Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008930.1 Corchorus capsularis cultivar CVL-1 contig08951, 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: 2099
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Found at i:1114 original size:323 final size:322
Alignment explanation
Indices: 1--1494 Score: 2226
Period size: 323 Copynumber: 4.6 Consensus size: 322
*
1 ATTCGGAATAAAAATGAAAAAAATGATATTAGAAGCGTGAAAAATCCTCGATTTTTATGGTGATG
1 ATTCGGAATAAAAATGAAAAAAATCATATTAGAAGCGTGAAAAATCCTCGATTTTTATGGTGATG
*
66 AATTATAAAATTTTTTTAGTATTGTGGGAAAAATTGAGAAAAAAAAACTTTT-GGGTCAGTTTTT
66 AATTATAAATTTTTTTTAGTATTGTGGGAAAAATTGAG-AAAAAAAA-TTTTCGGGTCAGTTTTT
130 AGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCA-TTCTGGCGCACCGGCTCA
129 AGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCATTTC-GGCGCACCGGCTCA
* * ** * *
194 GTTTTGCATGATTTTTGACGGAGGGAATCCTTGTAATATCTG---TC-T---AACAAATCTCAGA
193 GTTTTGCATGATTTCTGACAGAAAGACTCCTTGTAATATCTGTATTCATCAAAACAAATCTCAGC
* * * *
252 CACAATAGCTTTAAGGA-TTTCTTTTACGAGCATCTGAATCTAGTTTCGATATAATTTGAAATAA
258 CACAATGGATTTAAGGATTTTTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTTGAAATAA
* *
316 ATTCGGAATAAAAATGAAAAAAATGATATTAGAAGCGTGAAAAAATCCACGATTTTTATGGTGAT
1 ATTCGGAATAAAAATGAAAAAAATCATATTAGAAGCGTG-AAAAATCCTCGATTTTTATGGTGAT
* *
381 GAATTATAAATTTTTTGTAGTATTGTGGGAAAAATTGAGAATAAAAAAAATTTCGGGTCAGTTTT
65 GAATTATAAATTTTTTTTAGTATTGTGGGAAAAATTGAG-A-AAAAAAATTTTCGGGTCAGTTTT
*
446 TAGCCGAAATCGTGTACTAACCATCACGGTTTTAGGCTAAAAATGCATTTCGGCGCACCGGCTCA
128 TAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCATTTCGGCGCACCGGCTCA
* * ** *
511 GTTTTGCATGATTTTTGACGGAGGGACTCCTTGTAATATCTGTATTAATCAAAACAAATCTCAGC
193 GTTTTGCATGATTTCTGACAGAAAGACTCCTTGTAATATCTGTATTCATCAAAACAAATCTCAGC
* *
576 CACAAAGGATTGAAGGATCTTTTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTTGAAATA
258 CACAATGGATTTAAGGAT-TTTTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTTGAAATA
641 A
322 A
* * * * ** *
642 ATTCGGAATAAAGATG-GAAAAATCATATTAGAAGCATGAAAAAACTCTTAATTTTTTTGGTGAT
1 ATTCGGAATAAAAATGAAAAAAATCATATTAGAAGCGTGAAAAATC-CTCGATTTTTATGGTGAT
* * * * * *
706 GAATAATAATTTTTTTTTAGTATTCTGGCAAAAAATTGAGAAATAAAATTTTCGTGTCAGTTTTT
65 GAATTATAAATTTTTTTTAGTATTGTGG-GAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTT
* *
771 AGCCGAAATCGTGTACTAACTATCACGGTTCTTGGCTAAAAATGCATTTCGGCGCACCGGCTCAG
129 AGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCATTTCGGCGCACCGGCTCAG
* *
836 TTTTGCATCATTTCTGGCAGAAAGACTACC-TGTAATATCTGTATTCATCAAAACAAATCTCAGC
194 TTTTGCATGATTTCTGACAGAAAGACT-CCTTGTAATATCTGTATTCATCAAAACAAATCTCAGC
900 CACAATGGATTTAAGGATTTTTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTTGAAATAA
258 CACAATGGATTTAAGGATTTTTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTTGAAATAA
965 ATTCGGAATAAAAATGAAAAAAATCATATTAGAAGCGTG-AAAATCCTCGATTTTTATGGTGATG
1 ATTCGGAATAAAAATGAAAAAAATCATATTAGAAGCGTGAAAAATCCTCGATTTTTATGGTGATG
* * * * * * *
1029 AATAATAATTTTTTTTTAGTATTCTGGCAAAAAAATTGAGAAATAAAATTTTCGTGTAAGTTTTT
66 AATTATAAATTTTTTTTAGTATTGTGG--GAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTT
* *
1094 AGCCGAAATCGTGTACTAACTATCACGGTTTTTGGCTAAAAATGCACTTCGGCGCACCGGCTCAG
129 AGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCATTTCGGCGCACCGGCTCAG
*
1159 TTTTGCATGATTTCTGGCAGAAAGACTACC-TGTAATATCTGTATTCATCAAAACAAATCTCAGC
194 TTTTGCATGATTTCTGACAGAAAGACT-CCTTGTAATATCTGTATTCATCAAAACAAATCTCAGC
1223 CACAATGGATTTAAGGATTTTTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTTGAAATAA
258 CACAATGGATTTAAGGATTTTTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTTGAAATAA
1288 ATTCGGAATAAAAATGAAAAAAATCATATTAGAAGCGTGAAAAAATCCTCGATTTTTATGGTGAT
1 ATTCGGAATAAAAATGAAAAAAATCATATTAGAAGCGTG-AAAAATCCTCGATTTTTATGGTGAT
* * *
1353 GAATTATAAATTTTTTTTAGTATTGTGGGAAAAATTGTGAAAAAAAAATTTCGGGTAAGTTTTTA
65 GAATTATAAATTTTTTTTAGTATTGTGGGAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTTA
* * * *
1418 GCCGAAATCGTATACTAACCATCACGGTTTTTGGCTAAAAAT-AAATTCTGGCGCACCGACTCAG
130 GCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCATTTC-GGCGCACCGGCTCAG
1482 TTTTGCATGATTT
194 TTTTGCATGATTT
1495 TTTACGGATG
Statistics
Matches: 1090, Mismatches: 68, Indels: 34
0.91 0.06 0.03
Matches are distributed among these distances:
315 39 0.04
316 66 0.06
317 119 0.11
318 3 0.00
320 1 0.00
321 1 0.00
322 47 0.04
323 431 0.40
324 204 0.19
325 109 0.10
326 70 0.06
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Consensus pattern (322 bp):
ATTCGGAATAAAAATGAAAAAAATCATATTAGAAGCGTGAAAAATCCTCGATTTTTATGGTGATG
AATTATAAATTTTTTTTAGTATTGTGGGAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTTAG
CCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCATTTCGGCGCACCGGCTCAGTT
TTGCATGATTTCTGACAGAAAGACTCCTTGTAATATCTGTATTCATCAAAACAAATCTCAGCCAC
AATGGATTTAAGGATTTTTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTTGAAATAA
Found at i:1248 original size:647 final size:639
Alignment explanation
Indices: 1--1494 Score: 2216
Period size: 647 Copynumber: 2.3 Consensus size: 639
* *
1 ATTCGGAATAAAAATGAAAAAAATGATATTAGAAGCGTGAAAAATC-CTCGATTTTTATGGTGAT
1 ATTCGGAATAAAAATGAAAAAAATCATATTAGAAGCGTGAAAAAACTCTCGATTTTTATGGTGAT
*
65 GAATTATAAAATTTTTTTAGTATTGTGGGAAAAATTGAGAAAAAAAAACTTTT-GGGTCAGTTTT
66 GAATTATAAATTTTTTTTAGTATTGTGGGAAAAATTGAG-AAAAAAAA-TTTTCGGGTCAGTTTT
129 TAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCATTCTGGCGCACCGGCTCA
129 TAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCATTCTGGCGCACCGGCTCA
* * **
194 GTTTTGCATGATTTTTGACGGAGGGAATCCTTGTAATATCTGTCTAACAAATCTCAGACACAATA
194 GTTTTGCATGATTTCTGACAGAAAGAATCCTTGTAATATCTGTCTAACAAATCTCAGACACAATA
*
259 GCTTTAAGGATTTCTTTTACGAGCATCTGAATCTAGTTTCGATATAATTTGAAATAAATTCGGAA
259 GATTTAAGGATTTCTTTTACGAGCATCTGAATCTAGTTTCGATATAATTTGAAATAAATTCGGAA
* *
324 TAAAAATGAAAAAAATGATATTAGAAGCGTGAAAAAATCCACGATTTTTATGGTGATGAATTATA
324 TAAAAATGAAAAAAATCATATTAGAAGCGTG-AAAAATCCACGATTTTTATGGTGATGAATAATA
* * *
389 AATTTTTTGTAGTATTGTGGGAAAAATTGAGAATAAAAAAAATTTCGGGTCAGTTTTTAGCCGAA
388 AATTTTTTGTAGTATTCTGGAAAAAATTGAGAATAAAAAAAATTTCGGGTAAGTTTTTAGCCGAA
*
454 ATCGTGTACTAACCATCACGGTTTTAGGCTAAAAATGCATTTCGGCGCACCGGCTCAGTTTTGCA
453 ATCGTGTACTAACCATCACGGTTTTAGGCTAAAAATGCACTTCGGCGCACCGGCTCAGTTTTGCA
* * **
519 TGATTTTTGACGGAGGGACTCCTTGTAATATCTGTATTAATCAAAACAAATCTCAGCCACAAAGG
518 TGATTTCTGACAGAAAGACTCCTTGTAATATCTGTATTAATCAAAACAAATCTCAGCCACAAAGG
584 ATTGAAGGATCTTTTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTTGAAATAA
583 ATTGAAGGA-CTTTTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTTGAAATAA
* * * ** *
642 ATTCGGAATAAAGATG-GAAAAATCATATTAGAAGCATGAAAAAACTCTTAATTTTTTTGGTGAT
1 ATTCGGAATAAAAATGAAAAAAATCATATTAGAAGCGTGAAAAAACTCTCGATTTTTATGGTGAT
* * * * * *
706 GAATAATAATTTTTTTTTAGTATTCTGGCAAAAAATTGAGAAATAAAATTTTCGTGTCAGTTTTT
66 GAATTATAAATTTTTTTTAGTATTGTGG-GAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTT
* *
771 AGCCGAAATCGTGTACTAACTATCACGGTTCTTGGCTAAAAATGCATT-TCGGCGCACCGGCTCA
130 AGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCATTCT-GGCGCACCGGCTCA
* * *
835 GTTTTGCATCATTTCTGGCAGAAAGACTACC-TGTAATATCTGTATTCATCAAAACAAATCTCAG
194 GTTTTGCATGATTTCTGACAGAAAGAAT-CCTTGTAATATCTG---TC-T---AACAAATCTCAG
* * * *
899 CCACAATGGATTTAAGGATTTTTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTTGAAATA
251 ACACAATAGATTTAAGGA-TTTCTTTTACGAGCATCTGAATCTAGTTTCGATATAATTTGAAATA
*
964 AATTCGGAATAAAAATGAAAAAAATCATATTAGAAGCGTG-AAAATCCTCGATTTTTATGGTGAT
315 AATTCGGAATAAAAATGAAAAAAATCATATTAGAAGCGTGAAAAATCCACGATTTTTATGGTGAT
* * * * *
1028 GAATAATAATTTTTTTTTAGTATTCTGGCAAAAAAATTGAG-A-AATAAAATTTTCGTGTAAGTT
380 GAATAATAAATTTTTTGTAGTATTCTGG--AAAAAATTGAGAATAAAAAAAATTTCGGGTAAGTT
* *
1091 TTTAGCCGAAATCGTGTACTAACTATCACGGTTTTTGGCTAAAAATGCACTTCGGCGCACCGGCT
443 TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTAGGCTAAAAATGCACTTCGGCGCACCGGCT
* *
1156 CAGTTTTGCATGATTTCTGGCAGAAAGACTACC-TGTAATATCTGTATTCATCAAAACAAATCTC
508 CAGTTTTGCATGATTTCTGACAGAAAGACT-CCTTGTAATATCTGTATTAATCAAAACAAATCTC
* * *
1220 AGCCACAATGGATTTAAGGATTTTTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTTGAAA
572 AGCCACAAAGGATTGAAGGACTTTTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTTGAAA
1285 TAA
637 TAA
1288 ATTCGGAATAAAAATGAAAAAAATCATATTAGAAGCGTGAAAAAA-TCCTCGATTTTTATGGTGA
1 ATTCGGAATAAAAATGAAAAAAATCATATTAGAAGCGTGAAAAAACT-CTCGATTTTTATGGTGA
* * *
1352 TGAATTATAAATTTTTTTTAGTATTGTGGGAAAAATTGTGAAAAAAAAATTTCGGGTAAGTTTTT
65 TGAATTATAAATTTTTTTTAGTATTGTGGGAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTT
* ** *
1417 AGCCGAAATCGTATACTAACCATCACGGTTTTTGGCTAAAAATAAATTCTGGCGCACCGACTCAG
130 AGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCATTCTGGCGCACCGGCTCAG
1482 TTTTGCATGATTT
195 TTTTGCATGATTT
1495 TTTACGGATG
Statistics
Matches: 760, Mismatches: 74, Indels: 33
0.88 0.09 0.04
Matches are distributed among these distances:
640 30 0.04
641 164 0.22
642 12 0.02
644 2 0.00
645 1 0.00
646 162 0.21
647 266 0.35
648 30 0.04
649 93 0.12
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Consensus pattern (639 bp):
ATTCGGAATAAAAATGAAAAAAATCATATTAGAAGCGTGAAAAAACTCTCGATTTTTATGGTGAT
GAATTATAAATTTTTTTTAGTATTGTGGGAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTTA
GCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCATTCTGGCGCACCGGCTCAGT
TTTGCATGATTTCTGACAGAAAGAATCCTTGTAATATCTGTCTAACAAATCTCAGACACAATAGA
TTTAAGGATTTCTTTTACGAGCATCTGAATCTAGTTTCGATATAATTTGAAATAAATTCGGAATA
AAAATGAAAAAAATCATATTAGAAGCGTGAAAAATCCACGATTTTTATGGTGATGAATAATAAAT
TTTTTGTAGTATTCTGGAAAAAATTGAGAATAAAAAAAATTTCGGGTAAGTTTTTAGCCGAAATC
GTGTACTAACCATCACGGTTTTAGGCTAAAAATGCACTTCGGCGCACCGGCTCAGTTTTGCATGA
TTTCTGACAGAAAGACTCCTTGTAATATCTGTATTAATCAAAACAAATCTCAGCCACAAAGGATT
GAAGGACTTTTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTTGAAATAA
Done.