Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016128.1 Corchorus capsularis cultivar CVL-1 contig16149, 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: 26570
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Found at i:1018 original size:2 final size:2
Alignment explanation
Indices: 1011--1043 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1001 TAATATTTAG
1011 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1044 CTTCCTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9120 original size:18 final size:20
Alignment explanation
Indices: 9084--9132 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
9074 TTTATAAATT
* *
9084 ATTATTAATCTCAATTAT-AA
1 ATTATT-ATATCAAATATAAA
9104 ATTA-TATATCAAATATAAA
1 ATTATTATATCAAATATAAA
9123 ATTATTATAT
1 ATTATTATAT
9133 TATATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 9 0.36
19 7 0.28
20 9 0.36
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTATTATATCAAATATAAA
Found at i:9145 original size:17 final size:16
Alignment explanation
Indices: 9118--9165 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
9108 TATATCAAAT
*
9118 ATAAAATTATTATATT-
1 ATAATATTATTA-ATTA
9134 ATATATATTATTAATTA
1 ATA-ATATTATTAATTA
9151 ATAATATATATTAAT
1 ATAATAT-TATTAAT
9166 GTTGATAGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 10 0.36
17 18 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATAATATTATTAATTA
Found at i:9423 original size:18 final size:18
Alignment explanation
Indices: 9402--9436 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9392 AGTGAAATGG
*
9402 GTCGGTTGAGTCGGTTTT
1 GTCGGGTGAGTCGGTTTT
*
9420 GTCGGGTGATTCGGTTT
1 GTCGGGTGAGTCGGTTT
9437 GGGAAGTCGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.11, G:0.40, T:0.43
Consensus pattern (18 bp):
GTCGGGTGAGTCGGTTTT
Found at i:9631 original size:17 final size:18
Alignment explanation
Indices: 9609--9661 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
9599 GAATCATTTT
*
9609 TATTTTAATATGTAA-AA
1 TATTTTAATATATAAGAA
*
9626 TATTTTATTATATAAGAA
1 TATTTTAATATATAAGAA
*
9644 TATATATATATATATAAG
1 TAT-TTTA-ATATATAAG
9662 TAAGAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 13 0.45
18 5 0.17
19 3 0.10
20 8 0.28
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
TATTTTAATATATAAGAA
Found at i:11657 original size:29 final size:30
Alignment explanation
Indices: 11610--11668 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
11600 CGTTAGATTG
11610 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
* *
11640 AGGGGGTAAAATGT-CCAAAATTGAAGTTC
1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
11669 GGGAGGCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.20
Consensus pattern (30 bp):
AGGGGGCAAAACGTCCCAAAATTGAAGTTC
Found at i:14905 original size:16 final size:17
Alignment explanation
Indices: 14862--14967 Score: 88
Period size: 16 Copynumber: 6.7 Consensus size: 17
14852 GGCTTGAATC
*
14862 GGGTTCG-GGTTGGATTT
1 GGGTTCGAGGTT-AATTT
*
14879 GGG-TC-AGGTTAATTC
1 GGGTTCGAGGTTAATTT
14894 GGGTTCGA-GTTAATTT
1 GGGTTCGAGGTTAATTT
* *
14910 GGG-TC-AGGCTAATTC
1 GGGTTCGAGGTTAATTT
14925 GGGTTCG-GGTTGAATTT
1 GGGTTCGAGGTT-AATTT
14942 GGG-TC-AGGTTAATTT
1 GGGTTCGAGGTTAATTT
14957 GGGTTCG-GGTT
1 GGGTTCGAGGTT
14968 CTGTTTGGGT
Statistics
Matches: 72, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
14 1 0.01
15 25 0.35
16 35 0.49
17 11 0.15
ACGTcount: A:0.14, C:0.09, G:0.39, T:0.38
Consensus pattern (17 bp):
GGGTTCGAGGTTAATTT
Found at i:14946 original size:32 final size:32
Alignment explanation
Indices: 14860--14967 Score: 173
Period size: 32 Copynumber: 3.4 Consensus size: 32
14850 CGGGCTTGAA
*
14860 TCGGGTTCGGGTTGGATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
* *
14892 TCGGGTTCGAGTT-AATTTGGGTCAGGCTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
14923 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
*
14955 TTGGGTTCGGGTT
1 TCGGGTTCGGGTT
14968 CTGTTTGGGT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
31 28 0.41
32 41 0.59
ACGTcount: A:0.14, C:0.10, G:0.38, T:0.38
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
Found at i:21749 original size:18 final size:18
Alignment explanation
Indices: 21726--21761 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21716 AGGTTAGTCC
21726 TATGGCTTTGTGATTGTT
1 TATGGCTTTGTGATTGTT
21744 TATGGCTTTGTGATTGTT
1 TATGGCTTTGTGATTGTT
21762 GATGATTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.06, G:0.28, T:0.56
Consensus pattern (18 bp):
TATGGCTTTGTGATTGTT
Done.