Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018640.1 Corchorus olitorius cultivar O-4 contig18673, 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: 14847
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:4308 original size:49 final size:48
Alignment explanation
Indices: 4250--4378 Score: 172
Period size: 49 Copynumber: 2.7 Consensus size: 48
4240 TTACATTTCC
*
4250 TGCACTTTTTCTCAATTTTTACTACAAAATTGAACCTTTA-TTTTTACT
1 TGCACTTTTTCTCAATTTTTAATACAAAATTGAACCTTTACTTTTTA-T
* * *
4298 TGCACCTTTTTCTCAATTTTTAAGACAAAATTGATCTTTTACTTTTTAT
1 TGCA-CTTTTTCTCAATTTTTAATACAAAATTGAACCTTTACTTTTTAT
* *
4347 TGCACTTTTTATCAATTTTT-GTACAAAATTGA
1 TGCACTTTTTCTCAATTTTTAATACAAAATTGA
4379 TTGGCACGCC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
47 10 0.14
48 19 0.26
49 37 0.51
50 6 0.08
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (48 bp):
TGCACTTTTTCTCAATTTTTAATACAAAATTGAACCTTTACTTTTTAT
Found at i:5105 original size:18 final size:18
Alignment explanation
Indices: 5084--5151 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 18
5074 CACCAAGTGA
*
5084 CCGCACTGCACCAAATAG
1 CCGCACCGCACCAAATAG
* * * *
5102 CCGCGCCACACCCAATAC
1 CCGCACCGCACCAAATAG
* *
5120 CCGCACCGTACCAAATGG
1 CCGCACCGCACCAAATAG
5138 CCGCACCGCACCAA
1 CCGCACCGCACCAA
5152 GTTGCCACAA
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.29, C:0.47, G:0.16, T:0.07
Consensus pattern (18 bp):
CCGCACCGCACCAAATAG
Found at i:5110 original size:36 final size:36
Alignment explanation
Indices: 5070--5153 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 36
5060 AACAAATGGT
*
5070 GCCACACCAAGTGA-CCGCACTGCACCAAATAGCCGC
1 GCCACACCAAGT-ACCCGCACCGCACCAAATAGCCGC
* *
5106 GCCACACCCAA-TACCCGCACCGTACCAAATGGCCGC
1 GCCACA-CCAAGTACCCGCACCGCACCAAATAGCCGC
* *
5142 ACCGCACCAAGT
1 GCCACACCAAGT
5154 TGCCACAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
35 5 0.12
36 31 0.77
37 4 0.10
ACGTcount: A:0.30, C:0.44, G:0.18, T:0.08
Consensus pattern (36 bp):
GCCACACCAAGTACCCGCACCGCACCAAATAGCCGC
Found at i:6413 original size:30 final size:30
Alignment explanation
Indices: 6379--6441 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
6369 TGTCATGGAA
*
6379 GAAGATGATGGCACCAAAATCGACGGCATC
1 GAAGATGATGGCACCAAAATCGACGGCACC
*
6409 GAAGATGATGGCACCAAAATCGATGGCACC
1 GAAGATGATGGCACCAAAATCGACGGCACC
6439 GAA
1 GAA
6442 AGTGTTTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.13
Consensus pattern (30 bp):
GAAGATGATGGCACCAAAATCGACGGCACC
Found at i:6438 original size:15 final size:15
Alignment explanation
Indices: 6385--6438 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
6375 GGAAGAAGAT
6385 GATGGCACCAAAATC
1 GATGGCACCAAAATC
* * *
6400 GACGGCATCGAAGAT-
1 GATGGCA-CCAAAATC
6415 GATGGCACCAAAATC
1 GATGGCACCAAAATC
6430 GATGGCACC
1 GATGGCACC
6439 GAAAGTGTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
14 5 0.16
15 21 0.68
16 5 0.16
ACGTcount: A:0.35, C:0.26, G:0.26, T:0.13
Consensus pattern (15 bp):
GATGGCACCAAAATC
Found at i:9136 original size:49 final size:48
Alignment explanation
Indices: 9076--9204 Score: 154
Period size: 49 Copynumber: 2.7 Consensus size: 48
9066 TTACATTTCC
* *
9076 TGCACTTTTTCTCAATTTTTACTACAAAATTGAACCTTTA-TTTTTACT
1 TGCACATTTTCTCAATTTTTAATACAAAATTGAACCTTTATTTTTTA-T
* * *
9124 TGCACCATTTTCTCAATTTTTAAGACAAAATTGATCTTTTATTTTTTAT
1 TGCA-CATTTTCTCAATTTTTAATACAAAATTGAACCTTTATTTTTTAT
* * *
9173 TGCACTTTTTATCAATTTTT-GTACAAAATTGA
1 TGCACATTTTCTCAATTTTTAATACAAAATTGA
9205 TTGGCACGTC
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
47 10 0.14
48 18 0.26
49 36 0.51
50 6 0.09
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.50
Consensus pattern (48 bp):
TGCACATTTTCTCAATTTTTAATACAAAATTGAACCTTTATTTTTTAT
Found at i:9857 original size:23 final size:23
Alignment explanation
Indices: 9827--9872 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
9817 TGTTTGATTA
9827 TGGTAAGTTTACTTAGTTAAGTC
1 TGGTAAGTTTACTTAGTTAAGTC
9850 TGGTAAGTTTACTTAGTTAAGTC
1 TGGTAAGTTTACTTAGTTAAGTC
9873 AGCAGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (23 bp):
TGGTAAGTTTACTTAGTTAAGTC
Found at i:13630 original size:49 final size:48
Alignment explanation
Indices: 13529--13674 Score: 156
Period size: 49 Copynumber: 3.0 Consensus size: 48
13519 GAGCGTGCCA
* * * *
13529 ATCAATTTTG-ACCAGAAATTGATAAAAAGTGCAA-TGAAAATTAAAAG
1 ATCAATTTTGTAGCAAAAATTGAGAAAAAGTGCAAGT-AAAAATAAAAG
***
13576 ATCAATTTTGTCTTAAAAATTGTA-AAAAAGATGCAAGTAAAAATAAAAG
1 ATCAATTTTGTAGCAAAAATTG-AGAAAAAG-TGCAAGTAAAAATAAAAG
*
13625 TTCAATTTTGTAGCAAAAATTGAGAAAAAGTGC-AGTAAAAAGTAAAAG
1 ATCAATTTTGTAGCAAAAATTGAGAAAAAGTGCAAGTAAAAA-TAAAAG
13673 AT
1 AT
13675 TGCTTTGAGT
Statistics
Matches: 83, Mismatches: 10, Indels: 11
0.80 0.10 0.11
Matches are distributed among these distances:
47 18 0.22
48 24 0.29
49 40 0.48
50 1 0.01
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.27
Consensus pattern (48 bp):
ATCAATTTTGTAGCAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG
Done.