Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010831.1 Corchorus capsularis cultivar CVL-1 contig10852, 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: 2068
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:741 original size:334 final size:332
Alignment explanation
Indices: 1--2068 Score: 3063
Period size: 334 Copynumber: 6.2 Consensus size: 332
* * * * * * * *
1 AGTTTT-TTTGATTTTTGACGCCAAGAGTCATTGGATTATCGATATTCATCTGCCCAAATCTCAT
1 AGTTTTGTGTGATTTTTGGCTCCAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCAT
* * * *
65 CAACATAGGAATTAAAGATTTGTTTTAACGAGCATCAGAATGCAATTTCAATTTAACTGGAAATT
66 CCACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATT
** *
130 AATTTAGAAAAGCATAGGAAAAACTGTATTTA-AAGCGCGAAAAACTCTTCAAACATTTTGGCGT
131 AATTCGGAAAAGCATAGGAAAAACTGTA-TTAGAAGCGCGAAAAACCCTTCAAACATTTTGGCGT
* * * *
194 TGATTTGTATATTTTCTATACGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCCATTTT
195 TGATTTATATATTTTTTATAAGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTTT
* * * *
259 TGCAAAATCTTGAACGAAACTGTGTGCTAATC-TGTACGATTTTAT-GCT-AAAATGCGTTCCGG
260 TGCAAAATCTTGACCGAAACCGTGTGCTAATCAT-CACGATTTT-TGGCTAAAAACGCGTTCCGG
321 GGTCCCGGCTC
323 GG-CCCGGCTC
** * * * *
332 AGTTTTGTGTGATTTTTTACACCAAGAATCCTTAGATTATCTATATTCATCTACCAAAATCTCAT
1 AGTTTTGTGTGATTTTTGGCTCCAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCAT
* * * *
397 CCATATAGGATTTAAATATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAACTGGAAATT
66 CCACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATT
*
462 AATTCGGAAAAGCATAGGAAAAACTATATTAGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTT
131 AATTCGGAAAAGCATAGGAAAAACTGTATTAGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTT
* * *
527 G-TTATATATATATTTTTATAAGTATTTTCGCCAAAAATTGAGGAAAAATCATTCGGGTCAACTT
196 GATT-TATATAT-TTTTTATAAGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTT
591 TTGCAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGCTAAAAACGCGTTCCGGG
259 TTGCAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGCTAAAAACGCGTTCCGGG
656 GCACCGGCTC
324 GC-CCGGCTC
666 AGTTTTGTGTGATTTTTGGCTCCAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCAT
1 AGTTTTGTGTGATTTTTGGCTCCAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCAT
*
731 CCACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCAATTTAACTGGAAATT
66 CCACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATT
*
796 AATTCGGAAAAGCATAGGAAAAAGCTGTATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGT
131 AATTCGGAAAAGCATAGGAAAAA-CTGTATTAGAAGCGCGAAAAACCCTTCAAACATTTTGGCGT
* *
861 TGATTTGTATATTTTTTGTAAGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTTT
195 TGATTTATATATTTTTTATAAGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTTT
* * * *
926 TGCAAAATCTTGACCGAAACCGTGTGCTAATCATCAAGATTTTTGGCT-AAAATGCATACCGGGG
260 TGCAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGCTAAAAACGCGTTCC-GGG
*
990 GCCCGACTC
324 GCCCGGCTC
** * * * *
999 AGTTTTGTGTGATTTTTTACGCCAAGAATCCTTAGATTATCTATATTCATCTACCAAAATCTCAT
1 AGTTTTGTGTGATTTTTGGCTCCAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCAT
* * *
1064 ACACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAACTGGAAATT
66 CCACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATT
*
1129 AATTCGGAAAAGCATAGGAAAAACTATATTAGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTT
131 AATTCGGAAAAGCATAGGAAAAACTGTATTAGAAGCGCGAAAAACCCTTCAAACATTTTGGCG-T
* * *
1194 TGATTTGA-ATATTTTTTATACGTATTTTGGCCAAAAATTGAGGAAAAATCAATCGGGTCAATTT
195 TGATTT-ATATATTTTTTATAAGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTT
* * *
1258 TTACAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGATAAAAAACGCTTTCCGG
259 TTGCAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGCT-AAAAACGCGTTCCGG
* *
1323 GGTCTCGACTC
323 GG-CCCGGCTC
* *
1334 TGTTTTGTGAGATTTTTGGCT-CAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCAT
1 AGTTTTGTGTGATTTTTGGCTCCAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCAT
* *
1398 CCACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAACTTCAATTTAACTGGATATT
66 CCACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATT
* *
1463 AAATCGGAAAAGCATAGGAAAAAGCTGTATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGT
131 AATTCGGAAAAGCATAGGAAAAA-CTGTATTAGAAGCGCGAAAAACCCTTCAAACATTTTGGCGT
* *
1528 TGATTTGA-ATTTTTTTTATACGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTT
195 TGATTT-ATATATTTTTTATAAGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTT
* *
1592 TTGCAAAATCTTGACCGAAACCGTGTGCT--TGATCACGATTTTTGGATAAAAACGCGTTCCGGG
259 TTGCAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGCTAAAAACGCGTTCC-GG
* *
1655 GGACTGGCTC
323 GGCCCGGCTC
* *
1665 AGTTGTGTGTGATTTTTGGCT-CTAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCAT
1 AGTTTTGTGTGATTTTTGGCTCCAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCAT
* * *
1729 CCACATAGGATTTAAAGATTTGATTTTACGAGCATCAGAATCCAATTTCAATTTTACTTGAAATT
66 CCACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATT
*
1794 AATTCGGAAAAGTATAGGAAAAACTGTATTTA-AAGCGCGAAAAACCCTTCAAACATTTTGGCGT
131 AATTCGGAAAAGCATAGGAAAAACTGTA-TTAGAAGCGCGAAAAACCCTTCAAACATTTTGGCGT
* * * *
1858 TGATTTGTATATTTTTTGTAAGTATTTTGGCAAAAAATTGAGGAAAAATTATTCAGGTCAATTTT
195 TGATTTATATATTTTTTATAAGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTTT
*
1923 TGCAAAATCTTGACCGAAACCGTGTGCT--TGATCACGATTTTTGGCTAAAAACGCGTTCCGGGG
260 TGCAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGCTAAAAACGCGTTCCGGGG
1986 CACCGGCTC
325 C-CCGGCTC
*
1995 AGTTTTGTGCGATTTTTGGCT-CAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCAT
1 AGTTTTGTGTGATTTTTGGCTCCAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCAT
2059 CCACATAGGA
66 CCACATAGGA
Statistics
Matches: 1591, Mismatches: 125, Indels: 43
0.90 0.07 0.02
Matches are distributed among these distances:
329 4 0.00
330 230 0.14
331 170 0.11
332 230 0.14
333 354 0.22
334 484 0.30
335 117 0.07
336 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (332 bp):
AGTTTTGTGTGATTTTTGGCTCCAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCAT
CCACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATT
AATTCGGAAAAGCATAGGAAAAACTGTATTAGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTT
GATTTATATATTTTTTATAAGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTTTT
GCAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGCTAAAAACGCGTTCCGGGGC
CCGGCTC
Found at i:1281 original size:667 final size:665
Alignment explanation
Indices: 1--2068 Score: 3248
Period size: 667 Copynumber: 3.1 Consensus size: 665
* * * * * *
1 AGTTTT-TTTGATTTTTGACGC-CAAGAGTCATTGGATTATCGATATTCATCTGCCCAAATCTCA
1 AGTTTTGTGTGATTTTTG--GCTCAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCA
* * * *
64 TCAACATAGGAATTAAAGATTTGTTTTAACGAGCATCAGAATGCAATTTCAATTTAACTGGAAAT
64 TCCACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAAT
** ** *
129 TAATTTAGAAAAGCATAGGAAAAA-CTGTATTTAAAGCGCGAAAAACTCTTCAAACATTTTGGCG
129 TAATTCGGAAAAGCATAGGAAAAAGCTGTATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCG
* *
193 TTGATTTGTATATTTTCTATACGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCCATTT
194 TTGATTTGTATATTTTTTATACGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTT
* * *
258 TTGCAAAATCTTGAACGAAACTGTGTGCTAATC-TGTACGATTTTAT-GCTAAAATGCGTTCCGG
259 TTGCAAAATCTTGACCGAAACCGTGTGCTAATCAT-CACGATTTT-TGGCTAAAATGCGTTCCGG
* *
321 GGTCCCGGCTCAGTTTTGTGTGATTTTTTACACCAAGAATCCTTAGATTATCTATATTCATCTAC
322 GGGCCCGGCTCAGTTTTGTGTGATTTTTTACGCCAAGAATCCTTAGATTATCTATATTCATCTAC
* *
386 CAAAATCTCATCCATATAGGATTTAAATATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTT
387 CAAAATCTCATCCACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTT
451 AACTGGAAATTAATTCGGAAAAGCATAGGAAAAACTATATTAGAAGCGCGAAAAACCCTTCAAAC
452 AACTGGAAATTAATTCGGAAAAGCATAGGAAAAACTATATTAGAAGCGCGAAAAACCCTTCAAAC
*
516 ATTTTGGCGTTG-TTAT-ATATATATTTTTATAAGTATTTTCGCCAAAAATTGAGGAAAAATCAT
517 ATTTTGGCGTTGATT-TGA-ATAT-TTTTTATAAGTATTTTGGCCAAAAATTGAGGAAAAATCAT
*
579 TCGGGTCAACTTTTGCAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGCTAAAA
579 TCGGGTCAATTTTTGCAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGCTAAAA
644 ACGCGTTCCGGGGCACCGGCTC
644 ACGCGTTCCGGGGCACCGGCTC
666 AGTTTTGTGTGATTTTTGGCTCCAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCAT
1 AGTTTTGTGTGATTTTTGGCT-CAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCAT
*
731 CCACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCAATTTAACTGGAAATT
65 CCACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATT
796 AATTCGGAAAAGCATAGGAAAAAGCTGTATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGT
130 AATTCGGAAAAGCATAGGAAAAAGCTGTATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGT
* *
861 TGATTTGTATATTTTTTGTAAGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTTT
195 TGATTTGTATATTTTTTATACGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTTT
* * *
926 TGCAAAATCTTGACCGAAACCGTGTGCTAATCATCAAGATTTTTGGCTAAAATGCATACCGGGGG
260 TGCAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGCTAAAATGCGTTCCGGGGG
*
991 CCCGACTCAGTTTTGTGTGATTTTTTACGCCAAGAATCCTTAGATTATCTATATTCATCTACCAA
325 CCCGGCTCAGTTTTGTGTGATTTTTTACGCCAAGAATCCTTAGATTATCTATATTCATCTACCAA
*
1056 AATCTCATACACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAAC
390 AATCTCATCCACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAAC
1121 TGGAAATTAATTCGGAAAAGCATAGGAAAAACTATATTAGAAGCGCGAAAAACCCTTCAAACATT
455 TGGAAATTAATTCGGAAAAGCATAGGAAAAACTATATTAGAAGCGCGAAAAACCCTTCAAACATT
* *
1186 TTGGCGTTTGATTTGAATATTTTTTATACGTATTTTGGCCAAAAATTGAGGAAAAATCAATCGGG
520 TTGGCG-TTGATTTGAATATTTTTTATAAGTATTTTGGCCAAAAATTGAGGAAAAATCATTCGGG
* *
1251 TCAATTTTTACAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGATAAAAAACGC
584 TCAATTTTTGCAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGCT-AAAAACGC
* * *
1316 TTTCCGGGGTC-TCGACTC
648 GTTCCGGGG-CACCGGCTC
* *
1334 TGTTTTGTGAGATTTTTGGCTCAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCATC
1 AGTTTTGTGTGATTTTTGGCTCAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCATC
* *
1399 CACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAACTTCAATTTAACTGGATATTA
66 CACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATTA
*
1464 AATCGGAAAAGCATAGGAAAAAGCTGTATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTT
131 ATTCGGAAAAGCATAGGAAAAAGCTGTATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTT
* *
1529 GATTTGAATTTTTTTTATACGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTTTT
196 GATTTGTATATTTTTTATACGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTTTT
* * *
1594 GCAAAATCTTGACCGAAACCGTGTGCT--TGATCACGATTTTTGGATAAAAACGCGTTCCGGGGG
261 GCAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGCT-AAAATGCGTTCCGGGGG
* * * * * * * *
1657 ACTGGCTCAGTTGTGTGTGA-TTTTT-GGCTCTAGAATCCTTGGATTATCTATATTTATCTACCC
325 CCCGGCTCAGTTTTGTGTGATTTTTTACGC-CAAGAATCCTTAGATTATCTATATTCATCTACCA
* * * *
1720 AAATCTCATCCACATAGGATTTAAAGATTTGATTTTACGAGCATCAGAATCCAATTTCAATTTTA
389 AAATCTCATCCACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAA
* * *
1785 CTTGAAATTAATTCGGAAAAGTATAGGAAAAACTGTATTTA-AAGCGCGAAAAACCCTTCAAACA
454 CTGGAAATTAATTCGGAAAAGCATAGGAAAAACTATA-TTAGAAGCGCGAAAAACCCTTCAAACA
* * * * *
1849 TTTTGGCGTTGATTTGTATATTTTTTGTAAGTATTTTGGCAAAAAATTGAGGAAAAATTATTCAG
518 TTTTGGCGTTGATTTGAATATTTTTTATAAGTATTTTGGCCAAAAATTGAGGAAAAATCATTCGG
*
1914 GTCAATTTTTGCAAAATCTTGACCGAAACCGTGTGCT--TGATCACGATTTTTGGCTAAAAACGC
583 GTCAATTTTTGCAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGCTAAAAACGC
1977 GTTCCGGGGCACCGGCTC
648 GTTCCGGGGCACCGGCTC
*
1995 AGTTTTGTGCGATTTTTGGCTCAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCATC
1 AGTTTTGTGTGATTTTTGGCTCAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCATC
2060 CACATAGGA
66 CACATAGGA
Statistics
Matches: 1299, Mismatches: 89, Indels: 34
0.91 0.06 0.02
Matches are distributed among these distances:
660 1 0.00
661 93 0.07
662 16 0.01
664 90 0.07
665 181 0.14
666 163 0.13
667 702 0.54
668 49 0.04
669 4 0.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (665 bp):
AGTTTTGTGTGATTTTTGGCTCAAGAATCCTTGGATTATCTATATTTATCTACCCAAATCTCATC
CACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATTA
ATTCGGAAAAGCATAGGAAAAAGCTGTATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTT
GATTTGTATATTTTTTATACGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTTTT
GCAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGCTAAAATGCGTTCCGGGGGC
CCGGCTCAGTTTTGTGTGATTTTTTACGCCAAGAATCCTTAGATTATCTATATTCATCTACCAAA
ATCTCATCCACATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAACT
GGAAATTAATTCGGAAAAGCATAGGAAAAACTATATTAGAAGCGCGAAAAACCCTTCAAACATTT
TGGCGTTGATTTGAATATTTTTTATAAGTATTTTGGCCAAAAATTGAGGAAAAATCATTCGGGTC
AATTTTTGCAAAATCTTGACCGAAACCGTGTGCTAATCATCACGATTTTTGGCTAAAAACGCGTT
CCGGGGCACCGGCTC
Done.