Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012512.1 Corchorus olitorius cultivar O-4 contig12545, 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: 14292
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Found at i:7425 original size:2 final size:2
Alignment explanation
Indices: 7418--7456 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
7408 CATCATCATC
7418 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7457 AGATGGTTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8372 original size:29 final size:30
Alignment explanation
Indices: 8338--8409 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
8328 CCAAACTTAG
* * *
8338 AAGTAGAGGGACTAAATTGATCGTTTTT-T-
1 AAGTAGAGGGACGAAAATGAT-ATTTTTGTA
8367 AAGTAGAGGGACGAAAATGATATTTTTGTGA
1 AAGTAGAGGGACGAAAATGATATTTTTGT-A
8398 AAGTAGAGGGAC
1 AAGTAGAGGGAC
8410 CTCCTAGGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 5 0.14
29 20 0.54
31 12 0.32
ACGTcount: A:0.36, C:0.06, G:0.29, T:0.29
Consensus pattern (30 bp):
AAGTAGAGGGACGAAAATGATATTTTTGTA
Found at i:9729 original size:131 final size:131
Alignment explanation
Indices: 9487--10137 Score: 817
Period size: 131 Copynumber: 5.0 Consensus size: 131
9477 ATGCAACGAC
*
9487 TTATAAAGTTGTTACGAATAGATTATGATTTCGCAACAACTTAAGAATTTGTTGTTACGAATACT
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACAACTTAAGAATTTGTTGTTACGAATACT
* * * * * * *
9552 GTATATATTGGTAACAACTAAAAAAGTGTTGTGTAAAGTACTATCAAAATAACTTAGACAACGTT
66 GTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGTT
9617 T
131 T
* * *
9618 TTATAAAGTTGTTACGAATAGTTTATGATTTC-CTAGCAACTTAAGAAGTAGTTGTTACGAATAC
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGC-AACAACTTAAGAATTTGTTGTTACGAATAC
* * *
9682 TGTAAACATTAGCAATAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCAGTTAGGCAACGT
65 TGTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGT
9747 TT
130 TT
* *
9749 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACAACTTCAA-AATTTGTTGTTACAAATAT
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACAACTT-AAGAATTTGTTGTTACGAATAC
* * *
9813 TGTAAACATCGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACATAGGCAATGT
65 TGTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGT
9878 TT
130 TT
* * ** * *
9880 TTATAAAGTTGTTACAAATAGTTTATGATTTCGCAACGAA-TT-TGTTTTTGTTGTTACGAAAAT
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAAC-AACTTAAGAATTTGTTGTTACGAATAC
* *** * *
9943 TGTAAGCATTGGCAATGTCTAAAAAATTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGA
65 TGTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGT
*
10008 CT
130 TT
* * * * * * ** *
10010 TTATAAAATTGTTACAAATAGATTATGATTTCACAACGACTT-TGTTTTTGTTGTTACGAAAACT
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACAACTTAAGAATTTGTTGTTACGAATACT
* * * * *
10074 GTAAGCATTGGCAACAATTAAAAAAGTCATTGGGTAAAATACCATCAAAATCACTAAGGCAACG
66 GTAAACATTGGCAACAACTAAAAAAGT-GTTGTGTAAAATACCATCAAAATCACTTAGGCAACG
10138 ACTTTTAATT
Statistics
Matches: 459, Mismatches: 54, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
129 1 0.00
130 152 0.33
131 301 0.66
132 5 0.01
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (131 bp):
TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACAACTTAAGAATTTGTTGTTACGAATACT
GTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGTT
T
Found at i:10839 original size:25 final size:24
Alignment explanation
Indices: 10811--10861 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
10801 TTTTGAACTC
10811 ATTATTCA-TTATTTAA-AATATAT
1 ATTATT-ATTTATTTAATAATATAT
10834 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
10857 ATTAT
1 ATTAT
10862 ATATAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 1 0.04
22 13 0.52
23 7 0.28
24 4 0.16
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:12569 original size:27 final size:26
Alignment explanation
Indices: 12530--12615 Score: 93
Period size: 27 Copynumber: 3.3 Consensus size: 26
12520 GTTTCCTTTA
*
12530 TGGATTCCGATGGTCATGAGACAAAAT
1 TGGATCCCGATGGTCATGAGAC-AAAT
* * *
12557 TGGATCCCAATGGTCGTGAGATGAAAT
1 TGGATCCCGATGGTCATGAGA-CAAAT
* *
12584 TAGATCCCGATGGTCATGAG-CAATT
1 TGGATCCCGATGGTCATGAGACAAAT
12609 TGGATCC
1 TGGATCC
12616 GACGTGTTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
25 9 0.19
27 39 0.81
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (26 bp):
TGGATCCCGATGGTCATGAGACAAAT
Found at i:12763 original size:15 final size:15
Alignment explanation
Indices: 12743--12772 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12733 TAAAGAATAG
12743 CACACCATCAGGACA
1 CACACCATCAGGACA
12758 CACACCATCAGGACA
1 CACACCATCAGGACA
12773 ACTTATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.40, G:0.13, T:0.07
Consensus pattern (15 bp):
CACACCATCAGGACA
Done.