Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015388.1 Corchorus olitorius cultivar O-4 contig15421, 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: 3055
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:1048 original size:333 final size:333
Alignment explanation
Indices: 1--2569 Score: 3458
Period size: 333 Copynumber: 7.7 Consensus size: 333
* ** * * *
1 ATATCGATTTTCCTATATATTTCTTAATTAATTTCTGATTAAATCGAATCACGATT-TAGATGCT
1 ATATCGATTTTCCTATATCTTTCCGAATTAATTTCTGGTTAAATCGAAACATGATTCT-GATGCT
* * *
65 CGTAAAATCAAATCCTTTAATCCAATTTGGCTGAAATATGGTTAGATGAATATAGATATGTCGAG
65 CGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATATGTCAAG
* * * * ** * *
130 GAGTCTCGGGGTCAAAAATCATTGAAAACTGAGCTGGAGCCCCGGAACATGTTTTTGGCAAAAAA
130 GAGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGGAACGCGTTTTTAGC-CAAAA
* ** * *
195 ACCGTGAAGAATTCTATAAGTACACAATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGGTT
194 A-C-TG-TG-ATGGT-T-AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATT
* * * *
260 TTTTCCACAATCTTTGGCCAAAACACTTATAGAATATGTATAATTCAATGCCAAAAAGATTAAAT
253 TTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGA-TGAAG
325 GGTTTTTCACGCTTCTA
317 GGTTTTTCACGCTTCTA
* ** * *
342 ATATCGATTTTCCTATATATTTCTTAATTAATTTCTGATTAAATC-AAATCACGATTCTGATGCT
1 ATATCGATTTTCCTATATCTTTCCGAATTAATTTCTGGTTAAATCGAAA-CATGATTCTGATGCT
* * *
406 CGTAAAGTCAAATCCTTAAATCCAAATTTGGCTAAAAT-TCGGTTAGATGAATATAGATATGTCA
65 CGTAAAATCAAATCCTTAAATCC-AATTTGGCTGAGATAT-GGTTAGATGAATATAGATATGTCA
*
470 AGGAGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGGAACACGTTTTTAGCCAAA
128 AGGAGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCCAAA
* * * *
535 AACCGTGA----T-GTA-ACGATTTTGACTAAAATTTTGCAAAAACTT-ACCCAAAAGATTTTTT
193 AACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAA-TTGACCCGAAAGATTTTTT
* * *
593 CAACAATATTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGAATGAAGGATT
257 CCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAG-ATGAAGGGTT
* *
658 TTTTACGCTTATA
321 TTTCACGCTTCTA
* * * *
671 ATATTGATTTTCCTATATCTTTTCGAATTAATTTCCGGTTAAATCGAAACATGATTCTGATGCTT
1 ATATCGATTTTCCTATATCTTTCCGAATTAATTTCTGGTTAAATCGAAACATGATTCTGATGCTC
* * *
736 GTAAAA-GAAATCCTTAAATCTAATTTGGCTGAGATATGGTTAGATGAATATAGATATGTAAAGG
66 GTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATATGTCAAGG
800 AGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCCAAAAAC
131 AGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCCAAAAAC
* * * *
865 TATGATGGTTAGTGCACGATTTCGGGTAAAATTTTGCAAAAGTTGACCCGAAAGATTTTTTCCAC
196 TGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCCAC
* *
930 AATCTTTGGCAAAAACACTTATAGAATATATATAATTGAACGCCAAAAAGATGAAAGGGTTTTTC
261 AATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATG-AAGGGTTTTTC
995 ACGCTTCTA
325 ACGCTTCTA
* * * *
1004 ATATCGATTTTCATATATTTTTCCTAATTAATTTCTGGTTAAATCGAAACATGATTCTGATGCTT
1 ATATCGATTTTCCTATATCTTTCCGAATTAATTTCTGGTTAAATCGAAACATGATTCTGATGCTC
* *
1069 GTAAAATCAAATCCTTATATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATATGTCAAGG
66 GTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATATGTCAAGG
* * *
1134 ACTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGG-CCTAGAACACGTTTTTAGCCAAAAAC
131 AGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCCAAAAAC
1198 TGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCCAC
196 TGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCCAC
* * * *
1263 ATTCTTTGGCCAAAACACTTATAAAATATGTATAATTCAACGCCAAAAAGATTGAAGGGGTTTTC
261 AATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGA-TGAAGGGTTTTTC
1328 ACGCTTC-A
325 ACGCTTCTA
* * * *
1336 GATATCGATTTT-CTATATCTTTCCAAATTAATTTCTTGCTAAATCGAAACATG-TGCTGATGCT
1 -ATATCGATTTTCCTATATCTTTCCGAATTAATTTCTGGTTAAATCGAAACATGATTCTGATGCT
* *
1399 CGTAAAATCAAATCCTTAAATCCAATTTGGCCGAGATATGGTTAGATGAATATAGATATATCAAG
65 CGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATATGTCAAG
* * * * ** ** *
1464 GAGTCTTGGGGCCAAAAGTAATAGAAAACTGAGCCAGGAACCC-GGAACGCAATTTTAGACAAAA
130 GAGTCTCGGGGCCAAAAATCATTGAAAACTGAGCC-GGGGCCCTGGAACGCGTTTTTAGCCAAAA
* * * * * **
1528 ACCGTGAT-G--AGCACATGATTTCGACTAAAATTTTGGAAAAACTT-ACCTAAAAGATTTTTTC
194 ACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAA-TTGACCCGAAAGATTTTTTC
* * **
1589 AACAATATTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATTGAAGCATTT
258 CACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGA-TGAAGGGTTT
1654 TTCACGCTTCTA
322 TTCACGCTTCTA
* * * * *
1666 ATATTGATTTTCCTATCTCTTTCCGAATTAATTTTTGATTAAATCGAAACATGATTTTGATGCTC
1 ATATCGATTTTCCTATATCTTTCCGAATTAATTTCTGGTTAAATCGAAACATGATTCTGATGCTC
** * *
1731 GTAAAATCAAATAATTAAATCCAATTTGGCTGAGATTTGGTTAGATGAGTATAGATATGTCAAGG
66 GTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATATGTCAAGG
* * * * *
1796 ACTCTCGGGGGCAAAAATCATTGAAAACTAAGCTGGGGCCCTGTAACGCGTTTTTAGCCAAAAAA
131 AGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCC-AAAAA
* * *
1861 CAGTGATGGTTAGTACACGATTTCGGCTAAAATTTTCCAAAAATTGACCCGATAGATTTTTTCCA
195 CTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCCA
* * *
1926 CAATCTTTTGCAAAAACACTTATAGAATATATATAATTCAACGGCAAAAAGATGGAAGGGTTTTT
260 CAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGAT-GAAGGGTTTTT
1991 CACGCTTCTA
324 CACGCTTCTA
* * * *
2001 ATATTGATTTTCATATATCTTTCCGAATTAATTTCTGGTTAAATCGGAACATGATTTTGATGCTC
1 ATATCGATTTTCCTATATCTTTCCGAATTAATTTCTGGTTAAATCGAAACATGATTCTGATGCTC
* * * *
2066 GTAAAATCAAATTCTTAAATCAAATTTGGCTGA-AT-TAGGTTAGATGGATATAGATATGTCTAG
66 GTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATAT-GGTTAGATGAATATAGATATGTCAAG
*
2129 GAGTCTCGGGGCCAAAAATCATTGAAAAACTGAGCCGGGGACCTGGAACGCGTTTTTAGCCAAAA
130 GAGTCTCGGGGCCAAAAATCATTG-AAAACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCCAAAA
* *
2194 ACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGA-TTTTTCT
194 ACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCC
* * * *
2258 ACATTCTTTGGCCCAAACACTTATAAAATAAATATAATTCAACGCCAAAAAGATTGAAGGGTTTT
259 ACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGA-TGAAGGGTTTT
2323 TCACGCTTCTA
323 TCACGCTTCTA
* *** * *
2334 ATATCGATTCTAAAATATCATTCCGAATTAATTTCTGGTTAAATCGAAACATGATTCTGATGCTT
1 ATATCGATTTTCCTATATCTTTCCGAATTAATTTCTGGTTAAATCGAAACATGATTCTGATGCTC
* *
2399 GTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATATTTAAAGG
66 GTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATATGTCAAGG
* *
2464 AGTCTCGGGGCCAAAAATCATTGAAAACTGAACCGGGGCCCTGGAATGC-TTTTTAAGCCAAAAA
131 AGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGGAACGCGTTTTT-AGCCAAAAA
*
2528 CTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAA
195 CTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAA
2570 GTTCAGCAAA
Statistics
Matches: 1977, Mismatches: 213, Indels: 84
0.87 0.09 0.04
Matches are distributed among these distances:
327 105 0.05
328 14 0.01
329 282 0.14
330 52 0.03
331 208 0.11
332 86 0.04
333 566 0.29
334 249 0.13
335 232 0.12
337 1 0.00
338 1 0.00
339 1 0.00
340 3 0.00
341 85 0.04
342 92 0.05
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (333 bp):
ATATCGATTTTCCTATATCTTTCCGAATTAATTTCTGGTTAAATCGAAACATGATTCTGATGCTC
GTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATATGTCAAGG
AGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCCAAAAAC
TGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCCAC
AATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATGAAGGGTTTTTCA
CGCTTCTA
Found at i:1550 original size:662 final size:665
Alignment explanation
Indices: 1--2569 Score: 3461
Period size: 662 Copynumber: 3.9 Consensus size: 665
* ** * * *
1 ATATCGATTTTCCTATATATTTCTTAATTAATTTCTGATTAAATCGAATCACGATT-TAGATGCT
1 ATATCGATTTTCCTATATCTTTCCGAATTAATTTCTGGTTAAATCGAAACATGATTCT-GATGCT
* * *
65 CGTAAAATCAAATCCTTTAATCCAATTTGGCTGAAATATGGTTAGATGAATATAGATATGTCGAG
65 CGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATATGTCAAG
* * * ** * *
130 GAGTCTCGGGGTCAAAAATCATTGAAAACTGAGCTGGAGCCCCGGAACATGTTTTTGGCAAAAAA
130 GAGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGA-ACCCGGAACGCGTTTTTAG-ACAAAA
** * *
195 ACCGTGAAGAATTCTATAAGTACACAATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGGTT
193 ACCGT---G-A-T-GGT-AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATT
* * * *
260 TTTTCCACAATCTTTGGCCAAAACACTTATAGAATATGTATAATTCAATGCCAAAAAGATTAAAT
251 TTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATTGAAG
* * **
325 GGTTTTTCACGCTTCTAATATCGATTTTCCTATATATTTCTTAATTAATTTCTGATTAAATC-AA
316 GGTTTTTCACGCTTCTAATATCGATTTTCATATATCTTTCCGAATTAATTTCTGATTAAATCGAA
* * * * *
389 ATCACGATTCTGATGCTCGTAAAGTCAAATCCTTAAATCCAAATTTGGCTAAAATTCGGTTAGAT
381 A-CATGATTCTGATGCTCGTAAAATCAAATCCTTAAATCC-AATTTGGCTGAGATTTGGTTAGAT
*
454 GAATATAGATATGTCAAGGAGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGGAA
444 GAATATAGATATGTCAAGGACTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGGAA
* * *
519 CACGTTTTTAGCCAAAAACCGTGA----T-GTA-ACGATTTTGACTAAAATTTTGCAAAAACTT-
509 CACGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAA-TTG
* * *
577 ACCCAAAAGATTTTTTCAACAATATTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCA
573 ACCCGAAAGATTTTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCA
* * * *
642 AAAAGAATGAAGGATTTTTTACGCTTATA
638 AAAAGATTGAAGGGTTTTTCACGCTT-CA
* * * *
671 ATATTGATTTTCCTATATCTTTTCGAATTAATTTCCGGTTAAATCGAAACATGATTCTGATGCTT
1 ATATCGATTTTCCTATATCTTTCCGAATTAATTTCTGGTTAAATCGAAACATGATTCTGATGCTC
* * *
736 GTAAAA-GAAATCCTTAAATCTAATTTGGCTGAGATATGGTTAGATGAATATAGATATGTAAAGG
66 GTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATATGTCAAGG
** *
800 AGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCCAAAAAC
131 AGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGAACCC-GGAACGCGTTTTTAGACAAAAAC
** * * *
865 TATGATGGTTAGTGCACGATTTCGGGTAAAATTTTGCAAAAGTTGACCCGAAAGATTTTTTCCAC
195 CGTGATGG-TAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCCAC
* *
930 AATCTTTGGCAAAAACACTTATAGAATATATATAATTGAACGCCAAAAAGA-TGAAAGGGTTTTT
259 AATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATTG-AAGGGTTTTT
* * *
994 CACGCTTCTAATATCGATTTTCATATATTTTTCCTAATTAATTTCTGGTTAAATCGAAACATGAT
323 CACGCTTCTAATATCGATTTTCATATATCTTTCCGAATTAATTTCTGATTAAATCGAAACATGAT
* *
1059 TCTGATGCTTGTAAAATCAAATCCTTATATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGA
388 TCTGATGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGA
*
1124 TATGTCAAGGACTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGG-CCTAGAACACGTTTTT
453 TATGTCAAGGACTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGGAACACGTTTTT
1188 AGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGA
518 AGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGA
* * *
1253 TTTTTTCCACATTCTTTGGCCAAAACACTTATAAAATATGTATAATTCAACGCCAAAAAGATTGA
583 TTTTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATTGA
*
1318 AGGGGTTTTCACGCTTCA
648 AGGGTTTTTCACGCTTCA
* * * *
1336 GATATCGATTTT-CTATATCTTTCCAAATTAATTTCTTGCTAAATCGAAACATG-TGCTGATGCT
1 -ATATCGATTTTCCTATATCTTTCCGAATTAATTTCTGGTTAAATCGAAACATGATTCTGATGCT
* *
1399 CGTAAAATCAAATCCTTAAATCCAATTTGGCCGAGATATGGTTAGATGAATATAGATATATCAAG
65 CGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATATGTCAAG
* * * * **
1464 GAGTCTTGGGGCCAAAAGTAATAGAAAACTGAGCCAGGAACCCGGAACGCAATTTTAGACAAAAA
130 GAGTCTCGGGGCCAAAAATCATTGAAAACTGAGCC-GGAACCCGGAACGCGTTTTTAGACAAAAA
* * * * ** *
1529 CCGTGAT-G-AGCACATGATTTCGACTAAAATTTTGGAAAAACTT-ACCTAAAAGATTTTTTCAA
194 CCGTGATGGTAGTACACGATTTCGGCTAAAATTTTGCAAAAA-TTGACCCGAAAGATTTTTTCCA
* **
1591 CAATATTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATTGAAGCATTTTT
258 CAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTT
* * * *
1656 CACGCTTCTAATATTGATTTTCCTATCTCTTTCCGAATTAATTTTTGATTAAATCGAAACATGAT
323 CACGCTTCTAATATCGATTTTCATATATCTTTCCGAATTAATTTCTGATTAAATCGAAACATGAT
* ** *
1721 TTTGATGCTCGTAAAATCAAATAATTAAATCCAATTTGGCTGAGATTTGGTTAGATGAGTATAGA
388 TCTGATGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGA
* * * * *
1786 TATGTCAAGGACTCTCGGGGGCAAAAATCATTGAAAACTAAGCTGGGGCCCTGTAACGCGTTTTT
453 TATGTCAAGGACTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGGAACACGTTTTT
* * *
1851 AGCCAAAAAACAGTGATGGTTAGTACACGATTTCGGCTAAAATTTTCCAAAAATTGACCCGATAG
518 AGCC-AAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAG
* * * *
1916 ATTTTTTCCACAATCTTTTGCAAAAACACTTATAGAATATATATAATTCAACGGCAAAAAGATGG
582 ATTTTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATTG
1981 AAGGGTTTTTCACGCTTCTA
647 AAGGGTTTTTCACGCTTC-A
* * * *
2001 ATATTGATTTTCATATATCTTTCCGAATTAATTTCTGGTTAAATCGGAACATGATTTTGATGCTC
1 ATATCGATTTTCCTATATCTTTCCGAATTAATTTCTGGTTAAATCGAAACATGATTCTGATGCTC
* * * *
2066 GTAAAATCAAATTCTTAAATCAAATTTGGCTGA-AT-TAGGTTAGATGGATATAGATATGTCTAG
66 GTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATAT-GGTTAGATGAATATAGATATGTCAAG
* * *
2129 GAGTCTCGGGGCCAAAAATCATTGAAAAACTGAGCCGGGGACCTGGAACGCGTTTTTAGCCAAAA
130 GAGTCTCGGGGCCAAAAATCATTG-AAAACTGAGCC-GGAACCCGGAACGCGTTTTTAGACAAAA
*
2194 ACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGA-TTTTTCT
193 ACCGTGATGG-TAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCC
* * * *
2258 ACATTCTTTGGCCCAAACACTTATAAAATAAATATAATTCAACGCCAAAAAGATTGAAGGGTTTT
257 ACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATTGAAGGGTTTT
* * * * *
2323 TCACGCTTCTAATATCGATTCTAAAATATCATTCCGAATTAATTTCTGGTTAAATCGAAACATGA
322 TCACGCTTCTAATATCGATTTTCATATATCTTTCCGAATTAATTTCTGATTAAATCGAAACATGA
* *
2388 TTCTGATGCTTGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAG
387 TTCTGATGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAG
* * * * **
2453 ATATTTAAAGGAGTCTCGGGGCCAAAAATCATTGAAAACTGAACCGGGGCCCTGGAATGC-TTTT
452 ATATGTCAAGGACTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGGAACACGTTTT
*
2517 TAAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAA
517 T-AGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAA
2570 GTTCAGCAAA
Statistics
Matches: 1669, Mismatches: 201, Indels: 61
0.86 0.10 0.03
Matches are distributed among these distances:
660 29 0.02
661 78 0.05
662 451 0.27
663 26 0.02
664 161 0.10
665 232 0.14
666 202 0.12
667 50 0.03
668 246 0.15
669 134 0.08
670 59 0.04
671 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (665 bp):
ATATCGATTTTCCTATATCTTTCCGAATTAATTTCTGGTTAAATCGAAACATGATTCTGATGCTC
GTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATATGTCAAGG
AGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGAACCCGGAACGCGTTTTTAGACAAAAACC
GTGATGGTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCCACAA
TCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCAC
GCTTCTAATATCGATTTTCATATATCTTTCCGAATTAATTTCTGATTAAATCGAAACATGATTCT
GATGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATAT
GTCAAGGACTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGGAACACGTTTTTAGC
CAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTT
TTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATTGAAGG
GTTTTTCACGCTTCA
Found at i:2264 original size:997 final size:991
Alignment explanation
Indices: 1--2509 Score: 3659
Period size: 997 Copynumber: 2.5 Consensus size: 991
* * * * *
1 ATATCGATTTTCCTATATATTTCTTAATTAATTTCTGATTAAATC-GAATCACGATTTAGATGCT
1 ATATCGATTTTCATATATATTTCCTAATTAATTTCTGGTTAAATCGGAA-CATGATTTTGATGCT
* * *
65 CGTAAAATCAAATCCTTTAATCCAATTTGGCTGAAATATGGTTAGATGAATATAGATATGTCGAG
65 CGTAAAATCAAATCCTTAAATCCAATTTGGCTGAATTA-GGTTAGATGAATATAGATATGTCAAG
* * * * * * *
130 GAGTCTCGGGGTCAAAAATCATTGAAAACTGAGCTGGAGCCCCGGAACATGTTTTTGGCAAAAAA
129 GAGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGG-GGCCTGGAACACGTTTTTAGC-CAAAA
** * *
195 ACCGTGAAGAATTCTATAAGTACACAATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGGTT
192 ACCGT---G-ATGGT-T-AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-GAT
* * * * *
260 TTTTCCACAATCTTTGGCCAAAACACTTATAGAATATGTATAATTCAATGCCAAAAAGATTAAAT
250 TTTTCCACATTCTTTGGCCAAAACACTTATAAAATATGTATAATTCAACGCCAAAAAGATTGAAG
* **
325 GGTTTTTCACGCTTCTAATATCGATTTTCCTATATATTTCTTAATTAATTTC-TGATTAAATC-A
315 GGTTTTTCACGCTTCTAATATCGATTTT-CTATATCTTTCCAAATTAATTTCTTG-TTAAATCGA
* * * *
388 AATCACGATTCTGATGCTCGTAAAGTCAAATCCTTAAATCCAAATTTGGCTAAAAT-TCGGTTAG
378 AA-CATGATTCTGATGCTCGTAAAATCAAATCCTTAAATCC-AATTTGGCTGAGATAT-GGTTAG
* **
452 ATGAATATAGATATGTCAAGGAGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCTGG
440 ATGAATATAGATATATCAAGGAGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGAACCCTGG
** * *
517 AACACGTTTTTAGCCAAAAACCGTGATGTAACGATTTTGACTAAAATTTTGCAAAAACTTACCCA
505 AACACAATTTTAGACAAAAACCGTGATGTAACGATTTCGACTAAAATTTTGCAAAAACTTACCCA
582 AAAGATTTTTTCAACAATATTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAG
570 AAAGATTTTTTCAACAATATTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAG
* * * *
647 AATGAAGGATTTTTTACGCTTATAATATTGATTTTCCTATATCTTTTCGAATTAATTTCCGGTTA
635 AATGAAGCATTTTTCACGCTTATAATATTGATTTTCCTATATCTTTCCGAATTAATTTCCGATTA
* * ** *
712 AATCGAAACATGATTCTGATGCTTGTAAAAGAAATCCTTAAATCTAATTTGGCTGAGATATGGTT
700 AATCGAAACATGATTCTGATGCTCGTAAAACAAATAATTAAATCCAATTTGGCTGAGATATGGTT
* *
777 AGATGAATATAGATATGTAAAGGAGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCCT
765 AGATGAATATAGATATGTAAAGGACTCTCGGGGCCAAAAATCATTGAAAACTAAGCCGGGGCCCT
* * * *
842 GGAACGCGTTTTTAGCCAAAAACTATGATGGTTAGTGCACGATTTCGGGTAAAATTTTGCAAAAG
830 GGAACGCGTTTTTAGCCAAAAACTATGATGGTTAGTACACGATTTCGGCTAAAATTTTCCAAAAA
*
907 TTGACCCGAAAGATTTTTTCCACAATCTTTGGCAAAAACACTTATAGAATATATATAATTGAACG
895 TTGACCCGAAAGATTTTTTCCACAATCTTTGGCAAAAACACTTATAGAATATATATAATTCAACG
972 CCAAAAAGATGAAAGGGTTTTTCACGCTTCTA
960 CCAAAAAGATGAAAGGGTTTTTCACGCTTCTA
* * * *
1004 ATATCGATTTTCATATATTTTTCCTAATTAATTTCTGGTTAAATCGAAACATGATTCTGATGCTT
1 ATATCGATTTTCATATATATTTCCTAATTAATTTCTGGTTAAATCGGAACATGATTTTGATGCTC
* *
1069 GTAAAATCAAATCCTTATATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATATGTCAAGG
66 GTAAAATCAAATCCTTAAATCCAATTTGGCTGA-ATTAGGTTAGATGAATATAGATATGTCAAGG
* * *
1134 ACTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCTAGAACACGTTTTTAGCCAAAAACT
130 AGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCTGGAACACGTTTTTAGCCAAAAACC
1199 GTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCCACA
195 GTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGA-TTTTTCCACA
*
1264 TTCTTTGGCCAAAACACTTATAAAATATGTATAATTCAACGCCAAAAAGATTGAAGGGGTTTTCA
259 TTCTTTGGCCAAAACACTTATAAAATATGTATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCA
* *
1329 CGCTTC-AGATATCGATTTTCTATATCTTTCCAAATTAATTTCTTGCTAAATCGAAACATG-TGC
324 CGCTTCTA-ATATCGATTTTCTATATCTTTCCAAATTAATTTCTTGTTAAATCGAAACATGATTC
*
1392 TGATGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCCGAGATATGGTTAGATGAATATAGATA
388 TGATGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATA
* * * * *
1457 TATCAAGGAGTCTTGGGGCCAAAAGTAATAGAAAACTGAGCCAGGAACCC-GGAACGCAATTTTA
453 TATCAAGGAGTCTCGGGGCCAAAAATCATTGAAAACTGAGCC-GGAACCCTGGAACACAATTTTA
* *
1521 GACAAAAACCGTGATG-AGCACATGATTTCGACTAAAATTTTGGAAAAACTTACCTAAAAGATTT
517 GACAAAAACCGTGATGTA--AC--GATTTCGACTAAAATTTTGCAAAAACTTACCCAAAAGATTT
*
1585 TTTCAACAATATTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATTGAAGC
578 TTTCAACAATATTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGAATGAAGC
* * **
1650 ATTTTTCACGCTTCTAATATTGATTTTCCTATCTCTTTCCGAATTAATTTTTGATTAAATCGAAA
643 ATTTTTCACGCTTATAATATTGATTTTCCTATATCTTTCCGAATTAATTTCCGATTAAATCGAAA
* * *
1715 CATGATTTTGATGCTCGTAAAATCAAATAATTAAATCCAATTTGGCTGAGATTTGGTTAGATGAG
708 CATGATTCTGATGCTCGTAAAA-CAAATAATTAAATCCAATTTGGCTGAGATATGGTTAGATGAA
* * * *
1780 TATAGATATGTCAAGGACTCTCGGGGGCAAAAATCATTGAAAACTAAGCTGGGGCCCTGTAACGC
772 TATAGATATGTAAAGGACTCTCGGGGCCAAAAATCATTGAAAACTAAGCCGGGGCCCTGGAACGC
1845 GTTTTTAGCCAAAAAAC-AGTGATGGTTAGTACACGATTTCGGCTAAAATTTTCCAAAAATTGAC
837 GTTTTTAGCC-AAAAACTA-TGATGGTTAGTACACGATTTCGGCTAAAATTTTCCAAAAATTGAC
* * *
1909 CCGATAGATTTTTTCCACAATCTTTTGCAAAAACACTTATAGAATATATATAATTCAACGGCAAA
900 CCGAAAGATTTTTTCCACAATCTTTGGCAAAAACACTTATAGAATATATATAATTCAACGCCAAA
*
1974 AAGATGGAAGGGTTTTTCACGCTTCTA
965 AAGATGAAAGGGTTTTTCACGCTTCTA
* * *
2001 ATATTGATTTTCATATATCTTTCCGAATTAATTTCTGGTTAAATCGGAACATGATTTTGATGCTC
1 ATATCGATTTTCATATATATTTCCTAATTAATTTCTGGTTAAATCGGAACATGATTTTGATGCTC
* * * *
2066 GTAAAATCAAATTCTTAAATCAAATTTGGCTGAATTAGGTTAGATGGATATAGATATGTCTAGGA
66 GTAAAATCAAATCCTTAAATCCAATTTGGCTGAATTAGGTTAGATGAATATAGATATGTCAAGGA
*
2131 GTCTCGGGGCCAAAAATCATTGAAAAACTGAGCCGGGGACCTGGAACGCGTTTTTAGCCAAAAAC
131 GTCTCGGGGCCAAAAATCATTG-AAAACTGAGCCGGGG-CCTGGAACACGTTTTTAGCCAAAAAC
*
2196 CGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCTACA
194 CGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCACA
* **
2261 TTCTTTGGCCCAAACACTTATAAAATAAATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCA
259 TTCTTTGGCCAAAACACTTATAAAATATGTATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCA
*** * * *
2326 CGCTTCTAATATCGATTCTAAAATATCATTCCGAATTAATTTCTGGTTAAATCGAAACATGATTC
324 CGCTTCTAATATCGATT-TTCTATATCTTTCCAAATTAATTTCTTGTTAAATCGAAACATGATTC
*
2391 TGATGCTTGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATA
388 TGATGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATA
* * * **
2456 TTTAAAGGAGTCTCGGGGCCAAAAATCATTGAAAACTGAACCGGGGCCCTGGAA
453 TATCAAGGAGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGAACCCTGGAA
2510 TGCTTTTTAA
Statistics
Matches: 1355, Mismatches: 130, Indels: 46
0.89 0.08 0.03
Matches are distributed among these distances:
991 1 0.00
992 93 0.07
993 39 0.03
994 31 0.02
995 312 0.23
996 157 0.12
997 326 0.24
998 121 0.09
999 104 0.08
1001 8 0.01
1002 16 0.01
1003 143 0.11
1004 4 0.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (991 bp):
ATATCGATTTTCATATATATTTCCTAATTAATTTCTGGTTAAATCGGAACATGATTTTGATGCTC
GTAAAATCAAATCCTTAAATCCAATTTGGCTGAATTAGGTTAGATGAATATAGATATGTCAAGGA
GTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCCTGGAACACGTTTTTAGCCAAAAACCG
TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCACATT
CTTTGGCCAAAACACTTATAAAATATGTATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACG
CTTCTAATATCGATTTTCTATATCTTTCCAAATTAATTTCTTGTTAAATCGAAACATGATTCTGA
TGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATATAT
CAAGGAGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGAACCCTGGAACACAATTTTAGACA
AAAACCGTGATGTAACGATTTCGACTAAAATTTTGCAAAAACTTACCCAAAAGATTTTTTCAACA
ATATTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGAATGAAGCATTTTTCA
CGCTTATAATATTGATTTTCCTATATCTTTCCGAATTAATTTCCGATTAAATCGAAACATGATTC
TGATGCTCGTAAAACAAATAATTAAATCCAATTTGGCTGAGATATGGTTAGATGAATATAGATAT
GTAAAGGACTCTCGGGGCCAAAAATCATTGAAAACTAAGCCGGGGCCCTGGAACGCGTTTTTAGC
CAAAAACTATGATGGTTAGTACACGATTTCGGCTAAAATTTTCCAAAAATTGACCCGAAAGATTT
TTTCCACAATCTTTGGCAAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATGAAAGG
GTTTTTCACGCTTCTA
Found at i:2649 original size:100 final size:101
Alignment explanation
Indices: 2475--2669 Score: 270
Period size: 100 Copynumber: 1.9 Consensus size: 101
2465 GTCTCGGGGC
* * ** * *
2475 CAAAAATCATTGAAAACTGAACCGGGGCCCTGGAATGCTTTTTAAGCCAAAAACTGTGATGGTTA
1 CAAAAAGCATGGAAAACTGAACCGGGGCCCCAGAACGCTTTTTAAGCCAAAAACTGTGATGATTA
*
2540 GTACACGATTTCGGCTAAAATTTTGTAAAAGTTCAG
66 GTACACGATTTCGGCTAAAATTTTGCAAAAGTTCAG
*
2576 CAAAAAGCATGGAAAACTGAGCCGGGGCCCCAGAACGCATTTTT-AG-CAAAAA-TCGTGATGAT
1 CAAAAAGCATGGAAAACTGAACCGGGGCCCCAGAACGC-TTTTTAAGCCAAAAACT-GTGATGAT
*
2638 TAGTACACGATTTCGGTTAAAATTTTGCAAAA
64 TAGTACACGATTTCGGCTAAAATTTTGCAAAA
2670 ATGGTCCCGA
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
99 1 0.01
100 43 0.52
101 34 0.41
102 5 0.06
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (101 bp):
CAAAAAGCATGGAAAACTGAACCGGGGCCCCAGAACGCTTTTTAAGCCAAAAACTGTGATGATTA
GTACACGATTTCGGCTAAAATTTTGCAAAAGTTCAG
Done.