Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011693.1 Corchorus olitorius cultivar O-4 contig11726, 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: 3094
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:630 original size:329 final size:329
Alignment explanation
Indices: 24--1446 Score: 2098
Period size: 329 Copynumber: 4.3 Consensus size: 329
14 AAATCGTGTA
*
24 TTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTATTGCGGCAAAAAATTGAGGAAAAAC
1 TTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTATTGTGGCAAAAAATTGAGGAAAAAC
* *
89 TTTTCGGGTCAGTTTTTGCAAAATTTT-GCCGAAATCGTGTATAAACCATCACGGTTTCAGGCAA
66 TTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGGTTTCTGGCAA
* * *
153 AAAACGCGTTTCGTAGCCCCGGCTCAATTTTGCTTGATTTTAGGCGCAAAGACTCATTGAAATAT
131 AAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGCGCAAAGACTCATTGAAATAT
* *
218 CTATATTTATCTAACCAAATATTAGCCACAATGGATTTTGAA--ATTTGTTTTTACGAGCATCTG
196 CTATATTCATCTAACCAAATATTAGCCACAATAGA-TTT-AAGGATTTGTTTTTACGAGCATCTG
* * * * *
281 AATCTTGTTTCGATTTAACTAAAAATAAATTCGAAAAAAATG-GAAAACGATATTGGAAGCGTGA
259 AATCTTGTTTCGAATTAACTAAAAATAAATTCG-AAAAAATGCAAAAACGAAATTGGAAACATGA
345 AAATCCAT
323 AAA-CCAT
* ** *
353 TTTAACTTTTTGGGGTTGAATAATATAGTTTTTCTGAGTACTGTGGCAAAAAAATTGAGGAAAAA
1 TTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTATTGTGGC-AAAAAATTGAGGAAAAA
418 CTTTTCGGGTCAG-TTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGGTTTCTGGCA
65 CTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGGTTTCTGGCA
** * *
482 AAAAACGCGTTCCGGAGCCCCAACTCAATTTCGCTTGATTTTTGGCGCAAAGACTCCTTGAAA-A
130 AAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGCGCAAAGACTCATTGAAATA
* *
546 TCTATATTCATCTAACCAAATCTTAGGCACAATAGATTTAAGGATTTGTTTTTACGAGCATCTGA
195 TCTATATTCATCTAACCAAATATTAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCATCTGA
*
611 ATCTTGTTTCGAATTAACTAAAAAAAAATTCGAAAAAATGCAAAAACGAAATTGGAAACATGAAA
260 ATCTTGTTTCGAATTAACTAAAAATAAATTCGAAAAAATGCAAAAACGAAATTGGAAACATGAAA
676 ACC-T
325 ACCAT
* * * *
680 TTTAATTTCTTGGGGTTGAATAATATAATACATCAGAGTATTGTGGCAAAAAATTGAGGAAAAAC
1 TTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTATTGTGGCAAAAAATTGAGGAAAAAC
* * *
745 TTTTCGGGTCAGTTTTTGCAAAAATTTAGACGAAATCGTGTA-T---CATCACGGTTTTTGGCAA
66 TTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGGTTTCTGGCAA
* * *
806 AAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGGGCAAAGTCTCATTAAAATAT
131 AAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGCGCAAAGACTCATTGAAATAT
* * * *
871 CTATATTCATCTAACCAACTCTTAGCCACAATAGATTTAAGGAATTGTTTTCACGAGCATCTGAA
196 CTATATTCATCTAACCAAATATTAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCATCTGAA
* * * *
936 TCTTGTTTCGAATTAACTAAAAATAAATTCGAAAAAATGGAAAAATGAAATTGGAAACGTGGAAA
261 TCTTGTTTCGAATTAACTAAAAATAAATTCGAAAAAATGCAAAAACGAAATTGGAAACATGAAAA
*
1001 CCCT
326 CCAT
* *
1005 TTTAATTTTTTGGGGTTGAATAATATAGTAT-TTCAGAGTATTGTGGCAAAAAATTGAGGAAAAA
1 TTTAATTTTTTGGGGTTGAATAATATAGT-TCATCTGAGTATTGTGGCAAAAAATTGAGGAAAAA
* * *
1069 CTTTTCGGGTCAGTTTTTGCAAAATTTTAGCC-AAACTCGTGTATTAAACATTACGGTTTTTGGC
65 CTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAA-TCGTGTATTAACCATCACGGTTTCTGGC
* *
1133 AAAAAACGCGTTCTGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGCGCAAAGACTCCTTGAAAT
129 AAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGCGCAAAGACTCATTGAAAT
* **
1198 ATCTATATTCATCTAACCAAATATTAGCCACAATGGATTTTGGGATTTGTTTTTACGAGCATCTG
194 ATCTATATTCATCTAACCAAATATTAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCATCTG
* * * * *
1263 AATCTTTTTTCGATTTAATTAAAAATAAATTCGAAAAAAATGCCAAAAACGATATTGGAAGCATG
259 AATCTTGTTTCGAATTAACTAAAAATAAATTCG-AAAAAATG-CAAAAACGAAATTGGAAACATG
1328 AAAAACCAT
322 -AAAACCAT
* *
1337 TTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTATTGCGGCAAAAAATTGAGGAATAAC
1 TTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTATTGTGGCAAAAAATTGAGGAAAAAC
* * *
1402 TTTTCTGGTCAGTTTTTTCAAAATTTTAGCCTAAATCGTGTATTA
66 TTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTATTA
1447 GGATTTATTG
Statistics
Matches: 989, Mismatches: 86, Indels: 35
0.89 0.08 0.03
Matches are distributed among these distances:
323 72 0.07
324 128 0.13
325 97 0.10
326 32 0.03
327 69 0.07
328 13 0.01
329 325 0.33
330 128 0.13
331 18 0.02
332 104 0.11
333 3 0.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (329 bp):
TTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTATTGTGGCAAAAAATTGAGGAAAAAC
TTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGGTTTCTGGCAA
AAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGCGCAAAGACTCATTGAAATAT
CTATATTCATCTAACCAAATATTAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCATCTGAA
TCTTGTTTCGAATTAACTAAAAATAAATTCGAAAAAATGCAAAAACGAAATTGGAAACATGAAAA
CCAT
Found at i:1295 original size:653 final size:658
Alignment explanation
Indices: 24--1444 Score: 2198
Period size: 653 Copynumber: 2.2 Consensus size: 658
14 AAATCGTGTA
24 TTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTATTGCGGCAAAAAATTGAGGAAAAAC
1 TTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTATTGCGGCAAAAAATTGAGGAAAAAC
*
89 TTTTCGGGTCAGTTTTTGC-AAAATTTTGCCGAAATCGTGTATAAACCATCACGGTTTCAGGCAA
66 TTTTCGGGTCAGTTTTTGCAAAAATTTAGCCGAAATCGTGTAT--A-CATCACGGTTTCAGGCAA
* * *
153 AAAACGCGTTTCGTAGCCCCGGCTCAATTTTGCTTGATTTTAGGCGCAAAGACTCATTGAAATAT
128 AAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTAGGCGCAAAGACTCATTAAAATAT
* * * *
218 CTATATTTATCTAACCAAATATTAGCCACAATGGATTTTGAAATTTGTTTTTACGAGCATCTGAA
193 CTATATTCATCTAACCAAATATTAGCCACAATAGATTTAGAAATTTGTTTTCACGAGCATCTGAA
* * *
283 TCTTGTTTCGATTTAACTAAAAATAAATTCGAAAAAAATGGAAAACGATATTGGAAGCGTGAAAA
258 TCTTGTTTCGAATTAACTAAAAATAAATTCGAAAAAAATGGAAAACGAAATTGGAAACGTGAAAA
* *
348 TCCATTTTAACTTTTTGGGGTTGAATAATATAGTTTTTCTGAGTACTGTGGCAAAAAAATTGAGG
323 TCCATTTTAACTTTTTGGGGTTGAATAATATAGTATTTCAGAGTACTGTGGCAAAAAAATTGAGG
*
413 AAAAACTTTTCGGGTCAGTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGGTTTCT
388 AAAAACTTTTCGGGTCAGTTTTGCAAAATTTTAGCCGAAATCGTGTATTAAACATCACGGTTTCT
478 GGCAAAAAACGCGTTCCGGAGCCCCAACTCAATTTCGCTTGATTTTTGGCGCAAAGACTCCTTGA
453 GGCAAAAAACGCGTTCCGGAGCCCCAACTCAATTTCGCTTGATTTTTGGCGCAAAGACTCCTTGA
* *
543 AAATCTATATTCATCTAACCAAATCTTAGGCACAATAGATTTAAGGATTTGTTTTTACGAGCATC
518 AAATCTATATTCATCTAACCAAATATTAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCATC
608 TGAATCTTGTTTCGAATTAACTAAAAAAAAATTCG-AAAAAATG-CAAAAACGAAATTGGAAACA
583 TGAATCTTGTTTCGAATTAACTAAAAAAAAATTCGAAAAAAATGCCAAAAACGAAATTGGAAACA
671 TG-AAAACC-T
648 TGAAAAACCAT
* * * * *
680 TTTAATTTCTTGGGGTTGAATAATATAATACATCAGAGTATTGTGGCAAAAAATTGAGGAAAAAC
1 TTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTATTGCGGCAAAAAATTGAGGAAAAAC
* **
745 TTTTCGGGTCAGTTTTTGCAAAAATTTAGACGAAATCGTGTAT-CATCACGGTTTTTGGCAAAAA
66 TTTTCGGGTCAGTTTTTGCAAAAATTTAGCCGAAATCGTGTATACATCACGGTTTCAGGCAAAAA
* * *
809 ACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGGGCAAAGTCTCATTAAAATATCTA
131 ACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTAGGCGCAAAGACTCATTAAAATATCTA
* * *
874 TATTCATCTAACCAACTCTTAGCCACAATAGATTTAAGGAA-TTGTTTTCACGAGCATCTGAATC
196 TATTCATCTAACCAAATATTAGCCACAATAGATTT-AGAAATTTGTTTTCACGAGCATCTGAATC
* *
938 TTGTTTCGAATTAACTAAAAATAAATTCG-AAAAAATGGAAAAATGAAATTGGAAACGTGGAAA-
260 TTGTTTCGAATTAACTAAAAATAAATTCGAAAAAAATGG-AAAACGAAATTGGAAACGTGAAAAT
* * *
1001 CCCTTTTAATTTTTTGGGGTTGAATAATATAGTATTTCAGAGTATTGTGGC-AAAAAATTGAGGA
324 CCATTTTAACTTTTTGGGGTTGAATAATATAGTATTTCAGAGTACTGTGGCAAAAAAATTGAGGA
* *
1065 AAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCC-AAACTCGTGTATTAAACATTACGGTTTT
389 AAAACTTTTCGGGTCAG-TTTTGCAAAATTTTAGCCGAAA-TCGTGTATTAAACATCACGGTTTC
* ** *
1129 TGGCAAAAAACGCGTTCTGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGCGCAAAGACTCCTTG
452 TGGCAAAAAACGCGTTCCGGAGCCCCAACTCAATTTCGCTTGATTTTTGGCGCAAAGACTCCTTG
* **
1194 AAATATCTATATTCATCTAACCAAATATTAGCCACAATGGATTTTGGGATTTGTTTTTACGAGCA
517 AAA-ATCTATATTCATCTAACCAAATATTAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCA
* * * * * *
1259 TCTGAATCTTTTTTCGATTTAATTAAAAATAAATTCGAAAAAAATGCCAAAAACGATATTGGAAG
581 TCTGAATCTTGTTTCGAATTAACTAAAAAAAAATTCGAAAAAAATGCCAAAAACGAAATTGGAAA
1324 CATGAAAAACCAT
646 CATGAAAAACCAT
*
1337 TTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTATTGCGGCAAAAAATTGAGGAATAAC
1 TTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTATTGCGGCAAAAAATTGAGGAAAAAC
* * * *
1402 TTTTCTGGTCAGTTTTTTCAAAATTTTAGCCTAAATCGTGTAT
66 TTTTCGGGTCAGTTTTTGCAAAAATTTAGCCGAAATCGTGTAT
1445 TAGGATTTAT
Statistics
Matches: 694, Mismatches: 61, Indels: 19
0.90 0.08 0.02
Matches are distributed among these distances:
651 33 0.05
652 158 0.23
653 268 0.39
654 11 0.02
655 20 0.03
656 85 0.12
657 119 0.17
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (658 bp):
TTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTATTGCGGCAAAAAATTGAGGAAAAAC
TTTTCGGGTCAGTTTTTGCAAAAATTTAGCCGAAATCGTGTATACATCACGGTTTCAGGCAAAAA
ACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTAGGCGCAAAGACTCATTAAAATATCTA
TATTCATCTAACCAAATATTAGCCACAATAGATTTAGAAATTTGTTTTCACGAGCATCTGAATCT
TGTTTCGAATTAACTAAAAATAAATTCGAAAAAAATGGAAAACGAAATTGGAAACGTGAAAATCC
ATTTTAACTTTTTGGGGTTGAATAATATAGTATTTCAGAGTACTGTGGCAAAAAAATTGAGGAAA
AACTTTTCGGGTCAGTTTTGCAAAATTTTAGCCGAAATCGTGTATTAAACATCACGGTTTCTGGC
AAAAAACGCGTTCCGGAGCCCCAACTCAATTTCGCTTGATTTTTGGCGCAAAGACTCCTTGAAAA
TCTATATTCATCTAACCAAATATTAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCATCTGA
ATCTTGTTTCGAATTAACTAAAAAAAAATTCGAAAAAAATGCCAAAAACGAAATTGGAAACATGA
AAAACCAT
Found at i:2794 original size:330 final size:329
Alignment explanation
Indices: 2098--3086 Score: 1595
Period size: 330 Copynumber: 3.0 Consensus size: 329
2088 TACTCTTTTG
* * *
2098 CATCACGGTTTATGGCAAAAAACGCGTTCCAGAGCCCCAGCTCAATTTTGCTTGATTTTTGGCGC
1 CATCACGGTTTCTGGCAAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGCGC
* * * * **
2163 AAAGACTCCTTGAAATATCTATATTCATCCAACCAAATATAAGCCACAACGGATTTTTGGATTTG
66 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTTAG-CACAATGGATTTAAGGATTTG
2228 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAAAAATAAATTCGAAAAAAATGCAAAAAA
130 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAAAAATAAATTCGAAAAAAATGC-AAAAA
*
2293 CGATATTGGAAGCATAAAAAACCATTTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTA
194 CGATATTGGAAGCATGAAAAACCATTTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTA
* *
2358 TTGCGGCAAAAAATTGAGTAAAAACTTTTCTGGTCAGTTTTTTCAAAATTTTAGCCGAAATCGTG
259 TTGCGGCAAAAAATTGAGGAAAAACTTTTCTGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTG
*
2423 TATTAA
324 TATAAA
*
2429 CATCACGGTTTCTGGCAAAAATCGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGCGC
1 CATCACGGTTTCTGGCAAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGCGC
* *
2494 AAAGACTCCTTAAAATATCTATATTTATCTAACCAAATCTTAGACACAATGGATTTAAGGATTTG
66 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTTAG-CACAATGGATTTAAGGATTTG
*
2559 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAAAAATAAATTCGAAACAAATGCAAAAAC
130 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAAAAATAAATTCGAAAAAAATGCAAAAAC
*
2624 GATATTGGAAGCATGAAAAACCATTTTAATTTCTTGGGGTTGAATAATATAGTTCATCTGAGTAT
195 GATATTGGAAGCATGAAAAACCATTTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTAT
*
2689 TGCGGCAAAAAGTTGAGGAAAAACTTTTCTGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGT
260 TGCGGCAAAAAATTGAGGAAAAACTTTTCTGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGT
2754 ATAAA
325 ATAAA
* *
2759 CATCACGGTTTCTGGCAAAAAACGCGTTTCGGAGCCCCGACTCAATTTTGCTTGATTTTTGGCGC
1 CATCACGGTTTCTGGCAAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGCGC
* * *
2824 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTTTGCAACAATGGATTTAACGATTTA
66 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTTAGC-ACAATGGATTTAAGGATTTG
*
2889 TTTTTACGTAGCATCTGAATCTTGTTTCGATTTAACTAAAAATAAATACGAAAAAAAAATG-AAG
130 TTTTTACG-AGCATCTGAATCTTGTTTCGATTTAACTAAAAATAAATTCG--AAAAAAATGCAA-
* * * * *
2953 AAACGATATTAGAGGCGTGAAAATCCATTTTAATTTTTTGGGGTTGAATAATATAGTTCATCTCA
191 AAACGATATTGGAAGCATGAAAAACCATTTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGA
* *
3018 GTACTT-TGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAAT
256 GTA-TTGCGGCAAAAAATTGAGGAAAAACTTTTCTGGTCAGTTTTTGCAAAATTTTAGCCGAAAT
3082 CGTGT
320 CGTGT
3087 TTTAACCA
Statistics
Matches: 613, Mismatches: 39, Indels: 10
0.93 0.06 0.02
Matches are distributed among these distances:
329 1 0.00
330 263 0.43
331 215 0.35
332 2 0.00
333 130 0.21
334 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (329 bp):
CATCACGGTTTCTGGCAAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGCGC
AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTTAGCACAATGGATTTAAGGATTTGT
TTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAAAAATAAATTCGAAAAAAATGCAAAAACG
ATATTGGAAGCATGAAAAACCATTTTAATTTTTTGGGGTTGAATAATATAGTTCATCTGAGTATT
GCGGCAAAAAATTGAGGAAAAACTTTTCTGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTA
TAAA
Done.