Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022428.1 Corchorus olitorius cultivar O-4 contig22461, 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: 1835
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:1386 original size:317 final size:315
Alignment explanation
Indices: 1--1835 Score: 2373
Period size: 323 Copynumber: 5.8 Consensus size: 315
*
1 AAATTTTAGAAAAAATTTTTCGAGACACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
1 AAATTTCAGAAAAAATTTTTC-AGACACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
**
66 TGGGCTAAAAACAAGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTT
65 TGGGCTAAAAACGCGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTT
* * *
131 GAAAAATCTGTAATCATCGAACCAAATCTCAACCACAATGGATTTAAAGATATGTTTTTACGAGC
130 GAAAAATCTGTAATCATCAAACCAAATCTCAGCCACAATGGATTTAAGGATATGTTTTTACGAGC
* *
196 ATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAACGATATTGGATG
195 ATCTGAATTTGTTTCGATTTAATTAGAAATAAATTC-GGAAAAAATGGAAAAACGATATTGGAAG
* * * *
261 CGTGAAAAA-CC-GC---------TTGAACTCTATATTTTTCTGAGTATTTTGGCAA
259 CGTGAAAAACCCTTCAATTTTTTTTTGAATTATATATTTTTCTGAGTATTGTGGCAA
** * * * *
307 ACAA-TTCAG-AAATTTTTTTCAGGTCACTTTTTAGCCTAAATCGTGTACTAACCATCATGGTTT
1 A-AATTTCAGAAAAAATTTTTCA-GACACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTT
* * * * * ** *
370 TTAGCCTAAAAACGCGTTTCGGGGACCCGGCTTAGTTTTGCATCACATTTGGCAGAGAGCCTCCT
64 TTGGGCTAAAAACGCGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCT
* * *
435 TGAAATATCTGTATTCATCAAACCAAATCTCAGCCTCAATGGATTTAAGGATATGTTTTTACGAG
129 TGAAAAATCTGTAATCATCAAACCAAATCTCAGCCACAATGGATTTAAGGATATGTTTTTACGAG
* * * *
500 CATCTGAATTTAGTTTTGATTTAATTAGATATATATTC-GTAAAAATGGAAAAAACGATATTGGA
194 CATCTGAATTT-GTTTCGATTTAATTAGAAATAAATTCGGAAAAAATGG-AAAAACGATATTGGA
* *
564 TGCGTGAAAAACCCTTCAAATTTTAGTTTGTTTTGAATTATATATTTTTCCGAGTATTGTGGCAA
257 AGCGTGAAAAACCCTTC-AA--TT--TTT-TTTTGAATTATATATTTTTCTGAGTATTGTGGCAA
629 AAATTTCAGAAAAAATTTTTCGAGACACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
1 AAATTTCAGAAAAAATTTTTC-AGACACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
*
694 TGGGATAAAAACGCGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTT
65 TGGGCTAAAAACGCGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTT
* * *
759 GAAAAATTTGTAAACATCAAACCAAATCTCAGCGACAATGGATTTAAGGATATGTTTTTACGAGC
130 GAAAAATCTGTAATCATCAAACCAAATCTCAGCCACAATGGATTTAAGGATATGTTTTTACGAGC
* * * * *
824 ATCTGAATTTGTTTCGATTTAATCAGAAATAAATTCGGAAAAAA-AGCAAAACAATATTGAAAGC
195 ATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATGGAAAAACGATATTGGAAGC
*
888 GTGAAAAACCCTTAAATATTTTTTTTTGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAA
260 GTGAAAAACCCTT-CA-A--TTTTTTT---TTGAATTATATA-TTTTTCTGAGTATTGTGGCAA
* * * * *
952 ACAA-ATCAGAAAATATTTTTCAGGTCACTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTT
1 A-AATTTCAGAAAAAATTTTTCA-GACACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTT
* * * * **
1016 TTGGCCTAAAAACGCGTTTCGGGGAACCGGCTTAGTTTTGCATCACATTTGGCAGAAAGCCTCCT
64 TTGGGCTAAAAACGCGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCT
* **
1081 TGAAATAA-CTGTATTCATCAAACCAAATCTCAGCTTCAATGGATTTAAGGATATGTTTTTACGA
129 TGAAA-AATCTGTAATCATCAAACCAAATCTCAGCCACAATGGATTTAAGGATATGTTTTTACGA
* ** * * *
1145 GCATCTAAATTTAGTTTTTATTTAATTAGAAATATATTCGGAAAAAATGGAAAAATGATATTTGA
193 GCATCTGAATTT-GTTTCGATTTAATTAGAAATAAATTCGGAAAAAATGGAAAAACGATATTGGA
* * *
1210 AGAGTGAAAAACCCATCAATTTTTTTTTGAATTATATATTTTTCCGAGTATTGTGGCAA
257 AGCGTGAAAAACCCTTCAATTTTTTTTTGAATTATATATTTTTCTGAGTATTGTGGCAA
*
1269 AAATTTTAGAAAAAATTTTTCGAGACACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
1 AAATTTCAGAAAAAATTTTTC-AGACACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
**
1334 TGGGCTAAAAACAAGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTT
65 TGGGCTAAAAACGCGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTT
* * * *
1399 GAAAAATCTGTAATCATCGAATCAAATCTCAACCACAATGGATTTAAAGATATGTTTTTACGAGC
130 GAAAAATCTGTAATCATCAAACCAAATCTCAGCCACAATGGATTTAAGGATATGTTTTTACGAGC
* *
1464 ATCTGAATTTGTTTGGATTTAATTAGAAATAAATTCGGAAAAAAATTGAAAAACGATATTGGAAG
195 ATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCGG-AAAAAATGGAAAAACGATATTGGAAG
* *
1529 CGTGAAAAACCCTTCAATTTTTTTACGTTCAATTATATAATTTTTCTGAGTATTGTGGGAA
259 CGTGAAAAACCCTTCAATTTTTTT---TTGAATTATAT-ATTTTTCTGAGTATTGTGGCAA
*** * *
1590 AAATTTCAGAAATTTTTTTTCAGATCACTTTTTAGCCGAAATCGTGTACT---TATCACGGTTTT
1 AAATTTCAGAAAAAATTTTTCAGA-CACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
* * *
1652 TGGGCT-AAAACGCGTTTCGGGGACCCGGCTCAGTTTTGCATTATTTTTGACAGAAGGCCTCCTT
65 TGGGCTAAAAACGCGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTT
* * * *
1716 GAAAAATTTTTAATCAT-AGAACCAAATCTCAGTCACAATGGATTTAAGGATATATTTTTACGAG
130 GAAAAATCTGTAATCATCA-AACCAAATCTCAGCCACAATGGATTTAAGGATATGTTTTTACGAG
*
1780 TCATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGAAAAAC
194 -CATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCG-GAAAAAATGGAAAAAC
Statistics
Matches: 1328, Mismatches: 153, Indels: 84
0.85 0.10 0.05
Matches are distributed among these distances:
304 9 0.01
305 197 0.15
306 30 0.02
307 3 0.00
316 29 0.02
317 348 0.26
318 80 0.06
319 2 0.00
320 16 0.01
321 99 0.07
322 76 0.06
323 378 0.28
324 36 0.03
325 25 0.02
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (315 bp):
AAATTTCAGAAAAAATTTTTCAGACACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTT
GGGCTAAAAACGCGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTTG
AAAAATCTGTAATCATCAAACCAAATCTCAGCCACAATGGATTTAAGGATATGTTTTTACGAGCA
TCTGAATTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATGGAAAAACGATATTGGAAGCG
TGAAAAACCCTTCAATTTTTTTTTGAATTATATATTTTTCTGAGTATTGTGGCAA
Found at i:1551 original size:640 final size:640
Alignment explanation
Indices: 1--1835 Score: 2758
Period size: 640 Copynumber: 2.9 Consensus size: 640
1 AAATTTTAGAAAAAATTTTTCGAGACACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
1 AAATTTTAGAAAAAATTTTTCGAGACACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
66 TGGGCTAAAAACAAGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTT
66 TGGGCTAAAAACAAGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTT
131 GAAAAATCTGTAATCATCGAACCAAATCTCAACCACAATGGATTTAAAGATATGTTTTTACGAGC
131 GAAAAATCTGTAATCATCGAACCAAATCTCAACCACAATGGATTTAAAGATATGTTTTTACGAGC
* *
196 ATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAACGATATTGGATG
196 ATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAT-GAAAAACGATATTGGAAG
* * *
261 CGTGAAAAA--C--C---------GC-TTGAACTCTATATTTTTCTGAGTATTTTGGCAAACAAT
260 CGTGAAAAACCCTTCAATTTTTTTGCGTTGAATTATATATTTTTCTGAGTATTGTGGCAAACAAT
* * * *
312 TCAG-AAATTTTTTTCAGGTCACTTTTTAGCCTAAATCGTGTACTAACCATCATGGTTTTTAGCC
325 TCAGAAAATTTTTTTCAGGTCACTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGCC
*
376 TAAAAACGCGTTTCGGGGACCCGGCTTAGTTTTGCATCACATTTGGCAGAGAGCCTCCTTGAAAT
390 TAAAAACGCGTTTCGGGGACCCGGCTTAGTTTTGCATCACATTTGGCAGAAAGCCTCCTTGAAAT
* *
441 ATCTGTATTCATCAAACCAAATCTCAGCCTCAATGGATTTAAGGATATGTTTTTACGAGCATCTG
455 AACTGTATTCATCAAACCAAATCTCAGCTTCAATGGATTTAAGGATATGTTTTTACGAGCATCTG
* * * *
506 AATTTAGTTTTGATTTAATTAGATATATATTC-GTAAAAATGGAAAAAACGATATTGGATGCGTG
520 AATTTAGTTTTGATTTAATTAGAAATATATTCGGAAAAAATGG-AAAAACGATATTGGAAGAGTG
*
570 AAAAACCCTTCAAATTTTAGTTTGTTTTGAATTATATATTTTTCCGAGTATTGTGGCAA
584 AAAAACCCATCAAA-TTTA-TTTGTTTTGAATTATATATTTTTCCGAGTATTGTGGCAA
*
629 AAATTTCAGAAAAAATTTTTCGAGACACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
1 AAATTTTAGAAAAAATTTTTCGAGACACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
* **
694 TGGGATAAAAACGCGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTT
66 TGGGCTAAAAACAAGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTT
* * * * * *
759 GAAAAATTTGTAAACATCAAACCAAATCTCAGCGACAATGGATTTAAGGATATGTTTTTACGAGC
131 GAAAAATCTGTAATCATCGAACCAAATCTCAACCACAATGGATTTAAAGATATGTTTTTACGAGC
* * * *
824 ATCTGAATTTGTTTCGATTTAATCAGAAATAAATTCGGAAAAAAA-GCAAAACAATATTGAAAGC
196 ATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGAAAAACGATATTGGAAGC
*
888 GTGAAAAACCCTTAAATATTTTTTTTTGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAA
261 GTGAAAAACCCTT-CA-A--TTTTTTTGCGTTGAATTATATA-TTTTTCTGAGTATTGTGGCAAA
* *
953 CAAATCAGAAAATATTTTTCAGGTCACTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTT
321 CAATTCAGAAAATTTTTTTCAGGTCACTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTT
*
1018 GGCCTAAAAACGCGTTTCGGGGAACCGGCTTAGTTTTGCATCACATTTGGCAGAAAGCCTCCTTG
386 GGCCTAAAAACGCGTTTCGGGGACCCGGCTTAGTTTTGCATCACATTTGGCAGAAAGCCTCCTTG
1083 AAATAACTGTATTCATCAAACCAAATCTCAGCTTCAATGGATTTAAGGATATGTTTTTACGAGCA
451 AAATAACTGTATTCATCAAACCAAATCTCAGCTTCAATGGATTTAAGGATATGTTTTTACGAGCA
* * * *
1148 TCTAAATTTAGTTTTTATTTAATTAGAAATATATTCGGAAAAAATGGAAAAATGATATTTGAAGA
516 TCTGAATTTAGTTTTGATTTAATTAGAAATATATTCGGAAAAAATGGAAAAACGATATTGGAAGA
1213 GTGAAAAACCCATC-AA-TT-TTT-TTTTGAATTATATATTTTTCCGAGTATTGTGGCAA
581 GTGAAAAACCCATCAAATTTATTTGTTTTGAATTATATATTTTTCCGAGTATTGTGGCAA
1269 AAATTTTAGAAAAAATTTTTCGAGACACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
1 AAATTTTAGAAAAAATTTTTCGAGACACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
1334 TGGGCTAAAAACAAGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTT
66 TGGGCTAAAAACAAGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTT
*
1399 GAAAAATCTGTAATCATCGAATCAAATCTCAACCACAATGGATTTAAAGATATGTTTTTACGAGC
131 GAAAAATCTGTAATCATCGAACCAAATCTCAACCACAATGGATTTAAAGATATGTTTTTACGAGC
*
1464 ATCTGAATTTGTTTGGATTTAATTAGAAATAAATTCGGAAAAAAATTGAAAAACGATATTGGAAG
196 ATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAA-TGAAAAACGATATTGGAAG
* * *
1529 CGTGAAAAACCCTTCAATTTTTTTACGTTCAATTATATAATTTTTCTGAGTATTGTGGGAAA-AA
260 CGTGAAAAACCCTTCAATTTTTTTGCGTTGAATTATAT-ATTTTTCTGAGTATTGTGGCAAACAA
* *
1593 TTTCAGAAATTTTTTTTCAGATCACTTTTTAGCCGAAATCGTGTACT--T-ATCACGGTTTTTGG
324 -TTCAGAAAATTTTTTTCAGGTCACTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGG
* * * ** * *
1655 GCT-AAAACGCGTTTCGGGGACCCGGCTCAGTTTTGCATTATTTTTGACAGAAGGCCTCCTTGAA
388 CCTAAAAACGCGTTTCGGGGACCCGGCTTAGTTTTGCATCACATTTGGCAGAAAGCCTCCTTGAA
* * * * *
1719 A-AATTTTTAATCAT-AGAACCAAATCTCAG-TCACAATGGATTTAAGGATATATTTTTACGAGT
453 ATAA-CTGTATTCATCA-AACCAAATCTCAGCT-TCAATGGATTTAAGGATATGTTTTTACGAG-
* * *
1781 CATCTGAATTT-GTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGAAAAAC
514 CATCTGAATTTAGTTTTGATTTAATTAGAAATATATTCG-GAAAAAATGGAAAAAC
Statistics
Matches: 1095, Mismatches: 82, Indels: 53
0.89 0.07 0.04
Matches are distributed among these distances:
626 23 0.02
628 229 0.21
633 4 0.00
634 127 0.12
635 40 0.04
636 1 0.00
637 2 0.00
638 82 0.07
639 1 0.00
640 263 0.24
641 4 0.00
642 29 0.03
643 4 0.00
644 10 0.01
645 30 0.03
646 237 0.22
647 9 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (640 bp):
AAATTTTAGAAAAAATTTTTCGAGACACTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
TGGGCTAAAAACAAGTTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTT
GAAAAATCTGTAATCATCGAACCAAATCTCAACCACAATGGATTTAAAGATATGTTTTTACGAGC
ATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGAAAAACGATATTGGAAGC
GTGAAAAACCCTTCAATTTTTTTGCGTTGAATTATATATTTTTCTGAGTATTGTGGCAAACAATT
CAGAAAATTTTTTTCAGGTCACTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGCCT
AAAAACGCGTTTCGGGGACCCGGCTTAGTTTTGCATCACATTTGGCAGAAAGCCTCCTTGAAATA
ACTGTATTCATCAAACCAAATCTCAGCTTCAATGGATTTAAGGATATGTTTTTACGAGCATCTGA
ATTTAGTTTTGATTTAATTAGAAATATATTCGGAAAAAATGGAAAAACGATATTGGAAGAGTGAA
AAACCCATCAAATTTATTTGTTTTGAATTATATATTTTTCCGAGTATTGTGGCAA
Done.