Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015825.1 Corchorus capsularis cultivar CVL-1 contig15846, 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: 13041
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:4492 original size:7 final size:7
Alignment explanation
Indices: 4480--4506 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4470 GAGTATAATG
4480 TAAAATT
1 TAAAATT
4487 TAAAATT
1 TAAAATT
4494 TAAAATT
1 TAAAATT
4501 TAAAAT
1 TAAAAT
4507 ATCTATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TAAAATT
Found at i:6991 original size:385 final size:393
Alignment explanation
Indices: 6502--7259 Score: 1112
Period size: 385 Copynumber: 1.9 Consensus size: 393
6492 TTCTAAAAAA
* * *
6502 CTGTAAAATTGAACAATGTCATTTAAGAAATATATTTTAAAAAATATAATATATATATAAGTTTT
1 CTGTAAAATTAAACAATGTAATTTAAGAAATATATCTTAAAAAATATAATATATATATAAGTTTT
*
6567 TTAATTAAATTAGTAAAATGGTAAAACCAAAACAGGTATAAGGATATTAAATTTAATTAAACAAA
66 TTAATTAAATTAGTAAAATGGTAAAAACAAAACAGGTATAAGGATATTAAATTTAATTAAACAAA
* *
6632 AATAGTGTTTTTATTTGAGTAAAATTATAAAAGTATATTTTAAAAAAATTCTAATATATATA-A-
131 AATAGTGTTTTTAGTTGAGTAAAACTATAAAAGTAT-TTTTAAAAAAATTCTAATATATATATAG
* * *
6695 G-TTTT-TT-AA-A-TAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAGTTAAATA
195 GTTTTTATTAAATAGTAAAATGATAAAAATAAAATAGTTACAAGGATATTAGATTTAATTAAATA
* *
6755 AAAA-TACAGTATTTCGTTGAGT-AAACTTATAAATGTTTAAACAATGGCATTTAAGAAATATAT
260 AAAAGTACAGTATTTAGTTGAGTAAAAC-TATAAAAGTTTAAACAATGGCATTTAAGAAATATAT
* *
6818 TTGAAAAATAAGAG-TAT-ATCGGCGATTCAAAAGTTTTACAAGAACTGGTACTATTTATATTTT
324 TCGAAAAATAAG-GTTATAATCGGCGATTCAAAAGTTTTACAAAAACTGGTACTATTTATATTTT
6881 CAAGGG
388 CAAGGG
* *
6887 CTGTAAAATTTAAACAATGTAATTTAAGAAATATATCTTAAAAATTAT-A-ATATATCTAAGTTT
1 CTGTAAAA-TTAAACAATGTAATTTAAGAAATATATCTTAAAAAATATAATATATATATAAG-TT
* * * *
6950 TTTTAATTAAATTA-TCAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAAT
64 TTTTAATTAAATTAGT-AAAATGGTAAAAACAAAACAGGTATAAGGATATTAAATTTAATTAAAC
*
7014 AAAAATAGTGTTTTTAGTTGAGTAAAACTATAAAAGTATTTTTTAAAAAATTCTAATATATATAT
128 AAAAATAGTGTTTTTAGTTGAGTAAAACTATAAAAGTATTTTTAAAAAAATTCTAATATATATAT
*
7079 AGGTTTTTTAATTAAAATAGTAAAATGATAAAAATAAATTAGTTACAAGGATATTAGATTTAATT
193 AGG-TTTTT-ATT-AAATAGTAAAATGATAAAAATAAAATAGTTACAAGGATATTAGATTTAATT
* * *
7144 AAATAAAAAGTAGAGTTTTTAGTTGAGTAAAACTATAAAAGTTTAAACAATGTCATTTAAGAAAT
255 AAATAAAAAGTACAGTATTTAGTTGAGTAAAACTATAAAAGTTTAAACAATGGCATTTAAGAAAT
*
7209 ATATTCGAAAAATAAGGTTATAATGGGCGATTCAAAAGTTTTACAAAAACT
320 ATATTCGAAAAATAAGGTTATAATCGGCGATTCAAAAGTTTTACAAAAACT
7260 CATACTTTTT
Statistics
Matches: 331, Mismatches: 25, Indels: 23
0.87 0.07 0.06
Matches are distributed among these distances:
384 35 0.11
385 106 0.32
386 36 0.11
388 4 0.01
390 2 0.01
392 2 0.01
393 1 0.00
394 51 0.15
395 63 0.19
396 31 0.09
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (393 bp):
CTGTAAAATTAAACAATGTAATTTAAGAAATATATCTTAAAAAATATAATATATATATAAGTTTT
TTAATTAAATTAGTAAAATGGTAAAAACAAAACAGGTATAAGGATATTAAATTTAATTAAACAAA
AATAGTGTTTTTAGTTGAGTAAAACTATAAAAGTATTTTTAAAAAAATTCTAATATATATATAGG
TTTTTATTAAATAGTAAAATGATAAAAATAAAATAGTTACAAGGATATTAGATTTAATTAAATAA
AAAGTACAGTATTTAGTTGAGTAAAACTATAAAAGTTTAAACAATGGCATTTAAGAAATATATTC
GAAAAATAAGGTTATAATCGGCGATTCAAAAGTTTTACAAAAACTGGTACTATTTATATTTTCAA
GGG
Found at i:7111 original size:134 final size:134
Alignment explanation
Indices: 6926--7185 Score: 407
Period size: 134 Copynumber: 1.9 Consensus size: 134
6916 AATATATCTT
* * * * *
6926 AAAAATTATAATATATCTAAGTTTTTTTAATTAAATTATCAAAATGGTAAAAATAAAATAGGTAT
1 AAAAATTATAATATATATAAGGTTTTTTAATTAAAATATCAAAATGATAAAAATAAAATAGGTAC
*
6991 AAGGATATTAGATTTAATTAAATAAAAA-TAGTGTTTTTAGTTGAGTAAAACTATAAAAGTATTT
66 AAGGATATTAGATTTAATTAAATAAAAAGTAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATTT
7055 TTTA
131 TTTA
* * *
7059 AAAAATTCTAATATATATATAGGTTTTTTAATTAAAATAGT-AAAATGATAAAAATAAATTAGTT
1 AAAAATTATAATATATATA-AGGTTTTTTAATTAAAATA-TCAAAATGATAAAAATAAAATAGGT
7123 ACAAGGATATTAGATTTAATTAAATAAAAAGTAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
64 ACAAGGATATTAGATTTAATTAAATAAAAAGTAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
7186 TTAAACAATG
Statistics
Matches: 115, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
133 17 0.15
134 66 0.57
135 32 0.28
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.38
Consensus pattern (134 bp):
AAAAATTATAATATATATAAGGTTTTTTAATTAAAATATCAAAATGATAAAAATAAAATAGGTAC
AAGGATATTAGATTTAATTAAATAAAAAGTAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATTT
TTTA
Found at i:7294 original size:6 final size:6
Alignment explanation
Indices: 7271--7302 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
7261 ATACTTTTTA
7271 ATATAG -TATAG A-ATAG ATATAG ATATAG ATAT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATAT
7303 GAATATTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.42
6 14 0.58
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:11612 original size:18 final size:18
Alignment explanation
Indices: 11571--11612 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
11561 GGGTTTTTAC
11571 TAAATGAATCCATATTCA
1 TAAATGAATCCATATTCA
*
11589 -AAATGACTCCATGA-TCA
1 TAAATGAATCCAT-ATTCA
11606 TAAATGA
1 TAAATGA
11613 TTAACTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.29
Consensus pattern (18 bp):
TAAATGAATCCATATTCA
Done.