Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014654.1 Corchorus olitorius cultivar O-4 contig14687, 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: 2079
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:824 original size:331 final size:328
Alignment explanation
Indices: 8--1886 Score: 2923
Period size: 331 Copynumber: 5.7 Consensus size: 328
1 ATGGAAA
*
8 GGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATATCTAATTAAATGGATA
1 GGATTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTCCGAATTAATATCTAATTAAATGGAAA
* * * *
73 TCAGATTTTGATTCTCGTAAAAACAAATCTATAAATCCAATGTGGCTAAGATTTGTTTAGAAGAT
65 TCGGATTTTGATTCTCGTAAAAACAAATCCATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAA
* *
138 TATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGAAAAACAGAGCCGGGCCCCGGAACGCG
130 TATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGCCGGGCCCCGGAACGCG
* *
203 TTTTTAGCTAAAAACCGTGATGGTTAGTACATGAATTCGGCTAAAATTCTGTG-AAAACTGACCC
195 TTTTTAGCCAAAAACCGTGATGGTTAGTACATGAATTCGGCTAAAATTCTG-GCAAAACTGGCCC
267 GACAAATTTTTCTCAATTTTCGGCCACAATACTCATAGAAAATATATAATTCAACGCCAAAATGA
259 GACAAATTTTTCTCAATTTT-GGCCACAATACTCATAGAAAATATATAATTCAACGCCAAAATGA
332 TTGAAG
323 TTGAAG
* * * * *
338 GGCTTTTCTCGCTTCTAATATCGTTTTTACAATCTTTTCCAAATTAATATCTAATTAAATGGAAA
1 GGATTTTCACGCTTCTAATATCGTTTTTCCTAT-TTTTCCGAATTAATATCTAATTAAATGGAAA
* * * *
403 TCGGATTTAGATTCTCGTAAAAACAAAT-CATAAATCCAATTTGGCTGAAATTTGTTTAGAAGTA
65 TCGGATTTTGATTCTCGTAAAAACAAATCCATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAA
*
467 TATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGACGGGACCCCGGAACGC
130 TATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGCCGGG-CCCCGGAACGC
*
532 GTTTTTAGCCTAAAACCGTGATGGTTAGTACATG-ATTCCGGCTAAAATT-TGGCAAAAACTGGC
194 GTTTTTAGCCAAAAACCGTGATGGTTAGTACATGAATT-CGGCTAAAATTCTGGC-AAAACTGGC
* *
595 CCGACAAACTTTTTCTCAATTCTTGACCACAATAGTCAT-GAAAATTATATAATTCAACGCCAAA
257 CCGACAAA-TTTTTCTCAATT-TTGGCCACAATACTCATAGAAAA-TATATAATTCAACGCCAAA
* *
659 ATGATGGAAA
319 ATGATTGAAG
*
669 GGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTTCCGAATTAATATCTAATTAAATGGATAT
1 GGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTTCCGAATTAATATCTAATTAAATGGAAAT
*
734 CGGATTTTGATTCTCGTAAAAACAAATCTATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAAT
66 CGGATTTTGATTCTCGTAAAAACAAATCCATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAAT
*
799 ATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCGAAATAGAGCCGGGGCCCCGGAACGCG
131 ATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGCC-GGGCCCCGGAACGCG
864 TTTTTAGCCAAAAACCGTGATGGTTAGTACATGAATTCGGCTAAAATTCTGTG-AAAACTGAG-C
195 TTTTTAGCCAAAAACCGTGATGGTTAGTACATGAATTCGGCTAAAATTCTG-GCAAAACTG-GCC
*
927 CGACAAATTATTTCTCAATTTTTGGCCACAATACTCATAGAAAATATATAATTTAACGCCAAAAT
258 CGACAAATT-TTTCTCAA-TTTTGGCCACAATACTCATAGAAAATATATAATTCAACGCCAAAAT
*
992 AATTGAAG
321 GATTGAAG
* *
1000 GGCTTTTCTCGCTTCTAATATCGTTTTTCCTATTTTTCCGAATTAATATCTAATTAAATGGAAAT
1 GGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTTCCGAATTAATATCTAATTAAATGGAAAT
*
1065 CGAATTTTGATTCTCGTAAAAACAAATCCATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAAT
66 CGGATTTTGATTCTCGTAAAAACAAATCCATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAAT
1130 ATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGCCGCGGCCCCGGAACGCG
131 ATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGCCG-GGCCCCGGAACGCG
* * * * * *
1195 TTTTTAGCCAAAAACAGTGATGGTTAGTTCATGATTTCAGCTAAAATTTTAGCAAAAACTGGCCC
195 TTTTTAGCCAAAAACCGTGATGGTTAGTACATGAATTCGGCTAAAATTCTGGC-AAAACTGGCCC
* * * *
1260 GACAAATTTTTAATCAATTTTTAGCCACACTACTCAT-GAAAATTATATAATTCAATGCCAAAAT
259 GACAAATTTTT-CTCAA-TTTTGGCCACAATACTCATAGAAAA-TATATAATTCAACGCCAAAAT
1324 GATTGAAG
321 GATTGAAG
*
1332 GGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCAGAATTAATATCTAATTAAATGGAAA
1 GGATTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTCCGAATTAATATCTAATTAAATGGAAA
*
1397 TCGGATTTTGATTCTCGTAAAAACAAATCCATAAATGCAATGTGGCTGAGATTT-TTTAGAAGAA
65 TCGGATTTTGATTCTCGTAAAAACAAATCCATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAA
* *
1461 TATAGATATTGCAATGAGTCTGGGCACCAAAAATGATGCAAAATAGAGACGGGACCCCGGAACGC
130 TATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGCCGGG-CCCCGGAACGC
* *
1526 GTTTTTAGCCAAAAACCGTGATGCTTAGTACATGAATTCGGCTAAAATTCT-GCGAAAACTGACC
194 GTTTTTAGCCAAAAACCGTGATGGTTAGTACATGAATTCGGCTAAAATTCTGGC-AAAACTGGCC
*
1590 TGACAAATTATTTCTCAATTTTTGGCCACAATACTCATAGAAAATATATAATTCAACGCCAAAAT
258 CGACAAATT-TTTCTCAA-TTTTGGCCACAATACTCATAGAAAATATATAATTCAACGCCAAAAT
1655 GATTGAAG
321 GATTGAAG
* *
1663 GGCTTTTCTCGCTTCTAATATCGTTTTTCCTATTTTTCCGAATTAATATCTAATTAAATGGAAAT
1 GGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTTCCGAATTAATATCTAATTAAATGGAAAT
* *
1728 CGAATTTTGATTCTCGTAAAAACAAATCCATAAATCCAATGTGGCTGAGATTTGATTAGAAGAAT
66 CGGATTTTGATTCTCGTAAAAACAAATCCATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAAT
* * * *
1793 TTAGATATTGCAATGAGTCTGGGCAACAAAAATCACGCAAAATAGAGTCGGGGCCCCGGAACGCG
131 ATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAG-CCGGGCCCCGGAACGCG
* *
1858 TTTTTAGCCATAAACAGTGATGGTTAGTA
195 TTTTTAGCCAAAAACCGTGATGGTTAGTA
1887 GGCTAAAATC
Statistics
Matches: 1423, Mismatches: 97, Indels: 57
0.90 0.06 0.04
Matches are distributed among these distances:
328 1 0.00
329 86 0.06
330 301 0.21
331 712 0.50
332 239 0.17
333 84 0.06
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (328 bp):
GGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTTCCGAATTAATATCTAATTAAATGGAAAT
CGGATTTTGATTCTCGTAAAAACAAATCCATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAAT
ATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGCCGGGCCCCGGAACGCGT
TTTTAGCCAAAAACCGTGATGGTTAGTACATGAATTCGGCTAAAATTCTGGCAAAACTGGCCCGA
CAAATTTTTCTCAATTTTGGCCACAATACTCATAGAAAATATATAATTCAACGCCAAAATGATTG
AAG
Found at i:1597 original size:663 final size:660
Alignment explanation
Indices: 1--1886 Score: 3208
Period size: 663 Copynumber: 2.8 Consensus size: 660
1 ATGGAAAGGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATATCTAATTAA
1 ATGGAAAGGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATATCTAATTAA
* *
66 ATGGATATCAGATTTTGATTCTCGTAAAAACAAATCTATAAATCCAATGTGGCTAAGATTTGTTT
66 ATGGATATCGGATTTTGATTCTCGTAAAAACAAATCTATAAATCCAATGTGGCTGAGATTTGTTT
* * *
131 AGAAGATTATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGAAAAACAGAGCCGGGCCCCG
131 AGAAGAATATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGCCGGGCCCCG
*
196 GAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTACATGAATTCGGCTAAAATTCTGTGAAAAC
196 GAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGAATTCGGCTAAAATTCTGTGAAAAC
*
261 TGACCCGACAAATT-TTTCTCAATTTTCGGCCACAATACTCATAGAAAATATATAATTCAACGCC
261 TGA-CCGACAAATTATTTCTCAATTTTTGGCCACAATACTCATAGAAAATATATAATTCAACGCC
* * *
325 AAAATGATTGAAGGGCTTTTCTCGCTTCTAATATCGTTTTTACAATCTTTTCCAAATTAATATCT
325 AAAATGATTGAAGGGCTTTTCTCGCTTCTAATATCGTTTTTCCTAT-TTTTCCGAATTAATATCT
* * * *
390 AATTAAATGGAAATCGGATTTAGATTCTCGTAAAAACAAAT-CATAAATCCAATTTGGCTGAAAT
389 AATTAAATGGAAATCGAATTTTGATTCTCGTAAAAACAAATCCATAAATCCAATGTGGCTGAGAT
*
454 TTGTTTAGAAGTATATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGACGG
454 TTGTTTAGAAGAATATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGACGG
* * * *
519 GACCCCGGAACGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACATGATTCCGGCTAAAATTTGG
519 G-CCCCGGAACGCGTTTTTAGCCAAAAACAGTGATGGTTAGTACATGATTCCAGCTAAAATTTAG
* *
584 CAAAAACTGGCCCGACAAACTTTTTCTCAATTCTTGACCACAATAGTCATGAAAATTATATAATT
583 CAAAAACTGGCCCGACAAACTTTTTATCAATTCTTGACCACAATACTCATGAAAATTATATAATT
649 CAACGCCAAAATG
648 CAACGCCAAAATG
662 ATGGAAAGGATTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTCCGAATTAATATCTAATTAA
1 ATGGAAAGGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATATCTAATTAA
726 ATGGATATCGGATTTTGATTCTCGTAAAAACAAATCTATAAATCCAATGTGGCTGAGATTTGTTT
66 ATGGATATCGGATTTTGATTCTCGTAAAAACAAATCTATAAATCCAATGTGGCTGAGATTTGTTT
*
791 AGAAGAATATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCGAAATAGAGCCGGGGCCCC
131 AGAAGAATATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGCC-GGGCCCC
856 GGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGAATTCGGCTAAAATTCTGTGAAAA
195 GGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGAATTCGGCTAAAATTCTGTGAAAA
*
921 CTGAGCCGACAAATTATTTCTCAATTTTTGGCCACAATACTCATAGAAAATATATAATTTAACGC
260 CTGA-CCGACAAATTATTTCTCAATTTTTGGCCACAATACTCATAGAAAATATATAATTCAACGC
*
986 CAAAATAATTGAAGGGCTTTTCTCGCTTCTAATATCGTTTTTCCTATTTTTCCGAATTAATATCT
324 CAAAATGATTGAAGGGCTTTTCTCGCTTCTAATATCGTTTTTCCTATTTTTCCGAATTAATATCT
1051 AATTAAATGGAAATCGAATTTTGATTCTCGTAAAAACAAATCCATAAATCCAATGTGGCTGAGAT
389 AATTAAATGGAAATCGAATTTTGATTCTCGTAAAAACAAATCCATAAATCCAATGTGGCTGAGAT
*
1116 TTGTTTAGAAGAATATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGCCGC
454 TTGTTTAGAAGAATATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGACG-
* *
1181 GGCCCCGGAACGCGTTTTTAGCCAAAAACAGTGATGGTTAGTTCATGATTTCAGCTAAAATTTTA
518 GGCCCCGGAACGCGTTTTTAGCCAAAAACAGTGATGGTTAGTACATGATTCCAGCTAAAA-TTTA
* *
1246 GCAAAAACTGGCCCGACAAA-TTTTTAATCAATT-TTTAGCCACACTACTCATGAAAATTATATA
582 GCAAAAACTGGCCCGACAAACTTTTT-ATCAATTCTTGA-CCACAATACTCATGAAAATTATATA
*
1309 ATTCAATGCCAAAATG
645 ATTCAACGCCAAAATG
* * *
1325 ATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCAGAATTAATATCTAATTAA
1 ATGGAAAGGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATATCTAATTAA
* * *
1390 ATGGAAATCGGATTTTGATTCTCGTAAAAACAAATCCATAAATGCAATGTGGCTGAGATTT-TTT
66 ATGGATATCGGATTTTGATTCTCGTAAAAACAAATCTATAAATCCAATGTGGCTGAGATTTGTTT
* *
1454 AGAAGAATATAGATATTGCAATGAGTCTGGGCACCAAAAATGATGCAAAATAGAGACGGGACCCC
131 AGAAGAATATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGCCGGG-CCCC
* *
1519 GGAACGCGTTTTTAGCCAAAAACCGTGATGCTTAGTACATGAATTCGGCTAAAATTCTGCGAAAA
195 GGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGAATTCGGCTAAAATTCTGTGAAAA
1584 CTGACCTGACAAATTATTTCTCAATTTTTGGCCACAATACTCATAGAAAATATATAATTCAACGC
260 CTGACC-GACAAATTATTTCTCAATTTTTGGCCACAATACTCATAGAAAATATATAATTCAACGC
1649 CAAAATGATTGAAGGGCTTTTCTCGCTTCTAATATCGTTTTTCCTATTTTTCCGAATTAATATCT
324 CAAAATGATTGAAGGGCTTTTCTCGCTTCTAATATCGTTTTTCCTATTTTTCCGAATTAATATCT
1714 AATTAAATGGAAATCGAATTTTGATTCTCGTAAAAACAAATCCATAAATCCAATGTGGCTGAGAT
389 AATTAAATGGAAATCGAATTTTGATTCTCGTAAAAACAAATCCATAAATCCAATGTGGCTGAGAT
* * * * *
1779 TTGATTAGAAGAATTTAGATATTGCAATGAGTCTGGGCAACAAAAATCACGCAAAATAGAGTCGG
454 TTGTTTAGAAGAATATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGAC-G
*
1844 GGCCCCGGAACGCGTTTTTAGCCATAAACAGTGATGGTTAGTA
518 GGCCCCGGAACGCGTTTTTAGCCAAAAACAGTGATGGTTAGTA
1887 GGCTAAAATC
Statistics
Matches: 1163, Mismatches: 51, Indels: 20
0.94 0.04 0.02
Matches are distributed among these distances:
660 141 0.12
661 180 0.15
662 240 0.21
663 519 0.45
664 83 0.07
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (660 bp):
ATGGAAAGGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATATCTAATTAA
ATGGATATCGGATTTTGATTCTCGTAAAAACAAATCTATAAATCCAATGTGGCTGAGATTTGTTT
AGAAGAATATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGCCGGGCCCCG
GAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGAATTCGGCTAAAATTCTGTGAAAAC
TGACCGACAAATTATTTCTCAATTTTTGGCCACAATACTCATAGAAAATATATAATTCAACGCCA
AAATGATTGAAGGGCTTTTCTCGCTTCTAATATCGTTTTTCCTATTTTTCCGAATTAATATCTAA
TTAAATGGAAATCGAATTTTGATTCTCGTAAAAACAAATCCATAAATCCAATGTGGCTGAGATTT
GTTTAGAAGAATATAGATATTGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGACGGGC
CCCGGAACGCGTTTTTAGCCAAAAACAGTGATGGTTAGTACATGATTCCAGCTAAAATTTAGCAA
AAACTGGCCCGACAAACTTTTTATCAATTCTTGACCACAATACTCATGAAAATTATATAATTCAA
CGCCAAAATG
Done.