explanation
Indices: 4035--4970 Score: 1143
Period size: 333 Copynumber: 2.8 Consensus size: 326
4025 ATATTTTCTG
* * ** * ** *
4035 AATTTTTTGCCACAATACTCAGAAAGAA-TATCTAATTCAACTCAAAAAAAAATT-GTAGGGTTT
1 AATTTTTTGCCACAATACTCAGAAA-AACTATATTATTCAAC-C-CCAAAATATTAAAATGGTTT
* * *
4098 TTCACGATTCCAATATTGTTTTTCCATTTTTATTACCGAATTTATTTCTAATTAAATCGAAACAA
63 TTCACGCTTCCAATATCGTTTTTCCATTTTT-TT--CGAATTTATTTTTAATTAAATCGAAACAA
* * * * * * *
4163 AATTCAGATTCTCGTAAAAATAAATCCTTAAATCCATTGTGTCTGAGAATTGGTTCGATGAATAT
125 GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCAGAGATTTGGTTAGATGAATAT
* * * **
4228 AGATATTT-AGAGTAGGCTTTCTGCCAAAAATCATGTAAAACTGAGCCGGTTCCCCGAAACGCGT
190 AGATATTTCA-AGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGG-AGCCCGAAACGCGT
* * *
4292 TTTTAGCCCAAAAATCGTGATGCATAAACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAA
253 TTTTAG-CCAAAAACCGTGAT-CATAAACGATTTCAGCTAAAATTTTGCAAAAACTGACCCAAAA
*
4357 AGTTTTTCCTC
316 AGTTTTTCCTA
*
4368 AATTTTTTGCTACAATACTCAGAAAAACTATATTATTCAACCCCAAAATATTAAAATGGTTTTTC
1 AATTTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCCAAAATATTAAAATGGTTTTTC
4433 ACGCTTCCAATATCGTTTTTCCATTTATTTTTTTCGAATTTATTTTTAATTAAATCGAAACAAGA
66 ACGCTTCCAATATCGTTTTTCC----ATTTTTTTCGAATTTATTTTTAATTAAATCGAAACAAGA
* * * *
4498 TTCAAATGCTCGTAAAAACAAATCCATAAATCCATTGAGGGTA-AGATTTGGTTAGATGAATATA
127 TTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTG-TGGCAGAGATTTGGTTAGATGAATATA
* * * *
4562 GATATTTCAAGGAGTCTTTGC-GCCAACAATCAAGCAAAATTGAGCCGGAGCTCCGGAACGCGTT
191 GATATTTCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAACTGAGCCGGAGC-CCGAAACGCGTT
* * *
4626 TTTAGCAAAAAACCGTGAT-A-ACACGATTTCAGCTAAAATTTTGCAAAAACTGACTCAAAAAGT
254 TTTAGCCAAAAACCGTGATCATAAACGATTTCAGCTAAAATTTTGCAAAAACTGACCCAAAAAGT
*
4689 TTTTTCTA
319 TTTTCCTA
* ***
4697 AATTTTTTGCCACAGTACTCAGAAAAACTATATTATTCAACATTGAAAA-ATTAAAATGGTTTTT
1 AATTTTTTGCCACAATACTCAGAAAAACTATATTATTCAAC-CCCAAAATATTAAAATGGTTTTT
4761 -ATGCGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATTTTTAATTAAATCGAAACAAGAT
65 CA--CGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATTTTTAATTAAATCGAAACAAGAT
* *
4825 TCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCAGAGATTTTGTTAGATGACTATAGA
128 TCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCAGAGATTTGGTTAGATGAATATAGA
* * * * * *
4890 TATTTCCAGGAGTTTTTCTTCCAAAAATCATGCAAAACTGAACCGGGGCCCTGAAACGCTTTTTT
193 TATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGAGCCC-GAAACGCGTTTTT
*
4955 AGTCAAAAACCGTGAT
257 AGCCAAAAACCGTGAT
4971 GTTTTTCACG
Statistics
Matches: 524, Mismatches: 63, Indels: 39
0.84 0.10 0.06
Matches are distributed among these distances:
325 6 0.01
326 159 0.30
328 1 0.00
329 99 0.19
330 26 0.05
331 7 0.01
332 45 0.09
333 170 0.32
334 3 0.01
335 2 0.00
336 6 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (326 bp):
AATTTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCCAAAATATTAAAATGGTTTTTC
ACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATTTTTAATTAAATCGAAACAAGATTCA
GATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCAGAGATTTGGTTAGATGAATATAGATAT
TTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGAGCCCGAAACGCGTTTTTAGCC
AAAAACCGTGATCATAAACGATTTCAGCTAAAATTTTGCAAAAACTGACCCAAAAAGTTTTTCCT
A
Found at i:6090 original size:331 final size:330
Alignment explanation
Indices: 4973--8565 Score: 3982
Period size: 331 Copynumber: 10.9 Consensus size: 330
4963 ACCGTGATGT
*
4973 TTTTCACGCTTCCAATATCGATTTTCCATTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAG
1 TTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATTT-TAATTAAATCGAAACAAG
* *
5038 ATTCAGATGCTCGT-AAAA-AAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAAACGAATATA
65 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATA
* * *
5101 GATATTTCAAGGAGCCTTTGCGCCAAAAATCAAGCAAAATTGAG-CTGGGGCTCCGGAACACGTT
130 GATATTTCAAGGAGTCTTTTCGCCAAAAATCAAGCAAAATTGAGTC-GGGGCTCCGGAACGCGTT
* * *
5165 TTTAGCAAAAAAACAGTGATGGTTAATACATGATTTCGTCTAAAATTTTGCAAAAACTGACCCG-
194 TTTAGC-AAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGA
* **
5229 AAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCCAAAAAACA
258 AAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACCCCAAAAAATT
*
5294 AAAATGAG
323 AAAATGGG
*
5302 TTTTCACGCTTCCAATATCGATTTTCCATTTTTTTCGAATTTATTTTTAATTAAATCGAAACAAG
1 TTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTA-TTTTAATTAAATCGAAACAAG
* *
5367 ATTCAGATGCTCGT-AAAACAAATCCTTAAATCCATTGTGACTAAGATTTGGTTAGATAAATATA
65 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATA
* * * * ***
5431 GATATTTCAAGGAGTCTTTGCACCAAAAATCAAGCAAAATTGAGCCGAGGCTGTTGAACGCGTTT
130 GATATTTCAAGGAGTCTTTTCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAACGCGTTT
* *
5496 TTAGCTAAAAAACCGTGA-----CATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAA
195 TTAGC-AAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAA
* * * * *
5556 AAGTTTTTCCTTAATTTTTTGCCACAATACTCAGAAGAACTATATTATTCAATCCCAAAAAACTA
259 AAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACCCCAAAAAATTA
5621 AAATGGG
324 AAATGGG
*
5628 TTTTCACGCTT--AATATCGTTTTTCCATTTTTTTCGAATTTATTTTTAATTAAATCGAAATAAG
1 TTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTA-TTTTAATTAAATCGAAACAAG
* *
5691 ATTCAGATGCTCGTATAAACAAATCCATAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATA
65 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATA
* *
5756 GATATTTAAAGGAGTCTTTTCCCCAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAACGCGTTT
130 GATATTTCAAGGAGTCTTTTCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAACGCGTTT
* * *
5821 TTAGCCAAAAACTGTTATGGTTAATACACGATTTCGGCTAAAATTTTGTAAAAACTGACCCGAAA
195 TTAGCAAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAA
*
5886 AGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACCCCAAAAAACTAA
260 AGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACCCCAAAAAATTAA
5951 AATGGG
325 AATGGG
5957 TTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATGTTTAATTAAATCGAAACAAG
1 TTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTAT-TTTAATTAAATCGAAACAAG
6022 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATA
65 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATA
* **
6087 GATATTTCAAGGAGTCTTTGCGCCAAAAATCAAGCAAAATTGAGTCAGGGGCTCTTGAACGCGTT
130 GATATTTCAAGGAGTCTTTTCGCCAAAAATCAAGCAAAATTGAGTC-GGGGCTCCGGAACGCGTT
* *
6152 TTTAGCTAAAAAACCGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTTACCCGA
194 TTTAGC-AAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGA
* * *
6217 AAATTTTTTCCTCAATTTTTTGCCACAATACTCAGAAGAACTATATTATTCAACCCCAAAAAATT
258 AAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACCCCAAAAAATT
*
6282 AAAATGGT
323 AAAATGGG
6290 TTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATTTTTAATTAAATCGAAACAAG
1 TTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTA-TTTTAATTAAATCGAAACAAG
6355 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATA
65 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATA
*
6420 GATATTTGAAGGAGTCTTTTCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAACGCGTTT
130 GATATTTCAAGGAGTCTTTTCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAACGCGTTT
*
6485 TTAGCCAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAA
195 TTAGCAAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAA
* * *
6550 AGTTTTTCCTCAATTTTTTGCTACAATACTCAGAAAAACTATATTATTCAACCCCAAAATATTAA
260 AGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACCCCAAAAAATTAA
6615 AATGGG
325 AATGGG
6621 TTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATGTTTAATTAAATCGAAACAAG
1 TTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTAT-TTTAATTAAATCGAAACAAG
*
6686 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTTGTTAGATGAATATA
65 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATA
* * **
6751 GATATTTCAAGGAGTCTTTGCGCCAAAAATCAAGCAAAATTGAGACGGGGCTCTTGAACGCGTTT
130 GATATTTCAAGGAGTCTTTTCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAACGCGTTT
* *
6816 TTAGCTAAAAAACTGTGATGG-T-ATACACGATTTCGACTAAAATTTTGCAAAAACTTACCCGAA
195 TTAGC-AAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAA
** *
6879 AAGTTTTTCCTCAATTTTTTGCCACAATACTCATTAAAACTATATTATTCAACCCCAAAAAATTA
259 AAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACCCCAAAAAATTA
6944 AAA-GGG
324 AAATGGG
** *
6950 TTTTTCACGCTTCCAATATCGTTTTTTTTATTTTTTTTCGAATTTATTTCTAATTAAATTGAAAC
1 -TTTTCACGCTTCCAATATCG-TTTTTCCA-TTTTTTTCGAATTTATTT-TAATTAAATCGAAAC
* * *
7015 AAGATTCAGTTGCTCGTAGAAACAAATCCTTAAATCCATTGTGGCTAATATTTGGTTAGATGAAT
62 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAAT
* ** * ** * * *
7080 ATCGATATTTTGAGGACTCTTTTTTCCAAAAAT-AATGCAAAACTGAGTCGGGGC-CCTGAAAG-
127 ATAGATATTTCAAGGAGTCTTTTCGCCAAAAATCAA-GCAAAATTGAGTCGGGGCTCCGGAACGC
* ** ** * * ** * * *
7142 G---CT-G--AAACTCAT-TTTTAGTTAA-AAATCG-TGAC-G-TACACGATTTGGGCTAAAAAT
191 GTTTTTAGCAAAAAAC-TGTGATGGTTAATACA-CGATTTCGGCTA-A-AATTT-TGC-AAAAAC
* * * * * * *
7196 TGACCCGAAAAATTTTTTCTCAATTTATTG-CAAAATATTCAGAAAAAATATATAATTCAACACC
250 TGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACCCC
* * *
7260 AAAAAGATTGACA-GGC
315 AAAAA-ATTAAAATGGG
* * *
7276 TTTTCACGCTTCTAATATCGTTTTCCCATTTTTTTCCGAATTAATTTATAATTAAATC-AAAGCA
1 TTTTCACGCTTCCAATATCGTTTTTCCATTTTTTT-CGAATTTATTT-TAATTAAATCGAAA-CA
* * * * * ** *
7340 AGATTCAGAAGCTCGT-AAAACTAAATCGTTAAATCCAATGAGACTGGGATTTGGTTCGATGAAT
63 AGATTCAGATGCTCGTAAAAAC-AAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAAT
** * * * * * * **
7404 ATAGATATTTCTTGGAGTCTTTACGTCAGAAATCATGCAAAATTGATTCGGAGC-CTCGGAACAA
127 ATAGATATTTCAAGGAGTCTTTTCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTC-CGGAACGC
* * * * * * * *
7468 ATTTTAAGGC-AAAAACAGTAATGAG-T-A-A-ACGATTTTGACTAAAATTTTGTAAAAATTGAC
191 GTTTTTA-GCAAAAAACTGTGATG-GTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGAC
* ** ** * * * * *
7528 CCGAAAATTTTTTCCTTGATTCCTTGCAATAATACTC-GTAAAAAATATATAATTCAACAACAAA
254 CCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAG-AAAAAATATATTATTCAAC-CCCAA
*
7592 AAAATT-GAA-GGG
317 AAAATTAAAATGGG
* * *
7604 TTTTTAACGCTTCCTATATCATTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAAC
1 -TTTTCACGCTTCCAATATC-GTTTTTCCATTTTTTT-CGAATTTATTT-TAATTAAATCGAAAC
* * *
7669 GAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGACT
62 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAAT
* * * * * ** *
7734 ACAGATATTTCAAGGAGTCTTGCTT--CCAAAAATCATGAAAAACTGAGCCGGGGC-CCTCAA-A
127 ATAGATATTTCAAGGAGTCTT--TTCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAACG
* * * *
7795 CGTATTTTAG-TAAAAACTGTGAAGGTTAGTAAACGATTTCGGC--------T--AAAAACTGAC
190 CGT-TTTTAGCAAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGAC
* * * * * *
7849 CCGAAAAGATTTTT-CTCGATTTTTTG-CAAAATATTCAGAAAAATTATATAATTCAACGCCAAA
254 CCGAAAAG-TTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACCCCAAA
* *
7912 AAGATT--GACGGG
318 AA-ATTAAAATGGG
* * * *
7924 CTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATCTCTAATTAAATCGAAACA
1 -TTTTCACGCTTCCAATATCGTTTTTCCATTTTTTT-CGAATTTAT-TTTAATTAAATCGAAACA
*
7989 AGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATA
63 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATA
* * * * * *
8054 TAGATATTTCAAGGAGTC-TTTCTTCCAAAAATCATGC-AAACTGAGTCTGGGC-CTTGAAAGGC
128 TAGATATTTCAAGGAGTCTTTTC-GCCAAAAATCAAGCAAAATTGAGTCGGGGCTC-CGGAA--C
* * * * *
8116 TGAAAAACATTTTTAGTTAAAAATCATG-G-TGGTTAGTACACTATTTCGGC--------T-C-A
189 -G-----CGTTTTTAG-CAAAAAAC-TGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAA
* * * * * * *
8169 AAACTTACCTGAAAAATTTTTTCTCAATTTTTTGTCACAATACTCATAAAAAATATATAATTCAA
246 AAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAA
* **
8234 CGCCAAAAAATATTGAA-GGG
311 CCCCAAAAAAT-TAAAATGGG
* * * *
8254 TTTTTCACGCTTCTAATATTGTTTTTCCATTTTTTTTCTGAATTAAATTCTAATTAAATCGAAAC
1 -TTTTCACGCTTCCAATATCGTTTTTCCA-TTTTTTTC-GAATT-TATTTTAATTAAATCGAAAC
* * * ** * ** ** * *
8319 AAGATTCAAATGCTCTTAAAAATAAATTGTTAAATCCAATGTATCTGGGATTTGATTCGATGAAT
62 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAAT
* * * * * * **
8384 ATAGATATTTCAAAGAGGCTTTTCGCCAAAAATCATGCAAAATTGAGT--TGGCCCCGAAAAACG
127 ATAGATATTTCAAGGAGTCTTTTCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAACGCG
* * * * * *
8447 TTTTTAAGC-AAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAATTTTACAAAAATTGACCA
192 TTTTT-AGCAAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCC
* * * * * * *
8511 G-AAAGATTTTTGCTCAATTTCTAGCGAAAATACTCATAAAAAATATATAATTCAA
256 GAAAAG-TTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAA
8566 TGTCAAAAAA
Statistics
Matches: 2836, Mismatches: 317, Indels: 219
0.84 0.09 0.06
Matches are distributed among these distances:
316 2 0.00
318 15 0.01
319 139 0.05
320 49 0.02
321 32 0.01
322 33 0.01
323 25 0.01
324 196 0.07
325 206 0.07
326 118 0.04
327 13 0.00
328 96 0.03
329 298 0.11
330 423 0.15
331 628 0.22
332 268 0.09
333 294 0.10
334 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (330 bp):
TTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATTTTAATTAAATCGAAACAAGA
TTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATAG
ATATTTCAAGGAGTCTTTTCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTT
TAGCAAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAA
GTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACCCCAAAAAATTAAA
ATGGG
Found at i:6469 original size:664 final size:660
Alignment explanation
Indices: 4971--8565 Score: 4240
Period size: 664 Copynumber: 5.5 Consensus size: 660
4961 AAACCGTGAT
*
4971 GTTTTTCACGCTTCCAATATCGATTTTCCATTTTTTTCGAATTTATTTCTAATTAAATCGAAACA
1 GTTTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATTTCTAATTAAATCGAAACA
* *
5036 AGATTCAGATGCTCGT-AAAA-AAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAAACGAATA
66 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATA
* *
5099 TAGATATTTCAAGGAGCCTTTGCGCCAAAAATCAAGCAAAATTGAG-CTGGGGCTCCGGAACACG
131 TAGATATTTCAAGGAGTCTTTTCGCCAAAAATCAAGCAAAATTGAGTC-GGGGCTCCGGAACACG
* * *
5163 TTTTTAGCAAAAAAACAGTGATGGTTAATACATGATTTCGTCTAAAATTTTGCAAAAACTGACCC
195 TTTTTAGC--AAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCC
* * *
5228 G-AAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCCAAAAAA
258 GAAAAGTTTTTCCTCAATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACCCCAAAAAA
* * * *
5292 CAAAAATGAGTTTTCACGCTTCCAATATCGATTTTCCATTTTTTTCGAATTTATTTTTAATTAAA
323 CTAAAATGGGTTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATGTTTAATTAAA
*
5357 TCGAAACAAGATTCAGATGCTCGT-AAAACAAATCCTTAAATCCATTGTGACTAAGATTTGGTTA
388 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTA
* * * * *
5421 GATAAATATAGATATTTCAAGGAGTCTTTGCACCAAAAATCAAGCAAAATTGAGCCGAGGCTGTT
453 GATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCTT
*
5486 GAACGCGTTTTTAGCTAAAAAACCGTGA---CATACACGATTTCGGCTAAAATTTTGCAAAAACT
518 GAACGCGTTTTTAGCTAAAAAACCGTGATGGTATACACGATTTCGGCTAAAATTTTGCAAAAACT
* * * * *
5548 GACCCGAAAAGTTTTTCCTTAATTTTTTGCCACAATACTCAGAAGAACTATATTATTCAATCCCA
583 TACCCGAAAATTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCCA
*
5613 AAAAACTAAAATGG
648 AAAAATTAAAA-GG
* *
5627 G-TTTTCACGCTT--AATATCGTTTTTCCATTTTTTTCGAATTTATTTTTAATTAAATCGAAATA
1 GTTTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATTTCTAATTAAATCGAAACA
* *
5689 AGATTCAGATGCTCGTATAAACAAATCCATAAATCCATTGTGGCTAAGATTTGGTTAGATGAATA
66 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATA
* * *
5754 TAGATATTTAAAGGAGTCTTTTCCCCAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAACGCGT
131 TAGATATTTCAAGGAGTCTTTTCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAACACGT
* *
5819 TTTTAGCCAAAAACTGTTATGGTTAATACACGATTTCGGCTAAAATTTTGTAAAAACTGACCCGA
196 TTTTAG-CAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGA
* *
5884 AAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACCCCAAAAAACT
260 AAAGTTTTTCCTCAATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACCCCAAAAAACT
5949 AAAATGGGTTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATGTTTAATTAAATC
325 AAAATGGGTTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATGTTTAATTAAATC
6014 GAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGA
390 GAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGA
6079 TGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCAAGCAAAATTGAGTCAGGGGCTCTTG
455 TGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCAAGCAAAATTGAGTC-GGGGCTCTTG
6144 AACGCGTTTTTAGCTAAAAAACCGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAAC
519 AACGCGTTTTTAGCTAAAAAACCGTGATGG-T-ATACACGATTTCGGCTAAAATTTTGCAAAAAC
*
6209 TTACCCGAAAATTTTTTCCTCAATTTTTTGCCACAATACTCAGAAGAACTATATTATTCAACCCC
582 TTACCCGAAAATTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCC
*
6274 AAAAAATTAAAATG
647 AAAAAATTAAAAGG
*
6288 GTTTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATTTTTAATTAAATCGAAACA
1 GTTTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATTTCTAATTAAATCGAAACA
6353 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATA
66 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATA
* *
6418 TAGATATTTGAAGGAGTCTTTTCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAACGCGT
131 TAGATATTTCAAGGAGTCTTTTCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAACACGT
6483 TTTTAGCCAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGA
196 TTTTAG-CAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGA
* * * * * *
6548 AAAGTTTTTCCTCAATTTTTTGCTACAATACTCAGAAAAACTATATTATTCAACCCCAAAATATT
260 AAAGTTTTTCCTCAATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACCCCAAAAAACT
6613 AAAATGGGTTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATGTTTAATTAAATC
325 AAAATGGGTTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATGTTTAATTAAATC
*
6678 GAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTTGTTAGA
390 GAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGA
*
6743 TGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCAAGCAAAATTGAGACGGGGCTCTTGA
455 TGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCTTGA
* *
6808 ACGCGTTTTTAGCTAAAAAACTGTGATGGTATACACGATTTCGACTAAAATTTTGCAAAAACTTA
520 ACGCGTTTTTAGCTAAAAAACCGTGATGGTATACACGATTTCGGCTAAAATTTTGCAAAAACTTA
* **
6873 CCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCATTAAAACTATATTATTCAACCCCAAA
585 CCCGAAAATTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCCAAA
6938 AAATTAAAAGG
650 AAATTAAAAGG
** *
6949 GTTTTTCACGCTTCCAATATCGTTTTTTTTATTTTTTTTCGAATTTATTTCTAATTAAATTGAAA
1 GTTTTTCACGCTTCCAATATCG-TTTTTCCA-TTTTTTTCGAATTTATTTCTAATTAAATCGAAA
* * *
7014 CAAGATTCAGTTGCTCGTAGAAACAAATCCTTAAATCCATTGTGGCTAATATTTGGTTAGATGAA
64 CAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAA
* ** * ** * *
7079 TATCGATATTTTGAGGACTCTTTTTTCCAAAAAT-AATGCAAAACTGAGTCGGGGC-CCTGAA-A
129 TATAGATATTTCAAGGAGTCTTTTCGCCAAAAATCAA-GCAAAATTGAGTCGGGGCTCCGGAACA
** ** ** * * ** * * *
7141 -G--GCT-G-AAACTCAT-TTTTAGTTAA-AAATCG-TGAC-G-TACACGATTTGGGCTAAAAAT
193 CGTTTTTAGCAAAAAC-TGTGATGGTTAATACA-CGATTTCGGCTA-A-AATTT-TGC-AAAAAC
* * * * *
7196 TGACCCGAAAAATTTTTTCTCAATTTATTG-CAAAATATTCAGAAAAAATATATAATTCAACACC
252 TGACCCGAAAAGTTTTTCCTCAATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACCCC
* * * * * * *
7260 AAAAAGATTGACA-GGCTTTTCACGCTTCTAATATCGTTTTCCCATTTTTTTCCGAATTAAT-TT
317 AAAAA-ACTAAAATGGGTTTTCACGCTTCCAATATCGTTTTTCCATTTTTTT-CGAATTTATGTT
* * * * * *
7323 ATAATTAAATC-AAAGCAAGATTCAGAAGCTCGT-AAAACTAAATCGTTAAATCCAATGAGACTG
380 -TAATTAAATCGAAA-CAAGATTCAGATGCTCGTAAAAAC-AAATCCTTAAATCCATTGTGGCTA
* * ** * * * * *
7386 GGATTTGGTTCGATGAATATAGATATTTCTTGGAGTCTTTACGTCAGAAATCATGCAAAATTGAT
442 AGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCAAGCAAAATTGAG
* * *** * * * * *
7451 TCGGAGC-CTCGGAACAAATTTTAAGGC--AAAAACAGTAATGAGTA-A-ACGATTTTGACTAAA
507 TCGGGGCTCT-TGAACGCGTTTTTA-GCTAAAAAACCGTGATG-GTATACACGATTTCGGCTAAA
* ** ** * * *
7511 ATTTTGTAAAAA-TTGACCCGAAAATTTTTTCCTTGATTCCTTGCAATAATACTC-GTAAAAAAT
569 ATTTTGCAAAAACTT-ACCCGAAAATTTTTTCCTCAATTTTTTGCCACAATACTCAG-AAAAACT
* * * *
7574 ATATAATTCAACAACAAAAAAATT-GAAGG
632 ATATTATTCAAC-CCCAAAAAATTAAAAGG
* * *
7603 GTTTTTAACGCTTCCTATATCATTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAA
1 GTTTTTCACGCTTCCAATATC-GTTTTTCCATTTTTTT-CGAATTTATTTCTAATTAAATCGAAA
* * *
7668 CGAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAC
64 CAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAA
* * * * * **
7733 TACAGATATTTCAAGGAGTCTTGCTT--CCAAAAATCATGAAAAACTGAGCCGGGGC-CCTCAA-
129 TATAGATATTTCAAGGAGTCTT--TTCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAAC
* * * *
7794 ACGTATTTTAGTAAAAACTGTGAAGGTTAGTAAACGATTTCGGC--------T--AAAAACTGAC
192 ACGT-TTTTAGCAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGAC
* * * *
7849 CCGAAAAGATTTTT-CTCGATTTTTTG-CAAAATATTCAGAAAAATTATATAATTCAACGCCAAA
256 CCGAAAAG-TTTTTCCTCAATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACCCCAAA
** * * * * * *
7912 AAGA-T-TGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATCTCTA
320 AA-ACTAAAATGGG-TTTTCACGCTTCCAATATCGTTTTTCCATTTTTTT-CGAATTTATGTTTA
*
7975 ATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATT
382 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATT
* * * *
8040 TGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTTCCAAAAATCATGC-AAACTGAGTCTG
447 TGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGC-GCCAAAAATCAAGCAAAATTGAGTCGG
* * * * * *
8103 GGC-CTTGAAAGGCTGAAAAACATTTTTAG-TTAAAAATCATGGTGGTTAGTACACTATTTCGGC
511 GGCTCTTG-AA--C-G-----CGTTTTTAGCTAAAAAACCGTGATGG-TA-TACACGATTTCGGC
* * *
8166 --------T-C-AAAACTTACCTGAAAAATTTTTT-CTCAATTTTTTGTCACAATACTCATAAAA
565 TAAAATTTTGCAAAAACTTACCCG-AAAATTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAA
* * * **
8220 AATATATAATTCAACGCCAAAAAATATTGAAGG
629 ACTATATTATTCAACCCCAAAAAAT-TAAAAGG
* * * *
8253 GTTTTTCACGCTTCTAATATTGTTTTTCCATTTTTTTTCTGAATTAAATTCTAATTAAATCGAAA
1 GTTTTTCACGCTTCCAATATCGTTTTTCCA-TTTTTTTC-GAATTTATTTCTAATTAAATCGAAA
* * * ** * ** ** * *
8318 CAAGATTCAAATGCTCTTAAAAATAAATTGTTAAATCCAATGTATCTGGGATTTGATTCGATGAA
64 CAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAA
* * * * * * *
8383 TATAGATATTTCAAAGAGGCTTTTCGCCAAAAATCATGCAAAATTGAGT--TGGCCCCGAAAAAC
129 TATAGATATTTCAAGGAGTCTTTTCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAACAC
* * * * * *
8446 GTTTTTAAGCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAATTTTACAAAAATTGACCA
194 GTTTTT-AGCAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCC
* * * * *
8511 G-AAAGATTTTTGCTCAATTTCTAGCGAAAATACTCATAAAAAATATATAATTCAA
258 GAAAAG-TTTTTCCTCAATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAA
8566 TGTCAAAAAA
Statistics
Matches: 2571, Mismatches: 271, Indels: 189
0.85 0.09 0.06
Matches are distributed among these distances:
647 2 0.00
648 32 0.01
649 261 0.10
650 204 0.08
651 1 0.00
652 2 0.00
653 74 0.03
654 295 0.11
655 381 0.15
656 277 0.11
657 38 0.01
658 4 0.00
659 20 0.01
660 32 0.01
661 160 0.06
662 130 0.05
663 177 0.07
664 481 0.19
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (660 bp):
GTTTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATTTCTAATTAAATCGAAACA
AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATA
TAGATATTTCAAGGAGTCTTTTCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAACACGT
TTTTAGCAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAA
AAGTTTTTCCTCAATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACCCCAAAAAACTA
AAATGGGTTTTCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTTATGTTTAATTAAATCG
AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGAT
GAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCAAGCAAAATTGAGTCGGGGCTCTTGAA
CGCGTTTTTAGCTAAAAAACCGTGATGGTATACACGATTTCGGCTAAAATTTTGCAAAAACTTAC
CCGAAAATTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCCAAAA
AATTAAAAGG
Found at i:37898 original size:13 final size:12
Alignment explanation
Indices: 37865--37902 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
37855 AAAAGTCTTC
37865 TTTAATTTATGA
1 TTTAATTTATGA
37877 TTTAATTTAT-A
1 TTTAATTTATGA
37888 TTGTGAATTTATGA
1 TT-T-AATTTATGA
37902 T
1 T
37903 GTGTTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.13
12 11 0.48
13 7 0.30
14 2 0.09
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TTTAATTTATGA
Found at i:37934 original size:24 final size:24
Alignment explanation
Indices: 37907--37955 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
37897 TATGATGTGT
*
37907 TTATATCAAAAATAGGGTAGGAAA
1 TTATATCAAAAATAGGATAGGAAA
37931 TTATATCAAAAATAGGATAGGAAA
1 TTATATCAAAAATAGGATAGGAAA
37955 T
1 T
37956 GAAAATTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.27
Consensus pattern (24 bp):
TTATATCAAAAATAGGATAGGAAA
Found at i:41049 original size:104 final size:101
Alignment explanation
Indices: 40935--41204 Score: 317
Period size: 104 Copynumber: 2.7 Consensus size: 101
40925 AATTTTTCTA
* * *
40935 ACCCTTAAAATAAAATTTTAATTTTAATTTGGACTAAACTTAGTG-AATTAGTTATATAATTTAT
1 ACCCTTAAAATAAAATTTTAA-TTT-A-TTGG-CTAAACTTAGTGAAATTAATTTTATATTTTAT
40999 TTCTAAAACCCTATAACAAT-ATTATTAATTATGAAATTT
62 TTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
** *
41038 ACCCTT---A-AAAA-TTTAATTT-GGGGCTAAACTTAGTGAAATTAATTTTGTATTTTATTTCT
1 ACCCTTAAAATAAAATTTTAATTTATTGGCTAAACTTAGTGAAATTAATTTTATATTTTATTTCT
*
41097 AAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 AAAACCCTATAACAAT-AATTATTAATTATGAAATTT
*
41134 ACCCTTAGAAAAATAAAATTTTAA--TCTTGAGCTAAACTTAGTGAAATTAATTTTATATTTTAT
1 ACCCTT---AAAATAAAATTTTAATTTATTG-GCTAAACTTAGTGAAATTAATTTTATATTTTAT
41197 TTCTAAAA
62 TTCTAAAA
41205 TTCTACTATA
Statistics
Matches: 144, Mismatches: 10, Indels: 25
0.80 0.06 0.14
Matches are distributed among these distances:
93 12 0.08
94 37 0.26
96 24 0.17
97 3 0.02
98 5 0.03
99 4 0.03
100 1 0.01
102 2 0.01
103 11 0.08
104 45 0.31
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (101 bp):
ACCCTTAAAATAAAATTTTAATTTATTGGCTAAACTTAGTGAAATTAATTTTATATTTTATTTCT
AAAACCCTATAACAATAATTATTAATTATGAAATTT
Found at i:50315 original size:32 final size:33
Alignment explanation
Indices: 50269--50337 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
50259 CTAAAGTCCT
*
50269 CTGTTTAACTCTG-TTTCTATGCAAAAACTCCC
1 CTGTCTAACTCTGTTTTCTATGCAAAAACTCCC
*
50301 CTGTCTAACTCTGTTTTCTATGCAAAAACTCCT
1 CTGTCTAACTCTGTTTTCTATGCAAAAACTCCC
50334 CTGT
1 CTGT
50338 TTTTTACAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 12 0.35
33 22 0.65
ACGTcount: A:0.23, C:0.28, G:0.10, T:0.39
Consensus pattern (33 bp):
CTGTCTAACTCTGTTTTCTATGCAAAAACTCCC
Found at i:71942 original size:102 final size:103
Alignment explanation
Indices: 71766--71975 Score: 395
Period size: 102 Copynumber: 2.0 Consensus size: 103
71756 GTTTAGCTTA
71766 TGTAAATATACAAAAGAAGATACAGTGGCCTTCACGTTATAATTAAGAGTTTATAGACTAAAAAT
1 TGTAAATATACAAAAGAAGATACAGTGGCCTTCACGTTATAATTAAGAGTTTATAGACTAAAAAT
**
71831 TAAGCAAAGAGTTTAACAAAAGTTACTCAATTGCAA-T
66 TAAGCAAAGAGTTTAACAAAAAATACTCAATTGCAATT
71868 TGTAAATATACAAAAGAAGATACAGTGGCCTTCACGTTATAATTAAGAGTTTATAGACTAAAAAT
1 TGTAAATATACAAAAGAAGATACAGTGGCCTTCACGTTATAATTAAGAGTTTATAGACTAAAAAT
71933 TAAGCAAAGAGTTTAACAAAAAATACTCAATTGCAATT
66 TAAGCAAAGAGTTTAACAAAAAATACTCAATTGCAATT
71971 TGTAA
1 TGTAA
71976 CTGACCAAAG
Statistics
Matches: 105, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
102 99 0.94
103 6 0.06
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (103 bp):
TGTAAATATACAAAAGAAGATACAGTGGCCTTCACGTTATAATTAAGAGTTTATAGACTAAAAAT
TAAGCAAAGAGTTTAACAAAAAATACTCAATTGCAATT
Found at i:76462 original size:21 final size:21
Alignment explanation
Indices: 76438--76479 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
76428 CCTAAGTTTC
*
76438 CAAAAAGAAAATAAGAAAAAA
1 CAAAAAGAAAATAAAAAAAAA
* *
76459 CAAAAATAATATAAAAAAAAA
1 CAAAAAGAAAATAAAAAAAAA
76480 TGAAGTACAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.81, C:0.05, G:0.05, T:0.10
Consensus pattern (21 bp):
CAAAAAGAAAATAAAAAAAAA
Found at i:76659 original size:2 final size:2
Alignment explanation
Indices: 76652--76685 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
76642 AAAATAAAGG
*
76652 GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
76686 ATTTTGATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:77769 original size:54 final size:56
Alignment explanation
Indices: 77703--77828 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 56
77693 TATACAAAAT
* * *
77703 GACTAATTTGTCTCT-TTTTACAAG-GTGTGTAATTGCCAATTTCGGAAGTTAAAG
1 GACTAATTTGTCTATCTTTTACAAGTGTGTGTAATTGACAATTTCAGAAGTTAAAG
* * *
77757 GGCTAATTTGTCTATCTTTTACAAGTTCATGTGTGTAATTGACAATTTTAGAAGTTAAAT
1 GACTAATTTGTCTATCTTTTACAAG----TGTGTGTAATTGACAATTTCAGAAGTTAAAG
77817 GACTAATTTGTC
1 GACTAATTTGTC
77829 CATTTCTTAC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
54 13 0.22
55 9 0.15
60 37 0.63
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (56 bp):
GACTAATTTGTCTATCTTTTACAAGTGTGTGTAATTGACAATTTCAGAAGTTAAAG
Found at i:77795 original size:60 final size:60
Alignment explanation
Indices: 77727--77845 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
77717 TTTTTACAAG
* * * * *
77727 GTGTGTAATTGCCAATTTCGGAAGTTAAAGGGCTAATTTGTCTATCTT-TTACAAGTTCAT
1 GTGTGTAATTGACAATTTCAGAAGTTAAAGGACTAATTTGTCCAT-TTCTTACAAATTCAT
* *
77787 GTGTGTAATTGACAATTTTAGAAGTTAAATGACTAATTTGTCCATTTCTTACAAATTCA
1 GTGTGTAATTGACAATTTCAGAAGTTAAAGGACTAATTTGTCCATTTCTTACAAATTCA
77846 ATAGACAAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 2 0.04
60 49 0.96
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (60 bp):
GTGTGTAATTGACAATTTCAGAAGTTAAAGGACTAATTTGTCCATTTCTTACAAATTCAT
Found at i:104840 original size:14 final size:16
Alignment explanation
Indices: 104811--104842 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
104801 AGACAAGCTA
104811 CTTTGTTTCGTTTTCC
1 CTTTGTTTCGTTTTCC
104827 CTTT-TTTC-TTTTCC
1 CTTTGTTTCGTTTTCC
104841 CT
1 CT
104843 ATGGTAAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.00, C:0.28, G:0.06, T:0.66
Consensus pattern (16 bp):
CTTTGTTTCGTTTTCC
Found at i:111756 original size:29 final size:29
Alignment explanation
Indices: 111687--111757 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
111677 CCTGAGGGGG
*
111687 CAAAACGTCCCAAAATTGAAATTCAAGGGA
1 CAAAACGT-CCAAAATTGAAATTCAAGCGA
* *
111717 CAAAATGTCCAAAATTGAAGTTC-AGACGA
1 CAAAACGTCCAAAATTGAAATTCAAG-CGA
*
111746 CAAAACATCCAA
1 CAAAACGTCCAA
111758 CCACTACAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.06
29 26 0.74
30 7 0.20
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (29 bp):
CAAAACGTCCAAAATTGAAATTCAAGCGA
Found at i:128923 original size:65 final size:65
Alignment explanation
Indices: 128815--128948 Score: 234
Period size: 65 Copynumber: 2.1 Consensus size: 65
128805 TTTCCAAACC
* *
128815 TGGA-CTCGAACTCTAGTTTTTGAAGATAAAATGTAAGCATCCAACCATTAAAACAAGACGAGAA
1 TGGATCTCGAACTCTAGTTTTTGAAGATAAAATGCAAGCATCCAACCATTAAAAAAAGACGAGAA
*
128879 TGGATCTCGAACTCTAGTTTTTGAAGATAAAATGCAAGCATCCAATCATTAAAAAAAGACGAGAA
1 TGGATCTCGAACTCTAGTTTTTGAAGATAAAATGCAAGCATCCAACCATTAAAAAAAGACGAGAA
128944 TGGAT
1 TGGAT
128949 GCAAATACTG
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
64 4 0.06
65 62 0.94
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.25
Consensus pattern (65 bp):
TGGATCTCGAACTCTAGTTTTTGAAGATAAAATGCAAGCATCCAACCATTAAAAAAAGACGAGAA
Found at i:131971 original size:25 final size:26
Alignment explanation
Indices: 131926--131976 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
131916 GCTAAAATGG
*
131926 AGAGAAGAAAATGAAATGAAGCAGAA
1 AGAGAAGAAAATGAAATGAAGAAGAA
131952 AGAGAA-AAAATGAAGA-GAAGAAGAA
1 AGAGAAGAAAATGAA-ATGAAGAAGAA
131977 GAAGAGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.65, C:0.02, G:0.27, T:0.06
Consensus pattern (26 bp):
AGAGAAGAAAATGAAATGAAGAAGAA
Found at i:131976 original size:19 final size:20
Alignment explanation
Indices: 131918--131976 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
131908 AAAGAAGAGC
*
131918 TAAAATGGAGAGAAGAA-AA
1 TAAAATGAAGAGAAGAAGAA
*
131937 TGAAATGAAGCAGAA-AGAGAA
1 TAAAATGAAG-AGAAGA-AGAA
131958 -AAAATGAAGAGAAGAAGAA
1 TAAAATGAAGAGAAGAAGAA
131977 GAAGAGGAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
19 17 0.52
20 14 0.42
21 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.27, T:0.08
Consensus pattern (20 bp):
TAAAATGAAGAGAAGAAGAA
Done.