Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016740.1 Corchorus olitorius cultivar O-4 contig16773, 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: 15454
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Found at i:573 original size:22 final size:22
Alignment explanation
Indices: 532--573 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
522 GACAAACTCG
**
532 TAACCCGAATGACCCGAGAAGT
1 TAACCCGAATGACCAAAGAAGT
*
554 TAACCCGGATGACCAAAGAA
1 TAACCCGAATGACCAAAGAA
574 TATTATTAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.12
Consensus pattern (22 bp):
TAACCCGAATGACCAAAGAAGT
Found at i:639 original size:24 final size:20
Alignment explanation
Indices: 584--629 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
574 TATTATTAAG
*
584 TAAAATTATGTTTTGTTCAA
1 TAAAATTATGTTTTATTCAA
604 TAAAATTATGTTTTATTCAA
1 TAAAATTATGTTTTATTCAA
624 TAAAAT
1 TAAAAT
630 CAATATTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (20 bp):
TAAAATTATGTTTTATTCAA
Found at i:2026 original size:13 final size:13
Alignment explanation
Indices: 1984--2028 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
1974 TCATGCACCC
*
1984 AAAACAATTTATTT
1 AAAACAATTTA-AT
*
1998 AAAACCATTT-AT
1 AAAACAATTTAAT
2010 AAAACAATTTAAT
1 AAAACAATTTAAT
2023 AAAACA
1 AAAACA
2029 GTAATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.37
13 8 0.30
14 9 0.33
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAACAATTTAAT
Found at i:3630 original size:133 final size:133
Alignment explanation
Indices: 3424--3678 Score: 372
Period size: 133 Copynumber: 1.9 Consensus size: 133
3414 ATATTTTTAG
*
3424 AAATTCTAATATAACTAAGTTTTTTTAATTAAATTAGTAAAATGGAAAAAATAAAATAGGTATAA
1 AAATTCTAATATAACTAAGTTTTTTTAATTAAATTAATAAAATGGAAAAAATAAAATAGGTATAA
* *
3489 GGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTACAAAAGCATATTT
66 GAATATTAGATTTAATCAAAT-AAAAATAGAGTTTTTAGTTGAGTAAAACTACAAAAGCATATTT
3554 AAAA
130 AAAA
* * * *
3558 AAATTCTAATATTTA-TAAGTTTTTTTAATTGAA-TAATAAAATGGTAAAAACT-AAATAGTTAT
1 AAATTCTAATA-TAACTAAGTTTTTTTAATTAAATTAATAAAATGG-AAAAAATAAAATAGGTAT
* * *
3620 AAGAATATTAGATTTAATCAAATATAAATAGAGTTTTTAGTTGAGTAAGACTATAAAAG
64 AAGAATATTAGATTTAATCAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTACAAAAG
3679 TTTAAACAAT
Statistics
Matches: 109, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
132 33 0.30
133 40 0.37
134 34 0.31
135 2 0.02
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (133 bp):
AAATTCTAATATAACTAAGTTTTTTTAATTAAATTAATAAAATGGAAAAAATAAAATAGGTATAA
GAATATTAGATTTAATCAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTACAAAAGCATATTTA
AAA
Found at i:4022 original size:130 final size:131
Alignment explanation
Indices: 3836--4098 Score: 379
Period size: 130 Copynumber: 2.0 Consensus size: 131
3826 TTGTTTAGAC
*
3836 TTTTATAGTTTTATTCAACTAAAAAATCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
1 TTTTATAGTTTTACTCAACTAAAAAATCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
* * * *
3901 TTTAATTTTTACCATTTTACTATTTTAATTAAAA-ACTTATATATATATTAGAATTTTTTAAATA
66 TTTAATTTTTACCAATTTACTAATTTAATTAAAAGAC-T-TAGATATATTAGAATTTTTAAAATA
3965 TAT
129 TAT
* * * * *
3968 TTTTATAGTTTTACTCAACT-AAAACTCT-TTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAAATCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
* *
4031 TTTTATTTTTATCAATTTACTAATTTAATTAAAAGACTTAGATATATTAGAATTTTTAAAATATA
66 TTTAATTTTTACCAATTTACTAATTTAATTAAAAGACTTAGATATATTAGAATTTTTAAAATATA
4096 T
131 T
4097 TT
1 TT
4099 CTTAAATGAC
Statistics
Matches: 118, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
129 28 0.24
130 62 0.53
131 9 0.08
132 19 0.16
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (131 bp):
TTTTATAGTTTTACTCAACTAAAAAATCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
TTTAATTTTTACCAATTTACTAATTTAATTAAAAGACTTAGATATATTAGAATTTTTAAAATATA
T
Found at i:4974 original size:21 final size:22
Alignment explanation
Indices: 4950--4990 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
4940 GTTTAAAATA
*
4950 TTCTTGGGTCATT-GGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
4971 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
4991 AGAGTTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.10, C:0.15, G:0.29, T:0.46
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:5271 original size:15 final size:15
Alignment explanation
Indices: 5251--5280 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5241 AGATTTACAG
5251 CTGAGCGTACTTTTT
1 CTGAGCGTACTTTTT
5266 CTGAGCGTACTTTTT
1 CTGAGCGTACTTTTT
5281 AATATAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (15 bp):
CTGAGCGTACTTTTT
Found at i:8470 original size:7 final size:7
Alignment explanation
Indices: 8458--8492 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
8448 GAGATTGCTA
8458 TGATTGT
1 TGATTGT
8465 TGATTGT
1 TGATTGT
8472 TGATTGT
1 TGATTGT
8479 TGATTGT
1 TGATTGT
8486 TGATTGT
1 TGATTGT
8493 AATTGATTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (7 bp):
TGATTGT
Found at i:14838 original size:19 final size:19
Alignment explanation
Indices: 14814--14859 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
14804 CGGACCGTGT
14814 CAAACCGG-TCCGATCCGAC
1 CAAACCGGTTCCGA-CCGAC
*
14833 CAAACCGGTTCGGACCGAC
1 CAAACCGGTTCCGACCGAC
*
14852 CAAGCCGG
1 CAAACCGG
14860 CTCATGAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.26, C:0.39, G:0.26, T:0.09
Consensus pattern (19 bp):
CAAACCGGTTCCGACCGAC
Done.