Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014612.1 Corchorus olitorius cultivar O-4 contig14645, 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: 6787
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:2601 original size:665 final size:658
Alignment explanation
Indices: 33--5317 Score: 5047
Period size: 665 Copynumber: 8.0 Consensus size: 658
23 TCCGAGGCCT
* * * * * *
33 GGCTCAGTTTTACATGATTTTTGCCACCAAGACTCATTGAGATATCTATATTCATCTAACCAAAT
1 GGCTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
* * * ** * * *
98 CTCAACCATATTGGATATAAACATTTGTTTTTACAAGCATCTGAAT-TATGTTTCGATTTAATTT
66 CTCAGCCAGATTGGATTTAAGTATTTGTTTTTACGAGCATCTGAATCT-TGTTTCAATTTAATTA
* * *
162 GAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAGCAA-CGTTAAAAGCCCTTCAATCTTGT
130 GAAATAAATTC-GAAAAAAAT-GGAAAAACGATATTAG-AAGCGTGAAAAACCCTTCAAT-TT-T
* * * ** * * **
226 TGGTG-GTT-AATTATATA-CTTTTTCTGACTATTGTTACCAAAAATTGGGGGAAAAAC-TTTCA
190 T-TTGCGTTGAATTATATATATTTTTCTGAGTATTGTGGCAAAAAATT--GAGAAAAACTTTTTG
* * * *
287 GTTCAATTTTTGCAAAATTTAAGCAGAAATC--GT--T---CATCACAATTTATTAGCTAAAAAC
252 GTTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTT-TTGGCTAAAAAC
* * * * *
345 ACGCTCCGGGGCCCCGGCTCAGTTTTGCATTATTTTTGGCGCCAAGACTCCTTGTAATATGTATA
316 GCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCG-CAAGACTCCTTGTAATATCTATA
* ** * **
410 TTCATCTAACCAAATCTCAGGCATGTCAGATTTAAGGATTTGTTTCTACGAGCATCATAAA-CCG
380 TTCATCTAACCAAATCTCAGCCAT-TTGGATTTAAGGATTTGTTTTTACGAGCATC-TAAATCTT
* * * *
474 GTTTCAATTTAATTAGAAATTAATTCGGAAAAAAACAGGAAAAATGATATTAGAAGCGTGAAAAG
443 GTTTCAATTTAATTAGAAATAAATTCGGAAAAAAA-TGGAAAAACGATATTAGAAGCGTGAAAAA
* * ** * * * * * *
539 CCCTTCAATCTTCTTCGGCGATGAATTATATACTTTTTATGAGTATTGTGACCAAAAATTGAGGG
507 TCCTTCAAT-TTTTTTTGCGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTGA-GA
* * * **
604 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTAC---GCATCACAATTTTT
570 AAAAACTTTCGGTTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGTTTTTT
* * * *
666 AGC-AAAAACGCGCTACGGGGCCCT
635 GGCAAAAAACGCG-TTCGGGACCCC
* ** * * ** *
690 GTCTCAGTAGTGCATTATTTTTGGCGCCAAGACTCCTTCTAATATCTATATCCATCTAACCAAAT
1 GGCTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
* ** * * * **
755 CTCAGGCATG-TCAGATTTAAGGATTTGTTTTTACGAGCATCAGAAACCAGTTTCAATTTAATTA
66 CTCAGCCA-GATTGGATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTA
* * * * *
819 GAAATTAATTCGGAAAAAAACAGGAAAAATGAAATTAGAAGCGTGAAAAGCCCTTCAATCTTCTT
130 GAAATAAATTC-GAAAAAAA-TGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAT-TT-TT
* * * * * * *
884 TCGCGATGAATTATATACA-TTTTATGAGTATTGTGACCAAAAATTGAGGGAAAAAC-TTTCGGT
191 TTGCGTTGAATTATATATATTTTTCTGAGTATTGTGGCAAAAAATTGA--GAAAAACTTTTTGGT
* *
947 TCAATTTTTGGAAAATTTAAGCCGAAATCGTGTA-T---CA-CA--ATTTTTTAGG--ACAAAAC
254 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGA-TTTTT-GGCTA-AAAAC
* * *
1003 GCGCTCCGGAGCCTCGGCTCAGTTTTGCATTATTTTTGGCGCCAAGACTCCTTGTAATATCTATA
316 GCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCG-CAAGACTCCTTGTAATATCTATA
* * * **
1068 TTCATCTAACCAAATCTCAGGCATGTTAGATTTAAGGATTTGTTTTTACGAGCATC-AGAAACCG
380 TTCATCTAACCAAATCTCAGCCAT-TTGGATTTAAGGATTTGTTTTTACGAGCATCTA-AATCTT
* * * ** ** * *
1132 GTTTGAATTTAATTATAAATTAATTATGAAAAAAACAAGAAAAACGATATTAGAAGCCTGAAAAG
443 GTTTCAATTTAATTAGAAATAAATTCGGAAAAAAA-TGGAAAAACGATATTAGAAGCGTGAAAAA
* * * ** * * * * *
1197 CCCTTCAATCTTCTTTGGCAATGAATTATATACTTTTTATGAGTATTGTGACCAAAAATTGAGGG
507 TCCTTCAAT-TTTTTTTGCGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTGA-GA
* * * *
1262 AAAAACTTTCGGTTCAATTTCTGGAAAATTTAAGCCGAAATCGTGTACTAACCATCATAGTTTTT
570 AAAAACTTTCGGTTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA-CGTTTTT
*
1327 TAGCAAAAAACGCGCTTCGGGACCCC
634 TGGCAAAAAACGCG-TTCGGGACCCC
* * *
1353 GGCTCAGTTTTGCATTATTTTTGGCGCCAAGACTCCTTGTAATATCTATATTCATCTAACCAAAT
1 GGCTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
* ** * * * ** *
1418 CTCAGGCATG-TCAGATTTAAGGATTTGTTTTTACGAGCATCAGAAACCGGTTTCAATTTAACTA
66 CTCAGCCA-GATTGGATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTA
* ** *
1482 GAAA-ATAATTATGAAAAAAACAAGAAAAACGATATTAGAAGTC-TGAAAAGCCCTTCAATCTTC
130 GAAATA-AATT-CGAAAAAAA-TGGAAAAACGATATTAGAAG-CGTGAAAAACCCTTCAAT-TT-
* ** * * * * * *
1545 TTTGGCAAT-AATTATATACA-TTTTATGATTATTGTGACCAAAAATTGAGGGAAAAAC-TTTCG
189 TTTTGCGTTGAATTATATATATTTTTCTGAGTATTGTGGCAAAAAATTGA--GAAAAACTTTTTG
* * * * * *
1607 GTTCAATTTTTGGAAAATTTAAGCCGAAATCGTATACTAACCATCACAGTTTTTTAGCAAAAAAC
252 GTTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-GATTTTTGGCTAAAAAC
* * * *
1672 GCGCTT-C-GAGGCCCCGACTCAGTTTTGCATTATTTTTGGCGCCAACACTCCTTGTAATATATA
316 GCG-TTCCGGA-GCCCCGGCTCAGTTTTGCATGATTTTTGGCG-CAAGACTCCTTGTAATATCTA
* ** * *
1735 TATTCATCTAACCAAATCTCAGGCATGTCAGATTTAAGAATTTGTTTTTACGAGCATC-AGAAAC
378 TATTCATCTAACCAAATCTCAGCCAT-TTGGATTTAAGGATTTGTTTTTACGAGCATCTA-AATC
** *
1799 AGGTTTCAATTTAATTAGAAATTAATTCGG-AAAAAATAGGAAAAACGATATTAGAAGCGTGAAA
441 TTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAAT-GGAAAAACGATATTAGAAGCGTGAAA
** * * * * * * *
1863 AGCCCTTCAATCTTCTTTGGCGATGAATTATTTACA-TTTTATGAGTATTGTGACCAAAAATTGA
505 AATCCTTCAAT-TTTTTTTGCGTTGAATTATATA-ATTTTTCTGAGTATTGTGGCAAAAAATTGA
* *
1927 GGGAAAAACTTTCGGTTCAATTTTTGGAAAA-TTTATGCCGAAATCGTGTACTAACCATCACAGT
568 -GAAAAAACTTTCGGTTCAATTTTTGCAAAATTTTA-GCCGAAATCGTGTACTAACCATCAC-G-
*
1991 TTTTTTTAGCAAAAAAACGCGCTTCGGGACCCC
629 -TTTTTTGGC-AAAAAACGCG-TTCGGGACCCC
* * *
2024 GGCTTAGTTTTGCATTATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCCTCTAACCAAA
1 GGCTCAGTTTTGCATGATTTTTGGC-GCAAAGACTCCTTGAAATATCTATATTCATCTAACCAAA
** *
2088 TCTCAGCCAGATTGGATTTAAGTATTTGTTTTTAAAAGCATCTCAATCTTGTTTCAATTTAATTA
65 TCTCAGCCAGATTGGATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTA
*
2153 GAAATAAATTCGAAAAAAATGG-AAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGC
130 GAAATAAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGC
* * * *
2217 GTTGAAGTATATATATTTCTTCTGAGTATTATGGCAAAAAATTCAGAAAAACTTTTTGAG-CCAA
195 GTTGAATTATATATATTT-TTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTTG-GTTCAA
* * * *
2281 TTTCTACAAAATTTTAGCCGAAATCGTGTA-T-CCCATCACGGTTTTTGGCTAAAAACGCGTTCC
258 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTCC
* * * * *
2344 AGAGCCCCGGCTTAATTTTGCATGAATTTTGGCGCAATGACTCCATGTAATATCTATATTCATCT
323 GGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCAA-GACTCCTTGTAATATCTATATTCATCT
* *
2409 AACCAAATCTCAGCCACTTTGGATTT-AGGTATTTGTTTTTAGGAGCATCTAAATCTTGTTTCGA
387 AACCAAATCTCAGCCA-TTTGGATTTAAGG-ATTTGTTTTTACGAGCATCTAAATCTTGTTTCAA
2473 TTTAATTAGAAATAAATTCGGAAAAGAAATGG-AAAACGATATTAGAAGCGTGAAAAATCCTTCA
450 TTTAATTAGAAATAAATTCGGAAAA-AAATGGAAAAACGATATTAGAAGCGTGAAAAATCCTTCA
* *
2537 ATTTTTTTTGCGTTGAATTATATATATTTCTTCTGAGTATTGTGTCAAAAAATTCAGAAAAAACT
514 ATTTTTTTTGCGTTGAATTATATA-ATTT-TTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAC-
* * * * * * *
2602 TTTTGGGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTA-TAACCATCACGGTTTTTGGCTAG
576 TTTCGGTTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGTTTTTTGGCAAA
*
2666 AAACGCGTTCCGGAGCCCC
641 AAACGCGTTCGGGA-CCCC
* * * * *
2685 GGCTTAATTTTGCATGAATTTTGGCGCAATGACTCCTTGTAATATCTATATTCATCTAACCAAAT
1 GGCTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
** * * * *
2750 CTCAGCCACTTTGGATTTAGGTATTTGTTTTTAGGAGCATCTAAATCTTGTTTCGATTTAATTAG
66 CTCAGCCAGATTGGATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAG
* * *
2815 AAATAAATTCGAAAAAGAAATGG-AAAACGATATTTGAAGCGTGAAATATCCTTCAA-TTTTTTG
131 AAATAAATTCG-AAAA-AAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTG
* *
2878 CGTTGAATTATATATATTTCTTCTGAGTATTGTAGCAAAAAAATTGAGAAAAAACTTTTTGGATC
194 CGTTGAATTATATATATTT-TTCTGAGTATTGTGGC-AAAAAATTGAG-AAAAACTTTTTGGTTC
* * * *
2943 AGTTTTTGCAGAATTTTAGCCGAAATTGTGTACTAACCATCACAATTTTGTGGCTAAAAACGCGT
256 AATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTT-TGGCTAAAAACGCGT
* * * * * *
3008 TTCGG-GCCCCGACTCAGTTTTGCAGGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCC
320 TCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGC-GCAAGACTCCTTGTAATATCTATATTCA
* * ** *
3072 TCTAACCAAATCTCAGCCAGATTGGATTTAAGTATTTGTTTTTAAAAGCATCTCAATCTTGTTTC
384 TCTAACCAAATCTCAGCCA-TTTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTC
* *
3137 AATTTAATTAGAAATAAATTC-GAAAAATATGGAAAAACGATGTTAGAAGCGTGAAAAATCCTTC
448 AATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAATCCTTC
* *
3201 AA-TTTTTTTGCGTTGAAGTATATATATTTTTTCTGAGTATTGTGGCAAAAACTTGAGAAAAAAC
513 AATTTTTTTTGCGTTGAA-T-TATATAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAC
* * * * *
3265 ATTT-GGTGCCAATTTCTGCAAAATTTTAGCAGAAATCGTGTA-T-CCCATCACGGTTTTTGGCA
576 -TTTCGGT-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGTTTTTTGGCA
* **
3327 AAAAACACGTTCCAGAGCCCC
639 AAAAACGCGTTCGGGA-CCCC
* * * *
3348 GGCTTAATTTTGCATGAATTTTGGCGCAATGACTCCTT-ATAATATCTATATTCATCTAACCAAA
1 GGCTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGA-AATATCTATATTCATCTAACCAAA
** * * * *
3412 TCTCAGCCACTTTGGATTTAGGTATTTGTTTTTAGGAGCATCTAAATCTTGTTTCGATTTAATTA
65 TCTCAGCCAGATTGGATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTA
* * *
3477 GAAATAAATTCGAAAAAGAAATGG-AAAACGATATTAGAAGCATAAAAAATCCTTCAATTTTTTT
130 GAAATAAATTCG-AAAA-AAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAA-TTTTTT
*
3541 TGCGTTGAATTATATATATTTCTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTTGGGT
192 TGCGTTGAATTATATATATTT-TTCTGAGTATTGTGGCAAAAAATTGAG-AAAAACTTTTTGGTT
* * ** *
3606 CAGTTTTTGCAGAATTTTAGCCGAAATAATGTACTAACCATCACGATTTTTGGCAAAAAAACGCG
255 CAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGC-TAAAAACGCG
** * * * * *
3671 TTCCGTTGCCCCGGCTTAATTTTGAATGAATTTTGGCGCAATGAATCCTTGTAATATCTATATTC
319 TTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCAA-GACTCCTTGTAATATCTATATTC
* * * * * *
3736 AAT-GAACCAAATATCAGCCACCTTGGATTTAAGGATTTATCTTTACGAGCATCTGAATCTTGTT
383 -ATCTAACCAAATCTCAGCCA-TTTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTT
* ** * * * * * *
3800 TCGATAAAAATAGAAATGATTTCGGAAAAAAAATTGTAAAAACGATATTAGAAACTTG--AAATC
446 TCAATTTAATTAGAAATAAATTCGG-AAAAAAA-TGGAAAAACGATATTAGAAGCGTGAAAAATC
* * *
3863 CTTCAA-TTTTTTTGCGTTGAATCATATACTTTTTCTGAGTATTGTGGCAACAAATTGAGTAAAA
509 CTTCAATTTTTTTTGCGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTGAG-AAAA
* * * * *
3927 AATTTTCGGTT-AAGTTTTTGCAAAATTTTAACCGAAATCGTATACTAACTATCACGATTTTGTG
573 AACTTTCGGTTCAA-TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACG-TTTTTTG
* * *
3991 GCTAAAAACGTGTTTCGGGGCCCC
636 GCAAAAAACGCG-TTCGGGACCCC
* *
4015 GGCTCAGTTTTGCACGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCCTCTAACCAAA
1 GGCTCAGTTTTGCATGATTTTTGGC-GCAAAGACTCCTTGAAATATCTATATTCATCTAACCAAA
** *
4079 TCTCAGCCAGATTGGATTTAAGTATTTGTTTTTAATAGCATCTCAATCTTGTTTCAATTTAATTA
65 TCTCAGCCAGATTGGATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTA
* *
4144 GAAATAAATTCGAAAAAAATGGAAAAACGATGTTAGAAGCGTGAAAAATCCTTCAATTTTTTTGC
130 GAAATAAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGC
* * **
4209 GTTGAAGTATATATACTTTTTTCTGAGTATTGTGGCAAAAACTTGAGAAATAACTTTTTGGGCCA
195 GTTGAATTATATATA--TTTTTCTGAGTATTGTGGCAAAAAATTGAGAAA-AACTTTTTGGTTCA
* * * * *
4274 ATTTCTGCAAAATTTTTGCAGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACGCGTTC
257 ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTC
* * * *
4339 CGGAGCCCCGACTTAATTTTGCATGAATTTTGGCGCAATGACTCCTTGTAATATCTATATTCAT-
322 CGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCAA-GACTCCTTGTAATATCTATATTCATC
* * * * * * *
4403 TGAACCAAATATCAGCCACCTTGGATTTAAGGATTTATCTTTACGAGCATCTGAATCTTATTTCG
386 T-AACCAAATCTCAGCCA-TTTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCA
** * * * * *
4468 ATAAAAATAGAAATAATTTCGGAAAAAAAAATTGTAAAAACGATATTAGAAACTTG--AAATCCT
449 ATTTAATTAGAAATAAATTCGG--AAAAAAA-TGGAAAAACGATATTAGAAGCGTGAAAAATCCT
* * *
4531 TCAATTTTTTTTGCGTTGAATCATATACTTTTTCTGAGTATTGTGGCAACAAATTGAGTAAAAAA
511 TCAATTTTTTTTGCGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTGAG-AAAAAA
* * * * * *
4596 TTTTCTG-TAAAGTTTTTGCAAAATTTTAGCCGAAATCGTATACTAACCATCACGGTTTTTGGCT
575 CTTTCGGTTCAA-TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGTTTTTTGGCA
* * * * *
4660 AAAAACACGTTCCGAAGGCTC
639 AAAAACGCGTTCGGGA-CCCC
* * * * * * * *
4681 GGCTCAATTTTACATGATTTTTGGCGTAAATAGTCATTGAAATATCTATATTCATCAAACCAAGT
1 GGCTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
* * * * * * ** ** *
4746 CTCAGCCACATTGTATATAAGGATTTGCTTTTATGAGCATCTGAAAGTTGTTTTGATTTAATTAA
66 CTCAGCCAGATTGGATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAG
* * * * * * *
4811 AAATAAACTCGGAAAAGAA-GGAAAAACGATATAATAAGTGTGAAAAGCCCGTT-AATCTTTTTG
131 AAATAAATTC-GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCC-TTCAATTTTTTTG
* * * * *
4874 TCGTTGAAATATATATATATATATAT-TGAGTATTTTGGTAAAAAATTTAAGAAAAAAATTTTTG
194 -CGTTG-AAT-TATATATAT-T-TTTCTGAGTATTGTGGCAAAAAA-TTGAG-AAAAACTTTTT-
* * *
4938 GGTT-AGTTTTT----AA--TT----GAATTTGTGTACTAACCATCACGATTTTGTGGCTAAAAA
251 GGTTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTT-TGGCTAAAAA
* * * * * *
4992 CGCGTTTCGGGGCCCCGGCTCAGTTTTGTATGATTTTTGGCAGAAAGACTCCTGGAAATATCTAT
315 CGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGC-GCAAGACTCCTTGTAATATCTAT
* * * * ** * *
5057 ATTCCTCAAACCAAATCTCAGCCAGATTGGATTTAAGTATTTGTTTTTAATAGAATCTCAATCTT
379 ATTCATCTAACCAAATCTCAGCCA-TTTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTT
*
5122 GTTTCAATTTAATTAGAAATAAATTC-GAAAAAAATGGAAAAACGATGTTAGAAGCGTGAAAAAT
443 GTTTCAATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAAT
* * *
5186 CCTTCAA-TTTCTTTGCGTTGAAGTATATATACTTTTTCTGAGTATTGTGGCAAAAACTTGAGAA
508 CCTTCAATTTTTTTTGCGTTGAA-T-TATATAATTTTTCTGAGTATTGTGGCAAAAAATTGAG-A
* * * * * * *
5250 AAAAACTTTTTGGGTCAGTTTTTGCAAAATTTTAGCAGAGATTGTGTACTAACAATCACGGTTTT
570 AAAAAC-TTTCGGTTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-GTTTT
5315 TTG
633 TTG
5318 CGTTGAATTC
Statistics
Matches: 4038, Mismatches: 460, Indels: 256
0.85 0.10 0.05
Matches are distributed among these distances:
656 25 0.01
657 182 0.05
658 378 0.09
659 69 0.02
660 184 0.05
661 158 0.04
662 146 0.04
663 475 0.12
664 305 0.08
665 586 0.15
666 578 0.14
667 331 0.08
668 257 0.06
669 198 0.05
670 25 0.01
671 139 0.03
672 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (658 bp):
GGCTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
CTCAGCCAGATTGGATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAG
AAATAAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGCG
TTGAATTATATATATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTTGGTTCAATTT
TTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTCCGGA
GCCCCGGCTCAGTTTTGCATGATTTTTGGCGCAAGACTCCTTGTAATATCTATATTCATCTAACC
AAATCTCAGCCATTTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAAT
TAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTT
TTGCGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTCGGTTCA
ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGTTTTTTGGCAAAAAACGCGTTC
GGGACCCC
Found at i:2732 original size:333 final size:331
Alignment explanation
Indices: 4--5315 Score: 4885
Period size: 333 Copynumber: 16.0 Consensus size: 331
1 TAG
* ** * * * * *
4 TTTTTGGCTAAAAATGAATTCC-GAGGCCTGGCTCAGTTTTACATGATTTTTGCCACCAA-GACT
1 TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGC-GCAATGACT
* * * **
67 CATTG-AGATATCTATATTCATCTAACCAAATCTCAACCATATTGGATATAAACATTTGTTTTTA
65 CCTTGTA-ATATCTATATTCATCTAACCAAATCTCAGCCAT-TTGGAT-TTAGGATTTGTTTTTA
* * * * *
131 CAAGCATCTGAAT-TATGTTTCGATTTAATTTGAAATTAATTCGGAAAAAAATAGGAAAAACGAT
127 CGAGCATCTAAATCT-TGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAAT-GGAAAAACGAT
* ** ** * *
195 ATTAGCAA-CGTTAAAAGCCCTTCAATCTTGTTGGTG-GTT-AATTATATA-CTTTTTCTGACTA
190 ATTAG-AAGCGTGAAAAATCCTTCAAT-TT-TTTTTGCGTTGAATTATATATATTTTTCTGAGTA
** * * * ** * * *
256 TTGTTACCAAAAATTGGGGGAAAAAC-TTTCAGTTCAATTTTTGCAAAATTTAAGCAGAAATC--
252 TTGTGGCAAAAAATT-GAGAAAAAACTTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGT
*
318 GT--T---CATCACAA
316 GTACTAACCATCACGA
* * * * *
329 TTTATTAGCTAAAAACACGCTCCGGGGCCCCGGCTCAGTTTTGCATTATTTTTGGCGCCAA-GAC
1 TTT-TTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCG-CAATGAC
* * ** *
393 TCCTTGTAATATGTATATTCATCTAACCAAATCTCAGGCATGTCAGATTTAAGGATTTGTTTCTA
64 TCCTTGTAATATCTATATTCATCTAACCAAATCTCAGCCAT-TTGGATTT-AGGATTTGTTTTTA
** * * *
458 CGAGCATCATAAA-CCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAACAGGAAAAATGAT
127 CGAGCATC-TAAATCTTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAA-TGGAAAAACGAT
** * ** * * *
522 ATTAGAAGCGTGAAAAGCCCTTCAATCTTCTTCGGCGATGAATTATATA-CTTTTTATGAGTATT
190 ATTAGAAGCGTGAAAAATCCTTCAAT-TTTTTTTGCGTTGAATTATATATATTTTTCTGAGTATT
* * * * * * *
586 GTGACCAAAAATTGAGGGAAAAAC-TTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGT
254 GTGGCAAAAAATTGA-GAAAAAACTTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
* *
650 AC---GCATCACAA
318 ACTAACCATCACGA
* * * * * * ** *
661 TTTTTAGC-AAAAACGCGCTACGGGGCCCTGTCTCAGTAGTGCATTATTTTTGGCGCCAA-GACT
1 TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCG-CAATGACT
* * * **
724 CCTTCTAATATCTATATCCATCTAACCAAATCTCAGGCATGTCAGATTTAAGGATTTGTTTTTAC
65 CCTTGTAATATCTATATTCATCTAACCAAATCTCAGCCAT-TTGGATTT-AGGATTTGTTTTTAC
* ** * * * *
789 GAGCATC-AGAAACCAGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAACAGGAAAAATGAAA
128 GAGCATCTA-AATCTTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAA-TGGAAAAACGATA
** * * * * *
853 TTAGAAGCGTGAAAAGCCCTTCAATCTTCTTTCGCGATGAATTATATACA-TTTTATGAGTATTG
191 TTAGAAGCGTGAAAAATCCTTCAAT-TTTTTTTGCGTTGAATTATATATATTTTTCTGAGTATTG
* * * * * * *
917 TGACCAAAAATTGAGGGAAAAAC-TTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTA
255 TGGCAAAAAATTGA-GAAAAAACTTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA
981 -T---CA-CA--A
319 CTAACCATCACGA
* * *
987 TTTTTTAGG--ACAAAACGCGCTCCGGAGCCTCGGCTCAGTTTTGCATTATTTTTGGCGCCAA-G
1 -TTTTT-GGCTA-AAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCG-CAATG
* *
1049 ACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGGCATGTTAGATTTAAGGATTTGTTTT
62 ACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGCCAT-TTGGATTT-AGGATTTGTTTT
* ** * * * ** **
1114 TACGAGCATC-AGAAACCGGTTTGAATTTAATTATAAATTAATTATGAAAAAAACAAGAAAAACG
125 TACGAGCATCTA-AATCTTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAA-TGGAAAAACG
* ** * * ** * *
1178 ATATTAGAAGCCTGAAAAGCCCTTCAATCTTCTTTGGCAATGAATTATATA-CTTTTTATGAGTA
188 ATATTAGAAGCGTGAAAAATCCTTCAAT-TTTTTTTGCGTTGAATTATATATATTTTTCTGAGTA
* * * * * * * *
1242 TTGTGACCAAAAATTGAGGGAAAAAC-TTTCGGTTCAATTTCTGGAAAATTTAAGCCGAAATCGT
252 TTGTGGCAAAAAATTGA-GAAAAAACTTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGT
* *
1306 GTACTAACCATCATAGT
316 GTACTAACCATCA-CGA
* * * *
1323 TTTTTAGCAAAAAACGCGCTTCGGGA-CCCCGGCTCAGTTTTGCATTATTTTTGGCGCCAA-GAC
1 TTTTTGGCTAAAAACGCG-TTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCG-CAATGAC
* **
1386 TCCTTGTAATATCTATATTCATCTAACCAAATCTCAGGCATGTCAGATTTAAGGATTTGTTTTTA
64 TCCTTGTAATATCTATATTCATCTAACCAAATCTCAGCCAT-TTGGATTT-AGGATTTGTTTTTA
* ** * ** **
1451 CGAGCATC-AGAAACCGGTTTCAATTTAACTAGAAA-ATAATTATGAAAAAAACAAGAAAAACGA
127 CGAGCATCTA-AATCTTGTTTCAATTTAATTAGAAATA-AATTCGGAAAAAAA-TGGAAAAACGA
** * * ** * * *
1514 TATTAGAAGTC-TGAAAAGCCCTTCAATCTTCTTTGGCAAT-AATTATATACA-TTTTATGATTA
189 TATTAGAAG-CGTGAAAAATCCTTCAAT-TTTTTTTGCGTTGAATTATATATATTTTTCTGAGTA
* * * * * * *
1576 TTGTGACCAAAAATTGAGGGAAAAAC-TTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGT
252 TTGTGGCAAAAAATTGA-GAAAAAACTTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGT
* *
1640 ATACTAACCATCACAGT
316 GTACTAACCATCAC-GA
* * * * *
1657 TTTTTAGCAAAAAACGCGCTT-C-GAGGCCCCGACTCAGTTTTGCATTATTTTTGGCGCCAA-CA
1 TTTTTGGCTAAAAACGCG-TTCCGGA-GCCCCGGCTCAGTTTTGCATGATTTTTGGCG-CAATGA
* * ** *
1719 CTCCTTGTAATATATATATTCATCTAACCAAATCTCAGGCATGTCAGATTTAAGAATTTGTTTTT
63 CTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGCCAT-TTGGATTT-AGGATTTGTTTTT
* ** *
1784 ACGAGCATC-AGAAACAGGTTTCAATTTAATTAGAAATTAATTCGG-AAAAAATAGGAAAAACGA
126 ACGAGCATCTA-AATCTTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAAT-GGAAAAACGA
** * * * * * *
1847 TATTAGAAGCGTGAAAAGCCCTTCAATCTTCTTTGGCGATGAATTATTTACA-TTTTATGAGTAT
189 TATTAGAAGCGTGAAAAATCCTTCAAT-TTTTTTTGCGTTGAATTATATATATTTTTCTGAGTAT
* * * * * *
1911 TGTGACCAAAAATTGAGGGAAAAAC-TTTCGGTTCAATTTTTGGAAAA-TTTATGCCGAAATCGT
253 TGTGGCAAAAAATTGA-GAAAAAACTTTTTGGGTCAATTTTTGCAAAATTTTA-GCCGAAATCGT
*
1974 GTACTAACCATCACAGTTT
316 GTACTAACCATCAC-G--A
* * * * * *
1993 TTTTTAGCAAAAAAACGCGCTTCGGGA-CCCCGGCTTAGTTTTGCATTATTTTTGGCAG-AAAGA
1 TTTTTGGC-TAAAAACGCG-TTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGC-GCAATGA
* * * *
2056 CTCCTTGAAATATCTATATTCCTCTAACCAAATCTCAGCCAGATTGGATTTAAGTATTTGTTTTT
63 CTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGCCA-TTTGGATTT-AGGATTTGTTTTT
** *
2121 AAAAGCATCTCAATCTTGTTTCAATTTAATTAGAAATAAATTC-GAAAAAAATGG-AAAACGATA
126 ACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATA
* *
2184 TTAGAAGCGTGAAAAATCCTTCAA-TTTTTTTGCGTTGAAGTATATATATTTCTTCTGAGTATTA
191 TTAGAAGCGTGAAAAATCCTTCAATTTTTTTTGCGTTGAATTATATATATTT-TTCTGAGTATTG
* * * * *
2248 TGGCAAAAAATTCAG-AAAAACTTTTTGAGCCAATTTCTACAAAATTTTAGCCGAAATCGTGTA-
255 TGGCAAAAAATTGAGAAAAAACTTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC
* *
2311 T-CCCATCACGG
320 TAACCATCACGA
* * * *
2322 TTTTTGGCTAAAAACGCGTTCCAGAGCCCCGGCTTAATTTTGCATGAATTTTGGCGCAATGACTC
1 TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCAATGACTC
* *
2387 CATGTAATATCTATATTCATCTAACCAAATCTCAGCCACTTTGGATTTAGGTATTTGTTTTTAGG
66 CTTGTAATATCTATATTCATCTAACCAAATCTCAGCCA-TTTGGATTTAGG-ATTTGTTTTTACG
*
2452 AGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAGAAATGG-AAAACGATATT
129 AGCATCTAAATCTTGTTTCAATTTAATTAGAAATAAATTCGGAAAA-AAATGGAAAAACGATATT
2516 AGAAGCGTGAAAAATCCTTCAATTTTTTTTGCGTTGAATTATATATATTTCTTCTGAGTATTGTG
193 AGAAGCGTGAAAAATCCTTCAATTTTTTTTGCGTTGAATTATATATATTT-TTCTGAGTATTGTG
* * * *
2581 TCAAAAAATTCAGAAAAAACTTTTTGGGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTA-TA
257 GCAAAAAATTGAGAAAAAACTTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTA
*
2645 ACCATCACGG
322 ACCATCACGA
* * * *
2655 TTTTTGGCTAGAAACGCGTTCCGGAGCCCCGGCTTAATTTTGCATGAATTTTGGCGCAATGACTC
1 TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCAATGACTC
*
2720 CTTGTAATATCTATATTCATCTAACCAAATCTCAGCCACTTTGGATTTAGGTATTTGTTTTTAGG
66 CTTGTAATATCTATATTCATCTAACCAAATCTCAGCCA-TTTGGATTTAGG-ATTTGTTTTTACG
* *
2785 AGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAGAAATGG-AAAACGATATT
129 AGCATCTAAATCTTGTTTCAATTTAATTAGAAATAAATTCGGAAAA-AAATGGAAAAACGATATT
* * *
2849 TGAAGCGTGAAATATCCTTCAA--TTTTTTGCGTTGAATTATATATATTTCTTCTGAGTATTGTA
193 AGAAGCGTGAAAAATCCTTCAATTTTTTTTGCGTTGAATTATATATATTT-TTCTGAGTATTGTG
* * * *
2912 GCAAAAAAATTGAGAAAAAACTTTTTGGATCAGTTTTTGCAGAATTTTAGCCGAAATTGTGTACT
257 GC-AAAAAATTGAGAAAAAACTTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT
*
2977 AACCATCACAA
321 AACCATCACGA
* * * *
2988 TTTTGTGGCTAAAAACGCGTTTCGG-GCCCCGACTCAGTTTTGCAGGATTTTTGGCAG-AAAGAC
1 TTTT-TGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGC-GCAATGAC
* * * *
3051 TCCTTGAAATATCTATATTCCTCTAACCAAATCTCAGCCAGATTGGATTTAAGTATTTGTTTTTA
64 TCCTTGTAATATCTATATTCATCTAACCAAATCTCAGCCA-TTTGGATTT-AGGATTTGTTTTTA
** * * *
3116 AAAGCATCTCAATCTTGTTTCAATTTAATTAGAAATAAATTC-GAAAAATATGGAAAAACGATGT
127 CGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATAT
*
3180 TAGAAGCGTGAAAAATCCTTCAA-TTTTTTTGCGTTGAAGTATATATATTTTTTCTGAGTATTGT
192 TAGAAGCGTGAAAAATCCTTCAATTTTTTTTGCGTTGAATTATATATA-TTTTTCTGAGTATTGT
* * * * *
3244 GGCAAAAACTTGAGAAAAAAC-ATTTGGTGCCAATTTCTGCAAAATTTTAGCAGAAATCGTGTA-
256 GGCAAAAAATTGAGAAAAAACTTTTTGG-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC
* *
3307 T-CCCATCACGG
320 TAACCATCACGA
* * * * * *
3318 TTTTTGGCAAAAAACACGTTCCAGAGCCCCGGCTTAATTTTGCATGAATTTTGGCGCAATGACTC
1 TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCAATGACTC
* *
3383 CTTATAATATCTATATTCATCTAACCAAATCTCAGCCACTTTGGATTTAGGTATTTGTTTTTAGG
66 CTTGTAATATCTATATTCATCTAACCAAATCTCAGCCA-TTTGGATTTAGG-ATTTGTTTTTACG
* *
3448 AGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAGAAATGG-AAAACGATATT
129 AGCATCTAAATCTTGTTTCAATTTAATTAGAAATAAATTCGGAAAA-AAATGGAAAAACGATATT
* *
3512 AGAAGCATAAAAAATCCTTCAATTTTTTTTGCGTTGAATTATATATATTTCTTCTGAGTATTGTG
193 AGAAGCGTGAAAAATCCTTCAATTTTTTTTGCGTTGAATTATATATATTT-TTCTGAGTATTGTG
* * **
3577 GCAAAAAATTGAGAAAAAACTTTTTGGGTCAGTTTTTGCAGAATTTTAGCCGAAATAATGTACTA
257 GCAAAAAATTGAGAAAAAACTTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTA
3642 ACCATCACGA
322 ACCATCACGA
* ** * * * * *
3652 TTTTTGGCAAAAAAACGCGTTCCGTTGCCCCGGCTTAATTTTGAATGAATTTTGGCGCAATGAAT
1 TTTTTGGC-TAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCAATGACT
* * * * *
3717 CCTTGTAATATCTATATTCAAT-GAACCAAATATCAGCCACCTTGGATTTAAGGATTTATCTTTA
65 CCTTGTAATATCTATATTC-ATCTAACCAAATCTCAGCCA-TTTGGATTT-AGGATTTGTTTTTA
* * ** * * * *
3781 CGAGCATCTGAATCTTGTTTCGATAAAAATAGAAATGATTTCGGAAAAAAAATTGTAAAAACGAT
127 CGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATAAATTCGG-AAAAAAA-TGGAAAAACGAT
* * * *
3846 ATTAGAAACTTG--AAATCCTTCAA-TTTTTTTGCGTTGAATCATATA-CTTTTTCTGAGTATTG
190 ATTAGAAGCGTGAAAAATCCTTCAATTTTTTTTGCGTTGAATTATATATATTTTTCTGAGTATTG
* * * * *
3907 TGGCAACAAATTGAGTAAAAAA--TTTTCGGTTAAGTTTTTGCAAAATTTTAACCGAAATCGTAT
255 TGGCAAAAAATTGAG-AAAAAACTTTTTGGGTCAA-TTTTTGCAAAATTTTAGCCGAAATCGTGT
*
3970 ACTAACTATCACGA
318 ACTAACCATCACGA
* * * * *
3984 TTTTGTGGCTAAAAACGTGTTTCGGGGCCCCGGCTCAGTTTTGCACGATTTTTGGCAG-AAAGAC
1 TTTT-TGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGC-GCAATGAC
* * * *
4048 TCCTTGAAATATCTATATTCCTCTAACCAAATCTCAGCCAGATTGGATTTAAGTATTTGTTTTTA
64 TCCTTGTAATATCTATATTCATCTAACCAAATCTCAGCCA-TTTGGATTT-AGGATTTGTTTTTA
** * *
4113 ATAGCATCTCAATCTTGTTTCAATTTAATTAGAAATAAATTC-GAAAAAAATGGAAAAACGATGT
127 CGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATAT
*
4177 TAGAAGCGTGAAAAATCCTTCAA-TTTTTTTGCGTTGAAGTATATATACTTTTTTCTGAGTATTG
192 TAGAAGCGTGAAAAATCCTTCAATTTTTTTTGCGTTGAATTATATATA--TTTTTCTGAGTATTG
* * * * * * *
4241 TGGCAAAAACTTGAGAAATAACTTTTTGGGCCAATTTCTGCAAAATTTTTGCAGAAATCGTGTAA
255 TGGCAAAAAATTGAGAAAAAACTTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC
*
4306 TAACCATCACGG
320 TAACCATCACGA
* * * *
4318 TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTTAATTTTGCATGAATTTTGGCGCAATGACTC
1 TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCAATGACTC
* * * *
4383 CTTGTAATATCTATATTCAT-TGAACCAAATATCAGCCACCTTGGATTTAAGGATTTATCTTTAC
66 CTTGTAATATCTATATTCATCT-AACCAAATCTCAGCCA-TTTGGATTT-AGGATTTGTTTTTAC
* * * ** * * *
4447 GAGCATCTGAATCTTATTTCGATAAAAATAGAAATAATTTCGGAAAAAAAAATTGTAAAAACGAT
128 GAGCATCTAAATCTTGTTTCAATTTAATTAGAAATAAATTCGG--AAAAAAA-TGGAAAAACGAT
* * * *
4512 ATTAGAAACTTG--AAATCCTTCAATTTTTTTTGCGTTGAATCATATA-CTTTTTCTGAGTATTG
190 ATTAGAAGCGTGAAAAATCCTTCAATTTTTTTTGCGTTGAATTATATATATTTTTCTGAGTATTG
* * *
4574 TGGCAACAAATTGAGTAAAAAA-TTTTCT--GTAAAGTTTTTGCAAAATTTTAGCCGAAATCGTA
255 TGGCAAAAAATTGAG-AAAAAACTTTT-TGGGTCAA-TTTTTGCAAAATTTTAGCCGAAATCGTG
*
4636 TACTAACCATCACGG
317 TACTAACCATCACGA
* * * * * * * *
4651 TTTTTGGCTAAAAACACGTTCCGAAGGCTCGGCTCAATTTTACATGATTTTTGGCGTAAAT-AGT
1 TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCG-CAATGACT
* * * * * * * * *
4715 CATTGAAATATCTATATTCATCAAACCAAGTCTCAGCCACATTGTATATAAGGATTTGCTTTTAT
65 CCTTGTAATATCTATATTCATCTAACCAAATCTCAGCCA-TTTGGAT-TTAGGATTTGTTTTTAC
* ** * * *
4780 GAGCATCTGAAA-GTTGTTTTGATTTAATTAAAAATAAACTCGGAAAAGAA-GGAAAAACGATAT
128 GAGCATCT-AAATCTTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATAT
* * * ** * *
4843 AATAAGTGTGAAAAGCCCGTT-AA-TCTTTTTGTCGTTGAAATATATATATATATATAT-TGAGT
192 TAGAAGCGTGAAAAATCC-TTCAATTTTTTTTG-CGTTG-AAT-TATATATAT-T-TTTCTGAGT
* * * * * * * *
4905 ATTTTGGTAAAAAATTTAAGAAAAAAATTTTTGGGTTAGTTTTT----AA--TT----GAATTTG
251 ATTGTGGCAAAAAA-TTGAGAAAAAACTTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCG
4960 TGTACTAACCATCACGA
315 TGTACTAACCATCACGA
* * * *
4977 TTTTGTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGTATGATTTTTGGCAG-AAAGAC
1 TTTT-TGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGC-GCAATGAC
* * * * * *
5041 TCCTGGAAATATCTATATTCCTCAAACCAAATCTCAGCCAGATTGGATTTAAGTATTTGTTTTTA
64 TCCTTGTAATATCTATATTCATCTAACCAAATCTCAGCCA-TTTGGATTT-AGGATTTGTTTTTA
** * * *
5106 ATAGAATCTCAATCTTGTTTCAATTTAATTAGAAATAAATTC-GAAAAAAATGGAAAAACGATGT
127 CGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATAT
* *
5170 TAGAAGCGTGAAAAATCCTTCAA-TTTCTTTGCGTTGAAGTATATATACTTTTTCTGAGTATTGT
192 TAGAAGCGTGAAAAATCCTTCAATTTTTTTTGCGTTGAATTATATATA-TTTTTCTGAGTATTGT
* * * * *
5234 GGCAAAAACTTGAGAAAAAAACTTTTTGGGTCAGTTTTTGCAAAATTTTAGCAGAGATTGTGTAC
256 GGCAAAAAATTGAG-AAAAAACTTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC
* *
5299 TAACAATCACGG
320 TAACCATCACGA
5311 TTTTT
1 TTTTT
5316 TGCGTTGAAT
Statistics
Matches: 4328, Mismatches: 506, Indels: 298
0.84 0.10 0.06
Matches are distributed among these distances:
323 6 0.00
324 47 0.01
325 6 0.00
326 62 0.01
327 334 0.08
328 507 0.12
329 73 0.02
330 485 0.11
331 205 0.05
332 498 0.12
333 844 0.20
334 546 0.13
335 459 0.11
336 74 0.02
337 179 0.04
338 1 0.00
339 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (331 bp):
TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCAATGACTC
CTTGTAATATCTATATTCATCTAACCAAATCTCAGCCATTTGGATTTAGGATTTGTTTTTACGAG
CATCTAAATCTTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGA
AGCGTGAAAAATCCTTCAATTTTTTTTGCGTTGAATTATATATATTTTTCTGAGTATTGTGGCAA
AAAATTGAGAAAAAACTTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCA
TCACGA
Found at i:5919 original size:336 final size:333
Alignment explanation
Indices: 5311--6787 Score: 1928
Period size: 332 Copynumber: 4.4 Consensus size: 333
5301 ACAATCACGG
* * *
5311 TTTTTTGCGTTGAATTCTATATATTTCTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTT
1 TTTTTTGCGTTGAATTATATATATTTTTTCTGAGTATTGTGCCAAAAAATTGAGAAAAAACTTTT
* *
5376 TGGGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTA-T--TCATCACGGTTTTTGGC-TAAAA
66 TGGGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAAA
5437 CGCGTTCCGGAGCCCCGGCTTAACTTTTGCATTGAACTTTTGGCGCAATGACTCCTTGTAATATC
131 CGCGTTCCGGAGCCCCGGCTTAA-TTTTGCA-TGAA-TTTTGGCGCAATGACTCCTTGTAATATC
*
5502 TATATTCATCTAACCAAATCTCAGCCACTTTGGATTTAGGTATTTGTTTTTAGGAGCATCTAAAT
193 TATATTCATCTAACCAAATCTCAGCCACTTTGGATTTAGGTAATTGTTTTTAGGAGCATCTAAAT
*
5567 CTTGTTTCGGTTTAATTAGAAATAAATTCGGAAAAGAAATGGAAAACGATATTAGAAGCGTGAAA
258 CTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAGAAATGGAAAACGATATTAGAAGCGTGAAA
*
5632 AATCCTTCGA-
323 AATCCTTCAAT
*
5642 TTTTTTGCGTTGAATTATATATATTTATTCTGAGTATTGTGCCAAAAAATTGAGAAAAAACTTTT
1 TTTTTTGCGTTGAATTATATATATTTTTTCTGAGTATTGTGCCAAAAAATTGAGAAAAAACTTTT
* * * *
5707 TGGGTAAGTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGACAAAAA
66 TGGGTCAG-TTTTTGCAGAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGC---AA
** * * *
5772 AAAACGCGTTCTAGAGACCTGGCTTAATTTTTCATGAATTTTGGCGCAATGACTCCTTGTAATAT
127 AAAACGCGTTCCGGAGCCCCGGCTTAATTTTGCATGAATTTTGGCGCAATGACTCCTTGTAATAT
* * *
5837 CTATATTTAT-TGAACCAAATCTCAGCCACTTTGGATTTAGGTAATTGCTTTTAGGAGCATCTAG
192 CTATATTCATCT-AACCAAATCTCAGCCACTTTGGATTTAGGTAATTGTTTTTAGGAGCATCTAA
* *
5901 ATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAATGAAATGGAAAACGATATCAGAAGCGTGA
256 ATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAGAAATGGAAAACGATATTAGAAGCGTG-
5966 AAAAATCCTTCAAT
320 AAAAATCCTTCAAT
* * *
5980 TTTTTTGCGTTGAATTATATATATTTTTTCTGAGTATTGTGACAAAAAATTGAGAAAATACATTT
1 TTTTTTGCGTTGAATTATATATATTTTTTCTGAGTATTGTGCCAAAAAATTGAGAAAAAACTTTT
*
6045 TGGGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTACT--CCATCACGGTTTTTGGCTAAAAA
66 TGGGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAAA
* * * * *
6108 CGCGTTCCGGAGCCCCGGCTCAGTTTTGTATGAATTTTGGCAG-AAAGACTCCTTGAAATATCTA
131 CGCGTTCCGGAGCCCCGGCTTAATTTTGCATGAATTTTGGC-GCAATGACTCCTTGTAATATCTA
* ** * ** *
6172 TATTCCTCTAACCAAATCTCAGCCAGATTGGATTTAAGTAATTGTTTTTAAAAGCATCTGAATCT
195 TATTCATCTAACCAAATCTCAGCCACTTTGGATTTAGGTAATTGTTTTTAGGAGCATCTAAATCT
** *
6237 TGTTTTAATTTAATTAGAAATAAATTC-GAAAA-AAATGGGAAAACGATGTTAGAAGCGTG----
260 TGTTTCGATTTAATTAGAAATAAATTCGGAAAAGAAAT-GGAAAACGATATTAGAAGCGTGAAAA
6296 ATCCTTCAAT
324 ATCCTTCAAT
* *
6306 TTTTTT-CATTGGTTTATATATGTATATTTATACATATATATAAATTTTCTGAGTATTGCAGCAA
1 TTTTTTGC----G------T-TG-A-A-TTAT--ATATAT-T---TTTTCTGAGTATTG-TGCCA
** * * *
6370 AAAAATTGAGAAAAGTCTTTTTGTGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTAGTAACA
45 AAAAATTGAGAAAAAACTTTTTGGGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTACTAACC
*
6435 ATCACGGGTTTTT-GCTAAAAACGCGTTCCGGAGCCCCGGCTTAATTTTGCATGAATTTTGGCGC
110 ATCAC-GGTTTTTGGCAAAAAACGCGTTCCGGAGCCCCGGCTTAATTTTGCATGAATTTTGGCGC
* ** *
6499 AATGACTCCTTTGTAATATCTATATTCATCTGACCAAATCTCAGCCTTTTTGGATTTAGGTATTT
174 AATGACTCC-TTGTAATATCTATATTCATCTAACCAAATCTCAGCCACTTTGGATTTAGGTAATT
* * * * * *
6564 TTTTTTAGGAGCTTTTAAATCGTCTTTCGATTTAATTAGAAATAAATTCAGAAAAGAAATGGAAA
238 GTTTTTAGGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAGAAATGGAAA
*
6629 ACCATATTAGAAGCGTGAAAAATCCTTCAAT
303 ACGATATTAGAAGCGTGAAAAATCCTTCAAT
*
6660 TTTTTTGCGTTGAATTATATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG-AAAAACTTTT
1 TTTTTTGCGTTGAATTATATATATTTTTTCTGAGTATTGTGCCAAAAAATTGAGAAAAAACTTTT
* * * *
6724 TGGATCAGTTTTTGCAGAATTTTAGCCAAAATAGTGTACTAACCATCACGATTTTTGGCAAAAA
66 TGGGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAA
Statistics
Matches: 996, Mismatches: 102, Indels: 94
0.84 0.09 0.08
Matches are distributed among these distances:
325 1 0.00
326 16 0.02
329 1 0.00
330 4 0.00
331 93 0.09
332 170 0.17
333 60 0.06
334 12 0.01
335 45 0.05
336 148 0.15
337 48 0.05
338 76 0.08
339 33 0.03
341 10 0.01
342 2 0.00
343 1 0.00
344 2 0.00
345 15 0.02
346 58 0.06
347 1 0.00
348 60 0.06
349 93 0.09
350 25 0.03
351 5 0.01
354 16 0.02
355 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (333 bp):
TTTTTTGCGTTGAATTATATATATTTTTTCTGAGTATTGTGCCAAAAAATTGAGAAAAAACTTTT
TGGGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAAA
CGCGTTCCGGAGCCCCGGCTTAATTTTGCATGAATTTTGGCGCAATGACTCCTTGTAATATCTAT
ATTCATCTAACCAAATCTCAGCCACTTTGGATTTAGGTAATTGTTTTTAGGAGCATCTAAATCTT
GTTTCGATTTAATTAGAAATAAATTCGGAAAAGAAATGGAAAACGATATTAGAAGCGTGAAAAAT
CCTTCAAT
Found at i:6643 original size:681 final size:664
Alignment explanation
Indices: 5311--6787 Score: 1992
Period size: 681 Copynumber: 2.2 Consensus size: 664
5301 ACAATCACGG
* *
5311 TTTTTTGCGTTGAATTCTATATATTTCTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTT
1 TTTTTTGCGTTGAATTATATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG-AAAAACTTTT
*
5376 TGGGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTA-TTCATCACGGTTTTTGGCT-AAAACG
65 TGGGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTACTCCATCACGGTTTTTGGCTAAAAACG
* *
5439 CGTTCCGGAGCCCCGGCTTAACTTTTGCATTGAACTTTTGGCGCAATGACTCCTTGTAATATCTA
130 CGTTCCGGAGCCCCGGCTTAACTTTTGCATTGAACTTTTGGCGCAAAGACTCCTTGAAATATCTA
* * * **
5504 TATTCATCTAACCAAATCTCAGCCACTTTGGATTTAGGTATTTGTTTTTAGGAGCATCTAAATCT
195 TATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGTAATTGTTTTTAAAAGCATCTAAATCT
**
5569 TGTTTCGGTTTAATTAGAAATAAATTCGGAAAAGAAATGGAAAACGATATTAGAAGCGTGAAAAA
260 TGTTTCAATTTAATTAGAAATAAATTCGGAAAAGAAATGGAAAACGATATTAGAAGCGTG---AA
* * *
5634 TCCTTCGATTTTTTGCGTTGAATTATATATATTTATTCTGAGTATTGTGCCAAAAAATTGAGAAA
322 TCCTTCAATTTTTTGCGTTGAATTATATATATTTATTCTGAGTATTGAGCAAAAAAATTGAGAAA
*
5699 AAACTTTTTGGGTAAGTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTT
387 AAACTTTTTGGGTAAGTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACAATCACGATTTTT
* * *
5764 GACAAAAAAAAACGCGTTCTAGAGACCTGGCTTAATTTTTCATGAATTTTGGCGCAATGACTCCT
452 GAC--AAAAAAACGCGTTCCAGAGACCCGGCTTAATTTTGCATGAATTTTGGCGCAATGACTCCT
*
5829 TGTAATATCTATATTTATTGAACCAAATCTCAGCCACTTTGGATTTAGGTAATTGCTTTTAGGAG
515 TGTAATATCTATATTCATTGAACCAAATCTCAGCCACTTTGGATTTAGGTAATTGCTTTTAGGAG
* * * * * *
5894 CATCTAGATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAATGAAATGGAAAACGATATCAGA
580 CATCTAAATCGTCTTTCGATTTAATTAGAAATAAATTCAGAAAAGAAATGGAAAACCATATCAGA
5959 AGCGTGAAAAAATCCTTCAAT
645 AGCGTG-AAAAATCCTTCAAT
* *
5980 TTTTTTGCGTTGAATTATATATATTTTTTCTGAGTATTGTGACAAAAAATTGAGAAAATACATTT
1 TTTTTTGCGTTGAATTATATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAA-ACTTTT
6045 TGGGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTACTCCATCACGGTTTTTGGCTAAAAACG
65 TGGGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTACTCCATCACGGTTTTTGGCTAAAAACG
* * *
6110 CGTTCCGGAGCCCCGGC-TCAGTTTTGTA-TGAA-TTTTGGCAG-AAAGACTCCTTGAAATATCT
130 CGTTCCGGAGCCCCGGCTTAACTTTTGCATTGAACTTTTGGC-GCAAAGACTCCTTGAAATATCT
* * *
6171 ATATTCCTCTAACCAAATCTCAGCCAGATTGGATTTAAGTAATTGTTTTTAAAAGCATCTGAATC
194 ATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGTAATTGTTTTTAAAAGCATCTAAATC
* *
6236 TTGTTTTAATTTAATTAGAAATAAATTC-GAAAA-AAATGGGAAAACGATGTTAGAAGCGTG-AT
259 TTGTTTCAATTTAATTAGAAATAAATTCGGAAAAGAAAT-GGAAAACGATATTAGAAGCGTGAAT
* *
6298 CCTTCAATTTTTTTCATTGGTTTATATATGTATATTTATACATATATATAAATTTTCTGAGTATT
323 CCTTCAATTTTTTGC----G------T-TG-A-A-TTAT--ATATAT-T---TATTCTGAGTATT
** * * *
6363 GCAGCAAAAAAATTGAGAAAAGTCTTTTTGTGTCAG-TTTTTGCAGAATTTTAGCCGAAATCGTG
368 G-AGCAAAAAAATTGAGAAAAAACTTTTTGGGTAAGTTTTTTGCAAAATTTTAGCCGAAATCGTG
* * * * *
6427 TAGTAACAATCACGGGTTTTTG-C-TAAAAACGCGTTCCGGAGCCCCGGCTTAATTTTGCATGAA
432 TACTAACAATCAC-GATTTTTGACAAAAAAACGCGTTCCAGAGACCCGGCTTAATTTTGCATGAA
**
6490 TTTTGGCGCAATGACTCCTTTGTAATATCTATATTCATCTG-ACCAAATCTCAGCCTTTTTGGAT
496 TTTTGGCGCAATGACTCC-TTGTAATATCTATATTCAT-TGAACCAAATCTCAGCCACTTTGGAT
* ** * *
6554 TTAGGTATTTTTTTTTAGGAGCTTTTAAATCGTCTTTCGATTTAATTAGAAATAAATTCAGAAAA
559 TTAGGTAATTGCTTTTAGGAGCATCTAAATCGTCTTTCGATTTAATTAGAAATAAATTCAGAAAA
*
6619 GAAATGGAAAACCATATTAGAAGCGTGAAAAATCCTTCAAT
624 GAAATGGAAAACCATATCAGAAGCGTGAAAAATCCTTCAAT
6660 TTTTTTGCGTTGAATTATATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTT
1 TTTTTTGCGTTGAATTATATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTT
* * * *
6725 GGATCAGTTTTTGCAGAATTTTAGCCAAAATAGTGTACTAACCATCACGATTTTTGGC-AAAAA
66 GGGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTACT--CCATCACGGTTTTTGGCTAAAAA
Statistics
Matches: 715, Mismatches: 62, Indels: 51
0.86 0.07 0.06
Matches are distributed among these distances:
663 15 0.02
666 4 0.01
667 27 0.04
668 111 0.16
669 99 0.14
670 26 0.04
671 23 0.03
673 1 0.00
674 2 0.00
675 1 0.00
676 1 0.00
677 4 0.01
679 48 0.07
680 129 0.18
681 135 0.19
682 2 0.00
683 52 0.07
684 35 0.05
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (664 bp):
TTTTTTGCGTTGAATTATATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTT
GGGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTACTCCATCACGGTTTTTGGCTAAAAACGC
GTTCCGGAGCCCCGGCTTAACTTTTGCATTGAACTTTTGGCGCAAAGACTCCTTGAAATATCTAT
ATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGTAATTGTTTTTAAAAGCATCTAAATCTT
GTTTCAATTTAATTAGAAATAAATTCGGAAAAGAAATGGAAAACGATATTAGAAGCGTGAATCCT
TCAATTTTTTGCGTTGAATTATATATATTTATTCTGAGTATTGAGCAAAAAAATTGAGAAAAAAC
TTTTTGGGTAAGTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACAATCACGATTTTTGACA
AAAAAACGCGTTCCAGAGACCCGGCTTAATTTTGCATGAATTTTGGCGCAATGACTCCTTGTAAT
ATCTATATTCATTGAACCAAATCTCAGCCACTTTGGATTTAGGTAATTGCTTTTAGGAGCATCTA
AATCGTCTTTCGATTTAATTAGAAATAAATTCAGAAAAGAAATGGAAAACCATATCAGAAGCGTG
AAAAATCCTTCAAT
Done.