Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005523.1 Corchorus capsularis cultivar CVL-1 contig05541, 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: 1944
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:1396 original size:654 final size:642
Alignment explanation
Indices: 4--1944 Score: 2297
Period size: 653 Copynumber: 3.0 Consensus size: 642
1 CTT
* * *
4 CTTGAAATATCTATAATT-ATCGAACCAATTGTCAGCCACATTGGATATAAGGATTTGTTTTAAT
1 CTTGAAATATCTAT-ATTCATCGAACTAAATGTCAGCCATATTGGATATAAGGATTTGTTTT-AT
* * * * * *
68 GAGCATCTAAATCTTGTTTCGATATATTTGGAAATTAATTCGG--AAAAATTGAAAAAAACAATA
64 GAACATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGAAAAAAACAATA
* *
131 TTAGAAGCGTGAAAAGCCAGTCAATCATATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTA
129 TTAGAAGCTTGAAAAGCCAGTCAATC-T-T-TTTAT--CATTGAATTATATATTTTTTCTGAGTA
196 TTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTCAGCCGAAATCGAG-TACGTTACA
189 TTGTGG-AAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTCAGCCGAAATC-AGTTAC-TTACA
*
260 TCACGGTTTTTGGGGTAAAAACGCGTTCCAGGAGCCCCAGCTCAATTTTGCATGATTTTTGGCAG
251 TCACGGTTTTTGGGGTAAAAACGCGTTCCAGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCAG
* * * * ** * **
325 AAAGACTCCCTGAAAAATTTCTATGTTCATC-AAACAAAGTCTCAGCCATTTTAGATATTAGGAT
316 AAAGACTCCTTG--AAATATCTATATTCATCGAACCAAA-TCTCAGCCACATTGGATA-TAATAT
* * *
389 TTGTTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTGGGAAAAAAAATGA
377 TTGTTTTTAT-GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAATGA
* ** * *
454 AAAAACGCTATTCCAAGCTTTG-AAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTT
440 AAAAACGATATTAGAAGC-GTGAAAAG-CCATCAATCTTTTTGGCATTGAATTATATA-TTTTTT
*
518 TGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTGCTGCCGAAATCGTGTACT
502 TGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTT-CAGCCGAAATCGTGTACT
* * ** * *
583 AACCCCATCACGGTTTTTGGATAAAAACGCGTTATGGGAGCTCCGGCTCAATTTCGCATGATTTT
566 AA--ACACCACGGTTTTTGGATAAAAACGCGTTCCGGGAGCACCGACTCAATTTCGCATGATTTT
*
648 TGGCAGAAGGACTC
629 TGGCAGAAAGACTC
* * * * *
662 CTTGAAATATCTATATTCGTCAAACTAAATCTCAGCCATATTGGATATAAGGATTTGATTTGTGA
1 CTTGAAATATCTATATTCATCGAACTAAATGTCAGCCATATTGGATATAAGGATTTGTTTTATGA
* * *
727 AGATCTCAATCTTGTTTCGATTTAATTAGAAATTAGTTCGGAAAAAAAAATGAGAAAAACAATAT
66 ACATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAAATGAAAAAAACAATAT
* * * *
792 TAGAAGCTTGAAAAGTCTGTCAATCTTTTTATCATTGACTTATATATTTTTTCTCAGTATTGTGG
130 TAGAAGCTTGAAAAGCCAGTCAATCTTTTTATCATTGAATTATATATTTTTTCTGAGTATTGTGG
* * * *
857 TAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAACCGAAATCAGTTACTAACCATCACAGT
195 -AAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTCAGCCGAAATCAGTTACTTA-CATCACGGT
** * * * * * *
922 TTTT-GTCTAAACATGCGTTCC-GGAGCCCCGGCTGAATTTTGCATGATTTTTGGAACAAACACT
258 TTTTGGGGTAAAAACGCGTTCCAGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCAGAAAGACT
* * * * * *
985 TCTTGAAATATCTATATTTATCGAACCAATTGTCAGCCACATTGGAAATAAATATTTCTTTTTAT
323 CCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATAT-AATATTTGTTTTTAT
* * * * *
1050 AAGCATCTGAATCTTGTTTCGATTTATTTGGAAACTAATTCGGAAAAAATTGAAAAAACGATATT
387 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGAAAAAACGATATT
1115 AGAAGCGTGAAAAGCCAGTCAATCTTTTCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATT
452 AGAAGCGTGAAAAGCCA-TCAA-----TCTTTTTGGCATTGAATTATATATTTTTT-TGAGTATT
* * * *
1180 GAGGCAAAAAATTGAGAAAATATTTTTCGGGTCAGTATTCGGCCGAAATCGTGTACTAAACACCA
510 GTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGT-TTCAGCCGAAATCGTGTACTAAACACCA
* * * * * *
1245 CGATTTTGAGGGTAAAAACGCGTTCCGGGAGCCCCGTCTCAATTTCGCATGATTTTTTGCAGAAA
574 CGGTTTT-TGGATAAAAACGCGTTCCGGGAGCACCGACTCAATTTCGCATGATTTTTGGCAGAAA
1310 GACTC
638 GACTC
* *
1315 CTTGAAATATCTATATTCATCGAATTAAATGTCAGCCATATTGGATATAAGGATTTGTTTTTTCG
1 CTTGAAATATCTATATTCATCGAACTAAATGTCAGCCATATTGGATATAAGGATTTGTTTTAT-G
*
1380 AACATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGAAAAAAACGATAT
65 AACATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGAAAAAAACAATAT
* * ** *
1445 TAGAAGCTTGAAAAGCCCGTCAATATTTTTGGCATTGAATTAAATATTTTTTCTGAGTATTGTGG
130 TAGAAGCTTGAAAAGCCAGTCAATCTTTTTATCATTGAATTATATATTTTTTCTGAGTATTGTGG
* * * * *
1510 CAAAATTTGAGAAAATACTTTTCGGGGTCAGTTTTCGGCCGAAATC-GTGTACTTACACCACGGT
195 AAAAAATTGAGAAAAAACTTTTC-GGGTCAGTTTTCAGCCGAAATCAGT-TACTTACATCACGGT
* * * *
1574 TTTTGGGGTAAAAACGCGTTCCGGGAGCCCTGACTCAATTTCGCATGATTTTTGGCAGAAAGACT
258 TTTTGGGGTAAAAACGCGTTCCAGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCAGAAAGACT
* * *
1639 CCTCGAAATATCTATATTCATCGAACCAAATCTCAGTCACATTGGATATAATGATTTGTTTTTAC
323 CCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAT-ATTTGTTTTTAT
* * * * *
1704 GAGCATCTGGATCTTCTTTCGATTTAATTAGAAATTAATTCAGAAAAAGAACGAAAAAATGATAT
387 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAA-AATGAAAAAACGATAT
* ** * *
1769 TAGAAGGGTGAAAAGTCCAAAAATCTTTTTGGCGTTGAATTATATGTTTCTTTT-AGTATTGTGG
451 TAGAAGCGTGAAAAG-CCATCAATCTTTTTGGCATTGAATTATATATTT-TTTTGAGTATTGTGG
* * * * * *
1833 CAGAAAATTGAGAAAAAACATTTCGGGTCAATTTTTAGCCAAAATCATGTACT-AAC-CTCACGG
514 CAAAAAATTGAGAAAAAACTTTTCGGGTC-AGTTTCAGCCGAAATCGTGTACTAAACAC-CACGG
* * *
1896 TTTTTTTGTTAAAAACGCGTTCC-GGAGCACCGACTCAATTTTGCATGAT
577 -TTTTTGGATAAAAACGCGTTCCGGGAGCACCGACTCAATTTCGCATGAT
Statistics
Matches: 1094, Mismatches: 159, Indels: 71
0.83 0.12 0.05
Matches are distributed among these distances:
647 24 0.02
648 26 0.02
649 86 0.08
650 65 0.06
651 41 0.04
652 48 0.04
653 275 0.25
654 269 0.25
655 120 0.11
656 3 0.00
657 44 0.04
658 51 0.05
659 1 0.00
660 41 0.04
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (642 bp):
CTTGAAATATCTATATTCATCGAACTAAATGTCAGCCATATTGGATATAAGGATTTGTTTTATGA
ACATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGAAAAAAACAATATT
AGAAGCTTGAAAAGCCAGTCAATCTTTTTATCATTGAATTATATATTTTTTCTGAGTATTGTGGA
AAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTCAGCCGAAATCAGTTACTTACATCACGGTTTT
TGGGGTAAAAACGCGTTCCAGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCT
TGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAATATTTGTTTTTATGAGC
ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGAAAAAACGATATTAGAA
GCGTGAAAAGCCATCAATCTTTTTGGCATTGAATTATATATTTTTTTGAGTATTGTGGCAAAAAA
TTGAGAAAAAACTTTTCGGGTCAGTTTCAGCCGAAATCGTGTACTAAACACCACGGTTTTTGGAT
AAAAACGCGTTCCGGGAGCACCGACTCAATTTCGCATGATTTTTGGCAGAAAGACTC
Found at i:1625 original size:325 final size:322
Alignment explanation
Indices: 4--1944 Score: 2170
Period size: 325 Copynumber: 5.9 Consensus size: 322
1 CTT
* * *
4 CTTGAAATATCTATAATT-ATCGAACCAATTGTCAGCCACATTGGATATAAGGATTTGTTTTAAT
1 CTTGAAATATCTAT-ATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTT-TT
* * * * * * *
68 GAGCATCTAAATCTTGTTTCGATATATTTGGAAATTAATTCGG--AAAAATTGAAAAAAACAATA
64 GAACATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATG-AAAAAACGATA
*
131 TTAGAAGCGTGAAAAGCCAGTCAATCATATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTA
128 TTAGAAGCGTGAAAAGCC---C-GTCA-ATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTA
* * *
196 TTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTCAGCCGAAATCGAGTACGTTACAT
188 TTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTCAGCCGAAATCGTGTAC-TAACAC
* * *
261 CACGGTTTTTGGGGTAAAAACGCGTTCCAGGAGCCCCAGCTCAATTTTGCATGATTTTTGGCAGA
252 CACGGTTTTTGGGGTAAAAACGCGTTCCGGGAGCCCGA-CTCAATTTCGCATGATTTTTGGCAGA
326 AAGACTC
316 AAGACTC
* * * * ** * *
333 CCTGAAAAATTTCTATGTTCATC-AAACAAAGTCTCAGCCATTTTAGATATTAGGATTTGTTTTT
1 CTTG--AAATATCTATATTCATCGAACCAAA-TCTCAGCCACATTGGATATAAGGATTTG-TTTT
* * *
397 TTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTGGGAAAAAAAATGAAAAAACGC
62 TT-GAACATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGAAAAAACGA
** * * *
462 TATTCCAAGCTTTG-AAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTTTGAGTATT
126 TATTAGAAGC-GTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATT
* * *
526 GTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTGCTGCCGAAATCGTGTACTAACCCCAT
190 GTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTCAGCCGAAATCGTGTACTAA---CAC
* ** *
591 CACGGTTTTT-GGATAAAAACGCGTTATGGGAGCTCCGGCTCAATTTCGCATGATTTTTGGCAGA
252 CACGGTTTTTGGGGTAAAAACGCGTTCCGGGAGC-CCGACTCAATTTCGCATGATTTTTGGCAGA
*
655 AGGACTC
316 AAGACTC
* * * * * *
662 CTTGAAATATCTATATTCGTCAAACTAAATCTCAGCCATATTGGATATAAGGATTTGATTTGTGA
1 CTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTTGA
* * *
727 AGATCTCAATCTTGTTTCGATTTAATTAGAAATTAGTTCGGAAAAAAAAATGAGAAAAACAATAT
66 ACATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAAATGA-AAAAACGATAT
* * * ** * *
792 TAGAAGCTTGAAAAGTCTGTCAATCTTTTTATCATTGACTTATATATTTTTTCTCAGTATTGTGG
129 TAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGG
* * * * *
857 TAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAACCGAAATCAGT-TACTAACCATCACAG
194 CAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTCAGCCGAAATC-GTGTACTAA-CACCACGG
** * * * * * * * *
921 TTTTT-GTCTAAACATGCGTTCC-GGAGCCCCGGCTGAATTTTGCATGATTTTTGGAACAAACAC
257 TTTTTGGGGTAAAAACGCGTTCCGGGAG-CCCGACTCAATTTCGCATGATTTTTGGCAGAAAGAC
*
984 TT
321 TC
* * * * ** *
986 CTTGAAATATCTATATTTATCGAACCAATTGTCAGCCACATTGGAAATAAATATTTCTTTTTAT-
1 CTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTT-TG
* * * * *
1050 AAGCATCTGAATCTTGTTTCGATTTATTTGGAAACTAATTCGG-AAAAAATTGAAAAAACGATAT
65 AA-CATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGAAAAAACGATAT
*
1114 TAGAAGCGTGAAAAGCCAGTCAATCTTTTCTTTTTGGCATTGAATTATATATTTTTTCTGAGTAT
129 TAGAAGCGTGAAAAGCCCGTCAA-----TCTTTTTGGCATTGAATTATATATTTTTTCTGAGTAT
* * * * *
1179 TGAGGCAAAAAATTGAGAAAATATTTTTCGGGTCAGTATTCGGCCGAAATCGTGTACTAAACACC
189 TGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTCAGCCGAAATCGTGTACT-AACACC
* * *
1244 AC-GATTTTGAGGGTAAAAACGCGTTCCGGGAGCCCCGTCTCAATTTCGCATGATTTTTTGCAGA
253 ACGGTTTTTG-GGGTAAAAACGCGTTCCGGGAG-CCCGACTCAATTTCGCATGATTTTTGGCAGA
1308 AAGACTC
316 AAGACTC
** * *
1315 CTTGAAATATCTATATTCATCGAATTAAATGTCAGCCATATTGGATATAAGGATTTGTTTTTTCG
1 CTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTT-G
1380 AACATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGAAAAAAACGATAT
65 AACATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATG-AAAAAACGATAT
* * *
1445 TAGAAGCTTGAAAAGCCCGTCAATATTTTTGGCATTGAATTAAATATTTTTTCTGAGTATTGTGG
129 TAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGG
* * * *
1510 C-AAAATTTGAGAAAATACTTTTCGGGGTCAGTTTTCGGCCGAAATCGTGTACTTACACCACGGT
194 CAAAAAATTGAGAAAAAACTTTTC-GGGTCAGTTTTCAGCCGAAATCGTGTACTAACACCACGGT
1574 TTTTGGGGTAAAAACGCGTTCCGGGAGCCCTGACTCAATTTCGCATGATTTTTGGCAGAAAGACT
258 TTTTGGGGTAAAAACGCGTTCCGGGAGCCC-GACTCAATTTCGCATGATTTTTGGCAGAAAGACT
1639 C
322 C
* * * *
1640 CTCGAAATATCTATATTCATCGAACCAAATCTCAGTCACATTGGATATAATGATTTGTTTTTACG
1 CTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTT-TG
* ** * * * * *
1705 AGCATCTGGATCTTCTTTCGATTTAATTAGAAATTAATTCAGAAAAAGAACGAAAAAATGATATT
65 AACATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGAAAAAACGATATT
* * *** * *
1770 AGAAGGGTGAAAAGTCCAAAAATCTTTTTGGCGTTGAATTATATGTTTCTTT-T-AGTATTGTGG
130 AGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTT-TTTCTGAGTATTGTGG
* * * * * *
1833 CAGAAAATTGAGAAAAAACATTTCGGGTCAATTTTTAGCCAAAATCATGTACTAAC-CTCACGGT
194 CAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTCAGCCGAAATCGTGTACTAACAC-CACGGT
** * *
1897 TTTTTTGTTAAAAACGCGTTCC-GGAGCACCGACTCAATTTTGCATGAT
258 TTTTGGGGTAAAAACGCGTTCCGGGAGC-CCGACTCAATTTCGCATGAT
Statistics
Matches: 1371, Mismatches: 198, Indels: 93
0.82 0.12 0.06
Matches are distributed among these distances:
322 53 0.04
323 73 0.05
324 157 0.11
325 285 0.21
326 99 0.07
327 233 0.17
328 114 0.08
329 183 0.13
330 33 0.02
331 69 0.05
332 42 0.03
333 21 0.02
334 9 0.01
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (322 bp):
CTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTTGA
ACATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGAAAAAACGATATTA
GAAGCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCA
AAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTCAGCCGAAATCGTGTACTAACACCACGGTTTT
TGGGGTAAAAACGCGTTCCGGGAGCCCGACTCAATTTCGCATGATTTTTGGCAGAAAGACTC
Done.