Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020642.1 Corchorus olitorius cultivar O-4 contig20675, 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: 41490
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Found at i:2574 original size:52 final size:52
Alignment explanation
Indices: 2506--2714 Score: 258
Period size: 52 Copynumber: 3.9 Consensus size: 52
2496 TTCCAAGAGC
*
2506 TTTCAATTTAGGGAAAGATCCCATCCAGTTTTCAAAGTATTCAATTTAGGACT
1 TTTCAAATT-GGGAAAGATCCCATCCAGTTTTCAAAGTATTCAATTTAGGACT
* * * *
2559 TTTCAAAATGGGAAAGATCCCATCTAGTTTTCATAGTATTCAATTTAAGAGC-
1 TTTCAAATTGGGAAAGATCCCATCCAGTTTTCAAAGTATTCAATTTAGGA-CT
* * *
2611 TTTCAATTTAGGGAAAGATCCCATCCAGTTTTCGAAGTATTCAATATAGGACT
1 TTTCAAATT-GGGAAAGATCCCATCCAGTTTTCAAAGTATTCAATTTAGGACT
* * * *
2664 TTTCAAATTGGGAAAGATCCCATCAATTTTCTTCAAAATTTTCAATTTAGG
1 TTTCAAATTGGGAAAGATCCCATCCA-GTT-TTCAAAGTATTCAATTTAGG
2715 GAAAGATCCC
Statistics
Matches: 132, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
52 62 0.47
53 54 0.41
54 16 0.12
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (52 bp):
TTTCAAATTGGGAAAGATCCCATCCAGTTTTCAAAGTATTCAATTTAGGACT
Found at i:2719 original size:40 final size:39
Alignment explanation
Indices: 2663--2783 Score: 131
Period size: 41 Copynumber: 3.1 Consensus size: 39
2653 AATATAGGAC
2663 TTTTCAAATT-GGGAAAGATCCCATCAAT-TTTCTTCAAAA
1 TTTTC-AATTAGGGAAAGATCCCATCAATCTTT-TTCAAAA
* *
2702 TTTTCAATTTAGGGAAAGATCCCATCCAGTCTTTTTCAAAG
1 TTTTCAA-TTAGGGAAAGATCCCAT-CAATCTTTTTCAAAA
* **
2743 TTTTCAATTAGGGGAAAGATCTCATCAAAGTTTTT-AAAA
1 TTTTCAATTA-GGGAAAGATCCCATCAATCTTTTTCAAAA
2782 TT
1 TT
2784 GAGTCGTTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
38 2 0.03
39 12 0.17
40 24 0.34
41 29 0.41
42 3 0.04
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (39 bp):
TTTTCAATTAGGGAAAGATCCCATCAATCTTTTTCAAAA
Found at i:5699 original size:16 final size:16
Alignment explanation
Indices: 5678--5710 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5668 CATGTAAAAA
*
5678 TTATTAATTTAGAGAG
1 TTATTAATTTAAAGAG
5694 TTATTAATTTAAAGAG
1 TTATTAATTTAAAGAG
5710 T
1 T
5711 ATTCTTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.45
Consensus pattern (16 bp):
TTATTAATTTAAAGAG
Found at i:6489 original size:23 final size:22
Alignment explanation
Indices: 6436--6494 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
6426 ACTTGCAACG
*
6436 TGACTTTTTTTTCTTTAATAAA
1 TGACTTTTTTTTCCTTAATAAA
**
6458 TTTCATTTTTTTTCCTTAATAACA
1 TGAC-TTTTTTTTCCTTAATAA-A
6482 TGACTTTTTTTTC
1 TGACTTTTTTTTC
6495 ACATTAAGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 2 0.07
23 25 0.83
24 3 0.10
ACGTcount: A:0.22, C:0.14, G:0.03, T:0.61
Consensus pattern (22 bp):
TGACTTTTTTTTCCTTAATAAA
Found at i:9404 original size:25 final size:24
Alignment explanation
Indices: 9370--9425 Score: 94
Period size: 25 Copynumber: 2.3 Consensus size: 24
9360 TTTAATACAA
*
9370 ATATCCACGGATATATCGAACAGAT
1 ATATCGACGGATATATCG-ACAGAT
9395 ATATCGACGGATATATCGACAGAT
1 ATATCGACGGATATATCGACAGAT
9419 ATATCGA
1 ATATCGA
9426 GGTATCGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (24 bp):
ATATCGACGGATATATCGACAGAT
Found at i:9409 original size:12 final size:12
Alignment explanation
Indices: 9379--9425 Score: 76
Period size: 12 Copynumber: 3.8 Consensus size: 12
9369 AATATCCACG
9379 GATATATCGAACA
1 GATATATCG-ACA
*
9392 GATATATCGACG
1 GATATATCGACA
9404 GATATATCGACA
1 GATATATCGACA
9416 GATATATCGA
1 GATATATCGA
9426 GGTATCGGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 23 0.72
13 9 0.28
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (12 bp):
GATATATCGACA
Found at i:11213 original size:13 final size:13
Alignment explanation
Indices: 11195--11257 Score: 103
Period size: 13 Copynumber: 5.0 Consensus size: 13
11185 ACAGATATCC
11195 ACGGATATATCGA
1 ACGGATATATCGA
11208 ACGGATATATCGA
1 ACGGATATATCGA
11221 ACGGATATATCG-
1 ACGGATATATCGA
11233 ACGGATATATCG-
1 ACGGATATATCGA
*
11245 ACAGATATATCGA
1 ACGGATATATCGA
11258 GGTATCGGTG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
12 23 0.48
13 25 0.52
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (13 bp):
ACGGATATATCGA
Found at i:11225 original size:26 final size:25
Alignment explanation
Indices: 11189--11257 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
11179 TTTAATACAG
*
11189 ATATCCACGGATATATCGAACGGAT
1 ATATCGACGGATATATCGAACGGAT
11214 ATATCGAACGGATATATCG-ACGGAT
1 ATATCG-ACGGATATATCGAACGGAT
*
11239 ATATCGACAGATATATCGA
1 ATATCGACGGATATATCGA
11258 GGTATCGGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
24 11 0.28
25 17 0.43
26 12 0.30
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (25 bp):
ATATCGACGGATATATCGAACGGAT
Found at i:11254 original size:14 final size:12
Alignment explanation
Indices: 11189--11257 Score: 102
Period size: 12 Copynumber: 5.6 Consensus size: 12
11179 TTTAATACAG
*
11189 ATATCCACGGAT
1 ATATCGACGGAT
11201 ATATCGAACGGAT
1 ATATCG-ACGGAT
11214 ATATCGAACGGAT
1 ATATCG-ACGGAT
11227 ATATCGACGGAT
1 ATATCGACGGAT
*
11239 ATATCGACAGAT
1 ATATCGACGGAT
11251 ATATCGA
1 ATATCGA
11258 GGTATCGGTG
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
12 29 0.54
13 25 0.46
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (12 bp):
ATATCGACGGAT
Found at i:23148 original size:1 final size:1
Alignment explanation
Indices: 23142--23171 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
23132 GATCTTGGGG
23142 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
23172 AAATGCAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.