Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023498.1 Corchorus olitorius cultivar O-4 contig23531, 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: 16822
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:400 original size:196 final size:198
Alignment explanation
Indices: 1--515 Score: 833
Period size: 196 Copynumber: 2.6 Consensus size: 198
1 GGGAATATGTATTAATATTTTATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAAC
1 GGGAATATGTATTAATATTTTATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAAC
66 CCGCTTATGGAGTT-AAAATTTACACTGACAGTGTATTGTATAACAATCCTATCAAAAAATTATA
66 CCGCTTATGGAGTTCAAAATTTACACTGACAGTGTATTGTATAACAATCCTATCAAAAAATTATA
130 CAATACACCGTCAGTGGAGTTTAGCAGACTGCACGCGCAGGGCTTAAGGGTTGACATGTGTCCCC
131 CAATACACCGTCAGTGGAGTTTAGCAGACTGCACGCGCAGGGCTTAAGGGTTGACATGTGTCCCC
195 TTA
196 TTA
* *
198 -GGAATATGTATTAATATTTTATATTTAATTAATTATGAAATAGAGTATGTGTCAAATTCTTAAC
1 GGGAATATGTATTAATATTTTATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAAC
*
262 CCACTTATGGAGTTCAAAATTTACACTGACAGTGTATTGTATAACAATCCTAT-AAAAAAGTTAT
66 CCGCTTATGGAGTTCAAAATTTACACTGACAGTGTATTGTATAACAATCCTATCAAAAAA-TTAT
* * *
326 ACAATACACTGTCAGTGGAGTTTAGCAGACTGCACGCGCATGGTTTAA-GGTT-ACATGTGTCCC
130 ACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGCGCAGGGCTTAAGGGTTGACATGTGTCCC
389 CTTA
195 CTTA
393 GGGAATATGTATTAATATTAAATATTTAATATTTAATTAATTATGAAATAGGGTATGTGTCAACT
1 GGGAATATGTATT-A-A-T--AT-TTT-ATATTTAATTAATTATGAAATAGGGTATGTGTCAACT
* * * *
458 TCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACAGTATATTGTATAATAATCCT
59 TCTTAACCCGCTTATGGAGTTCAAAATTTACACTGACAGTGTATTGTATAACAATCCT
516 TATTATAAAG
Statistics
Matches: 295, Mismatches: 13, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
195 15 0.05
196 97 0.33
197 88 0.30
198 1 0.00
199 1 0.00
201 2 0.01
202 3 0.01
203 88 0.30
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (198 bp):
GGGAATATGTATTAATATTTTATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAAC
CCGCTTATGGAGTTCAAAATTTACACTGACAGTGTATTGTATAACAATCCTATCAAAAAATTATA
CAATACACCGTCAGTGGAGTTTAGCAGACTGCACGCGCAGGGCTTAAGGGTTGACATGTGTCCCC
TTA
Found at i:505 original size:203 final size:200
Alignment explanation
Indices: 10--515 Score: 801
Period size: 197 Copynumber: 2.5 Consensus size: 200
1 GGGAATATG
10 TATTAATATTTTATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATG
1 TATTAATA-TTTATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATG
*
75 GAGTTAAAATTTACACTGACAGTGTATTGTATAACAATCCTATCAAAAAATTATACAATACACCG
65 GAGTCAAAATTTACACTGACAGTGTATTGTATAACAATCCTATCAAAAAATTATACAATACACCG
140 TCAGTGGAGTTTAGCAGACTGCACGCGCAGGGCTTAAGGGTTGACATGTGTCCCCTTAGGAATAT
130 TCAGTGGAGTTTAGCAGACTGCACGCGCAGGGCTTAAGGGTTGACATGTGTCCCCTTAGGAATAT
205 GTATTA
195 GTATTA
* * *
211 -A-T-AT-TTTATATTTAATTAATTATGAAATAGAGTATGTGTCAAATTCTTAACCCACTTATGG
1 TATTAATATTTATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGG
*
272 AGTTCAAAATTTACACTGACAGTGTATTGTATAACAATCCTAT-AAAAAAGTTATACAATACACT
66 AG-TCAAAATTTACACTGACAGTGTATTGTATAACAATCCTATCAAAAAA-TTATACAATACACC
* *
336 GTCAGTGGAGTTTAGCAGACTGCACGCGCATGGTTTAA-GGTT-ACATGTGTCCCCTTAGGGAAT
129 GTCAGTGGAGTTTAGCAGACTGCACGCGCAGGGCTTAAGGGTTGACATGTGTCCCCTTA-GGAAT
399 ATGTATTAA
193 ATGTATT-A
408 TATTAAATATTTAATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTAT
1 TATT-AATATTT-ATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTAT
* * *
473 GGAGTCCAAAATTTACATTGACAGTATATTGTATAATAATCCT
64 GGAGT-CAAAATTTACACTGACAGTGTATTGTATAACAATCCT
516 TATTATAAAG
Statistics
Matches: 281, Mismatches: 13, Indels: 20
0.89 0.04 0.06
Matches are distributed among these distances:
195 15 0.05
196 78 0.28
197 89 0.32
198 3 0.01
199 2 0.01
200 1 0.00
201 2 0.01
202 4 0.01
203 87 0.31
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (200 bp):
TATTAATATTTATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGG
AGTCAAAATTTACACTGACAGTGTATTGTATAACAATCCTATCAAAAAATTATACAATACACCGT
CAGTGGAGTTTAGCAGACTGCACGCGCAGGGCTTAAGGGTTGACATGTGTCCCCTTAGGAATATG
TATTA
Found at i:877 original size:16 final size:16
Alignment explanation
Indices: 852--882 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
842 TCTACATATT
852 ATAAAGATTTAGTAAA
1 ATAAAGATTTAGTAAA
*
868 ATAAATATTTAGTAA
1 ATAAAGATTTAGTAA
883 TATTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
ATAAAGATTTAGTAAA
Found at i:2308 original size:23 final size:23
Alignment explanation
Indices: 2265--2308 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2255 TAATATTTTT
*
2265 AATTAAAATAGTAAAATGATAAA
1 AATTAAAATAGTAAAAGGATAAA
*
2288 AATT-AAATAGTTATAAGGATA
1 AATTAAAATAG-TAAAAGGATA
2309 TTATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (23 bp):
AATTAAAATAGTAAAAGGATAAA
Found at i:4452 original size:20 final size:21
Alignment explanation
Indices: 4427--4466 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4417 TCTTATTTTT
4427 TTTGAAAT-TTTTCTTTTTAA
1 TTTGAAATCTTTTCTTTTTAA
* *
4447 TTTGAATTCTTTTTTTTTTA
1 TTTGAAATCTTTTCTTTTTA
4467 GTTTAGGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTGAAATCTTTTCTTTTTAA
Found at i:5743 original size:15 final size:15
Alignment explanation
Indices: 5719--5755 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
5709 AAACAGGATT
*
5719 CGAAAGCCCAATCCA
1 CGAAACCCCAATCCA
5734 CGAAACCCCAATCCA
1 CGAAACCCCAATCCA
*
5749 CAAAACC
1 CGAAACC
5756 GTTGAACCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.43, C:0.43, G:0.08, T:0.05
Consensus pattern (15 bp):
CGAAACCCCAATCCA
Found at i:7628 original size:14 final size:17
Alignment explanation
Indices: 7584--7639 Score: 103
Period size: 17 Copynumber: 3.3 Consensus size: 17
7574 GAAGTAGTCC
*
7584 AATTAATATAATGACCA
1 AATTAATATGATGACCA
7601 AATTAATATGATGACCA
1 AATTAATATGATGACCA
7618 AATTAATATGATGACCA
1 AATTAATATGATGACCA
7635 AATTA
1 AATTA
7640 TATTTTACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (17 bp):
AATTAATATGATGACCA
Found at i:8188 original size:11 final size:11
Alignment explanation
Indices: 8172--8205 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
8162 AAGTTCGTGT
8172 TTGAAGATTTA
1 TTGAAGATTTA
**
8183 TTGAAGATAAA
1 TTGAAGATTTA
8194 TTGAAGATTTA
1 TTGAAGATTTA
8205 T
1 T
8206 CACACTGGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (11 bp):
TTGAAGATTTA
Found at i:13056 original size:21 final size:21
Alignment explanation
Indices: 13031--13085 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
13021 CCTTGGGGAT
13031 GATGAAATCGATTCTCATAAG
1 GATGAAATCGATTCTCATAAG
13052 GATGAAATCGATTCTCATAAG
1 GATGAAATCGATTCTCATAAG
*
13073 GATGAAACCGATT
1 GATGAAATCGATT
13086 TCTGAACTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (21 bp):
GATGAAATCGATTCTCATAAG
Done.