Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012550.1 Corchorus capsularis cultivar CVL-1 contig12571, 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: 3812
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:2998 original size:629 final size:630
Alignment explanation
Indices: 395--3755 Score: 3019
Period size: 630 Copynumber: 5.3 Consensus size: 630
385 TTTCGGCTAT
* * * * *
395 AATTTGGCAAAAAACTGACCCGAAA-TATTTTTCCT-AAATTTTTTGCCACAATACTAAGAAAAA
1 AATTCGGCTAAAAACTGACTCGAAATTTTTTTTCCTGAAA-TTTTTGCCACAATACTCAGAAAAA
* ** * *
458 ATTATATGATTCAACGCCAAAAA-ATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTCCCATTT
65 A-TATATAATTCAACGCCAAAAAGATTGAAGGATTTTTAACGCTTCTAATATCGTTTTTCCATTT
* *
522 TTATTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAA
129 TT-TT--AATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAA
*
587 ATCCAATGTGGCTGTGATTTAGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAAT
191 ATCCAATGTGGCTGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAAT
* * * *
652 CATGCGAAACTGAGTCGGGGCCCTGAAACGCGTTTTTAGCCCCAAAACCGTCATGGTTAGTACAC
256 CATGCGAAACTGAGTCGGGACCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATGGTTAGTACAC
**
717 GATTTCGGCTAAAAACTGAGTCGATTTTTTTTTCCTGAAATATTTGCCACAATACTCAGAAAAAA
321 GATTTCGGCTAAAAACTGA-TCGA----AATTT--T----T-TTTGCCACAATACTCAGAAAAAA
* * * *
782 TATATAATTCAACACTAAAAAGATTTACA-GATTTTTAACGCTTCTAACTATCGTTTTTCCATTT
374 TATATAATTCAACGCCAAAAAGATTGA-AGGATTTTTAACGCTTCTAA-TATCGTTTTCCCATTT
* * * * * * * *
846 TTTTT-ATTAATTTCTAATTAAATAGAATCAAGTTTCATAT-ACTTGTAAAAACAAGTCATTACA
437 TTTTTAATTTATTTCTAATTAAATAGAAACAAGATTCAGATGA-TCGTAAAAACAAATCCTTAAA
* * * * * *
909 TCCAATGCGGTTGAGATTTGGTTAGATGAATAGAGATATTTCAGGGAGTCTTTCTGCCAAAAATC
501 TCCAATGTGGCTGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATC
* * * * * * *
974 ATGCGAAACTCAGACGGAACCCCGAAACAC-TTTTGTA-ACCCAAAAATCGTGAT-TTTAGTACA
566 ATGCGAAACTGAGTCGGGACCCCGAAACGCGTTTT-TAGCCCCAAAACT-GTGATGGTTAGTACA
1036 C-
629 CG
*
1037 AATTTCGGCCAAAAACTGA-TCTGAAA-TTTTTTT-C-----------CCACAATACTCA-AAAA
1 AA-TTCGGCTAAAAACTGACTC-GAAATTTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAA
** * * *
1087 AATATATAATTCAACATCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCCCATTT
64 AATATATAATTCAACGCCAAAAAGATTGAAGGATTTTTAACGCTTCTAATATCGTTTTTCCA-TT
* * * * *
1152 TTATTTGAATTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAACCAAATCCTTAA
128 TT-TTT-AATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAA
* * * *
1217 ATCCAATGTGGCGGTGATTTGGTTAGATGAATATAGATATTTTAAGAAGACTTTCTGCTAAAAAT
191 ATCCAATGTGGCTGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAAT
* * * *
1282 CATGCGAAACGGAGTCGGGACCCCGAAACGCATTTTTAGCCCAAAAACTGTGATAGTTAGTACAC
256 CATGCGAAACTGAGTCGGGACCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATGGTTAGTACAC
*
1347 GATTTCGGCTAAAAACTGACCTGAAACTGTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAA
321 GATTTCGGCTAAAAACTGATC-GAAA-----TT--T----TTTTTGCCACAATACTCAGAAAAAA
* * * *
1412 TATATAATTCAGCGCCAAAAAGATTGACGGATTTTTAACACTTCTAAATATCGTTTTTCCATTTT
374 TATATAATTCAACGCCAAAAAGATTGAAGGATTTTTAACGCTTCT-AATATCGTTTTCCCATTTT
*
1477 TTTTATATTTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA
438 TTTTA-ATTT-ATTTCTAATTAAATAGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAA
*
1542 TCCAATGTGGCTGTGATTTGGTTAGATGAATATAAATATTTCAAGAAGTCTTTCTGCCAAAAATC
501 TCCAATGTGGCTGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATC
* * * *
1607 ATGCGAAACTAAGTCGGGGCCCCGAAACGCGTTTTTAGTCCCTAAAACCGTGATGGTTAGTACAC
566 ATGCGAAACTGAGTCGGGACCCCGAAACGCGTTTTTAG-CCCCAAAACTGTGATGGTTAGTACAC
1672 G
630 G
* * *
1673 ATTTCGGCTAAAAACTGAGTCGAAACTTTTTTTTCCTGAAATATTTGCCACAATACTCAGAAAAA
1 AATTCGGCTAAAAACTGACTCGAAA-TTTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAA
* ** * * *
1738 ATATATAATTCAACGCCAAAACGATTGTCGAGCTTTTCAGAC-C-TCTACT-TCGTTTTTCCATT
65 ATATATAATTCAACGCCAAAAAGATTGAAG-GATTTTTA-ACGCTTCTAATATCGTTTTTCCATT
** * * * * * ** *
1800 TATTTCCTAAAAAATTTCTAATTAAAAAGAATCAAGATACAGATACCCGTAAAAA-ATGTCCCTA
128 T-TTT--TAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * * * *
1864 TATCTAA--T-GC--TG--TTGAGTTTGATGAATATTGATATTTTAAGGAGT-TTTCTCGCCAAA
190 AATCCAATGTGGCTGTGATTTG-GTTAGATGAATATAGATATTTCAAGAAGTCTTTCT-GCCAAA
* * * * ** * * *
1921 AATCATGCAAAATTGAGCTAGGG-CTCCGGCATGCGTTTTTTG-CAAAAAACCGTGATGGTTAGT
253 AATCATGCGAAACTGAG-TCGGGACCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATGGTTAGT
*
1984 ACACGATTTCGGCTATAATTTTGCAAAAAACTGACCCGAAATGTTTTTCCTCAATTTTTTGCCAC
317 ACACGATTTCGGC--------T---AAAAACTGA-TCGAAA------T--T---TTTTTTGCCAC
* * * ** *
2049 AATACTGAGAAAAAATTTTATGATTCAACGCCAAAAA-ATTGAAGGGGTTTTCACGCTTCTAATA
359 AATACTCAGAAAAAA-TATATAATTCAACGCCAAAAAGATTGAAGGATTTTTAACGCTTCTAATA
* * *
2113 TCGTTTTCCCATTTTTATTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
423 TCGTTTTCCCATTTTT-TT-TAATTTATTTCTAATTAAATAGAAACAAGATTCAGATGATCGTAA
* * *
2178 AAACAAATTCTTAAATCCAATGTGGCTGTGATTTTGTTAGATGAATATTGATAATTTC-AGAAGT
486 AAACAAATCCTTAAATCCAATGTGGCTGTGATTTGGTTAGATGAATATAGAT-ATTTCAAGAAGT
* * *
2242 CTTTCTGCCATAAATCATGCGAAACTGAGTCGGGACTCTGAAACGCGTTTTTAGCCCCAAAAC--
550 CTTTCTGCCAAAAATCATGCGAAACTGAGTCGGGACCCCGAAACGCGTTTTTAGCCCCAAAACTG
2305 TGATGGTTAGTACACG
615 TGATGGTTAGTACACG
* * * *
2321 ATTTCGGCTAAAAACTGAGTCGAAATTTTTTTTCCTGAAATATTTGCCACAATACTCTGAAAAAA
1 AATTCGGCTAAAAACTGACTCGAAATTTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAA
* * *
2386 TATATAATTCAACACTAAAAAGAATGAAGGATTTTTAACGCTTCTAACTATCGTTTTTCCATTTT
66 TATATAATTCAACGCCAAAAAGATTGAAGGATTTTTAACGCTTCTAA-TATCGTTTTTCCATTTT
* * * * * * **
2451 TTTAATTAATTTCTAATTAAATAGAATCAAGTTTCAGATACTTGTAAAAACAAGTCATTGCATCC
130 TTTAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
* ** * * * *
2516 AATGCGATTGAGATTTGGTTAGATGAATAGAGATATTTCAGGGAGTCTTTCTGCCAAAAATCATG
195 AATGTGGCTGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATG
* * * * * * * * *
2581 CGAAACTCAGACGGAACCTCGAAACACGTTTTTAACCCAAAAATCGTGAT-TTTAGTACACAATT
260 CGAAACTGAGTCGGGACCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATGGTTAGTACACGATT
* * * *
2645 TCTGCCAAAAACTGATCTGAAATTTTTTTTGCCACAATACTCA-AAAAAATAAATAATTCAACGT
325 TCGGCTAAAAACTGATC-GAAATTTTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGC
* * *
2709 CAAAAA-ATTTAAGGGTTTTTCACGCTTCTAATATCGTTTTCCCATTTTTATTTGAATTTATTTC
389 CAAAAAGATTGAAGGATTTTTAACGCTTCTAATATCGTTTTCCCATTTTT-TTT-AATTTATTTC
* * * * * *
2773 TAATTATATCGAAACAAGATTTAGATGATTGTTAAAGA-AAATCCTTAAATCCAATGTGGCGGTG
452 TAATTAAATAGAAACAAGATTCAGATGATCG-TAAAAACAAATCCTTAAATCCAATGTGGCTGTG
* * * *
2837 ATCTGGTTAGATGAATATAGATATTTTAAGAAGTCTTTCTG-CGAAAATCATGTGAAACTGAGTC
516 ATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAACTGAGTC
*
2901 GGGACCCCGAAACGCGTTTTTAGCCCCAAAACTGTGATAGTTAGTACACG
581 GGGACCCCGAAACGCGTTTTTAGCCCCAAAACTGTGATGGTTAGTACACG
* * ** *
2951 AATTCGGCTAAAAACTAAC-CTGAAA-TTGTTTTCAAGATATTTTTGCCACAATACTCAGAAAAA
1 AATTCGGCTAAAAACTGACTC-GAAATTTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAA
* * *
3014 ATATATAATTAAACGCCAAAAAGATTGACGGATTTTTAACGCTTCTAAATATCGCTTTTCCATTT
65 ATATATAATTCAACGCCAAAAAGATTGAAGGATTTTTAACGCTTCT-AATATCGTTTTTCCA-TT
3079 TTTTATAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA
128 TTTT-TAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA
* * *
3144 TCCAATGTGGCAGTGATTTGGTTAGATGTATATAGATATTTCAAGAAGACTTTCTGCCAAAAATC
192 TCCAATGTGGCTGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATC
* * * *
3209 ATGCGAAACTAAGTCGGGCCCCCGAAACGCGTTTTTAGCCCCAAAACCGTGATGGTTAGTAGACG
257 ATGCGAAACTGAGTCGGGACCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATGGTTAGTACACG
*
3274 ATTTCGGCTAAAAACTGAGTCGAAATTTTTTTTTCCTGAAATATTTGCCACAATACTCA-TAAAA
322 ATTTCGGCTAAAAACTGA-TCGAAA------TTT--T----T-TTTGCCACAATACTCAGAAAAA
* * * ** * * * *
3338 ATTTATATTTCAATGCCAAAAAGATTGTCGAGCTTTTCAGAC-C-TCTACT-TCGTTTTTCCATT
373 ATATATAATTCAACGCCAAAAAGATTGAAG-GATTTTTA-ACGCTTCTAATATCGTTTTCCCATT
*** * * * ** *
3400 TTTTTCCTAAAAAAATTTCTAATTAAATAGAATCAAGATACAGAT-ACCCGTAAAAA-ATGTCCC
436 TTTTT--T-AATTTATTTCTAATTAAATAGAAACAAGATTCAGATGA-TCGTAAAAACAAATCCT
* * * * * * * *
3463 TATATCTAA--T-GC--TG--TTGAGTTTGATGAATATTGATATTTTAAGGAGTC-TTCACGTCA
497 TAAATCCAATGTGGCTGTGATTTG-GTTAGATGAATATAGATATTTCAAGAAGTCTTTC-TGCCA
* * * * ** ** *
3520 AAAATCATGCAAAATTGAGCTAGGG-CTCCGGCACGCGTTCTTT-G-CAAAAAACCGTGATGGTT
560 AAAATCATGCGAAACTGAG-TCGGGACCCCGAAACGCGTT-TTTAGCCCCAAAACTGTGATGGTT
3582 AGTACACG
623 AGTACACG
* * * * * *
3590 ATTTCGGCTAAAAAACTAAGTCGAAATGTTTTTGTCCTGAAATATTTGCCACAATATTCAGAAAA
1 AATTCGGCT-AAAAACTGACTCGAAAT-TTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAA
** * * *
3655 AATATATAATTCAACGCCAAAAAGATTGTCGAACTTTTCAGAC-C-TCTACT-TCGTTTTTCCAT
64 AATATATAATTCAACGCCAAAAAGATTGAAGGA-TTTTTA-ACGCTTCTAATATCGTTTTTCCA-
** *
3717 TTTTTTCCTAAAAAATTTCTAATTAAATAGAATCAAGAT
126 TTTTTT--TAATTAATTTCTAATTAAATAGAAACAAGAT
3756 ACGGATACCC
Statistics
Matches: 2264, Mismatches: 327, Indels: 257
0.79 0.11 0.09
Matches are distributed among these distances:
628 54 0.02
629 259 0.11
630 373 0.16
631 191 0.08
632 32 0.01
633 133 0.06
634 10 0.00
635 35 0.02
636 4 0.00
637 7 0.00
638 9 0.00
639 58 0.03
640 62 0.03
641 78 0.03
642 139 0.06
643 37 0.02
644 5 0.00
645 73 0.03
646 88 0.04
647 82 0.04
648 63 0.03
649 73 0.03
650 44 0.02
651 166 0.07
652 71 0.03
653 96 0.04
654 20 0.01
655 1 0.00
656 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (630 bp):
AATTCGGCTAAAAACTGACTCGAAATTTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAA
TATATAATTCAACGCCAAAAAGATTGAAGGATTTTTAACGCTTCTAATATCGTTTTTCCATTTTT
TTAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCA
ATGTGGCTGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGC
GAAACTGAGTCGGGACCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATGGTTAGTACACGATTT
CGGCTAAAAACTGATCGAAATTTTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCA
AAAAGATTGAAGGATTTTTAACGCTTCTAATATCGTTTTCCCATTTTTTTTAATTTATTTCTAAT
TAAATAGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCAATGTGGCTGTGATTTG
GTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAACTGAGTCGGGAC
CCCGAAACGCGTTTTTAGCCCCAAAACTGTGATGGTTAGTACACG
Done.