Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010879.1 Corchorus capsularis cultivar CVL-1 contig10900, 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, 961
Length: 1602
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Found at i:716 original size:323 final size:324
Alignment explanation
Indices: 1--1602 Score: 2456
Period size: 323 Copynumber: 5.0 Consensus size: 324
1 CAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGAA
1 CAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGAA
*
66 TATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTTAGCCGGGGCCTCGAAACGC
66 TATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCCGGGGCCTCGAAACGC
*
131 GTTTTTATGCCAAAAACAGTGATGGTTAGTATACGATTTCGGCTAGAAATTGACCCGAAAATTTT
131 GTTTTTATGCCAAAAACCGTGATGGTTAGTATACGATTTCGGCTAGAAATTGACCCGAAAATTTT
*
196 TTGTCACAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACACCAAAAAGATTGACGG
196 TTGTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACACCAAAAAGATTGACGG
*
261 GCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTTCCGAAATAATTTCTAATTAAATCGAAA
261 GCTTTTCACGCTTCTAATATCGTTTTTCAA-TTTTTTTCCGAAATAATTTCTAATTAAATCCAAA
* *
326 CAAGATTCAGATGCTCCTAAAAATAATTCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGAA
1 CAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGAA
391 TATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCCGGGGCCTCGAAACGC
66 TATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCCGGGGCCTCGAAACGC
*
456 GTTTTTATACCAAAAACCGTGATGGTTAGTATACGATTTCGGCTAGAAATTGACCCG-AAATTTT
131 GTTTTTATGCCAAAAACCGTGATGGTTAGTATACGATTTCGGCTAGAAATTGACCCGAAAATTTT
* * *
520 TTTTCACAATTTTTTGCCACAATACTCAGAAGAAATATATTATTCAACACCAAAAAGATTGACGG
196 TTGTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACACCAAAAAGATTGACGG
* *
585 GCTTTTCACGCTTCTAATATTGTTTTTCAATTTTTTTCTGAAATAATTTCTAATTAAATCCAAA
261 GCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTCCGAAATAATTTCTAATTAAATCCAAA
*
649 CAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTATGTCTAAGATTTGGTTAGAAGAA
1 CAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGAA
*
714 TATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCCGCGG-CTCCGAAACG
66 TATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCCGGGGCCT-CGAAACG
* *
778 CGTTTTTATGCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAGAAATTGACCCGAAAATTT
130 CGTTTTTATGCCAAAAACCGTGATGGTTAGTATACGATTTCGGCTAGAAATTGACCCGAAAATTT
*
843 TTTGTCTCAATTTTTTGCCACAATACTCAG----AA-A-A-TATTCAACACCAAAATGATTGACG
195 TTTGTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACACCAAAAAGATTGACG
*
901 GGCTTTTTACGCTTCTAATATCG-TTTTCAATTTTTTTTCCGAAATAATTTCTAATTAAA-CCGA
260 GGCTTTTCACGCTTCTAATATCGTTTTTCAA-TTTTTTTCCGAAATAATTTCTAATTAAATCC-A
964 AA
323 AA
* *
966 CAAGATTCAGATGCTCCTAAAAATAATTCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGAA
1 CAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGAA
*
1031 TATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGTCGGGGCCTCGAAACGC
66 TATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCCGGGGCCTCGAAACGC
* * * *
1096 GTTTTTATACCAAAAACCGTGATAGTAACGTATACGATTTCGGTTAGAAATTGACCCG-AAATTT
131 GTTTTTATGCCAAAAACCGTGATGGTTA-GTATACGATTTCGGCTAGAAATTGACCCGAAAATTT
* * * * * * *
1160 TTTTTCTCAATTTTTTGCCACAATACTTAG-AAAAATATCTAATTCAACACCATAAAGTTTGACA
195 TTTGTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACACCAAAAAGATTGACG
* * * *
1224 GGCTTTTCACGCTTCTAATATCATTTTT-AGTTTTTTTTCTGAAATAAATTCTAATTAAATCCAA
260 GGCTTTTCACGCTTCTAATATCGTTTTTCA-ATTTTTTTCCGAAATAATTTCTAATTAAATCCAA
1288 A
324 A
* * *
1289 CAAGATTCATATGCTCTTAAAAATAAATCCTTAAATCCATTTTGTCTAAAATTTGGTTAGAAGAA
1 CAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGAA
* * * *
1354 TATATATATTCTAAGGAGTCTTTCTGGTAAAAATCTTGCATAACTGAGCCGGAGTCC-CGAAACG
66 TATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCCGG-GGCCTCGAAACG
* * * * *
1418 CGTATTTATGCC-AACA-C----T-GTAACGTACACGATTTTCGGCTAAAAATTGACCCGAAAAT
130 CGTTTTTATGCCAAAAACCGTGATGGTTA-GTATACGA-TTTCGGCTAGAAATTGACCCGAAAAT
* * * *
1476 TTTTTATCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCATCACCAAAAATATTGA
193 TTTTTGTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACACCAAAAAGATTGA
* * *
1541 CGGGTTTTTCACACTTCTAATATCATTTTTTCAATTTTTTTCCCGAAATAATTTCTAATTAA
258 CGGGCTTTTCACGCTTCTAATATC-GTTTTTCAATTTTTTT-CCGAAATAATTTCTAATTAA
Statistics
Matches: 1178, Mismatches: 77, Indels: 48
0.90 0.06 0.04
Matches are distributed among these distances:
316 21 0.02
317 274 0.23
318 64 0.05
319 49 0.04
320 16 0.01
321 21 0.02
322 5 0.00
323 404 0.34
324 142 0.12
325 182 0.15
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (324 bp):
CAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGAA
TATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCCGGGGCCTCGAAACGC
GTTTTTATGCCAAAAACCGTGATGGTTAGTATACGATTTCGGCTAGAAATTGACCCGAAAATTTT
TTGTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACACCAAAAAGATTGACGG
GCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTCCGAAATAATTTCTAATTAAATCCAAA
Found at i:1230 original size:640 final size:641
Alignment explanation
Indices: 1--1602 Score: 2550
Period size: 640 Copynumber: 2.5 Consensus size: 641
*
1 CAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGAA
1 CAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTATGTCTAAGATTTGGTTAGAAGAA
*
66 TATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTTAGCCGGGGC-CTCGAAACG
66 TATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCC-GGGCTC-CGAAACG
*
130 CGTTTTTATGCCAAAAACAGTGATGGTTAGTATACGATTTCGGCTAGAAATTGACCCGAAAATTT
129 CGTTTTTATGCCAAAAAC-GTGATGGTTAGTACACGATTTCGGCTAGAAATTGACCCGAAAATTT
* *
195 TTTGTCACAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACACCAAAAAGATTGACG
193 TTTGTCTCAATTTTTTGCCACAATACTCAG---AAATATA-TATTCAACACCAAAATGATTGACG
* *
260 GGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTTCCGAAATAATTTCTAATTAAATCGAA
254 GGCTTTTTACGCTTCTAATATCG-TTTTCAATTTTTTTTCCGAAATAATTTCTAATTAAACCGAA
325 ACAAGATTCAGATGCTCCTAAAAATAATTCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGA
318 ACAAGATTCAGATGCTCCTAAAAATAATTCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGA
390 ATATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCCGGGGCCTCGAAACG
383 ATATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCCGGGGCCTCGAAACG
* *
455 CGTTTTTATACCAAAAACCGTGATGGTTAGTATACGATTTCGGCTAGAAATTGACCCGAAATTTT
448 CGTTTTTATACCAAAAACCGTGATAGTAAGTATACGATTTCGGCTAGAAATTGACCCGAAATTTT
* *
520 TTTTCACAATTTTTTGCCACAATACTCAGAAGAAATATATTATTCAACACCAAAAAGATTGACGG
513 TTTTCACAATTTTTTGCCACAATACTCAGAAGAAATATATAATTCAACACCAAAAAGATTGACAG
** *
585 GCTTTTCACGCTTCTAATATTGTTTTTCA-ATTTTTTTCTGAAATAATTTCTAATTAAATCCAAA
578 GCTTTTCACGCTTCTAATATCATTTTT-AGATTTTTTTCTGAAATAAATTCTAATTAAATCCAAA
649 CAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTATGTCTAAGATTTGGTTAGAAGAA
1 CAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTATGTCTAAGATTTGGTTAGAAGAA
714 TATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCCGCGGCTCCGAAACGC
66 TATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCCG-GGCTCCGAAACGC
779 GTTTTTATGCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAGAAATTGACCCGAAAATTTT
130 GTTTTTATGCCAAAAA-CGTGATGGTTAGTACACGATTTCGGCTAGAAATTGACCCGAAAATTTT
844 TTGTCTCAATTTTTTGCCACAATACTCAG-AA-A-ATATTCAACACCAAAATGATTGACGGGCTT
194 TTGTCTCAATTTTTTGCCACAATACTCAGAAATATATATTCAACACCAAAATGATTGACGGGCTT
906 TTTACGCTTCTAATATCGTTTTCAATTTTTTTTCCGAAATAATTTCTAATTAAACCGAAACAAGA
259 TTTACGCTTCTAATATCGTTTTCAATTTTTTTTCCGAAATAATTTCTAATTAAACCGAAACAAGA
971 TTCAGATGCTCCTAAAAATAATTCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGAATATAT
324 TTCAGATGCTCCTAAAAATAATTCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGAATATAT
*
1036 ATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGTCGGGGCCTCGAAACGCGTTTT
389 ATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCCGGGGCCTCGAAACGCGTTTT
*
1101 TATACCAAAAACCGTGATAGTAACGTATACGATTTCGGTTAGAAATTGACCCGAAATTTTTTTTC
454 TATACCAAAAACCGTGATAGTAA-GTATACGATTTCGGCTAGAAATTGACCCGAAATTTTTTTTC
* * * * *
1166 TCAATTTTTTGCCACAATACTTAGAA-AAATATCTAATTCAACACCATAAAGTTTGACAGGCTTT
518 ACAATTTTTTGCCACAATACTCAGAAGAAATATATAATTCAACACCAAAAAGATTGACAGGCTTT
*
1230 TCACGCTTCTAATATCATTTTTAGTTTTTTTTCTGAAATAAATTCTAATTAAATCCAAA
583 TCACGCTTCTAATATCATTTTTAGATTTTTTTCTGAAATAAATTCTAATTAAATCCAAA
* * *
1289 CAAGATTCATATGCTCTTAAAAATAAATCCTTAAATCCATTTTGTCTAAAATTTGGTTAGAAGAA
1 CAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTATGTCTAAGATTTGGTTAGAAGAA
* * *
1354 TATATATATTCTAAGGAGTCTTTCTGGTAAAAATCTTGCATAACTGAGCCGGAG-TCCCGAAACG
66 TATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCCGG-GCT-CCGAAACG
* * * *
1418 CGTATTTATGCC-AACAC----T-GTAACGTACACGATTTTCGGCTAAAAATTGACCCGAAAATT
129 CGTTTTTATGCCAAAAACGTGATGGTTA-GTACACGA-TTTCGGCTAGAAATTGACCCGAAAATT
* *
1477 TTTTATCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCATCACCAAAAAT-ATTGA
192 TTTTGTCTCAATTTTTTGCCACAATACTCAG---AAATATAT-ATTCAACACC-AAAATGATTGA
* * *
1541 CGGG-TTTTTCACACTTCTAATATCATTTTTTCAATTTTTTTCCCGAAATAATTTCTAATTAA
252 CGGGCTTTTT-ACGCTTCTAATATC--GTTTTCAATTTTTTTTCCGAAATAATTTCTAATTAA
Statistics
Matches: 897, Mismatches: 37, Indels: 44
0.92 0.04 0.04
Matches are distributed among these distances:
633 3 0.00
634 9 0.01
635 56 0.06
638 1 0.00
639 8 0.01
640 413 0.46
641 116 0.13
642 32 0.04
643 6 0.01
644 36 0.04
647 1 0.00
648 214 0.24
649 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (641 bp):
CAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTATGTCTAAGATTTGGTTAGAAGAA
TATATATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCCGGGCTCCGAAACGCG
TTTTTATGCCAAAAACGTGATGGTTAGTACACGATTTCGGCTAGAAATTGACCCGAAAATTTTTT
GTCTCAATTTTTTGCCACAATACTCAGAAATATATATTCAACACCAAAATGATTGACGGGCTTTT
TACGCTTCTAATATCGTTTTCAATTTTTTTTCCGAAATAATTTCTAATTAAACCGAAACAAGATT
CAGATGCTCCTAAAAATAATTCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGAATATATAT
ATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAACTGAGCCGGGGCCTCGAAACGCGTTTTTA
TACCAAAAACCGTGATAGTAAGTATACGATTTCGGCTAGAAATTGACCCGAAATTTTTTTTCACA
ATTTTTTGCCACAATACTCAGAAGAAATATATAATTCAACACCAAAAAGATTGACAGGCTTTTCA
CGCTTCTAATATCATTTTTAGATTTTTTTCTGAAATAAATTCTAATTAAATCCAAA
Done.