Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005726.1 Corchorus capsularis cultivar CVL-1 contig05744, 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: 2820
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1346 original size:322 final size:319
Alignment explanation
Indices: 10--1682 Score: 2131
Period size: 318 Copynumber: 5.2 Consensus size: 319
1 GAATACTTG
* *
10 AAATATCTATATACATTGAACCAAATGTCAGCCACATTCGATATAAGTATTTGTTTTTACGAGCA
1 AAATATCTATATACATTGAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTA-GAGCA
* * * * *
75 TCTAAATTATATTTCGATTTAATTAGAAATTATTTCGG--AAAAATGGAAAAATCATGTTAGATG
65 TCTAAATCATATTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAATGATATTAGAAG
* * ** *
138 CGTGAAAAGCCCATCAATCTTTTTGGCGTTGAATTATATATTTTTCTAAATATTGTGTCCAAAAA
130 CGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTCTATGTATTGTG-GCAAAAA
* ** * * * *
203 ATTGGGAAAAAAAATTTCGGAACTGTTTTTAGCCAAAATTGTGTACTTA-CATCACGGTTTTTGG
194 ATTGAG-AAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
* * * * *
267 ATAAAAACGCGTTCCGGAGCCCCGGCTCAATTTCGCATAAATTTTGGGACAAAGACT-CTTCA
258 CTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCACAAAGACTCCTT-A
* * * *
329 AAATGT-TATATACATTGAAACAAATGTCAGCCATATTGGATATAAGGATTTGTTTTTACAGCAT
1 AAATATCTATATACATTGAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTAGAGCAT
* * *
393 CTAAATCATATATCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAATTGATATCAGAAGC
66 CTAAATCATATTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAATGATATTAGAAGC
* *
458 GTGAAAAGCTCGTCAATCTTTTTGG-AGTTGAATTATATATTTTTTCTAAGTATTGTGGCGAAAA
131 GTGAAAAGCCCGTCAATCTTTTTGGCA-TTGAATTATATA-TTTTTCTATGTATTGTGGC-AAAA
* * * *
522 ATTTG-GAAAAAAATTTCGGGTAAGTTTTGAGCCGAAATCGTGTACTAACCATCACGGTTTTTGA
193 AATTGAGAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
* * *
586 CAAAAAAAAAACGCGTTCCGGAGCCCTGGCTCAATTTTGCTTGATTTTTTGG-ACAAAGACTCCT
258 C----TAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGA-TTTTTGGCACAAAGACTCCT
650 TA
318 TA
* * * *
652 AAATGTATATATACATTGAACCAAATGTCAGCCACATTGGATATAAGGATTCGTTTTTACAGCAT
1 AAATATCTATATACATTGAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTAGAGCAT
**
717 CTAAATCATATTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAAAAGAAAAATGATATTAGAA
66 CTAAATCATATTTCGATTTAATTAGAAATTAATTCGG--AAAAAAATGGAAAAATGATATTAGAA
*
782 GCGTGAAAAGCCCGTCAATCTTTTTGG-ACTTGAATTAT-TTTTTTTCT-TAGTATTGT--CAAA
129 GCGTGAAAAGCCCGTCAATCTTTTTGGCA-TTGAATTATATATTTTTCTAT-GTATTGTGGCAAA
* **
842 AAATTGAGAAAAAAAATTTCGGGTCA-ATTTTAGCCGAAATCGTGTACTAACCATCACGAATTTT
192 AAATTGAG-AAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT
* * * * * * * * *
906 GGCTAAAAACGCGTTTCGGAGCCCCGACTCAATTTCGAATGATTTTTGGCGCAGAGAATACTTG
256 GGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCACAAAGACTCCTTA
*
970 AAATATCTATATACATTGAACCAAATGCCAGCCACATTGGATATAAGGATTTGTTTTTATGAGCA
1 AAATATCTATATACATTGAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTA-GAGCA
* *
1035 TCTAAATCTTAGTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAATGATATTAGAA
65 TCTAAATCATATTTCGATTTAATTAGAAATTAATTCGG-AAAAAAATGGAAAAATGATATTAGAA
* *
1100 GCGTGAAAAGCTCGTCAATCTTTTTGGCATTGAATTATATATTTTTCTGTGTATTGTGGCAAAAA
129 GCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTCTATGTATTGTGGCAAAAA
* * * *
1165 ATTGAG-AAAAAATTCTTGGGTCAGTTTTTAACCAAAATCGTGTACTAACAATCACGGTTTTTGC
194 ATTGAGAAAAAAATT-TCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG-
* * **
1229 GCTGAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATTTTTGGCTTAAAGACTCCTTA
257 GCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCACAAAGACTCCTTA
* * * * * *
1292 AAATATTTATATACATTGAACCATATGTCAACCGCATTGAATATAAGGATTTGTTTTTACGAGGA
1 AAATATCTATATACATTGAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTA-GAGCA
1357 TCTAAATCATATTTCGATTTAATTAGAAATTAATTCGG---AAAATGGAAAAATGATATTAGAAG
65 TCTAAATCATATTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAATGATATTAGAAG
* * * * *
1419 CGTGAAAACCCCGTCAATCTTTTTGACGTTGAATTATATATTTTTTTTTAGTATTGTGGCAAAAA
130 CGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTCTAT-GTATTGTGGCAAAAA
*
1484 ATTGAGAAAAAAACATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTG
194 ATTGAG-AAAAAA-ATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
* * * * * *
1549 ACTAAAAACGCGTTCCGGAGCCCCGGCTTAATTTTGCATGATTTTTGACACAAAAACTCCCTG
257 GCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCACAAAGACTCCTTA
* * * * *
1612 AAATATCTACATACATTGAACCAAATGTTAGTCACATTGGATATAAGAATTTGCTTTTAGGAGCA
1 AAATATCTATATACATTGAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTA-GAGCA
1677 TCTAAA
65 TCTAAA
1683 CCTATATATA
Statistics
Matches: 1182, Mismatches: 140, Indels: 63
0.85 0.10 0.05
Matches are distributed among these distances:
317 46 0.04
318 305 0.26
319 162 0.14
320 144 0.12
321 101 0.09
322 185 0.16
323 66 0.06
324 114 0.10
325 1 0.00
326 58 0.05
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (319 bp):
AAATATCTATATACATTGAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTAGAGCAT
CTAAATCATATTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAATGATATTAGAAGC
GTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTCTATGTATTGTGGCAAAAAAT
TGAGAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTA
AAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCACAAAGACTCCTTA
Found at i:1595 original size:642 final size:639
Alignment explanation
Indices: 10--1691 Score: 2256
Period size: 642 Copynumber: 2.6 Consensus size: 639
1 GAATACTTG
* *
10 AAATATCTATATACATTGAACCAAATGTCAGCCACATTCGATATAAGTATTTGTTTTTACGAGCA
1 AAATATATATATACATTGAACCAAATGTCAGCCACATT-GATATAAGGATTTGTTTTTACGAGCA
* * * * *
75 TCTAAATTATATTTCGATTTAATTAGAAATTATTTCGGAAAAATGGAAAAATCATGTTAGATGCG
65 TCTAAATCATATTTCGATTTAATTAGAAATTAATTCGGAAAAATGGAAAAATGATATTAGAAGCG
* * * *
140 TGAAAAGCCCATCAATCTTTTTGGCGTTGAATTATATA-TTTTTCTAAATATTGTGTCCAAAAAA
130 TGAAAAGCCCGTCAATCTTTTTGACGTTGAATTATATATTTTTTCTTAGTATTGTG--CAAAAAA
* ** * * * * *
204 TTGGGAAAAAAAATTTCGGAACTGTTTTTAGCCAAAATTGTGTACTTA-CATCACGGTTTTTGGA
193 TTGAGAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTT-GA
* * * *
268 -TAAAAACGCGTTCCGGAGCCCCGGCTCAATTTCGCATAAATTTTGG-GACAAAGACTCTTCAAA
257 CTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTCGCATGATTTTTGGCG-C-AAGAATCTTGAAA
* * * *
331 -ATGTTATATACATTGAAACAAATGTCAGCCATATTGGATATAAGGATTTGTTTTTACAGCATCT
320 TAT-CTATATACATTGAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTAGAGCATCT
*
395 AAATCATATATCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAATTGATATCAGAAGCGT
384 AAATCATATATCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAATGATATCAGAAGCGT
*
460 GAAAAGCTCGTCAATCTTTTTGGAGTTGAATTATATATTTTTTCTAAGTATTGTGGCGAAAAATT
449 GAAAAGCTCGTCAATCTTTTTGGAGTTGAATTATATATTTTTTCTAAGTATTGTGGCGAAAAAAT
* * *
525 TGGAAAAAAATTTCGGGTAAGTTTTGAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACAAA
514 TGGAAAAAAATTTCGGGTAAGTTTTGAACCAAAATCGTGTACTAACAATCACGGTTTTTGAC-AA
*
590 AAAAAAACGCGTTCCGGAGCCCTGGCTCAATTTTGCTTGATTTTTTGGACAAAGACTCCTTA
578 AAAAAAACGCGTTCCGGAGCCCTGGCTCAATTTTGCATGATTTTTTGGACAAAGACTCCTTA
* *
652 AAATGTATATATACATTGAACCAAATGTCAGCCACATTGGATATAAGGATTCGTTTTTAC-AGCA
1 AAATATATATATACATTGAACCAAATGTCAGCCACATT-GATATAAGGATTTGTTTTTACGAGCA
**
716 TCTAAATCATATTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAAAAGAAAAATGATATTAGA
65 TCTAAATCATATTTCGATTTAATTAGAAATTAATTCGG----AAAAATGGAAAAATGATATTAGA
781 AGCGTGAAAAGCCCGTCAATCTTTTTGGAC-TTGAATTAT-T-TTTTTTCTTAGTATTGT-CAAA
126 AGCGTGAAAAGCCCGTCAATCTTTTT-GACGTTGAATTATATATTTTTTCTTAGTATTGTGCAAA
* *
842 AAATTGAGAAAAAAAATTTCGGGTCA-ATTTTAGCCGAAATCGTGTACTAACCATCACGAATTTT
190 AAATTGAGAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTT
* * * *
906 GGCTAAAAACGCGTTTCGGAGCCCCGACTCAATTTCGAATGATTTTTGGCGCAGAGAATACTTGA
255 GACTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTCGCATGATTTTTGGCGCA-AGAAT-CTTGA
*
971 AATATCTATATACATTGAACCAAATGCCAGCCACATTGGATATAAGGATTTGTTTTTATGAGCAT
318 AATATCTATATACATTGAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTA-GAGCAT
* *
1036 CTAAATCTTAGT-TCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAATGATATTAGAA
382 CTAAATCATA-TATCGATTTAATTAGAAATTAATTCGG-AAAAAAATGGAAAAATGATATCAGAA
**
1100 GCGTGAAAAGCTCGTCAATCTTTTTGGCA-TTGAATTATATA-TTTTTCTGTGTATTGTGGC-AA
445 GCGTGAAAAGCTCGTCAATCTTTTTGG-AGTTGAATTATATATTTTTTCTAAGTATTGTGGCGAA
* * *
1162 AAAATT-GAGAAAAAATTCTTGGGTCAGTTTTTAACCAAAATCGTGTACTAACAATCACGGTTTT
509 AAAATTGGA-AAAAAATT-TCGGGTAAGTTTTGAACCAAAATCGTGTACTAACAATCACGGTTTT
****
1226 TG-C-GCTGAAAACGCGTTCCGGAGTCCC-GGCTCAATTTTGCATGA-TTTTTGG-CTTAAAGAC
572 TGACAAAAAAAAACGCGTTCCGGAG-CCCTGGCTCAATTTTGCATGATTTTTTGGAC--AAAGAC
1286 TCCTTA
634 TCCTTA
* * * * *
1292 AAATATTTATATACATTGAACCATATGTCAACCGCATTGAATATAAGGATTTGTTTTTACGAGGA
1 AAATATATATATACATTGAACCAAATGTCAGCCACATTG-ATATAAGGATTTGTTTTTACGAGCA
1357 TCTAAATCATATTTCGATTTAATTAGAAATTAATTCGG-AAAATGGAAAAATGATATTAGAAGCG
65 TCTAAATCATATTTCGATTTAATTAGAAATTAATTCGGAAAAATGGAAAAATGATATTAGAAGCG
* *
1421 TGAAAACCCCGTCAATCTTTTTGACGTTGAATTATATATTTTTTTTTAGTATTGTGGCAAAAAAT
130 TGAAAAGCCCGTCAATCTTTTTGACGTTGAATTATATATTTTTTCTTAGTATTGT-GCAAAAAAT
1486 TGAGAAAAAAACATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGAC
194 TGAGAAAAAAA-ATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGAC
* * * * * *
1551 TAAAAACGCGTTCCGGAGCCCCGGCTTAATTTTGCATGATTTTTGACACAAAAACTCCCTGAAAT
258 TAAAAACGCGTTCCGGAGCCCCGGCTCAATTTCGCATGATTTTTGGCGCAAGAA-T-CTTGAAAT
* * * * *
1616 ATCTACATACATTGAACCAAATGTTAGTCACATTGGATATAAGAATTTGCTTTTAGGAGCATCTA
321 ATCTATATACATTGAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTA-GAGCATCTA
*
1681 AACCTATATAT
385 AATC-ATATAT
1692 ATAACATTTT
Statistics
Matches: 918, Mismatches: 89, Indels: 65
0.86 0.08 0.06
Matches are distributed among these distances:
635 3 0.00
636 54 0.06
637 1 0.00
638 17 0.02
639 8 0.01
640 137 0.15
641 183 0.20
642 278 0.30
643 103 0.11
644 79 0.09
645 53 0.06
646 2 0.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (639 bp):
AAATATATATATACATTGAACCAAATGTCAGCCACATTGATATAAGGATTTGTTTTTACGAGCAT
CTAAATCATATTTCGATTTAATTAGAAATTAATTCGGAAAAATGGAAAAATGATATTAGAAGCGT
GAAAAGCCCGTCAATCTTTTTGACGTTGAATTATATATTTTTTCTTAGTATTGTGCAAAAAATTG
AGAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGACTAA
AAACGCGTTCCGGAGCCCCGGCTCAATTTCGCATGATTTTTGGCGCAAGAATCTTGAAATATCTA
TATACATTGAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTAGAGCATCTAAATCAT
ATATCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAATGATATCAGAAGCGTGAAAAGC
TCGTCAATCTTTTTGGAGTTGAATTATATATTTTTTCTAAGTATTGTGGCGAAAAAATTGGAAAA
AAATTTCGGGTAAGTTTTGAACCAAAATCGTGTACTAACAATCACGGTTTTTGACAAAAAAAAAC
GCGTTCCGGAGCCCTGGCTCAATTTTGCATGATTTTTTGGACAAAGACTCCTTA
Found at i:1815 original size:19 final size:20
Alignment explanation
Indices: 1778--1818 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
1768 AAGTATGGGC
1778 CTAACCAAGTCATATATAGAT
1 CTAACCAAGTCA-ATATAGAT
1799 CTAACCAAGTC-ATATAGAT
1 CTAACCAAGTCAATATAGAT
1818 C
1 C
1819 AAATGGGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.45
21 11 0.55
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (20 bp):
CTAACCAAGTCAATATAGAT
Done.