Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016793.1 Corchorus olitorius cultivar O-4 contig16826, 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: 11800
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Found at i:2794 original size:15 final size:16
Alignment explanation
Indices: 2774--2807 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
2764 TTGATGTTTT
2774 GAATAATAAAAA-TAA
1 GAATAATAAAAAGTAA
2789 GAATAATAAAAAGTAA
1 GAATAATAAAAAGTAA
2805 GAA
1 GAA
2808 AATTGAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (16 bp):
GAATAATAAAAAGTAA
Found at i:3029 original size:22 final size:22
Alignment explanation
Indices: 3001--3109 Score: 182
Period size: 22 Copynumber: 4.9 Consensus size: 22
2991 TGGAAACATT
*
3001 TTTGCAGAGCATTATTTACCAC
1 TTTGCAGAGCATTATTTTCCAC
*
3023 TTTGCAGAGCATTATTTTCTAC
1 TTTGCAGAGCATTATTTTCCAC
3045 TTTGCAGAGCATTATTTTCCAC
1 TTTGCAGAGCATTATTTTCCAC
3067 TTTGCAGAGCATTATTTTCCAC
1 TTTGCAGAGCATTATTTTCCAC
3089 TTTGCAGAGTGCATTATTTTC
1 TTTGCAGA--GCATTATTTTC
3110 TTCAACTTCA
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
22 71 0.87
24 11 0.13
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (22 bp):
TTTGCAGAGCATTATTTTCCAC
Found at i:3803 original size:12 final size:12
Alignment explanation
Indices: 3786--3816 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3776 CCTGGCAATC
3786 CGTGTTTCGTGT
1 CGTGTTTCGTGT
3798 CGTGTTTCGTGT
1 CGTGTTTCGTGT
3810 CGTGTTT
1 CGTGTTT
3817 ACATAGGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.32, T:0.52
Consensus pattern (12 bp):
CGTGTTTCGTGT
Found at i:4367 original size:42 final size:43
Alignment explanation
Indices: 4296--4378 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
4286 CTTAAACGTG
* *
4296 TTAATCGTGTCTTGACACGATTAGGACACGAAACACGATAATC
1 TTAATCGTGTCTCGACACGATTAGAACACGAAACACGATAATC
*
4339 TTAATCGTGTC-CGACACGATTCA-AACACGAGACACGATAA
1 TTAATCGTGTCTCGACACGATT-AGAACACGAAACACGATAA
4379 GTCAAACACG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 24 0.67
43 12 0.33
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACGATTAGAACACGAAACACGATAATC
Found at i:5889 original size:22 final size:22
Alignment explanation
Indices: 5838--6052 Score: 127
Period size: 22 Copynumber: 9.7 Consensus size: 22
5828 CATATTATGG
* *
5838 TATCAAAAATTT-ATAGGGAGAT
1 TATC-AAAATTTCATAGAGAGGT
5860 TAAT-AAAATTTCATAGAGAGGT
1 T-ATCAAAATTTCATAGAGAGGT
**
5882 TATCAAAAAAATCATATG-GAGGT
1 TATC-AAAATTTCATA-GAGAGGT
* *
5905 TGTCAAAATTTCATAGAAAGGTT
1 TATCAAAATTTCATAGAGAGG-T
* ***
5928 TATGAAAATTTCATACTTAGGT
1 TATCAAAATTTCATAGAGAGGT
** * * *
5950 TATCAGTATTTCATTGGGAGTT
1 TATCAAAATTTCATAGAGAGGT
* * *
5972 TATCACAATTTCATAGGGTA-AT
1 TATCAAAATTTCATAGAG-AGGT
* *
5994 TATCAAAATTTCATAGTGTGGT
1 TATCAAAATTTCATAGAGAGGT
*
6016 TATCAAAATTTCTTA-AG-GTGAT
1 TATCAAAATTTCATAGAGAG-G-T
6038 TATCAAAATTTCATA
1 TATCAAAATTTCATA
6053 AAAATATTTA
Statistics
Matches: 150, Mismatches: 32, Indels: 22
0.74 0.16 0.11
Matches are distributed among these distances:
20 1 0.01
21 12 0.08
22 99 0.66
23 37 0.25
24 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATAGAGAGGT
Found at i:6157 original size:37 final size:37
Alignment explanation
Indices: 6114--6187 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
6104 AAACTAGTAT
6114 ATATAAAAGTACGAGTTCTTGTAAAACTGTTGAATCG
1 ATATAAAAGTACGAGTTCTTGTAAAACTGTTGAATCG
6151 ATATAAAAGTACGAGTTCTTGTAAAACTGTTGAATCG
1 ATATAAAAGTACGAGTTCTTGTAAAACTGTTGAATCG
6188 CCCATTATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (37 bp):
ATATAAAAGTACGAGTTCTTGTAAAACTGTTGAATCG
Found at i:9299 original size:54 final size:55
Alignment explanation
Indices: 9156--9301 Score: 231
Period size: 55 Copynumber: 2.7 Consensus size: 55
9146 AGCGTCACAA
* *
9156 GAACACTGGGAAATCACGGAGATTTCAGGCGAGCGTCAGCATTGAAGCTTTCAAG
1 GAACACTGGGAAATCACGGAGATCTCAGGCGAGTGTCAGCATTGAAGCTTTCAAG
* * *
9211 GAACACTGGGAAATCACGGAGATCTCTGGCGAGTGTCAGCATTGAAGGTTTTAAG
1 GAACACTGGGAAATCACGGAGATCTCAGGCGAGTGTCAGCATTGAAGCTTTCAAG
*
9266 GAACACT-GGAAATCACGGAGATCTCAAGCGAGTGTC
1 GAACACTGGGAAATCACGGAGATCTCAGGCGAGTGTC
9302 TGCAGAGAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
54 27 0.32
55 57 0.68
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (55 bp):
GAACACTGGGAAATCACGGAGATCTCAGGCGAGTGTCAGCATTGAAGCTTTCAAG
Found at i:10328 original size:2 final size:2
Alignment explanation
Indices: 10321--10346 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10311 CAAAAATGAA
10321 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
10347 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10471 original size:15 final size:15
Alignment explanation
Indices: 10451--10480 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
10441 TATTCCATGA
10451 TTGATTTCAATTAAT
1 TTGATTTCAATTAAT
10466 TTGATTTCAATTAAT
1 TTGATTTCAATTAAT
10481 AGATTGGCTC
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:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (15 bp):
TTGATTTCAATTAAT
Done.