Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014589.1 Corchorus capsularis cultivar CVL-1 contig14610, 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: 17790
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2508 original size:56 final size:57
Alignment explanation
Indices: 2440--2547 Score: 209
Period size: 56 Copynumber: 1.9 Consensus size: 57
2430 ATATATAAAC
2440 TAAATAAAATATATTTAACGTGATTTTGATAGATATAAATATATAAT-TAATTTATA
1 TAAATAAAATATATTTAACGTGATTTTGATAGATATAAATATATAATATAATTTATA
2496 TAAATAAAATATATTTAACGTGATTTTGATAGATATAAATATATAATATAAT
1 TAAATAAAATATATTTAACGTGATTTTGATAGATATAAATATATAATATAAT
2548 AATTTATATA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 47 0.92
57 4 0.08
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (57 bp):
TAAATAAAATATATTTAACGTGATTTTGATAGATATAAATATATAATATAATTTATA
Found at i:2831 original size:90 final size:88
Alignment explanation
Indices: 2656--2818 Score: 197
Period size: 90 Copynumber: 1.8 Consensus size: 88
2646 TTTCACGTGC
* * *
2656 GTTGCACGTGGCACAACGCGTGTGAACTAAATTAATTTTTTTTTAAATCTTTGAAAATAATAAGA
1 GTTGCACGTGGCACAACGCGTGTGAACGAAATTAA--TATGTTTAAATCTTTGAAAATAATAAGA
* * *
2721 GGTGAAAATATATTTAATTAATTTA
64 GATCAAAATATATTAAATTAATTTA
* *
2746 GTTGCACGTGGCAGAACGCGTGTGAACGAAA-TAA-ATGTTTAAATACTTT-AAAATAATGAGAG
1 GTTGCACGTGGCACAACGCGTGTGAACGAAATTAATATGTTTAAAT-CTTTGAAAATAATAAGAG
2808 ATCACAAATAT
65 ATCA-AAATAT
2819 TCTATTAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
86 22 0.34
87 10 0.16
89 3 0.05
90 29 0.45
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (88 bp):
GTTGCACGTGGCACAACGCGTGTGAACGAAATTAATATGTTTAAATCTTTGAAAATAATAAGAGA
TCAAAATATATTAAATTAATTTA
Found at i:5361 original size:2 final size:2
Alignment explanation
Indices: 5354--5387 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5344 CATATTAGTC
5354 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5388 ATAAGAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13715 original size:16 final size:17
Alignment explanation
Indices: 13696--13736 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
13686 GAAATTACCG
13696 GAACCCGAACCCG-CCC
1 GAACCCGAACCCGACCC
* *
13712 GAACCCAAACCCGACTC
1 GAACCCGAACCCGACCC
13729 GAACCCGA
1 GAACCCGA
13737 GATCAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.32, C:0.49, G:0.17, T:0.02
Consensus pattern (17 bp):
GAACCCGAACCCGACCC
Found at i:14506 original size:17 final size:17
Alignment explanation
Indices: 14479--14526 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
14469 TATCGAAAGT
*
14479 GAACCCAAACCCGACCC
1 GAACCCGAACCCGACCC
* *
14496 GTACCCGAACCCGATCC
1 GAACCCGAACCCGACCC
*
14513 GAACACGAACCCGA
1 GAACCCGAACCCGA
14527 AATACCCGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.33, C:0.46, G:0.17, T:0.04
Consensus pattern (17 bp):
GAACCCGAACCCGACCC
Found at i:14538 original size:15 final size:15
Alignment explanation
Indices: 14518--14574 Score: 80
Period size: 15 Copynumber: 3.8 Consensus size: 15
14508 GATCCGAACA
14518 CGAACCCGAAATACC
1 CGAACCCGAAATACC
14533 CGAACCCGAAAATACC
1 CGAACCCG-AAATACC
* *
14549 CGAACCCGAAGTGCC
1 CGAACCCGAAATACC
14564 CGAACCC-AAAT
1 CGAACCCGAAAT
14575 CGGCCCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
14 3 0.08
15 20 0.53
16 15 0.39
ACGTcount: A:0.39, C:0.39, G:0.16, T:0.07
Consensus pattern (15 bp):
CGAACCCGAAATACC
Found at i:14547 original size:16 final size:16
Alignment explanation
Indices: 14518--14558 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
14508 GATCCGAACA
14518 CGAACCCG-AAATACC
1 CGAACCCGAAAATACC
14533 CGAACCCGAAAATACC
1 CGAACCCGAAAATACC
14549 CGAACCCGAA
1 CGAACCCGAA
14559 GTGCCCGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.41, C:0.39, G:0.15, T:0.05
Consensus pattern (16 bp):
CGAACCCGAAAATACC
Found at i:14558 original size:6 final size:6
Alignment explanation
Indices: 14479--14542 Score: 51
Period size: 6 Copynumber: 10.5 Consensus size: 6
14469 TATCGAAAGT
* * * *
14479 GAACCC AAACCC G-ACCC GTACCC GAACCC G-ATCC GAACAC GAACCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC
14525 GAAATACCC GAACCC GAA
1 G--A-ACCC GAACCC GAA
14543 AATACCCGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
5 9 0.20
6 30 0.65
7 1 0.02
8 1 0.02
9 5 0.11
ACGTcount: A:0.36, C:0.44, G:0.16, T:0.05
Consensus pattern (6 bp):
GAACCC
Found at i:16964 original size:184 final size:184
Alignment explanation
Indices: 16655--16999 Score: 672
Period size: 184 Copynumber: 1.9 Consensus size: 184
16645 ACAATCGCCG
*
16655 TGTTGCCTCGAATCGCGTGCCAGTCGGTCACGTACACTAAGGCTCCACGAAGCGTCAATACCAGA
1 TGTTGCCTCGAATCGCGTGCCAGTCGGTCACGTACACCAAGGCTCCACGAAGCGTCAATACCAGA
16720 TCAAAAAGACAAAACACAAATAGAGTATAAATTTGAAATACATAAGTTTCCAAATCAGAATAAAA
66 TCAAAAAGACAAAACACAAATAGAGTATAAATTTGAAATACATAAGTTTCCAAATCAGAATAAAA
16785 GCGGAATGGTTAAAACCGAGAATAAAAGTAAAACGCTCCCTATCTTTAACAAGC
131 GCGGAATGGTTAAAACCGAGAATAAAAGTAAAACGCTCCCTATCTTTAACAAGC
*
16839 TGTTGCCTCGAATCGCGTGCCGGTCGGTCACGTACACCAAGGCTCCACGAAGCGTCAATACCAGA
1 TGTTGCCTCGAATCGCGTGCCAGTCGGTCACGTACACCAAGGCTCCACGAAGCGTCAATACCAGA
16904 TCAAAAAGACAAAACACAAATAGAGTATAAATTTGAAATACATAAGTTTCCAAATCAGAATAAAA
66 TCAAAAAGACAAAACACAAATAGAGTATAAATTTGAAATACATAAGTTTCCAAATCAGAATAAAA
16969 GCGGAATGGTTAAAACCGAGAATAAAAGTAA
131 GCGGAATGGTTAAAACCGAGAATAAAAGTAA
17000 TACGGGTCTC
Statistics
Matches: 159, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
184 159 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (184 bp):
TGTTGCCTCGAATCGCGTGCCAGTCGGTCACGTACACCAAGGCTCCACGAAGCGTCAATACCAGA
TCAAAAAGACAAAACACAAATAGAGTATAAATTTGAAATACATAAGTTTCCAAATCAGAATAAAA
GCGGAATGGTTAAAACCGAGAATAAAAGTAAAACGCTCCCTATCTTTAACAAGC
Done.