Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014222.1 Corchorus capsularis cultivar CVL-1 contig14243, 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: 2610
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.31
Found at i:518 original size:53 final size:52
Alignment explanation
Indices: 440--565 Score: 189
Period size: 53 Copynumber: 2.4 Consensus size: 52
430 CAACAATTTC
*
440 ATTTGCACCATTACACCTTTAACTATGTAATAGGAATGCATCATATGACTTCA
1 ATTTGCACCATTACACCTTTAACTATGTAATAGGAATGCATAATA-GACTTCA
* *
493 ATTTGCATCATTACACCTTTCACTATGTAATAGGAATGCATAATAGACTTCA
1 ATTTGCACCATTACACCTTTAACTATGTAATAGGAATGCATAATAGACTTCA
* * *
545 ACTGGCACCATTATACCTTTA
1 ATTTGCACCATTACACCTTTA
566 GTACAATAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
52 23 0.35
53 42 0.65
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Consensus pattern (52 bp):
ATTTGCACCATTACACCTTTAACTATGTAATAGGAATGCATAATAGACTTCA
Found at i:1519 original size:534 final size:528
Alignment explanation
Indices: 1--1659 Score: 1545
Period size: 534 Copynumber: 3.1 Consensus size: 528
1 AATAGACTTAAACTGGCACCATTATACCTTTAGTATAATAGGAATGCCTTATCTCTTCACCTTAC
1 AATAGACTTAAACTGGCACCATTATACCTTTAGTATAATAGGAATGCCTTATCTCTTCACCTTAC
* *
66 ATGGATTTATGTAGAGAGAAGCACATGCTCACCAATTTACCAAAACCAGTAAGTATTTGATCTCT
66 ATGG-TTTATGTAGTGAGAAGCACATGCTCACC-ATTTACCAAAATCAGTAAGTATTTGATCTCT
*
131 AGTTAGTACAAACAACATAGTTTATGCAGACAAATAATGCAAGAAAAGATTTTGCATCCAATTTT
129 AGTTAGTACAGACAACATAGTTTATGCAGACAAATAATGCAAGAAAAGATTTTGCATCCAATTTT
*
196 TACACCTCTACAT-AAAAAAATAAGAAAGATGATTTCAATCATATAAAATCAGTGCAATATCAAT
194 TACACCTCTACATAAAAAAAATAAGAAAGATGATTTCAATCATGTAAAATCAGTGCAATATCAAT
* * *
260 TTACTTGGTTAAATTGAAAGCTCCAATAAAAAGTTATCAATGAATTACACAAGTGTATCCTGTAC
259 TTACTTGGTTAAATTGAAAGATCCAATAAAAAGTTATCAATGAATTAC-CCAGTGTAT--TTTAC
* *
325 AAT--CAAAATTTGAATAAGAAGTACTAAAAGCCCCAACACCCAAGCTTGCTTTTCACATTAGCA
321 AATAACAAAA--TGAATAAGAAGTAATAAAAGCCCCAACACCCAGGCTTGCTTTTCACATTAGCA
* * *
388 TCATTGTGACTTTACTACACAATAGGAATGCCATGTAAAACTCAACAATTTCATTTGCACCATTA
384 TCATTGTGACTTTACTACACAATAGGAATACCATGTAAAATTCAACAAATTCATTTGCACCATTA
*
453 CACCTTTAACTATGTAATAGGAATGCATCATATGACTTCAATTTGCATCATTACACCTTTCACTA
449 CACCTTTAACTATGTAATAGGAATGCATCATGT-ACTTCAATTTGCATCATTACACCTTTCACTA
518 TGTAATAGGAATGCAT
513 TGTAATAGGAATGCAT
* * *
534 AATAGACTTCAACTGGCACCATTATACCTTTAGTACAATAGGAATGCCTTATATCTTCA--TTAA
1 AATAGACTTAAACTGGCACCATTATACCTTTAGTATAATAGGAATGCCTTATCTCTTCACCTT-A
* * * *** ** * * * * *
597 TGCATAGATTACT-T--TCATCTGCACCATTAT-ACC-TTT-CGTATAAT-AGGAATGCCAACAC
65 --CATGGTTTA-TGTAGTGAGAAGCA-CATGCTCACCATTTAC-CAAAATCAGTAA-G----TAT
** * * * *** * ** * *
655 TCAAGC-CATAATATGAATTTGGGTC-ACATCCTCTGAT--A-ACATCAATAA-G-ATAGTAAA-
120 TTGATCTC-TAGT-T--AGTACAGACAACATAGT-TTATGCAGACA--AATAATGCA-AGAAAAG
* * * * * *** * * * ***
712 A-TTT-C--CGAATTTCATAAAAGACT-TAAACTAAAATTGAT-GGTTAAACGCTTACCCCCCAT
177 ATTTTGCATCCAATTT--TTACA-CCTCTACA-TAAAAAAAATAAG--AAA-GATGA--TTTCA-
* * * * *
771 AGTCA-GCACAAA-AAGT----TATCAATAGATTACCATGGTT---TT----TA-CCAAT--AAG
232 A-TCATGTA-AAATCAGTGCAATATCAAT---TTA-CTTGGTTAAATTGAAAGATCCAATAAAAA
** * **
820 GCAAT-AACTGAA--A--C-GTGTATTCTGTACAATAA-AAAATTGAAAAAGAAGGGGA-AAAA-
291 GTTATCAA-TGAATTACCCAGTGTATT-T-TACAATAACAAAA-TGAATAAGAA-GTAATAAAAG
** * * * * *
876 TTCCAACACCAAGGCTTGCTTTTCATATTGGCATCATTCTGACTTTACTACGCAATAGGAATACC
351 CCCCAACACCCAGGCTTGCTTTTCACATTAGCATCATTGTGACTTTACTACACAATAGGAATACC
* *
941 ATGTAGAATTCAACAAATTCATTTGCACCATTACACCTTTAACTATGTAATAGATAATGCATCAT
416 ATGTAAAATTCAACAAATTCATTTGCACCATTACACCTTTAACTATGTAATAG-GAATGCATCAT
** * *
1006 GTAAAATCAATTTGCATCATTACACCTTTTCACTACGTAATACG-ATGCAT
480 GT-ACTTCAATTTGCATCATTACACC-TTTCACTATGTAATAGGAATGCAT
*
1056 AATAGACTTAAATTGGCACCATTATACCTTTAGTATAATAGGAATGCCTTATCTCTTCACCTTAC
1 AATAGACTTAAACTGGCACCATTATACCTTTAGTATAATAGGAATGCCTTATCTCTTCACCTTAC
1121 ATGGTTTATGTAGTGAGAAGCACATGCTCACCATTTACCAAAATCAGTAAGTATTTGATCTCTAG
66 ATGGTTTATGTAGTGAGAAGCACATGCTCACCATTTACCAAAATCAGTAAGTATTTGATCTCTAG
1186 TTAGTACAGACAACATAGTTTATGCAGACAAATAATGCAAGAAAAGATTTTGCATCCAATTTTTA
131 TTAGTACAGACAACATAGTTTATGCAGACAAATAATGCAAGAAAAGATTTTGCATCCAATTTTTA
1251 CACCTCTACATAAAAAAAATAAGAAAGATGATTTCAATCATGTAAAATCAGTGCAATATCAATTT
196 CACCTCTACATAAAAAAAATAAGAAAGATGATTTCAATCATGTAAAATCAGTGCAATATCAATTT
*
1316 ACTTGGTTAAATTGAAAGATCCAATAAAAAGTTATCAATGAATTACCCATTG-ATTTTCACCAAT
261 ACTTGGTTAAATTGAAAGATCCAATAAAAAGTTATCAATGAATTACCCAGTGTATTTT-A-CAAT
*
1380 AACTGAAACAAGAATAAGAAGTAATAAAAGCCCCAACACCCAGGCTTGCTTTTCACATTAGCATC
324 AAC--AAA-ATGAATAAGAAGTAATAAAAGCCCCAACACCCAGGCTTGCTTTTCACATTAGCATC
* *
1445 ACTGTGACCTTACTACACAATAGGAATACCATGTAAAATTCAACAAATTCATTTGCACCATTACA
386 ATTGTGACTTTACTACACAATAGGAATACCATGTAAAATTCAACAAATTCATTTGCACCATTACA
* * * *
1510 CCTTTAACTATGTAATAGGAATGCATTTATG-ACTTCAATTTGCATCATTACAGCTTTAACCATG
451 CCTTTAACTATGTAATAGGAATGCA-TCATGTACTTCAATTTGCATCATTACACCTTTCACTATG
*
1574 TAATAGGAACGCAT
515 TAATAGGAATGCAT
* * * * * * * * *
1588 AGTAGTCGTCAATTAGCACCATTATACCTTTAGTGTAATAGGAGTGCCTTATCTCTTCACCTTGC
1 AATAGACTTAAACTGGCACCATTATACCTTTAGTATAATAGGAATGCCTTATCTCTTCACCTTAC
1653 ATGGTTT
66 ATGGTTT
1660 TGAGGTTCCA
Statistics
Matches: 863, Mismatches: 164, Indels: 199
0.70 0.13 0.16
Matches are distributed among these distances:
515 6 0.01
516 12 0.01
517 12 0.01
518 10 0.01
519 13 0.02
520 24 0.03
521 127 0.15
522 131 0.15
523 30 0.03
524 21 0.02
525 5 0.01
526 10 0.01
527 4 0.00
528 16 0.02
529 15 0.02
530 15 0.02
531 31 0.04
532 104 0.12
533 98 0.11
534 136 0.16
535 15 0.02
536 6 0.01
537 5 0.01
538 11 0.01
539 6 0.01
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (528 bp):
AATAGACTTAAACTGGCACCATTATACCTTTAGTATAATAGGAATGCCTTATCTCTTCACCTTAC
ATGGTTTATGTAGTGAGAAGCACATGCTCACCATTTACCAAAATCAGTAAGTATTTGATCTCTAG
TTAGTACAGACAACATAGTTTATGCAGACAAATAATGCAAGAAAAGATTTTGCATCCAATTTTTA
CACCTCTACATAAAAAAAATAAGAAAGATGATTTCAATCATGTAAAATCAGTGCAATATCAATTT
ACTTGGTTAAATTGAAAGATCCAATAAAAAGTTATCAATGAATTACCCAGTGTATTTTACAATAA
CAAAATGAATAAGAAGTAATAAAAGCCCCAACACCCAGGCTTGCTTTTCACATTAGCATCATTGT
GACTTTACTACACAATAGGAATACCATGTAAAATTCAACAAATTCATTTGCACCATTACACCTTT
AACTATGTAATAGGAATGCATCATGTACTTCAATTTGCATCATTACACCTTTCACTATGTAATAG
GAATGCAT
Found at i:1600 original size:52 final size:52
Alignment explanation
Indices: 1495--1619 Score: 153
Period size: 52 Copynumber: 2.4 Consensus size: 52
1485 CAACAAATTC
* * * *
1495 ATTTGCACCATTACACCTTTAACTATGTAATAGGAATGCATTTATGACTTCA
1 ATTTGCACCATTACACCTTTAACCATGTAATAGGAACGCATGTATGACGTCA
* * *
1547 ATTTGCATCATTACAGCTTTAACCATGTAATAGGAACGCATAGTA-GTCGTCA
1 ATTTGCACCATTACACCTTTAACCATGTAATAGGAACGCAT-GTATGACGTCA
* *
1599 ATTAGCACCATTATACCTTTA
1 ATTTGCACCATTACACCTTTA
1620 GTGTAATAGG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
52 59 0.97
53 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (52 bp):
ATTTGCACCATTACACCTTTAACCATGTAATAGGAACGCATGTATGACGTCA
Done.