Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012161.1 Corchorus olitorius cultivar O-4 contig12194, 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: 23569
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Found at i:1456 original size:51 final size:52
Alignment explanation
Indices: 1355--1456 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 52
1345 GTTCATCAAA
* **
1355 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGTTT
1 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
* *
1407 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTCTCCTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGTT
1457 CTTCATTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 2 0.05
51 36 0.84
52 5 0.12
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (52 bp):
TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
Found at i:2174 original size:24 final size:25
Alignment explanation
Indices: 2140--2190 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
2130 ATTGGAGTAT
* *
2140 TTATTTATCTTGTTTCTTAATTTTA
1 TTATTTATCTTGCTTATTAATTTTA
*
2165 TTATTT-TCTTGCTTATTTATTTTA
1 TTATTTATCTTGCTTATTAATTTTA
2189 TT
1 TT
2191 GTTACTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGCTTATTAATTTTA
Found at i:3025 original size:22 final size:22
Alignment explanation
Indices: 2986--3031 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2976 AAAATCTCCT
*
2986 AATTCAACCTCTGGAGAGGTCG
1 AATTCAACCTCTGGAGAGATCG
*
3008 AATTCAACCT-TCGTAGAGATCG
1 AATTCAACCTCT-GGAGAGATCG
3030 AA
1 AA
3032 ACAACAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (22 bp):
AATTCAACCTCTGGAGAGATCG
Found at i:6559 original size:24 final size:25
Alignment explanation
Indices: 6525--6575 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
6515 ATTGGAGTAT
* *
6525 TTATTTATCTTGTTTGTTAATTTTA
1 TTATTTATCTTGCTTATTAATTTTA
*
6550 TTATTT-TCTTGCTTATTGATTTTA
1 TTATTTATCTTGCTTATTAATTTTA
6574 TT
1 TT
6576 GTTACTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.18, C:0.06, G:0.08, T:0.69
Consensus pattern (25 bp):
TTATTTATCTTGCTTATTAATTTTA
Found at i:7658 original size:38 final size:38
Alignment explanation
Indices: 7607--7693 Score: 174
Period size: 38 Copynumber: 2.3 Consensus size: 38
7597 GCCATCTGAT
7607 TAAATGGAGGCTAGTAGCAAAAAAATAAATAAATAAAA
1 TAAATGGAGGCTAGTAGCAAAAAAATAAATAAATAAAA
7645 TAAATGGAGGCTAGTAGCAAAAAAATAAATAAATAAAA
1 TAAATGGAGGCTAGTAGCAAAAAAATAAATAAATAAAA
7683 TAAATGGAGGC
1 TAAATGGAGGC
7694 CAGCCATGGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.57, C:0.06, G:0.18, T:0.18
Consensus pattern (38 bp):
TAAATGGAGGCTAGTAGCAAAAAAATAAATAAATAAAA
Found at i:9289 original size:24 final size:24
Alignment explanation
Indices: 9244--9289 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
9234 GATAGTTAAT
*
9244 TATTTATAATTTATAACAAAAAAC
1 TATTTATAATTTATAAAAAAAAAC
* *
9268 TATTTTTAATTTA-AAAAGAAAA
1 TATTTATAATTTATAAAAAAAAA
9290 TTAATTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (24 bp):
TATTTATAATTTATAAAAAAAAAC
Found at i:9404 original size:31 final size:31
Alignment explanation
Indices: 9342--9404 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
9332 GAAAATATCT
* ** *
9342 ATAGCTTATATATATCTTTTGTTTGGTTAAA
1 ATAGCTTATATATATCTATACTTAGGTTAAA
9373 ATAGCTTATATATATCTATACTATAGG-TAAA
1 ATAGCTTATATATATCTATACT-TAGGTTAAA
9404 A
1 A
9405 CTACAAGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (31 bp):
ATAGCTTATATATATCTATACTTAGGTTAAA
Found at i:9756 original size:69 final size:70
Alignment explanation
Indices: 9675--9816 Score: 180
Period size: 69 Copynumber: 2.0 Consensus size: 70
9665 AGAAATAAAC
* * * **
9675 TTTTACAGTTTTATTCTACTAAAAACTCTATTTTTAGTTAA-TAAATCTAATATTTTTATAACTA
1 TTTTACAGTTTTACTCAACTAAAAACTCTATTTTTAGTTAACTAAATATAATATCCTTATAACTA
9739 TTCTA
66 TTCTA
* * *
9744 TTTTACCA-TTTTACTCAACTAAAAAGTCTATTTTTATTTAACTAATTATAATATCCTTATAACT
1 TTTTA-CAGTTTTACTCAACTAAAAACTCTATTTTTAGTTAACTAAATATAATATCCTTATAACT
*
9808 ATTTTA
65 ATTCTA
9814 TTT
1 TTT
9817 CTTTAATATT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
69 34 0.55
70 28 0.45
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.51
Consensus pattern (70 bp):
TTTTACAGTTTTACTCAACTAAAAACTCTATTTTTAGTTAACTAAATATAATATCCTTATAACTA
TTCTA
Found at i:21069 original size:10 final size:9
Alignment explanation
Indices: 21045--21102 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
21035 ATTTCTTACC
*
21045 CTTATCTTT
1 CTTATTTTT
21054 -TTATTTTT
1 CTTATTTTT
21062 CGTTATTTTT
1 C-TTATTTTT
21072 CTT-TTTCTT
1 CTTATTT-TT
21081 -TTATTTTT
1 CTTATTTTT
*
21089 GTTTATTTTT
1 -CTTATTTTT
21099 CTTA
1 CTTA
21103 GTTACTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 14 0.34
9 10 0.24
10 17 0.41
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.76
Consensus pattern (9 bp):
CTTATTTTT
Found at i:21076 original size:16 final size:17
Alignment explanation
Indices: 21051--21088 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
21041 TACCCTTATC
21051 TTTTTATTTTTC-GTTA
1 TTTTTATTTTTCTGTTA
* *
21067 TTTTTCTTTTTCTTTTA
1 TTTTTATTTTTCTGTTA
21084 TTTTT
1 TTTTT
21089 GTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTATTTTTCTGTTA
Done.