Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013499.1 Corchorus capsularis cultivar CVL-1 contig13520, 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: 4244
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2516 original size:572 final size:571
Alignment explanation
Indices: 1270--2841 Score: 2069
Period size: 572 Copynumber: 2.7 Consensus size: 571
1260 AATTAACTAG
* * * *
1270 AACTAGAATTTCCCGGCCGCGCTTCGGGAGCGGCTGTTTTATTTTATAAATTATTTTAAAAAAAT
1 AACTAGAATTTCCCGGCCGCGCTTCGCGTGCGGCTGTTTTATTTTATAAATTCTTTTAAGAAAA-
* * *
1335 TTCAGTTAAGAAATGAAATTTTGTTGTAAAATGATAACAAAACAAA-CGAAGAGAATAGAAAATT
65 TTCAGTTAAGAAATGAAATTTTGTTGTGAAATGATAACAAAACAAAGC-AAGGGAGTAG--AATT
*
1399 GAAGTATGGAAAAGATAAGAGAATAGAGAGACAATAGAATATGGAGAAA-AAGAACATATGAA-A
127 GAAGTAT-GAAAAGATAAGAGAATAGAGAGACAATAGAATATGGA-AAAGAAGAAAATATGAAGA
* * * * * * * **
1462 AAGGGAGAAATAGTTTTTATTCATCATATTTCATAACAAAATAAGTGGTGTATTTATAAACACAT
190 AGGGGAGAAATAGTTCTCATTCATCTTATTCCATAACAAAGTAAGTGGTCTATTTATAGGCACAT
* *
1527 AGATACATCACCATAAATATAAGAGGATGAACTTAGT-TATAGGTATAT-ATGTATGAATGAACC
255 AGATACATCACTATAAATATAAGGGGATGAACTTAGTATATAGGTATATGATGTATGAATGAA-C
* * * *
1590 AAGTTATTAATCTTATCCATGCTTTAATTTTAGATTCATGGACATCCACAATATACATGTATATT
319 AAATCATCAATCTTAT-CATGCTTTAA--TTAGATTCATGGACATCCACAACATACATGTATATT
1655 CATAACAAATTTATAATTAATTTATAATCATTTGATTAATTTATTTTATATAGGAAAAGGGGATG
381 CATAACAAA-TT-T-A-TAA--T-T-A--ATTTGA-TAATTTATTTTATATAGGAAAAGGGGATG
*
1720 AATGTCTTTTGATTTTTCCAAACTAAATGAATACAATTATAATAAACAAAACATTAGAAAATTAA
435 AATGTCTTTTAATTTTTCCAAACTAAATGAATACAATTATAATAAACAAAACATTAGAAAATTAA
* * * * *
1785 CTATTGACACTTGTCAAAAAAACCTAATACCATGTGGCACTCAATGAAAGCTTTGCTTATAAAAT
500 CTATTCACACTTGTCAAAAAAACCAAATACCATGTGGCACTCAATGAAAGCCTTACTCATAAAAT
* *
1850 TAATAGT
565 TAAGAGA
** ** * * * * *
1857 AGGTTTAATTTCTCGGCCGCGCTTTGCGTGTGACTGTTTTATTTTATAAATTCTTCTAAGAAAAT
1 AACTAGAATTTCCCGGCCGCGCTTCGCGTGCGGCTGTTTTATTTTATAAATTCTTTTAAGAAAAT
1922 TCAGTTAAGAAATGAAATTTTGTTGTGAAATGATAACAAAACAAAGCAAGGGAGTAGAATTGAAG
66 TCAGTTAAGAAATGAAATTTTGTTGTGAAATGATAACAAAACAAAGCAAGGGAGTAGAATTGAAG
* * *
1987 TATGTAAAAGACAAGAGAATAGAGAGATAATAAAATATGGAAAAGAAGAAAATATGAAGAAGGGG
131 TATG-AAAAGATAAGAGAATAGAGAGACAATAGAATATGGAAAAGAAGAAAATATGAAGAAGGGG
* **
2052 AGAAATTGTTCTCATTCATCTTATTCCATAACAAAGTAAGTGACCTATTTATAGGCACATAGATA
195 AGAAATAGTTCTCATTCATCTTATTCCATAACAAAGTAAGTGGTCTATTTATAGGCACATAGATA
* * * * * **
2117 CATCACTAAAAATATAAGGGGATGAACTTAGTACATAGGTATATGCCATATGTGTATGAATGAAT
260 CATCACTATAAATATAAGGGGATGAACTTAGTATATAGGTATATG--ATGTATGAATGAACAAAT
2182 CATCAATCTTATCTATGCTTTAATTAGATTCATGGACATCCACAACATACATGTATATTCATAAC
323 CATCAATCTTATC-ATGCTTTAATTAGATTCATGGACATCCACAACATACATGTATATTCATAAC
2247 AAATTTATAATT-ATTTGATAATTTATTTTATATAGG-AAAGGGGATGAATGTCTTTTAATTTTT
387 AAATTTATAATTAATTTGATAATTTATTTTATATAGGAAAAGGGGATGAATGTCTTTTAATTTTT
2310 CCAAACTAAATGAATACAA-TATAATAAACAAAACATTAGAAAATTAACTATTCACACTTGTCAA
452 CCAAACTAAATGAATACAATTATAATAAACAAAACATTAGAAAATTAACTATTCACACTTGTCAA
* * * * *
2374 AGAAACCAAATGCCATGTGGCGCTCAATG-AGGACCTTACTCATAAAATTAAGGGAA
517 AAAAACCAAATACCATGTGGCACTCAATGAAAG-CCTTACTCATAAAATTAAGAG-A
** *
2430 AACTAGAACCTCCCGGCCGCGCTTCGCGTGCGGCTG-TTTATCTTATAAATTCTTTTAAGAAAAT
1 AACTAGAATTTCCCGGCCGCGCTTCGCGTGCGGCTGTTTTATTTTATAAATTCTTTTAAGAAAAT
* *
2494 TCAGTTAAGAAATGAAATTTTGTTTTGAAATGATAACAAAACAAAGCAAGGGAGTAAAATTGAAG
66 TCAGTTAAGAAATGAAATTTTGTTGTGAAATGATAACAAAACAAAGCAAGGGAGTAGAATTGAAG
**
2559 TATAGAAAAGATAAGAGAAT--AGAGACAATAGAATATGGGGAAGAAGAAAATATGAAGAAGGGG
131 TAT-GAAAAGATAAGAGAATAGAGAGACAATAGAATATGGAAAAGAAGAAAATATGAAGAAGGGG
* * *
2622 AGAAATCGTTCACATTCATCTTATTCCATAAAAAAGTAAGTGGTCTATTTATAGGCACATAGATA
195 AGAAATAGTTCTCATTCATCTTATTCCATAACAAAGTAAGTGGTCTATTTATAGGCACATAGATA
*
2687 CATCACTATAAATATAAGGGGATGAACTTAGTATATAGGTGTATG-TGTATGAATGAACCAAATC
260 CATCACTATAAATATAAGGGGATGAACTTAGTATATAGGTATATGATGTATGAATGAA-CAAATC
* *
2751 ATCAAT-AT-TCATGCTTTAATTAGATTTATGGACATTCACAAGTCACAACATACATGTATATTC
324 ATCAATCTTATCATGCTTTAATTAGATTCATGGACA-T--C----CACAACATACATGTATATTC
2814 ATAACAAATTTATAATTAATTT-ATAATT
382 ATAACAAATTTATAATTAATTTGATAATT
2842 ATAATTTAAT
Statistics
Matches: 872, Mismatches: 92, Indels: 57
0.85 0.09 0.06
Matches are distributed among these distances:
565 23 0.03
566 3 0.00
567 10 0.01
568 11 0.01
570 141 0.16
571 2 0.00
572 234 0.27
573 76 0.09
574 18 0.02
575 6 0.01
579 1 0.00
580 1 0.00
582 3 0.00
583 5 0.01
584 57 0.07
585 90 0.10
586 107 0.12
587 53 0.06
588 21 0.02
589 10 0.01
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (571 bp):
AACTAGAATTTCCCGGCCGCGCTTCGCGTGCGGCTGTTTTATTTTATAAATTCTTTTAAGAAAAT
TCAGTTAAGAAATGAAATTTTGTTGTGAAATGATAACAAAACAAAGCAAGGGAGTAGAATTGAAG
TATGAAAAGATAAGAGAATAGAGAGACAATAGAATATGGAAAAGAAGAAAATATGAAGAAGGGGA
GAAATAGTTCTCATTCATCTTATTCCATAACAAAGTAAGTGGTCTATTTATAGGCACATAGATAC
ATCACTATAAATATAAGGGGATGAACTTAGTATATAGGTATATGATGTATGAATGAACAAATCAT
CAATCTTATCATGCTTTAATTAGATTCATGGACATCCACAACATACATGTATATTCATAACAAAT
TTATAATTAATTTGATAATTTATTTTATATAGGAAAAGGGGATGAATGTCTTTTAATTTTTCCAA
ACTAAATGAATACAATTATAATAAACAAAACATTAGAAAATTAACTATTCACACTTGTCAAAAAA
ACCAAATACCATGTGGCACTCAATGAAAGCCTTACTCATAAAATTAAGAGA
Found at i:2854 original size:17 final size:19
Alignment explanation
Indices: 2823--2867 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
2813 CATAACAAAT
2823 TTATAA-TTAATTTA-TAA
1 TTATAATTTAATTTATTAA
2840 TTATAATTTAA-TTATTAA
1 TTATAATTTAATTTATTAA
*
2858 -TATATTTTAA
1 TTATAATTTAA
2868 AGACGAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 18 0.72
18 7 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATAATTTAATTTATTAA
Found at i:3457 original size:14 final size:14
Alignment explanation
Indices: 3440--3470 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3430 GATGGATATA
3440 TATCGTATAATTCT
1 TATCGTATAATTCT
3454 TATCGTATAATTCT
1 TATCGTATAATTCT
3468 TAT
1 TAT
3471 ATATTGTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (14 bp):
TATCGTATAATTCT
Done.