Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008058.1 Corchorus capsularis cultivar CVL-1 contig08079, 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: 40337
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Found at i:2489 original size:52 final size:52
Alignment explanation
Indices: 2411--2519 Score: 202
Period size: 52 Copynumber: 2.1 Consensus size: 52
2401 AATGAACTCA
2411 TTTGAATTTAATATGTAATAAGGGTTATTTAGTGT-TGCTATTGATTTTTGCT
1 TTTGAATTTAATATGTAATAAGGGTTATTTAGT-TCTGCTATTGATTTTTGCT
2463 TTTGAATTTAATATGTAATAAGGGTTATTTAGTTCTGCTATTGATTTTTGCT
1 TTTGAATTTAATATGTAATAAGGGTTATTTAGTTCTGCTATTGATTTTTGCT
2515 TTTGA
1 TTTGA
2520 GCTAAAAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
51 1 0.02
52 55 0.98
ACGTcount: A:0.25, C:0.05, G:0.18, T:0.52
Consensus pattern (52 bp):
TTTGAATTTAATATGTAATAAGGGTTATTTAGTTCTGCTATTGATTTTTGCT
Found at i:3065 original size:47 final size:47
Alignment explanation
Indices: 2997--3093 Score: 142
Period size: 48 Copynumber: 2.1 Consensus size: 47
2987 TATTGACCCC
*
2997 ATAAAACATTGGCTATTTTCACA-TATATGATATTTAAACTATATTT
1 ATAAAAAATTGGCTATTTTCACATTATATGATATTTAAACTATATTT
* * *
3043 ATAAAAAATTTGGCTATTTTCACATTTTCTTATATTTAAACTATATTT
1 ATAAAAAA-TTGGCTATTTTCACATTATATGATATTTAAACTATATTT
3091 ATA
1 ATA
3094 TCTTATCCTC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 7 0.16
47 15 0.33
48 23 0.51
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.46
Consensus pattern (47 bp):
ATAAAAAATTGGCTATTTTCACATTATATGATATTTAAACTATATTT
Found at i:4640 original size:25 final size:24
Alignment explanation
Indices: 4603--4654 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 24
4593 TAAAAATAAA
*
4603 AAAAAATCAATTTTTCTGTTTTTTTT
1 AAAAAATCAATTTTT-T-TCTTTTTT
*
4629 AAAAAA-CCATTTTTTTCTTTTTT
1 AAAAAATCAATTTTTTTCTTTTTT
4652 AAA
1 AAA
4655 GAAGAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 10 0.42
24 1 0.04
25 7 0.29
26 6 0.25
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.54
Consensus pattern (24 bp):
AAAAAATCAATTTTTTTCTTTTTT
Found at i:5086 original size:31 final size:31
Alignment explanation
Indices: 5044--5104 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
5034 ATGCAAATAG
*
5044 GTCCCTGAAGTGAACTTAAATGAGCAATTAA
1 GTCCCTAAAGTGAACTTAAATGAGCAATTAA
* * * *
5075 GTCCCTAAAGTGGAGTTAATTGAGTAATTA
1 GTCCCTAAAGTGAACTTAAATGAGCAATTA
5105 GGCCCCTGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (31 bp):
GTCCCTAAAGTGAACTTAAATGAGCAATTAA
Found at i:12137 original size:29 final size:30
Alignment explanation
Indices: 12094--12163 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
12084 CGTTTAGATG
12094 TTTTGCCTCCC-GAACTTCAA-TCTT-GGACA
1 TTTTGCC-CCCTGAACTTCAACT-TTGGGACA
*
12123 TTTTGCCCCCTGAACTTCAACTTTGGGACG
1 TTTTGCCCCCTGAACTTCAACTTTGGGACA
12153 TTTTGCCCCCT
1 TTTTGCCCCCT
12164 CAACCTAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
28 3 0.08
29 18 0.49
30 16 0.43
ACGTcount: A:0.16, C:0.33, G:0.16, T:0.36
Consensus pattern (30 bp):
TTTTGCCCCCTGAACTTCAACTTTGGGACA
Found at i:12352 original size:30 final size:30
Alignment explanation
Indices: 12318--12424 Score: 119
Period size: 29 Copynumber: 3.6 Consensus size: 30
12308 CGGAGCCGTT
*
12318 AAGTTGAGGGGGCAAAACGTCTCAAAATTG
1 AAGTTCAGGGGGCAAAACGTCTCAAAATTG
* * *
12348 AAGTTCATGGGGTAAAATGTC-CAAAATTG
1 AAGTTCAGGGGGCAAAACGTCTCAAAATTG
* **
12377 AAGTTCGGGGGGCAAAACGTCT-AAACACTAA
1 AAGTTCAGGGGGCAAAACGTCTCAAA-A-TTG
12408 AAGTTCAGGGGGCAAAA
1 AAGTTCAGGGGGCAAAA
12425 TTGTTGTTTA
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
29 28 0.44
30 18 0.29
31 17 0.27
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.20
Consensus pattern (30 bp):
AAGTTCAGGGGGCAAAACGTCTCAAAATTG
Found at i:24625 original size:17 final size:16
Alignment explanation
Indices: 24585--24627 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
24575 CATGTAATCT
*
24585 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
24601 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
24618 TTAGATCACT
1 TT-GATCACT
24628 AGTCATCTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:27570 original size:33 final size:33
Alignment explanation
Indices: 27533--27597 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
27523 TCAGTGGTAG
27533 CTTTGTTGATCCTCGTGGAGTTCTTGATAATTC
1 CTTTGTTGATCCTCGTGGAGTTCTTGATAATTC
27566 CTTTGTTGATCCTCGTGGAGTTCTTGATAATT
1 CTTTGTTGATCCTCGTGGAGTTCTTGATAATT
27598 GGGATGAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (33 bp):
CTTTGTTGATCCTCGTGGAGTTCTTGATAATTC
Found at i:33291 original size:13 final size:13
Alignment explanation
Indices: 33273--33297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33263 CATAAATAAT
33273 TATACAAAAAAAA
1 TATACAAAAAAAA
33286 TATACAAAAAAA
1 TATACAAAAAAA
33298 TGGAGTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (13 bp):
TATACAAAAAAAA
Done.