Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013655.1 Corchorus capsularis cultivar CVL-1 contig13676, 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: 2732
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Found at i:633 original size:335 final size:320
Alignment explanation
Indices: 22--997 Score: 988
Period size: 335 Copynumber: 3.0 Consensus size: 320
12 TTTAGCATTG
* * **** *
22 AATTATAT-AT-TGTTTCTGTGTATTGTGGCAAAAAATTGAGAAAAAAACTTTCGGGTCAATTTT
1 AATTATATAATAT-TTTCTGAGTATTGTGGCAAAAAATTAAGAAAAAAA-TTTCAAAACAGTTTT
* * * * * ** *
85 TAGCCGAAATCGTG---T-ACCAACACGATTTTTGACTAAAAACGCGTTCCAGAGCCCCAACT-G
64 TAGCCAAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACGCATTCCAGAGCCCCGGCTCA
* *
145 AATTTTACATGA-TTTTTGGCGCAAAGACTCTTTGAAATATCTACATTCATCAAAACAAATGTCA
129 AATTTGA-ATGAGTTTTT-GCGCAAAGACTCTTTGAAATATCTACATTCATC-AAACAAATCTCA
* *
209 GCTACACTGGATATAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAAA
191 GC-ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAAT
* *
274 TAATTCGAAAAAAATGGCAAAACGATGTTAGAAGTGTGAAAACCCTGCCAATCTTTTTGGCGTTG
255 TAATTCGGAAAAAATGGAAAAACGATGTTAGAAGTGTGAAAACCCTG-CAATCTTTTTGGCGTTG
339 AATTATATA
319 ------A-A
* **
348 TATATATATATATATATTTTCTGAGTATTGTGGTAAAAAATTAAGAAAATACTTTTCAAAACAGT
1 -A-AT-TATATA-ATATTTTCTGAGTATTGTGGCAAAAAATTAAGAAAA-AAATTTCAAAACAGT
* * * * * ** *
413 TTTTAGCCAGAATCGTGTACTAACCGTCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCTTCGTC
61 TTTTAGCCAAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACGCATTCCAGAGCCCCGGC
* * * *
478 TCAAATTTGAATG-GCTTTTTGCGCAAAGACTCCTTGGAATATCTATATTCATCAAACCAAACCT
126 TCAAATTTGAATGAG-TTTTTGCGCAAAGACTCTTTGAAATATCTACATTCATCAAA-CAAATCT
* * * * *
542 CAGCAACATTGGATATAAGGATTTGTTTTTTCGAGTATCTCAATCTTATTTCGATTTAATTAGAA
189 CAGC-ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAA
* * * * *
607 ATTAATTCGGAAAAAATGGAAAAACGATATGAGAAGCGTTAAAAACCCAT-CAATCTTTTCGGCG
253 ATTAATTCGGAAAAAATGGAAAAACGATGTTAGAAGTG-TGAAAACCC-TGCAATCTTTTTGGCG
671 TTG--
316 TTGAA
* * * ****
674 AATTATATAATATTTTCTGTGTATTGTGGCAAAAAGTTGAGAAAAAAATTTCGGGTCAGTTTTTA
1 AATTATATAATATTTTCTGAGTATTGTGGCAAAAAATTAAGAAAAAAATTTCAAAACAGTTTTTA
* * * * * *
739 GCCAAAATCGTGTAATTACTATCACGGTTTTTGGCTAAAAAGGCATTTCAGAGCCCCGGCTGAAT
66 GCCAAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACGCATTCCAGAGCCCCGGCTCAAA
* * *
804 TTTGCATGAGTTTTGGC-CAAAGACTCTTTGAAATATCTACATTCATCGAAACAAATTTCAGTCA
131 TTTGAATGAGTTTTTGCGCAAAGACTCTTTGAAATATCTACATTCATC-AAACAAATCTCAG-CA
* *
868 CATTGGATATAAGGATTTCTTTTTACGAGCATCTGAATATTGTTTCGATTGAATTAGAAATTAAT
194 CATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAAT
* * **
933 TCGGAAAAAAAATCGAAAAACGATGTTAGAAGTGCGAAAAGACTGTCAATCTTTTTGGCGTTGAA
259 TCGG--AAAAAATGGAAAAACGATGTTAGAAGTGTGAAAACCCTG-CAATCTTTTTGGCGTTGAA
998 CTTTGCATGA
Statistics
Matches: 534, Mismatches: 90, Indels: 53
0.79 0.13 0.08
Matches are distributed among these distances:
320 99 0.19
321 87 0.16
322 73 0.14
323 6 0.01
324 2 0.00
325 1 0.00
327 1 0.00
328 2 0.00
329 5 0.01
331 53 0.10
332 2 0.00
334 4 0.01
335 179 0.34
336 19 0.04
337 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (320 bp):
AATTATATAATATTTTCTGAGTATTGTGGCAAAAAATTAAGAAAAAAATTTCAAAACAGTTTTTA
GCCAAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACGCATTCCAGAGCCCCGGCTCAAA
TTTGAATGAGTTTTTGCGCAAAGACTCTTTGAAATATCTACATTCATCAAACAAATCTCAGCACA
TTGGATATAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTC
GGAAAAAATGGAAAAACGATGTTAGAAGTGTGAAAACCCTGCAATCTTTTTGGCGTTGAA
Found at i:1188 original size:192 final size:195
Alignment explanation
Indices: 799--1189 Score: 520
Period size: 196 Copynumber: 2.0 Consensus size: 195
789 GAGCCCCGGC
* * * *
799 TGAATTTTGCATGAGTTTTGGCCAAAGACTCTTTGAAATATCTACATTCATCGAAACAAATTTCA
1 TGAACTTTGCATGAGTTTTGGCCAAAGACTCCTTGAAATATCTACATTCATCGAAACAAATCTAA
* *
864 GTCACATTGGATATAAGGATTTCTTTTTACGAGCATCTGAATATTGTTTCGATTGAATTAGAAAT
66 GTCACATTGAATATAAGGATTTCTTTTTACGAGCATCTCAATATTGTTTCGATTGAATTAGAAAT
* * *
929 TAATTCGGAAAAAAAATCGAAAAACGATGTTAGAAGTGCGAAAAGACTGTCAATCTTTTTGGCGT
131 TAATTCGGAAAAAAAATCGAAAAACGATATTAGAAGCGCGAAAAGACAGTCAATCTTTTTGGCGT
* * * *
994 TGAACTTTGCATGATTTTTGGCGCAAATACTCCTTGAAATATCTATATTCATCGAACCAAATCTA
1 TGAACTTTGCATGAGTTTTGGC-CAAAGACTCCTTGAAATATCTACATTCATCGAAACAAATCTA
* * * * * *
1059 AGTTATATTGAATATAAGGATTTGTTTTT-TGAGCATCTCAATCTT-TTTCGATTTAATTAGAAA
65 AGTCACATTGAATATAAGGATTTCTTTTTACGAGCATCTCAATATTGTTTCGATTGAATTAGAAA
* * * * * *
1122 TTCATTCTG-AAAAAAA-GGAAAAACTATATTAGAAGCGTGAAAAGCCAGTCAATCTTTTTGGCG
130 TTAATTCGGAAAAAAAATCGAAAAACGATATTAGAAGCGCGAAAAGACAGTCAATCTTTTTGGCG
1185 T
195 T
1186 TGAA
1 TGAA
1190 TTATATATTG
Statistics
Matches: 170, Mismatches: 25, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
192 45 0.26
193 7 0.04
194 24 0.14
195 33 0.19
196 61 0.36
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (195 bp):
TGAACTTTGCATGAGTTTTGGCCAAAGACTCCTTGAAATATCTACATTCATCGAAACAAATCTAA
GTCACATTGAATATAAGGATTTCTTTTTACGAGCATCTCAATATTGTTTCGATTGAATTAGAAAT
TAATTCGGAAAAAAAATCGAAAAACGATATTAGAAGCGCGAAAAGACAGTCAATCTTTTTGGCGT
Found at i:1955 original size:514 final size:514
Alignment explanation
Indices: 493--2732 Score: 3130
Period size: 514 Copynumber: 4.3 Consensus size: 514
483 TTTGAATGGC
* * * * *
493 TTTTT-GCGCAAAGACTCCTTGGAATATCTATATTCATCAAACCAAACCTCAGCAACATTGGATA
1 TTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAATATTGAATA
* *
557 TAAGGATTTGTTTTTTCGAGTATCTCAATCTTATTTCGATTTAATTAGAAATTAATTCGGAAAAA
66 TAAGGATTTGTTTTTTGGAGCATCTCAATCTT-TTTCGATTTAATTAGAAATTAATTCGG-AAAA
* * * * *
622 ATGGAAAAACGATATGAGAAGCGTTAAAAACCCA-TCAATCTTTTCGGCGTTGAATTATATAATA
129 ATGGAAAAACGTTATTAGAAGCG-TGAAAAGCCAGTCAATTTTTTC-GCGTTGAATTATATAAT-
* * *
686 T-TTTCTGTGTATTGTGGCAAAAAGTTGAG-AAAAAAATTTCGGGTCAGTTTTTAGCCAAAATCG
191 TGTTTCTGTGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCAATTTTTAGCCGAAATCG
* * * * * * * * *
749 TGTAATTACTATCACGGTTTTTGGCTAAAAAGGCATTTCAGAGCCCCGGCTGAATTTTGCATGAG
256 TGTACTTACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTACATGAT
* *
814 TTTTGGC-CAAAGACTCTTTGAAATATCTACATTCATCGAAACAAATTTCAGTCACATTGGATAT
321 TTTTGGCGCAAAGACTCTTTGAAATATCTACATTCATCGAAACAAATGTCAGCCACATTGGATAT
* *
878 AAGGATTTCTTTTTACGAGCATCTGAATATTGTTTCGATTGAATTAGAAATTAATTCGGAAAAAA
386 AAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA
* * *
943 AATCGAAAAACGATGTTAGAAGTGCGAAAAGA-CTGTCAATCTTTTTGGCGTTGAACTTTGCATG
451 AAT-GGAAAACGATGTTAGAAGTGTGAAAA-ACCTGTCAATCTTTTTGGCGTTGAATTTTGCATG
1007 A
514 A
* * **
1008 TTTTTGGCGCAAATACTCCTTGAAATATCTATATTCATCGAACCAAATCTAAGTTATATTGAATA
1 TTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAATATTGAATA
* *
1073 TAAGGATTTGTTTTTT-GAGCATCTCAATCTTTTTCGATTTAATTAGAAATTCATTCTGAAAAAA
66 TAAGGATTTGTTTTTTGGAGCATCTCAATCTTTTTCGATTTAATTAGAAATTAATTC-GGAAAAA
* *
1137 AGGAAAAAC-TATATTAGAAGCGTGAAAAGCCAGTCAATCTTTTTGGCGTTGAATTATAT-ATTG
130 TGGAAAAACGT-TATTAGAAGCGTGAAAAGCCAGTCAAT-TTTTTCGCGTTGAATTATATAATTG
* * *
1200 TTTCTGTGTATTGTGGCAAAAAAATTGAGAAAACAATTTTCGGATCAATTTTTAGCCGAAATCGT
193 TTTCTGTGTATTGTGGC-AAAAAATTGAGAAAAAAAATTTCGGGTCAATTTTTAGCCGAAATCGT
* * * * * *
1265 GTACTTACCATCACGATTTCTGGTTAAAAACGCGTTTCGGAGCCCCGTCTCAATTTTGCATGATT
257 GTACTTACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTACATGATT
* * * * * *
1330 TTTGTCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATA
322 TTTGGCGCAAAGACTCTTTGAAATATCTACATTCATCGAAACAAATGTCAGCCACATTGGATATA
* * * * * *
1395 AGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTTGAATAAATTAGAAATTAATTCGGAAAAAAA
387 AGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAA
* *
1460 AATGGAAAACGGTGTTAGAAGTGTGAAAAACCTGTCAATCTTTTTGGCGTTGAATTTTGCATTA
451 AATGGAAAACGATGTTAGAAGTGTGAAAAACCTGTCAATCTTTTTGGCGTTGAATTTTGCATGA
*
1524 TTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGAATA
1 TTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAATATTGAATA
*
1589 TAAGGATTTGTTTTTTGGAGCATCTCAATCTTTTTCGATTTAATTAGAAATTAAATCGGAAAAAT
66 TAAGGATTTGTTTTTTGGAGCATCTCAATCTTTTTCGATTTAATTAGAAATTAATTCGGAAAAAT
*
1654 GG-AAAACGTTATTAGAAGCGTGAAAAGCCAGTCAATATTTTTCGTGTTGAATTATAT-ATTGTT
131 GGAAAAACGTTATTAGAAGCGTGAAAAGCCAGTCAAT-TTTTTCGCGTTGAATTATATAATTGTT
*
1717 TCTGGGTATTGTGGCAAAAAATTGAGAAAAAAAAATTT-GGGTCAATTTTTAGCCGAAATCGTGT
195 TCTGTGTATTGTGGCAAAAAATTGAG-AAAAAAAATTTCGGGTCAATTTTTAGCCGAAATCGTGT
* * * *
1781 ACTTACCATCACGGTTTTTTGCTAAAAACGTGTTCCGGAGCCCCGACTCTATTTTACATGATTTT
259 ACTTACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTACATGATTTT
* *
1846 TGGCGCAAAGACTCTTTGAAATATTTACATTCATCGAAACAAATGTCAGCCGCATTGGATATAAG
324 TGGCGCAAAGACTCTTTGAAATATCTACATTCATCGAAACAAATGTCAGCCACATTGGATATAAG
*
1911 GATTTGTTTTTACGAGCATCTAAATATTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAT
389 GATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAT
* * *
1976 GGAAAAACGATGTTAGAAGTGTGAAAAGCCTGTCGATCTTTTTGGCATTGAATTTTGCATGA
454 GG-AAAACGATGTTAGAAGTGTGAAAAACCTGTCAATCTTTTTGGCGTTGAATTTTGCATGA
* * * *
2038 TTTTTGGCGCAAAGACTCCTTGAAATATCTATATTTATCGAACCAAATCTCAACAACATTGGATA
1 TTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAATATTGAATA
* * * *
2103 TAAGGATTTGTTTTTTTGAGCATCTCAATCTTGTTTCGAATTAATAAGAAATTAATTTGGAAAAA
66 TAAGGATTTGTTTTTTGGAGCATCTCAATCTT-TTTCGATTTAATTAGAAATTAATTCGGAAAAA
* * * *
2168 TGGAAAAATGATATTAGAAGCGTGCAAAGCCAGTC-ATTCTTTTCGGCGTTGAATTATATAATTT
130 TGGAAAAACGTTATTAGAAGCGTGAAAAGCCAGTCAATT-TTTTC-GCGTTGAATTATATAATTG
* * * * *
2232 TTTCTGTGTATTGTGGTAAAAAAGTGAGAAAAACATTTTCGGGTCAGTTTTTAGCCGAAATCGTG
193 TTTCTGTGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCAATTTTTAGCCGAAATCGTG
* * * *
2297 TACTTACCATCACGGGTTTTT-GATAAAAACGCGTTCCGGAGTCTCGGCTCCATTTTACATGATT
258 TACTTACCATCAC-GGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTACATGATT
* * * * * *
2361 ATTGGCGCAATGACTCTTTGAAATATTTATATTCATCGAAACAAATGTCAGTCATATTGGATATA
322 TTTGGCGCAAAGACTCTTTGAAATATCTACATTCATCGAAACAAATGTCAGCCACATTGGATATA
* * *
2426 AGGATTTATTTTTACGAGCATCTGAGTATTATTTCGATTTAATTAGAAATTAATTCGGAAAAAAA
387 AGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAA
* * *
2491 TTGGAAAACGAATGTTAGAAGTGTG-AAAACCTATCAATC-TTTTGGCGTTGAATTTTGCTTGA
452 ATGGAAAACG-ATGTTAGAAGTGTGAAAAACCTGTCAATCTTTTTGGCGTTGAATTTTGCATGA
* *
2553 TTTTTGACGCAAAGACTCCTTAAAATATCTATATTCATCGAACCAAATCTCAGTC-ATATTGAAT
1 TTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAG-CAATATTGAAT
*
2617 ATAAGGATTTG-TTTTTGGAGCATCTCAATCTTTTTCGATTTAATTAGAAATTAAATCGGAAAAA
65 ATAAGGATTTGTTTTTTGGAGCATCTCAATCTTTTTCGATTTAATTAGAAATTAATTCGGAAAAA
*
2681 TGGAAAAACGATTATTAGAAGCGTGAAAAGCCAGTCAATATTTTTCGTGTTG
130 TGGAAAAACG-TTATTAGAAGCGTGAAAAGCCAGTCAAT-TTTTTCGCGTTG
Statistics
Matches: 1542, Mismatches: 156, Indels: 55
0.88 0.09 0.03
Matches are distributed among these distances:
512 1 0.00
513 75 0.05
514 469 0.30
515 326 0.21
516 378 0.25
517 286 0.19
518 7 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (514 bp):
TTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAATATTGAATA
TAAGGATTTGTTTTTTGGAGCATCTCAATCTTTTTCGATTTAATTAGAAATTAATTCGGAAAAAT
GGAAAAACGTTATTAGAAGCGTGAAAAGCCAGTCAATTTTTTCGCGTTGAATTATATAATTGTTT
CTGTGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCAATTTTTAGCCGAAATCGTGTAC
TTACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTACATGATTTTTG
GCGCAAAGACTCTTTGAAATATCTACATTCATCGAAACAAATGTCAGCCACATTGGATATAAGGA
TTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGG
AAAACGATGTTAGAAGTGTGAAAAACCTGTCAATCTTTTTGGCGTTGAATTTTGCATGA
Done.