Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005367.1 Corchorus capsularis cultivar CVL-1 contig05385, 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: 18167
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:134 original size:7 final size:7
Alignment explanation
Indices: 122--164 Score: 59
Period size: 7 Copynumber: 5.9 Consensus size: 7
112 TAAAAGGTTT
122 TCAAAAA
1 TCAAAAA
129 TCAAAAAAA
1 TC--AAAAA
138 TCAAAAA
1 TCAAAAA
145 TCAAAAA
1 TCAAAAA
*
152 TCAAAAT
1 TCAAAAA
159 TCAAAA
1 TCAAAA
165 CAAAATTCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
7 26 0.79
9 7 0.21
ACGTcount: A:0.70, C:0.14, G:0.00, T:0.16
Consensus pattern (7 bp):
TCAAAAA
Found at i:170 original size:12 final size:14
Alignment explanation
Indices: 133--172 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
123 CAAAAATCAA
*
133 AAAAATCAAAAATC
1 AAAAATCAAAATTC
147 AAAAATCAAAATTC
1 AAAAATCAAAATTC
161 -AAAA-CAAAATTC
1 AAAAATCAAAATTC
173 CATTCCAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 8 0.32
13 4 0.16
14 13 0.52
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAATCAAAATTC
Found at i:2192 original size:59 final size:60
Alignment explanation
Indices: 2113--2227 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
2103 AATAACTTTA
*
2113 CATTTTATTTCATTA-ATTTTTAAGAGAAACCTAATGAAAAACGCTTAACTATTATCGTG
1 CATTTTATTTCATTATATTTTTAAGAGAAACATAATGAAAAACGCTTAACTATTATCGTG
* * * * * *
2172 CATTTTCTTTTATTATTTTTTTGAGAGAAACATAATGAAAAATGCTTGACTATTAT
1 CATTTTATTTCATTATATTTTTAAGAGAAACATAATGAAAAACGCTTAACTATTAT
2228 TAGTCCCATT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 13 0.27
60 35 0.73
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (60 bp):
CATTTTATTTCATTATATTTTTAAGAGAAACATAATGAAAAACGCTTAACTATTATCGTG
Found at i:4573 original size:32 final size:32
Alignment explanation
Indices: 4532--4632 Score: 94
Period size: 32 Copynumber: 3.2 Consensus size: 32
4522 GAATCAGATT
4532 GGGTTAAATTTAGATCAGGTTGATTCGGGTTC
1 GGGTTAAATTTAGATCAGGTTGATTCGGGTTC
* * * *
4564 GGGTTAAATTTGGGTCAGGTTGCTTCGAGTTC
1 GGGTTAAATTTAGATCAGGTTGATTCGGGTTC
* * * * * * * *
4596 AGGTCAATTTTAGTTTAGGTTAATCCGGATTC
1 GGGTTAAATTTAGATCAGGTTGATTCGGGTTC
4628 GGGTT
1 GGGTT
4633 CGACCTGGAT
Statistics
Matches: 52, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.20, C:0.11, G:0.31, T:0.39
Consensus pattern (32 bp):
GGGTTAAATTTAGATCAGGTTGATTCGGGTTC
Found at i:7480 original size:169 final size:167
Alignment explanation
Indices: 7201--7605 Score: 438
Period size: 169 Copynumber: 2.4 Consensus size: 167
7191 TTTCCCTATT
* ** * * *
7201 TGTCCGATTAAGTTGATTCAAGTGTCAATTAAAAGGTAATTTCATGATCTACAATTTTCATTAAG
1 TGTCCGATTAAATT-ATTCAAGTGTCGGTTAAAAGGTTATTTCATGATCTACAACTTTCATAAAG
* * * ** * * * * *
7266 AACTCAGAAGGCCAATTTTAATGTTTTGATTCTAAAAAATGCTTCCGAAATTTTGTGGTTTTTTG
65 GACTCAAAAAGCCAATTTTAATGTTTCAATTCAAAAAAATGCTTCCCAAATTTGGTGG--GTTCG
* * *
7331 ATTGCCAG-TAATATAATATCGTATAATTTTTTATCCACA
128 ATTGCCAGTTAATATAATACCATATAATTTTTGATCCACA
* * *
7370 TGTCCGATTGAAATTATTGAAGTGTCGGTTAAAAGGTTATTTTATTATCTACAACTTTCATAAAG
1 TGTCCGATT-AAATTATTCAAGTGTCGGTTAAAAGGTTATTTCATGATCTACAACTTTCATAAAG
* *
7435 GACTCAAAAAGCCAATTTTTATGTTTCAATT-AAAGAAAATGCTTCCCCAATTTGGTGGGTTCGA
65 GACTCAAAAAGCCAATTTTAATGTTTCAATTCAAA-AAAATGCTTCCCAAATTTGGTGGGTTCGA
* * * *
7499 TTGCCGGTTTATTTAATACCATATGATTTTTGATCCACA
129 TTGCCAGTTAATATAATACCATATAATTTTTGATCCACA
* * * *
7538 TGTCCAATTAAATTTATTCAAGTGTTGGTTAAAAGGTT-TTTGCATGATTTACGACTTTCATAAA
1 TGTCCGATTAAA-TTATTCAAGTGTCGGTTAAAAGGTTATTT-CATGATCTACAACTTTCATAAA
7602 GGAC
64 GGAC
7606 CCGAAAAGTA
Statistics
Matches: 196, Mismatches: 35, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
167 16 0.08
168 80 0.41
169 96 0.49
170 4 0.02
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (167 bp):
TGTCCGATTAAATTATTCAAGTGTCGGTTAAAAGGTTATTTCATGATCTACAACTTTCATAAAGG
ACTCAAAAAGCCAATTTTAATGTTTCAATTCAAAAAAATGCTTCCCAAATTTGGTGGGTTCGATT
GCCAGTTAATATAATACCATATAATTTTTGATCCACA
Found at i:8487 original size:2 final size:2
Alignment explanation
Indices: 8482--8518 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
8472 CTAGTGTGTG
8482 TA TA 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 TA TA T
8519 GTGTGTGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12867 original size:18 final size:20
Alignment explanation
Indices: 12824--12876 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 20
12814 TTTGCTCTAT
12824 CACCAGTATCTGCTATAATC
1 CACCAGTATCTGCTATAATC
*
12844 GA--AGTATCTGCTA-AA-C
1 CACCAGTATCTGCTATAATC
*
12860 CACCAGTATTTGCTATA
1 CACCAGTATCTGCTATA
12877 TTACCAGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
16 2 0.07
17 2 0.07
18 21 0.78
19 1 0.04
20 1 0.04
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (20 bp):
CACCAGTATCTGCTATAATC
Found at i:17735 original size:13 final size:13
Alignment explanation
Indices: 17717--17741 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17707 TAAAAGTATT
17717 TATACTAATTATC
1 TATACTAATTATC
17730 TATACTAATTAT
1 TATACTAATTAT
17742 AATGTGAACC
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:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
TATACTAATTATC
Done.