Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008070.1 Corchorus capsularis cultivar CVL-1 contig08091, 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, 837
Length: 1396
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Found at i:748 original size:331 final size:333
Alignment explanation
Indices: 1--1395 Score: 2074
Period size: 331 Copynumber: 4.2 Consensus size: 333
* * *
1 AAAATATTAATAAAAATTATATAATTCAATGCCAAAAGTTTGAAGGGTTTTTCATGTTTCTAATA
1 AAAATATTAATAAAAATTATATAATTCAACGCCAAAAGTTTGAAGGGTTTTTCACGCTTCTAATA
* * * *
66 TCAATTTTCATATTTTTTTCCCGAATTTATTTCTAATTAAAACGAAACAAGATTCAGACGCTCGT
66 TCAATTTTCCTATTTTTTT-CTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
*
131 AAAAAGAAATCCTTAAATCCGTTGTGCCTGAGATTTGAATAGATAAATATAGATATTTTGATGAG
130 AAAAAGAAATCCTTAAATCCGTTGTGCCTGAGATTTGAATAGATAAATATAGATATTTTGAGGAG
* * * *
196 TCTTGACGCAAAAAATCATGCAGAACTGAACCAAGGACCTGGAACGCGTTTTTAGCAAAAAACCG
195 TCTTGACGCAAAAAATCATGCAGAACTGAGCCGAGGACCCGGAACACGTTTTTAGCAAAAAACCG
* * *
261 TG--A--TAGTACACGA-TTTCGGTTGAAATATTGAAAAAATTGAAAGAAAATTTTTTTCCCTCA
260 TGATAGTTAGTATACGATTTTCGGCTGAAATATTGAAAAAATTGACAGAAAATTTTTTT-CCTCA
321 ATTTTTTTGCC
324 A-TTTTTTGCC
*
332 AAAATATTAATAAAAATTATATAATTCAACACCAAAAGTTTGAAGGGTTTTTCACGCTTCTAATA
1 AAAATATTAATAAAAATTATATAATTCAACGCCAAAAGTTTGAAGGGTTTTTCACGCTTCTAATA
*
397 TAAATTTTCCTATTTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
66 TCAATTTTCCTA-TTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
*
462 AAAAAGCAATCCTTAAATCCGTTGTGCCTGAGATTTGAATAGATAAATATAGATATTTTGAGGAG
130 AAAAAGAAATCCTTAAATCCGTTGTGCCTGAGATTTGAATAGATAAATATAGATATTTTGAGGAG
* * * * * * *
527 TCTTGATG-TAAAAATAAAGCAGAATTTAGCCGAGGACCCGGAACGCGTTTTTAGCAAAAAACCG
195 TCTTGACGCAAAAAATCATGCAGAACTGAGCCGAGGACCCGGAACACGTTTTTAGCAAAAAACCG
* *
591 TGAAAGTTAGTAAACGA-TTTCGGCTGAAATATTGAAAAAATTGACAGAAAATTATTTTTCCTCA
260 TGATAGTTAGTATACGATTTTCGGCTGAAATATTGAAAAAATTGACAGAAAATT-TTTTTCCTCA
655 ATTTTTTGCC
324 ATTTTTTGCC
* *
665 AAAATATTAATAAAAATTATATAATTCAACGCCAAAAATTTGAAGGGTTTTTCAAGCTTCTAATA
1 AAAATATTAATAAAAATTATATAATTCAACGCCAAAAGTTTGAAGGGTTTTTCACGCTTCTAATA
730 TCAATTTTCCTA-TTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
66 TCAATTTTCCTATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* *
794 AAAAGCAATCCTTAAATCCGTTGTGCCTGAGATTTGAATAGATAAATATAGATATTTTGAGGAGC
131 AAAAGAAATCCTTAAATCCGTTGTGCCTGAGATTTGAATAGATAAATATAGATATTTTGAGGAGT
* *
859 CATGACGC-------CATGCAGAACTGAGCATG-GGACCCGGAACACGTTTTTAGCAAAAAACCG
196 CTTGACGCAAAAAATCATGCAGAACTGAGC-CGAGGACCCGGAACACGTTTTTAGCAAAAAACCG
**
916 TGATAGTTAGTATACGATTTTCGGCTGAAATATTGAAAAAATTGACA-AAAA-AATTTTCCTCAA
260 TGATAGTTAGTATACGATTTTCGGCTGAAATATTGAAAAAATTGACAGAAAATTTTTTTCCTCAA
979 -TTTTTGCC
325 TTTTTTGCC
*
987 AAAATATTAATAAAAATTATATAATTCAACGCCAAAAGTTTGAAGGGTTTATCACGCTTCTAATA
1 AAAATATTAATAAAAATTATATAATTCAACGCCAAAAGTTTGAAGGGTTTTTCACGCTTCTAATA
* * *
1052 TAAATGTTCCTATTTTTTTCTGAATTTATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTA
66 TCAATTTTCCTATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * * * *
1117 AAATGAAATCCTTAAATCCATTGTGGCTGAGATTTGAATAGATAAATAAATATATTTTGAGGAGT
131 AAAAGAAATCCTTAAATCCGTTGTGCCTGAGATTTGAATAGATAAATATAGATATTTTGAGGAGT
* * * * * * *
1182 CTTGACGCAAAAAATCATGCAGAATTGAGCCGGGGACCTGAAAAACGTTTTTAGGAAGAAACCGT
196 CTTGACGCAAAAAATCATGCAGAACTGAGCCGAGGACCCGGAACACGTTTTTAGCAAAAAACCGT
* *
1247 TATAGTTAGTATACGATTTTCGGTTGAAATATTGAAAAAATTGACAG-AAATTTTTTTCCTCAAT
261 GATAGTTAGTATACGATTTTCGGCTGAAATATTGAAAAAATTGACAGAAAATTTTTTTCCTCAAT
*
1311 TTTTTTCC
326 TTTTTGCC
* * *
1319 AAAATATTAATAAAAATTATTTTATTCAACACCAAAAAGTTTGAAGGGTTTTTCACGCTTCTAAT
1 AAAATATTAATAAAAATTATATAATTCAACGCC-AAAAGTTTGAAGGGTTTTTCACGCTTCTAAT
1384 ATCAATTTTCCT
65 ATCAATTTTCCT
1396 T
Statistics
Matches: 970, Mismatches: 72, Indels: 42
0.89 0.07 0.04
Matches are distributed among these distances:
322 80 0.08
323 126 0.13
325 60 0.06
326 30 0.03
329 1 0.00
330 138 0.14
331 314 0.32
332 45 0.05
333 122 0.13
334 49 0.05
335 5 0.01
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (333 bp):
AAAATATTAATAAAAATTATATAATTCAACGCCAAAAGTTTGAAGGGTTTTTCACGCTTCTAATA
TCAATTTTCCTATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
AAAAGAAATCCTTAAATCCGTTGTGCCTGAGATTTGAATAGATAAATATAGATATTTTGAGGAGT
CTTGACGCAAAAAATCATGCAGAACTGAGCCGAGGACCCGGAACACGTTTTTAGCAAAAAACCGT
GATAGTTAGTATACGATTTTCGGCTGAAATATTGAAAAAATTGACAGAAAATTTTTTTCCTCAAT
TTTTTGCC
Found at i:1265 original size:655 final size:655
Alignment explanation
Indices: 1--1395 Score: 2099
Period size: 655 Copynumber: 2.1 Consensus size: 655
* * * *
1 AAAATATTAATAAAAATTATATAATTCAATGCCAAAAGTTTGAAGGGTTTTTCATGTTTCTAATA
1 AAAATATTAATAAAAATTATATAATTCAACGCCAAAAATTTGAAGGGTTTTTCAAGCTTCTAATA
*
66 TCAATTTTCATATTTTTTTCCCGAATTTATTTCTAATTAAAACGAAACAAGATTCAGACGCTCGT
66 TCAATTTTCCTATTTTTTTCCCGAATTTATTTCTAATTAAAACGAAACAAGATTCAGACGCTCGT
*
131 AAAAAGAAATCCTTAAATCCGTTGTGCCTGAGATTTGAATAGATAAATATAGATATTTTGATGAG
131 AAAAAGAAATCCTTAAATCCGTTGTGCCTGAGATTTGAATAGATAAATATAGATATTTTGAGGAG
* * * *
196 TCTTGACGCAAAAAATCATGCAGAACTGAACCAAGGACCTGGAACGCGTTTTTAGCAAAAAACCG
196 CCATGACGC-----A-CATGCAGAACTGAACCAAGGACCCGGAACACGTTTTTAGCAAAAAACCG
* *
261 TGATAGTACACGATTTCGGTTGAAATATTGAAAAAATTGAAAGAAAATTTTTTTCCCTCAATTTT
255 TGATAGTACACGATTTCGGCTGAAATATTGAAAAAATTGAAAGAAAA-TATTTTCCCTCAA-TTT
*
326 TTTGCCAAAATATTAATAAAAATTATATAATTCAACACCAAAAGTTTGAAGGGTTTTTCACGCTT
318 TTTGCCAAAATATTAATAAAAATTATATAATTCAACACCAAAAGTTTGAAGGGTTTATCACGCTT
* *
391 CTAATATAAATTTTCCTATTTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAT
383 CTAATATAAATGTTCCTATTTTTTTTCTGAATTTATTTATAATTAAATCGAAACAAGATTCAGAT
* * *
456 GCTCGTAAAAAGCAATCCTTAAATCCGTTGTGCCTGAGATTTGAATAGATAAATATAGATATTTT
448 GCTCGTAAAAAGAAATCCTTAAATCCATTGTGCCTGAGATTTGAATAGATAAATAAAGATATTTT
* * * * **
521 GAGGAGTCTTGATGTAAAAATAAAGCAGAATTTAGCCGAGGACCCGGAACGCGTTTTTAGCAAAA
513 GAGGAGTCTTGACGAAAAAATAAAGCAGAATTGAGCCGAGGACCCGAAAAACGTTTTTAGCAAAA
586 AACCGTGAAAGTTAGTAAACGA-TTTCGGCTGAAATATTGAAAAAATTGACAGAAAATTATTTTT
578 AACCGTGAAAGTTAGTAAACGATTTTCGGCTGAAATATTGAAAAAATTGACAG-AAATT-TTTTT
650 CCTCAATTTTTTGCC
641 CCTCAATTTTTTGCC
665 AAAATATTAATAAAAATTATATAATTCAACGCCAAAAATTTGAAGGGTTTTTCAAGCTTCTAATA
1 AAAATATTAATAAAAATTATATAATTCAACGCCAAAAATTTGAAGGGTTTTTCAAGCTTCTAATA
* * *
730 TCAATTTTCCTA-TTTTTT-CTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
66 TCAATTTTCCTATTTTTTTCCCGAATTTATTTCTAATTAAAACGAAACAAGATTCAGACGCTCGT
*
793 AAAAAGCAATCCTTAAATCCGTTGTGCCTGAGATTTGAATAGATAAATATAGATATTTTGAGGAG
131 AAAAAGAAATCCTTAAATCCGTTGTGCCTGAGATTTGAATAGATAAATATAGATATTTTGAGGAG
* *
858 CCATGACGC-CATGCAGAACTG-AGCATGGGACCCGGAACACGTTTTTAGCAAAAAACCGTGATA
196 CCATGACGCACATGCAGAACTGAACCA-AGGACCCGGAACACGTTTTTAGCAAAAAACCGTG--A
*
921 GTTAGTATACGATTTTCGGCTGAAATATTGAAAAAATTGACAA-AAAA-ATTTT-CCTCAA-TTT
258 --TAGTACACGA-TTTCGGCTGAAATATTGAAAAAATTGA-AAGAAAATATTTTCCCTCAATTTT
*
982 TTGCCAAAATATTAATAAAAATTATATAATTCAACGCCAAAAGTTTGAAGGGTTTATCACGCTTC
319 TTGCCAAAATATTAATAAAAATTATATAATTCAACACCAAAAGTTTGAAGGGTTTATCACGCTTC
1047 TAATATAAATGTTCCTA-TTTTTTTCTGAATTTATTTATAATTAAATCGAAACAAGATTCAGATG
384 TAATATAAATGTTCCTATTTTTTTTCTGAATTTATTTATAATTAAATCGAAACAAGATTCAGATG
* * *
1111 CTCGTAAAATGAAATCCTTAAATCCATTGTGGCTGAGATTTGAATAGATAAATAAATATATTTTG
449 CTCGTAAAAAGAAATCCTTAAATCCATTGTGCCTGAGATTTGAATAGATAAATAAAGATATTTTG
* * * * * *
1176 AGGAGTCTTGACGCAAAAAATCATGCAGAATTGAGCCGGGGACCTGAAAAACGTTTTTAGGAAGA
514 AGGAGTCTTGACG-AAAAAATAAAGCAGAATTGAGCCGAGGACCCGAAAAACGTTTTTAGCAAAA
* * * *
1241 AACCGTTATAGTTAGTATACGATTTTCGGTTGAAATATTGAAAAAATTGACAGAAATTTTTTTCC
578 AACCGTGAAAGTTAGTAAACGATTTTCGGCTGAAATATTGAAAAAATTGACAGAAATTTTTTTCC
*
1306 TCAATTTTTTTCC
643 TCAATTTTTTGCC
* * * *
1319 AAAATATTAATAAAAATTATTTTATTCAACACCAAAAAGTTTGAAGGGTTTTTCACGCTTCTAAT
1 AAAATATTAATAAAAATTATATAATTCAACGCCAAAAA-TTTGAAGGGTTTTTCAAGCTTCTAAT
1384 ATCAATTTTCCT
65 ATCAATTTTCCT
1396 T
Statistics
Matches: 671, Mismatches: 50, Indels: 29
0.89 0.07 0.04
Matches are distributed among these distances:
654 174 0.26
655 226 0.34
656 29 0.04
657 7 0.01
658 4 0.01
659 9 0.01
660 30 0.04
661 2 0.00
662 112 0.17
663 6 0.01
664 72 0.11
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (655 bp):
AAAATATTAATAAAAATTATATAATTCAACGCCAAAAATTTGAAGGGTTTTTCAAGCTTCTAATA
TCAATTTTCCTATTTTTTTCCCGAATTTATTTCTAATTAAAACGAAACAAGATTCAGACGCTCGT
AAAAAGAAATCCTTAAATCCGTTGTGCCTGAGATTTGAATAGATAAATATAGATATTTTGAGGAG
CCATGACGCACATGCAGAACTGAACCAAGGACCCGGAACACGTTTTTAGCAAAAAACCGTGATAG
TACACGATTTCGGCTGAAATATTGAAAAAATTGAAAGAAAATATTTTCCCTCAATTTTTTGCCAA
AATATTAATAAAAATTATATAATTCAACACCAAAAGTTTGAAGGGTTTATCACGCTTCTAATATA
AATGTTCCTATTTTTTTTCTGAATTTATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAA
AAAGAAATCCTTAAATCCATTGTGCCTGAGATTTGAATAGATAAATAAAGATATTTTGAGGAGTC
TTGACGAAAAAATAAAGCAGAATTGAGCCGAGGACCCGAAAAACGTTTTTAGCAAAAAACCGTGA
AAGTTAGTAAACGATTTTCGGCTGAAATATTGAAAAAATTGACAGAAATTTTTTTCCTCAATTTT
TTGCC
Done.