Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020813.1 Corchorus olitorius cultivar O-4 contig20846, 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: 5109
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:852 original size:59 final size:59
Alignment explanation
Indices: 755--872 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
745 GATTTTTGCA
*
755 AAACTTTAGCCAAAATCGTGTACTATCCATCACGGTTTTTGGCCAAAAAGGTGTTCCGG
1 AAACTTTAGCCAAAATCGTGTACTATCCATCACAGTTTTTGGCCAAAAAGGTGTTCCGG
814 AAACTTTAGCCAAAATCGTGTACTATCCATCACAGTTTTTGGCCAAAAAGGTGTTCCGG
1 AAACTTTAGCCAAAATCGTGTACTATCCATCACAGTTTTTGGCCAAAAAGGTGTTCCGG
873 GGACCCGGCT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (59 bp):
AAACTTTAGCCAAAATCGTGTACTATCCATCACAGTTTTTGGCCAAAAAGGTGTTCCGG
Found at i:1256 original size:2 final size:2
Alignment explanation
Indices: 1249--1277 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1239 CTTGTTGAAT
1249 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1278 GACCGAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2565 original size:332 final size:331
Alignment explanation
Indices: 818--3209 Score: 3047
Period size: 332 Copynumber: 7.2 Consensus size: 331
808 TTCCGGAAAC
* * *
818 TTTAGCCAAAATCGTGTACTATCCATCACAGTTTTTGGCCAAAAAGGTGTTCCGGGGACCCGGCT
1 TTTAGCCGAAATCGTGTACTATCCATCACAGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCT
* *
883 CAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATTAAACCATATCTCA
66 CAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCA
* * * *
948 GCCACAATTGATTTAAAAGCTTATTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAT
131 GCCACAATTGATTTAAGA-CTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAAA
* * * *
1013 TTAATTC-AAAAAATAGGAAAAATGATATTAAAAGCGTGAAAAACCTTTTAATCTTTTTGGAATT
195 TTAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATT
* * * *
1077 GAATTATATAATTTTTACAACTATTGTGT-AAAAAATTAAGGAAAAATTTTTCGGCTCAGTTTTT
260 GAATTATATACTTTTTACGACTATTGTGTCAAAAAATTGAGGAAAAATTTTTCGGCTCAATTTTT
*
1141 GCAAAGT
325 GCAAAAT
* * * *** * * *
1148 TTTAGCAGAAATCGTGT-TTAACCATCACAGTTTTTGGCTAAAAACACGTTCC-GGGCCCAGACA
1 TTTAGCCGAAATCGTGTACTATCCATCACAGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCT
* ** * * *
1211 CAGTTTTGCATAATTTTTGGCGCCAAGACTTGTTGAATTATATATATATATATATATATATATAT
66 CAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTG------A-A-ATATCTATAT-T-CAT-CA-
* * * * * *
1276 ATGACCGAATCTTAGTCAC-ATTGGATTTAAGGATTTGTTTTTACGAGCATCAGAATCATATTTC
119 A--ACCAAATCTCAGCCACAATT-GATTTAA-GACTTGTTTTTACGAGCATCAGAATCTTGTTTC
* * * *
1340 GATTTTTATTATAAATTAATT-AAAAAAATAGGAAAAACAACATTAGAAGCGTGAGAA-CCTTTT
180 GATTTTTATTAGAAATTAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTT
*
1403 AATCTTTTTGGCATTGAATTATATACTTTTTACGACTATTGTGTCAAAAAATTGAGGAAAAA-AT
245 AATCTTTTTGGCATTGAATTATATACTTTTTACGACTATTGTGTCAAAAAATTGAGGAAAAATTT
* *
1467 TTCAGCTCAGTTTTTGCAAAAT
310 TTCGGCTCAATTTTTGCAAAAT
* * * * * * * * *
1489 TTTAGCTGAAATCATGCACTATCCATCACTGTTTATGGCTAAAATGGTCTTCTGGGGCCCCGACT
1 TTTAGCCGAAATCGTGTACTATCCATCACAGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCT
* * *
1554 CCGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGACATATCTATATTCATCAAACCAAAATCTC
66 CAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCAAACC-AAATCTC
*
1619 AGCCACAATTGATTTAAAGAC--ATTTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAA
130 AGCCACAATTGATTT-AAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAA
* * *
1682 ATTAATTTAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCC--TT-ATATTTTTGGCAT
194 ATTAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCAT
*
1744 TGAATTATATACTTTTTCCGACTATTGTGTCAAAAAA-TGAGGAAAAATTTTTCGGCTCAATTTT
259 TGAATTATATACTTTTTACGACTATTGTGTCAAAAAATTGAGGAAAAATTTTTCGGCTCAATTTT
1808 T-CAAAAT
324 TGCAAAAT
*
1815 TTTAGCCGAAATCGTG---------T-ACGGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCAC-GC
1 TTTAGCCGAAATCGTGTACTATCCATCACAGTTTTTGGCTAAAAAGGTGTTCCGGGGCCC-CGGC
* ** *
1869 TCAGTTTTGCATGATTTTTGGCGCTAAGACTCCTTGAAATATCTATATTCATCATTCCAAATCTT
65 TCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTC
* * * *
1934 AGCCACAATTGATTTAAAGACGTGTTTTTACTAGCATCGGAATCTTGTTTTGATTTTTATTAGAA
130 AGCCACAATTGATTT-AAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAA
* *
1999 CTTAATTCAAAAAAATGGGAAAAACGATATTAGAAGCGTCGAAAAGCCTTTTAATCTTTTTGGCA
194 ATTAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGT-GAAAAGCCTTTTAATCTTTTTGGCA
* * * * *
2064 TTAAATTATATA--TTTTACAACTATTGTGTGAAAAAATTGAGGAAAAATTTTTAGACTCAATTT
258 TTGAATTATATACTTTTTACGACTATTGTGTCAAAAAATTGAGGAAAAATTTTTCGGCTCAATTT
2127 TTGCAAAAT
323 TTGCAAAAT
* * ** *
2136 TTTTGCTGAAATTATGTACTATCCATCACAGTTTTTGGTTAAAAAGGTGTTCCGGGGCCCCGGCT
1 TTTAGCCGAAATCGTGTACTATCCATCACAGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCT
* * * * *
2201 CAGTTTTGCATGATTTTCGGTGCCAGGACTCCTTCAAATATCTATATTTATCAAACCAAATCTCA
66 CAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCA
* * *
2266 GCCACAATTGATTTATAGACGTGTTTTTACGAGCATCGGAATCTTGTTTCGATTTCTATTAGAAA
131 GCCACAATTGATTTA-AGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAAA
* *
2331 TTAATTCAAAAAAATAGGAAAAATGATATTAGAAGCGTTAAAAGCCTTTTAATCTTTTTGGCATT
195 TTAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATT
* *
2396 GAATTATATACCTTTTCCGACTATTGTGTCAAAAAATTGAGGAAAAATTTTTCGGCTCAATTTTT
260 GAATTATATACTTTTTACGACTATTGTGTCAAAAAATTGAGGAAAAATTTTTCGGCTCAATTTTT
*
2461 GTAAAAT
325 GCAAAAT
*
2468 TTTAGCCGAAATCGTGTAC-ATTCCATCACAGTTTTAGGCTAAAAAGGTGTTCCGGGGCCCCGGC
1 TTTAGCCGAAATCGTGTACTA-TCCATCACAGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGC
* * * *
2532 TCAGTTTTGCATGATTTTTTGCGCTAAGACTCCTTGAAATATTTATATTCATCATACCAAATCTC
65 TCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTC
* *
2597 ATCCACAATTGATTTAATGACTTGTTTTTACGCGCATCAGAATCTTGTTTCG-TTTTTAATTAGA
130 AGCCACAATTGATTTAA-GACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTT-ATTAGA
* * * *
2661 AATTAATTC-AAAAAATAGGAAAAACAATATTAAAAGCGTGAAAAGCCTTGTAATCATTTTGGCA
193 AATTAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCA
* *
2725 TTGAATTATATA-TTTATTACGACTATTTTGTCAAAAAATTGAGGAAAAAAATTTTCGGCTCAAT
258 TTGAATTATATACTTT-TTACGACTATTGTGTCAAAAAATTGAGG-AAAAATTTTTCGGCTCAAT
2789 TTTTGCAAAAT
321 TTTTGCAAAAT
* * * *
2800 TTTAGTCGAAATCGTGTACTAACCATTACAGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCTGGCT
1 TTTAGCCGAAATCGTGTACTATCCATCACAGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCT
* * *
2865 CAGTTTTGCATGATTTTTGGCGCCAAGACTCTTTGAAATATCTATATTCATCATACCAAATCTTA
66 CAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCA
*
2930 GCCACAATTGATTTAAAGACTTGTTTTTACGAGCATC-GAAATCTTGTTTCGATTTCTATTAGAA
131 GCCACAATTGATTT-AAGACTTGTTTTTACGAGCATCAG-AATCTTGTTTCGATTTTTATTAGAA
* * * *
2994 TTTAATTC-AAAAAATAGGAAAAATGATATTAAAAGCGTGAAAAGCCTTTTAATCTTTTTGGAAT
194 ATTAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCAT
* * * * * *
3058 TGAATTATATAATTTTTACAACTATTGTGTCAAAAGATTAAGGAAAAATTTTTCGGCTTAGTTTT
259 TGAATTATATACTTTTTACGACTATTGTGTCAAAAAATTGAGGAAAAATTTTTCGGCTCAATTTT
3123 TGCAAAAT
324 TGCAAAAT
* * ** * * *
3131 TTTAGCCGAAATCGTGTATTAACCATCACAGTTTTTGGCTAAAAACATGTTTC-GGGCCCAGCCT
1 TTTAGCCGAAATCGTGTACTATCCATCACAGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCT
3195 CAGTTTTGCAT-ATTT
66 CAGTTTTGCATGATTT
3210 AGTAAGGTCA
Statistics
Matches: 1800, Mismatches: 203, Indels: 119
0.85 0.10 0.06
Matches are distributed among these distances:
315 27 0.01
316 82 0.05
317 75 0.04
318 8 0.00
319 21 0.01
320 28 0.02
321 40 0.02
326 30 0.02
327 62 0.03
328 86 0.05
329 70 0.04
330 94 0.05
331 359 0.20
332 518 0.29
333 12 0.01
334 2 0.00
335 10 0.01
336 9 0.00
337 2 0.00
338 2 0.00
339 2 0.00
340 1 0.00
341 85 0.05
342 135 0.08
343 40 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (331 bp):
TTTAGCCGAAATCGTGTACTATCCATCACAGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCT
CAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCA
GCCACAATTGATTTAAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAAAT
TAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTG
AATTATATACTTTTTACGACTATTGTGTCAAAAAATTGAGGAAAAATTTTTCGGCTCAATTTTTG
CAAAAT
Found at i:2642 original size:663 final size:657
Alignment explanation
Indices: 826--3209 Score: 3182
Period size: 663 Copynumber: 3.6 Consensus size: 657
816 ACTTTAGCCA
* * *
826 AAATCGTGTACTATCCATCACAGTTTTTGGCCAAAAAGGTGTTCCGGGGACCCGGCTCAGTTTTG
1 AAATCATGTACTATCCATCACAGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTG
* *
891 CATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATTAAACCATATCTCAGCCACAAT
66 CATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACAAT
*
956 TGATTTAAA-AGCTTATTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAATTTAATTC
131 TGATTTAAAGA-CTTATTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAATTAATTC
*
1020 AAAAAATAGGAAAAATGATATTAAAAGCGTGAAAAACCTTTTAATCTTTTTGGAATTGAATTATA
195 AAAAAATAGGAAAAATGATATTAAAAGCGTGAAAAGCCTTTTAATCTTTTTGGAATTGAATTATA
* *
1085 TAATTTTTACAACTATTGTGT-AAAAAATTAAGGAAAAATTTTTCGGCTCAGTTTTTGCAAAGTT
260 TAATTTTTACAACTATTGTGTCAAAAAATTAAGGAAAAATTTTTCGGCTCAATTTTTGCAAAATT
* * * * *
1149 TTAGCAGAAATCGTGTTTAACCATCACAGTTTTTGGCTAAAAACACGTTCCGGGCCCAGACACAG
325 TTAGCCGAAATCGTG--TATCCATCACAGTTTTTGGCTAAAAACATGTTCCGGGCCCAGGCTCAG
* * ** * *
1214 TTTTGCATAATTTTTGGCGCCAAGACTTGTTGAATTATATATATATATATATATATATATATATG
388 TTTTGCATGATTTTTGGCGCTAAGACTCCTTG------A-A-ATAT-T-TATAT-T-CAT-CAT-
* * * * *
1279 ACCGAATCTTAGT-CAC-ATTGGATTTAAGGATTTGTTTTTACGAGCATCAGAATCATATTTCGA
439 ACCAAATCTTA-TCCACAATT-GATTTAAAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGA
* * *
1342 TTTTTATTATAAATTAATT-AAAAAAATAGGAAAAACAACATTAGAAGCGTGAGAA-CCTTTTAA
502 TTTTTATTAGAAATTAATTCAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCTTTTAA
*
1405 TCTTTTTGGCATTGAATTATATACTTTTTACGACTATTGTGTCAAAAAATTGAGGAAAAAATTTC
567 TCTTTTTGGCATTGAATTATATA-TTTTTACGACTATTGTGTCAAAAAATTGAGGAAAAAATTTT
*
1470 AGCTCAGTTTTTGCAAAATTTTAGCTG
631 AGCTCAATTTTTGCAAAATTTTAGCTG
* * * * * * * *
1497 AAATCATGCACTATCCATCACTGTTTATGGCTAAAATGGTCTTCTGGGGCCCCGACTCCGTTTTG
1 AAATCATGTACTATCCATCACAGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTG
* *
1562 CATGATTTTTGGCGCAAAGACTCCTTGACATATCTATATTCATCAAACCAAAATCTCAGCCACAA
66 CATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCAAACC-AAATCTCAGCCACAA
*
1627 TTGATTTAAAGAC--ATTTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAAATTAATTT
130 TTGATTTAAAGACTTATTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAATTAA-TT
* ** * * *
1690 AAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCC--TT-ATATTTTTGGCATTGAATTAT
194 CAAAAAATAGGAAAAATGATATTAAAAGCGTGAAAAGCCTTTTAATCTTTTTGGAATTGAATTAT
* * * *
1752 ATACTTTTTCCGACTATTGTGTCAAAAAA-TGAGGAAAAATTTTTCGGCTCAATTTTT-CAAAAT
259 ATAATTTTTACAACTATTGTGTCAAAAAATTAAGGAAAAATTTTTCGGCTCAATTTTTGCAAAAT
* ** *
1815 TTTAGCCGAAATCGTG------T-ACGGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCACGCTCAG
324 TTTAGCCGAAATCGTGTATCCATCACAGTTTTTGGCTAAAAACATGTTCC-GGGCCCAGGCTCAG
* * *
1873 TTTTGCATGATTTTTGGCGCTAAGACTCCTTGAAATATCTATATTCATCATTCCAAATCTTAGCC
388 TTTTGCATGATTTTTGGCGCTAAGACTCCTTGAAATATTTATATTCATCATACCAAATCTTATCC
* * * * *
1938 ACAATTGATTTAAAGACGTGTTTTTACTAGCATCGGAATCTTGTTTTGATTTTTATTAGAACTTA
453 ACAATTGATTTAAAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAAATTA
* * *
2003 ATTCAAAAAAATGGGAAAAACGATATTAGAAGCGTCGAAAAGCCTTTTAATCTTTTTGGCATTAA
518 ATTCAAAAAAATAGGAAAAACAATATTAGAAGCGT-GAAAAGCCTTTTAATCTTTTTGGCATTGA
* * *
2068 ATTATATA-TTTTACAACTATTGTGTGAAAAAATTGAGGAAAAATTTTTAGACTCAATTTTTGCA
582 ATTATATATTTTTACGACTATTGTGTCAAAAAATTGAGGAAAAAATTTTAG-CTCAATTTTTGCA
*
2132 AAATTTTTGCTG
646 AAATTTTAGCTG
* *
2144 AAATTATGTACTATCCATCACAGTTTTTGGTTAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTG
1 AAATCATGTACTATCCATCACAGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTG
* * * * *
2209 CATGATTTTCGGTGCCAGGACTCCTTCAAATATCTATATTTATCAAACCAAATCTCAGCCACAAT
66 CATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACAAT
* * * *
2274 TGATTTATAGACGTGTTTTTACGAGCATCGGAATCTTGTTTCGATTTCTATTAGAAATTAATTCA
131 TGATTTAAAGACTTATTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAATTAATTC-
* * *
2339 AAAAAATAGGAAAAATGATATTAGAAGCGTTAAAAGCCTTTTAATCTTTTTGGCATTGAATTATA
195 AAAAAATAGGAAAAATGATATTAAAAGCGTGAAAAGCCTTTTAATCTTTTTGGAATTGAATTATA
** * * * *
2404 TACCTTTTCCGACTATTGTGTCAAAAAATTGAGGAAAAATTTTTCGGCTCAATTTTTGTAAAATT
260 TAATTTTTACAACTATTGTGTCAAAAAATTAAGGAAAAATTTTTCGGCTCAATTTTTGCAAAATT
* ** *
2469 TTAGCCGAAATCGTGTACATTCCATCACAGTTTTAGGCTAAAAAGGTGTTCCGGGGCCCCGGCTC
325 TTAGCCGAAATCGTGT--A-TCCATCACAGTTTTTGGCTAAAAACATGTTCC-GGGCCCAGGCTC
* *
2534 AGTTTTGCATGATTTTTTGCGCTAAGACTCCTTGAAATATTTATATTCATCATACCAAATCTCAT
386 AGTTTTGCATGATTTTTGGCGCTAAGACTCCTTGAAATATTTATATTCATCATACCAAATCTTAT
* *
2599 CCACAATTGATTTAATGACTTGTTTTTACGCGCATCAGAATCTTGTTTCG-TTTTTAATTAGAAA
451 CCACAATTGATTTAAAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTT-ATTAGAAA
* * *
2663 TTAATTC-AAAAAATAGGAAAAACAATATTAAAAGCGTGAAAAGCCTTGTAATCATTTTGGCATT
515 TTAATTCAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATT
* *
2727 GAATTATATATTTATTACGACTATTTTGTCAAAAAATTGAGGAAAAAAATTTTCGGCTCAATTTT
580 GAATTATATATTT-TTACGACTATTGTGTCAAAAAATTGAGG-AAAAAATTTT-AGCTCAATTTT
2792 TGCAAAATTTTAG-TCG
642 TGCAAAATTTTAGCT-G
* * * *
2808 AAATCGTGTACTAACCATTACAGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCTGGCTCAGTTTTG
1 AAATCATGTACTATCCATCACAGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTG
* * *
2873 CATGATTTTTGGCGCCAAGACTCTTTGAAATATCTATATTCATCATACCAAATCTTAGCCACAAT
66 CATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACAAT
* *
2938 TGATTTAAAGACTTGTTTTTACGAGCATC-GAAATCTTGTTTCGATTTCTATTAGAATTTAATTC
131 TGATTTAAAGACTTATTTTTACGAGCATCAG-AATCTTGTTTCGATTTCTATTAGAAATTAATTC
3002 AAAAAATAGGAAAAATGATATTAAAAGCGTGAAAAGCCTTTTAATCTTTTTGGAATTGAATTATA
195 AAAAAATAGGAAAAATGATATTAAAAGCGTGAAAAGCCTTTTAATCTTTTTGGAATTGAATTATA
* * *
3067 TAATTTTTACAACTATTGTGTCAAAAGATTAAGGAAAAATTTTTCGGCTTAGTTTTTGCAAAATT
260 TAATTTTTACAACTATTGTGTCAAAAAATTAAGGAAAAATTTTTCGGCTCAATTTTTGCAAAATT
* *
3132 TTAGCCGAAATCGTGTATTAACCATCACAGTTTTTGGCTAAAAACATGTTTCGGGCCCAGCCTCA
325 TTAGCCGAAATCGTGTA-T--CCATCACAGTTTTTGGCTAAAAACATGTTCCGGGCCCAGGCTCA
3197 GTTTTGCAT-ATTT
387 GTTTTGCATGATTT
3210 AGTAAGGTCA
Statistics
Matches: 1515, Mismatches: 160, Indels: 86
0.86 0.09 0.05
Matches are distributed among these distances:
645 64 0.04
646 98 0.06
647 128 0.08
648 110 0.07
649 5 0.00
650 2 0.00
651 52 0.03
652 29 0.02
653 22 0.01
658 22 0.01
659 40 0.03
661 41 0.03
662 55 0.04
663 341 0.23
664 206 0.14
665 1 0.00
667 20 0.01
668 64 0.04
669 8 0.01
670 45 0.03
671 136 0.09
672 25 0.02
673 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (657 bp):
AAATCATGTACTATCCATCACAGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTG
CATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACAAT
TGATTTAAAGACTTATTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAATTAATTCA
AAAAATAGGAAAAATGATATTAAAAGCGTGAAAAGCCTTTTAATCTTTTTGGAATTGAATTATAT
AATTTTTACAACTATTGTGTCAAAAAATTAAGGAAAAATTTTTCGGCTCAATTTTTGCAAAATTT
TAGCCGAAATCGTGTATCCATCACAGTTTTTGGCTAAAAACATGTTCCGGGCCCAGGCTCAGTTT
TGCATGATTTTTGGCGCTAAGACTCCTTGAAATATTTATATTCATCATACCAAATCTTATCCACA
ATTGATTTAAAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAAATTAATT
CAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTGAATTA
TATATTTTTACGACTATTGTGTCAAAAAATTGAGGAAAAAATTTTAGCTCAATTTTTGCAAAATT
TTAGCTG
Found at i:3294 original size:25 final size:26
Alignment explanation
Indices: 3200--3312 Score: 105
Period size: 25 Copynumber: 4.5 Consensus size: 26
3190 AGCCTCAGTT
* * *
3200 TTGCATATTTAGTA-AGGTCATATAA
1 TTGCATATTCAGTAGGGGTCATATAG
3225 TTGCATATTCAGTAGGGG-C--AT-G
1 TTGCATATTCAGTAGGGGTCATATAG
3247 TT-CTATATTCAGTAGGGCGTCATATAG
1 TTGC-ATATTCAGTAGGG-GTCATATAG
*
3274 TTGCATATT-AGTTGGGGTCATATAG
1 TTGCATATTCAGTAGGGGTCATATAG
* *
3299 TTCCATAGTCAGTA
1 TTGCATATTCAGTA
3313 AGGACCATTT
Statistics
Matches: 72, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
21 1 0.01
22 15 0.21
23 3 0.04
24 1 0.01
25 30 0.42
26 13 0.18
27 8 0.11
28 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.37
Consensus pattern (26 bp):
TTGCATATTCAGTAGGGGTCATATAG
Found at i:3519 original size:4 final size:4
Alignment explanation
Indices: 3510--3550 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
3500 AGTAGTGTAC
* *
3510 ACAT ACAT ACAT ACAT ACAT ACAT ATAT ACAC ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
3551 TATATATAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:3551 original size:16 final size:16
Alignment explanation
Indices: 3508--3554 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
3498 ATAGTAGTGT
*
3508 ACACATACATACATAC
1 ACACATACATATATAC
*
3524 ATACATACATATATAC
1 ACACATACATATATAC
3540 ACACATACATATATA
1 ACACATACATATATA
3555 TATAGTAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (16 bp):
ACACATACATATATAC
Done.