Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014271.1 Corchorus olitorius cultivar O-4 contig14304, 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: 7788
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1267 original size:663 final size:664
Alignment explanation
Indices: 1--2066 Score: 3280
Period size: 663 Copynumber: 3.1 Consensus size: 664
* *
1 ACGCATTCCGGGAACCCGGCTCAGTTTTGCATGATTTTTTGCTCCAAGACTCCTTGAAATATCTA
1 ACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
* * * * *
66 TATTCATCTAGCCAAATCTCAGCCAGAACCGATTTAAGAATTTGTTTTTACGAGCAACGAAATCG
66 TATTCATCTAACCAAATCTCAGCCACAACCGATTTAAGGATTTGTTTTTACGAGCATCGGAATCG
131 TGTTTCGATTTTATTATAAATTAATTCAGAAAAACATAGCAAAAACGATATTCGAAGCGTGAAAT
131 TGTTTCGATTTTATTATAAATTAATTCAGAAAAACATAGCAAAAACGATATTCGAAGCGTGAAAT
*
196 GCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATTGTGGCAAAAAATAATAGA
196 GCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATTGTGGCCAAAAATAATAGA
261 AAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCATGTAC---CCATCACAGTTTTTG
261 AAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCATGTACTAACCATCACAGTTTTTG
* * *
323 GAGAAAAACGCATTCCGGGGCTCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAA
326 GCGAAAAACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAA
* * *
388 ATATCAATATTCTTCTAAACCAAACATGGTCACAT-TTGAAT-TAAGGATTTGTTTTTACGAGCA
391 ATATCTATATTCTTCT-AACCAAAC-TCGTC-CATATTGGATATAAGGATTTGTTTTTACGAGCA
* * * *
451 ACGGAATCGTGTTTCGATTTTATTATAAATTAATTCAGAAAAACATAGCAAAAACGATATTCGAA
453 TCAGAATCGTGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATAGGAAAAACGATATTCGAA
* * * * *
516 GCGTGAAATGCCC-TTAAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATTGTGGCTAA
518 GCGTGAAATGCCCTTTAAATATTTTTAGCATTAAAATATAAAATTTTTACAAGTATTGTGGCCAA
*
580 AAATAATAGAAAATTTTTTCGGGTCAATTTTGCAAAATTTTAGCAGAAATCGTGTACGTTAACCA
583 AAATAATAGAAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTAC--TAACCA
645 TCACAGTTTTTGGCGAAAA
646 TCACAGTTTTTGGCGAAAA
*
664 ACGCATTCCGGGACCCCGGCTCAGTTTTACATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
1 ACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
*
729 TATTCATCTAACCAAATCTCAGCCACAACCGATTTAAGGATTTGTTTTTACGAGCATCGGAATCA
66 TATTCATCTAACCAAATCTCAGCCACAACCGATTTAAGGATTTGTTTTTACGAGCATCGGAATCG
* * *
794 AGTTTCGATTTTATTATAAATTAATTC-GAAAAACATAGGAAAAACAATATTCGAAGCGTGAAAT
131 TGTTTCGATTTTATTATAAATTAATTCAGAAAAACATAGCAAAAACGATATTCGAAGCGTGAAAT
* *
858 GCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATTTTGGCCTAAAATAATAGA
196 GCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATTGTGGCCAAAAATAATAGA
*
923 AAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCATGTACTAACCATCACGGTTTTTG
261 AAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCATGTACTAACCATCACAGTTTTTG
* * * * * ** * *
988 GCTAAAAACGCGTTTCGGGACCCCGGCTCAGTTTTGCAT-A-TTTTCGCACCCGGACGCCATGAA
326 GCGAAAAACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAA
* * *
1051 ATATCTATATTCTTCTAGCCCAAACTCATCCATATTGGATATAAGGATTTGTTTTTACGAGTATC
391 ATATCTATATTCTTCTA-ACCAAACTCGTCCATATTGGATATAAGGATTTGTTTTTACGAGCATC
* * * *
1116 AAAATCTTGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATTGGAAAAACGATATTCGAATC
455 AGAATCGTGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATAGGAAAAACGATATTCGAAGC
*
1181 GTGAAATGCCCTTTAAAT-TTTTTAGCATTAAAATATACAATTTTTACAAGTATTGTGGCCAAAA
520 GTGAAATGCCCTTTAAATATTTTTAGCATTAAAATATAAAATTTTTACAAGTATTGTGGCCAAAA
*
1245 ATAATAGAAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGTAGAAATCGTGTACTAACCATCAC
585 ATAATAGAAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCATCAC
1310 AGTTTTTGGCGAAAA
650 AGTTTTTGGCGAAAA
* * *
1325 ACACATTCCGAGACCCTGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
1 ACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
* * * * *** * *
1390 TATTCTTCTAAACCAAA-CGCGGTCACATTGGAATTAAGGATTTGTTTTTACGAGCATCAGAATC
66 TATTCATCT-AACCAAATCTCAGCCACAACCGATTTAAGGATTTGTTTTTACGAGCATCGGAATC
*
1454 GTGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATAGCAAAAACGATATTCGAAGCGTGAAA
130 GTGTTTCGATTTTATTATAAATTAATTCAGAAAAACATAGCAAAAACGATATTCGAAGCGTGAAA
* * *
1519 TGCCCTTTAATATTTTTGGCATTCATTTATATAATTTTTACAAGTATTGTGGCCAAAAATAGTAG
195 TGCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATTGTGGCCAAAAATAATAG
* *
1584 AAAA-TTTTTCGGGTCAATTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCATCACAGTTTTT
260 AAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCATGTACTAACCATCACAGTTTTT
1648 GGCGAAAAACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGA
325 GGCGAAAAACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGA
* * *
1713 AATATCTATATTCATCTAACCAAATGTCGGT-CACATTGGA-ATTAAGGATTTGTTTTTACGAGC
390 AATATCTATATTCTTCTAACCAAA-CTC-GTCCATATTGGATA-TAAGGATTTGTTTTTACGAGC
1776 ATCAGAATCGTGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATAGGAAAAACGATATTCGA
452 ATCAGAATCGTGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATAGGAAAAACGATATTCGA
1841 AGCGTGAAATGCCCTTT-AATATTTTTAGCATTAAAATATAAAATTTTTACAAGTATTGTGGCCA
517 AGCGTGAAATGCCCTTTAAATATTTTTAGCATTAAAATATAAAATTTTTACAAGTATTGTGGCCA
*
1905 AAAATAATAGAAAATTTTTTCGGGTCAGTTTTGTAAAATTTTAGCAGAAATCGTGTACTAACCAT
582 AAAATAATAGAAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCAT
1970 CACAGTTTTTGGCGAAAA
647 CACAGTTTTTGGCGAAAA
*
1988 ACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTTCTTGAAATATCTA
1 ACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
2053 TATTCATCTAACCA
66 TATTCATCTAACCA
2067 CGTCATCGGT
Statistics
Matches: 1286, Mismatches: 102, Indels: 31
0.91 0.07 0.02
Matches are distributed among these distances:
661 256 0.20
662 272 0.21
663 703 0.55
664 8 0.01
665 47 0.04
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (664 bp):
ACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
TATTCATCTAACCAAATCTCAGCCACAACCGATTTAAGGATTTGTTTTTACGAGCATCGGAATCG
TGTTTCGATTTTATTATAAATTAATTCAGAAAAACATAGCAAAAACGATATTCGAAGCGTGAAAT
GCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATTGTGGCCAAAAATAATAGA
AAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCATGTACTAACCATCACAGTTTTTG
GCGAAAAACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAA
ATATCTATATTCTTCTAACCAAACTCGTCCATATTGGATATAAGGATTTGTTTTTACGAGCATCA
GAATCGTGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATAGGAAAAACGATATTCGAAGCG
TGAAATGCCCTTTAAATATTTTTAGCATTAAAATATAAAATTTTTACAAGTATTGTGGCCAAAAA
TAATAGAAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCATCACA
GTTTTTGGCGAAAA
Found at i:1746 original size:331 final size:332
Alignment explanation
Indices: 1--2066 Score: 3172
Period size: 329 Copynumber: 6.2 Consensus size: 332
* *
1 ACGCATTCCGGGAACCCGGCTCAGTTTTGCATGATTTTTTGCTCCAAGACTCCTTGAAATATCTA
1 ACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
* * * * *** * * *
66 TATTCATCTAGCCAAATCTCAGCCAGAACCGATTTAAGAATTTGTTTTTACGAGCAAC-GAAATC
66 TATTCATCTAACCAAATCTCGGTCACATTGGAATTAAGGATTTGTTTTTACGAGCATCAG-AATC
*
130 GTGTTTCGATTTTATTATAAATTAATTCAGAAAAACATAGCAAAAACGATATTCGAAGCGTGAAA
130 GTGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATAGCAAAAACGATATTCGAAGCGTGAAA
*
195 TGCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATTGTGGCAAAAAATAATAG
195 TGCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATTGTGGCCAAAAATAATAG
*
260 AAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCATGTAC---CCATCACAGTTTTT
260 AAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCATCACAGTTTTT
*
322 GGAGAAAA
325 GGCGAAAA
* * *
330 ACGCATTCCGGGGCTCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCAA
1 ACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
* * * *
395 TATTCTTCTAAACCAAA-CAT-GGTCACATTTGAATTAAGGATTTGTTTTTACGAGCAACGGAAT
66 TATTCATCT-AACCAAATC-TCGGTCACATTGGAATTAAGGATTTGTTTTTACGAGCATCAGAAT
*
458 CGTGTTTCGATTTTATTATAAATTAATTCAGAAAAACATAGCAAAAACGATATTCGAAGCGTGAA
129 CGTGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATAGCAAAAACGATATTCGAAGCGTGAA
* *
523 ATGCCCTTAAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATTGTGGCTAAAAATAATA
194 ATGCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATTGTGGCCAAAAATAATA
*
588 GAAAATTTTTTCGGGTCAATTTTGCAAAATTTTAGCAGAAATCGTGTACGTTAACCATCACAGTT
259 GAAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTAC--TAACCATCACAGTT
653 TTTGGCGAAAA
322 TTTGGCGAAAA
*
664 ACGCATTCCGGGACCCCGGCTCAGTTTTACATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
1 ACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
* * *** * * *
729 TATTCATCTAACCAAATCTCAGCCACAACCGATTTAAGGATTTGTTTTTACGAGCATCGGAATCA
66 TATTCATCTAACCAAATCTCGGTCACATTGGAATTAAGGATTTGTTTTTACGAGCATCAGAATCG
* * * *
794 AGTTTCGATTTTATTATAAATTAATTC-GAAAAACATAGGAAAAACAATATTCGAAGCGTGAAAT
131 TGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATAGCAAAAACGATATTCGAAGCGTGAAAT
* *
858 GCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATTTTGGCCTAAAATAATAGA
196 GCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATTGTGGCCAAAAATAATAGA
* *
923 AAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCATGTACTAACCATCACGGTTTTTG
261 AAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCATCACAGTTTTTG
*
988 GCTAAAA
326 GCGAAAA
* * * * ** * *
995 ACGCGTTTCGGGACCCCGGCTCAGTTTTGCAT-A-TTTTCGCACCCGGACGCCATGAAATATCTA
1 ACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
* * * * * *
1058 TATTCTTCTAGCCCAAA-CTC-ATCCATATTGG-ATATAAGGATTTGTTTTTACGAGTATCAAAA
66 TATTCATCTA-ACCAAATCTCGGT-CACATTGGAAT-TAAGGATTTGTTTTTACGAGCATCAGAA
* * * *
1120 TCTTGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATTGGAAAAACGATATTCGAATCGTGA
128 TCGTGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATAGCAAAAACGATATTCGAAGCGTGA
* * * *
1185 AATGCCCTTTAA-ATTTTTTAGCATTAAAATATACAATTTTTACAAGTATTGTGGCCAAAAATAA
193 AATGCCCTTTAATA-TTTTTGGCATTGAATTATATAATTTTTACAAGTATTGTGGCCAAAAATAA
*
1249 TAGAAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGTAGAAATCGTGTACTAACCATCACAGTT
257 TAGAAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCATCACAGTT
1314 TTTGGCGAAAA
322 TTTGGCGAAAA
* * *
1325 ACACATTCCGAGACCCTGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
1 ACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
* *
1390 TATTCTTCTAAACCAAA-CGCGGTCACATTGGAATTAAGGATTTGTTTTTACGAGCATCAGAATC
66 TATTCATCT-AACCAAATCTCGGTCACATTGGAATTAAGGATTTGTTTTTACGAGCATCAGAATC
1454 GTGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATAGCAAAAACGATATTCGAAGCGTGAAA
130 GTGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATAGCAAAAACGATATTCGAAGCGTGAAA
* * *
1519 TGCCCTTTAATATTTTTGGCATTCATTTATATAATTTTTACAAGTATTGTGGCCAAAAATAGTAG
195 TGCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATTGTGGCCAAAAATAATAG
*
1584 AAAA-TTTTTCGGGTCAATTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCATCACAGTTTTT
260 AAAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCATCACAGTTTTT
1648 GGCGAAAA
325 GGCGAAAA
1656 ACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
1 ACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
*
1721 TATTCATCTAACCAAATGTCGGTCACATTGGAATTAAGGATTTGTTTTTACGAGCATCAGAATCG
66 TATTCATCTAACCAAATCTCGGTCACATTGGAATTAAGGATTTGTTTTTACGAGCATCAGAATCG
*
1786 TGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATAGGAAAAACGATATTCGAAGCGTGAAAT
131 TGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATAGCAAAAACGATATTCGAAGCGTGAAAT
* * * *
1851 GCCCTTTAATATTTTTAGCATTAAAATATAAAATTTTTACAAGTATTGTGGCCAAAAATAATAGA
196 GCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATTGTGGCCAAAAATAATAGA
*
1916 AAATTTTTTCGGGTCAGTTTTGTAAAATTTTAGCAGAAATCGTGTACTAACCATCACAGTTTTTG
261 AAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCATCACAGTTTTTG
1981 GCGAAAA
326 GCGAAAA
*
1988 ACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTTCTTGAAATATCTA
1 ACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
2053 TATTCATCTAACCA
66 TATTCATCTAACCA
2067 CGTCATCGGT
Statistics
Matches: 1588, Mismatches: 126, Indels: 43
0.90 0.07 0.02
Matches are distributed among these distances:
328 1 0.00
329 371 0.23
330 206 0.13
331 361 0.23
332 341 0.21
333 154 0.10
334 154 0.10
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (332 bp):
ACGCATTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTA
TATTCATCTAACCAAATCTCGGTCACATTGGAATTAAGGATTTGTTTTTACGAGCATCAGAATCG
TGTTTCGATTTTATTATAAATTAATTCAGAAAAAAATAGCAAAAACGATATTCGAAGCGTGAAAT
GCCCTTTAATATTTTTGGCATTGAATTATATAATTTTTACAAGTATTGTGGCCAAAAATAATAGA
AAATTTTTTCGGGTCAGTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCATCACAGTTTTTG
GCGAAAA
Done.