Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010640.1 Corchorus olitorius cultivar O-4 contig10672, 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: 7355
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:3910 original size:20 final size:21
Alignment explanation
Indices: 3885--3928 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3875 TCTTTTTATA
3885 TTTA-TTTAAATTTCATTTTT
1 TTTATTTTAAATTTCATTTTT
* *
3905 TTTATTTTTATTTTCATTTTT
1 TTTATTTTAAATTTCATTTTT
3926 TTT
1 TTT
3929 TGGAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTATTTTAAATTTCATTTTT
Found at i:3929 original size:26 final size:26
Alignment explanation
Indices: 3872--3929 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
3862 GATTTTTCTC
*
3872 TTTTCTTTTTATATTTATTTAAATTT
1 TTTTTTTTTTATATTTATTTAAATTT
** * **
3898 CATTTTTTTTATTTTTATTTTCATTT
1 TTTTTTTTTTATATTTATTTAAATTT
3924 TTTTTT
1 TTTTTT
3930 GGAATTAATT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTTTTTTTATATTTATTTAAATTT
Found at i:6068 original size:38 final size:39
Alignment explanation
Indices: 6018--6461 Score: 373
Period size: 38 Copynumber: 11.6 Consensus size: 39
6008 TAAAAGGACT
*
6018 TGTTTCTAGTCAA-TTCTGATAACTGCTAAAAGATGACC
1 TGTTTCCAGTCAACTTCTGATAACTGCTAAAAGATGACC
* * *
6056 TGTCTT-GAGTCAACTTC-GATAAACTTCTGAAAA-ATGACA
1 TGT-TTCCAGTCAACTTCTGAT-AACTGCT-AAAAGATGACC
* * * *
6095 TGTTTCCAGTCAACTAC-GATAACTACTGAAAGGTGACC
1 TGTTTCCAGTCAACTTCTGATAACTGCTAAAAGATGACC
* * * * *
6133 TGTTTCTAGTCGA-TTTTGATAACTTCTGAAAGATGACC
1 TGTTTCCAGTCAACTTCTGATAACTGCTAAAAGATGACC
* * *
6171 TGTTTCCAGTCGA-TTTTGATAACTGCTGAAAGATGACC
1 TGTTTCCAGTCAACTTCTGATAACTGCTAAAAGATGACC
*
6209 TGTTTCCAGTCAACTTC-GATAACTGCTGAAAGATGACC
1 TGTTTCCAGTCAACTTCTGATAACTGCTAAAAGATGACC
*
6247 TGTTTCCAGTCAACTTC-GATAACTGCTGAAAGATGACC
1 TGTTTCCAGTCAACTTCTGATAACTGCTAAAAGATGACC
* * * * * * * *
6285 TATTTCTAGTCGA-TTTTGGTAAATTTCTGAAAA-ATGACA
1 TGTTTCCAGTCAACTTCTGAT-AACTGCT-AAAAGATGACC
* * * * *
6324 TGCTTCCAGTCAA-TTTTGGTAACTTCTGAAAA-ATGACA
1 TGTTTCCAGTCAACTTCTGATAACTGCT-AAAAGATGACC
* * * *
6362 TGTTTCTAGTCGA-TTTTGATAACTTCTAAAAGATGACC
1 TGTTTCCAGTCAACTTCTGATAACTGCTAAAAGATGACC
* *
6400 TGTTTCTAGTCAACTTC-GATAACTGC-AGAATGATGACC
1 TGTTTCCAGTCAACTTCTGATAACTGCTA-AAAGATGACC
6438 TGTTTCCAGTCAACTT-TGATAACT
1 TGTTTCCAGTCAACTTCTGATAACT
6462 TCTTTGAGTT
Statistics
Matches: 348, Mismatches: 43, Indels: 30
0.83 0.10 0.07
Matches are distributed among these distances:
37 11 0.03
38 269 0.77
39 61 0.18
40 7 0.02
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (39 bp):
TGTTTCCAGTCAACTTCTGATAACTGCTAAAAGATGACC
Found at i:6180 original size:76 final size:76
Alignment explanation
Indices: 6018--6464 Score: 502
Period size: 76 Copynumber: 5.9 Consensus size: 76
6008 TAAAAGGACT
* * * * * *
6018 TGTTTCTAGTCAA-TTCTGATAACTGCTAAAAGATGACCTGTCTT-GAGTCAACTTCGATAAACT
1 TGTTTCCAGTCAACTTC-GATAACTGCTGAAAGATGACCTGT-TTCTAGTCGATTTTGAT-AACT
* *
6081 TCTGAAAAATGACA
63 TCTGAAAGATGACC
* * *
6095 TGTTTCCAGTCAACTACGATAACTACTGAAAGGTGACCTGTTTCTAGTCGATTTTGATAACTTCT
1 TGTTTCCAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCTAGTCGATTTTGATAACTTCT
6160 GAAAGATGACC
66 GAAAGATGACC
* * * * * * * *
6171 TGTTTCCAGTCGATTTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCAACTTCGATAACTGCT
1 TGTTTCCAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCTAGTCGATTTTGATAACTTCT
6236 GAAAGATGACC
66 GAAAGATGACC
* * *
6247 TGTTTCCAGTCAACTTCGATAACTGCTGAAAGATGACCTATTTCTAGTCGATTTTGGTAAATTTC
1 TGTTTCCAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCTAGTCGATTTTGAT-AACTTC
* *
6312 TGAAAAATGACA
65 TGAAAGATGACC
* * * * * * *
6324 TGCTTCCAGTCAATTTTGGTAACTTCTGAAAAATGACATGTTTCTAGTCGATTTTGATAACTTCT
1 TGTTTCCAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCTAGTCGATTTTGATAACTTCT
*
6389 AAAAGATGACC
66 GAAAGATGACC
* * * * * *
6400 TGTTTCTAGTCAACTTCGATAACTGCAGAATGATGACCTGTTTCCAGTCAACTTTGATAACTTCT
1 TGTTTCCAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCTAGTCGATTTTGATAACTTCT
6465 TTGAGTTTGA
Statistics
Matches: 306, Mismatches: 61, Indels: 7
0.82 0.16 0.02
Matches are distributed among these distances:
76 198 0.65
77 106 0.35
78 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (76 bp):
TGTTTCCAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCTAGTCGATTTTGATAACTTCT
GAAAGATGACC
Found at i:6375 original size:191 final size:190
Alignment explanation
Indices: 6018--6461 Score: 568
Period size: 191 Copynumber: 2.3 Consensus size: 190
6008 TAAAAGGACT
* *
6018 TGTTTCTAGTCAA-TTCTGATAACTGCTAAAAGATGACCTGTCTT-GAGTCAACTTCGATAAACT
1 TGTTTCTAGTCAACTTC-GATAACTGCTGAAAGATGACCTGT-TTCCAGTCAACTTCGAT-AACT
* * ** * * * *
6081 TCTGAAAAATGACATGTTTCCAGTCAACTACGATAACTACTGAAAGGTGACCTGTTTCTAGTCGA
63 GCTGAAAAATGACATATTTCCAGTCAACTACGATAACTACTGAAAAATGACATGCTTCCAGTCAA
* * *
6146 TTTTGATAACTTCTGAAAGATGACCTGTTTCCAGTCGATTTTGATAACTGCTGAAAGATGACC
128 TTTTGATAACTTCTGAAAAATGACATGTTTCCAGTCGATTTTGATAACTGCTAAAAGATGACC
*
6209 TGTTTCCAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCCAGTCAACTTCGATAACTGCT
1 TGTTTCTAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCCAGTCAACTTCGATAACTGCT
* * * * * ** * * *
6274 GAAAGATGACCTATTTCTAGTCGATTTTGGTAAATTTCTGAAAAATGACATGCTTCCAGTCAATT
66 GAAAAATGACATATTTCCAGTCAACTACGAT-AACTACTGAAAAATGACATGCTTCCAGTCAATT
* * *
6339 TTGGTAACTTCTGAAAAATGACATGTTTCTAGTCGATTTTGATAACTTCTAAAAGATGACC
130 TTGATAACTTCTGAAAAATGACATGTTTCCAGTCGATTTTGATAACTGCTAAAAGATGACC
* * *
6400 TGTTTCTAGTCAACTTCGATAACTGCAGAATGATGACCTGTTTCCAGTCAACTTTGATAACT
1 TGTTTCTAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCCAGTCAACTTCGATAACT
6462 TCTTTGAGTT
Statistics
Matches: 219, Mismatches: 31, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
190 30 0.14
191 186 0.85
192 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (190 bp):
TGTTTCTAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCCAGTCAACTTCGATAACTGCT
GAAAAATGACATATTTCCAGTCAACTACGATAACTACTGAAAAATGACATGCTTCCAGTCAATTT
TGATAACTTCTGAAAAATGACATGTTTCCAGTCGATTTTGATAACTGCTAAAAGATGACC
Found at i:6437 original size:229 final size:229
Alignment explanation
Indices: 6018--6461 Score: 622
Period size: 229 Copynumber: 1.9 Consensus size: 229
6008 TAAAAGGACT
* *
6018 TGTTTCTAGTCAATTCTGATAACTGCTAAAAGATGACCTGTCTTGAGTCAACTTCGATAAACTTC
1 TGTTTCCAGTCAATTCTGATAACTGCTAAAAGATGACCTATCTTGAGTCAACTTCGATAAACTTC
* ** *
6083 TGAAAAATGACATGTTTCCAGTCAACTACGATAACTACTGAAAGGTGACCTGTTTCTAGTCGATT
66 TGAAAAATGACATGCTTCCAGTCAACTACGATAACTACTGAAAAATGACATGTTTCTAGTCGATT
* * * * *
6148 TTGATAACTTCTGAAAGATGACCTGTTTCCAGTCGATTTTGATAACTGCTGAAAGATGACCTGTT
131 TTGATAACTTCTAAAAGATGACCTGTTTCCAGTCAACTTCGATAACTGCAGAAAGATGACCTGTT
6213 TCCAGTCAACTTCGATAACTGCTGAAAGATGACC
196 TCCAGTCAACTTCGATAACTGCTGAAAGATGACC
* * * * * * *
6247 TGTTTCCAGTCAACTTC-GATAACTGCTGAAAGATGACCTAT-TTCTAGTCGATTTTGGTAAATT
1 TGTTTCCAGTCAA-TTCTGATAACTGCTAAAAGATGACCTATCTT-GAGTCAACTTCGATAAACT
* ** * *
6310 TCTGAAAAATGACATGCTTCCAGTCAATTTTGGTAACTTCTGAAAAATGACATGTTTCTAGTCGA
64 TCTGAAAAATGACATGCTTCCAGTCAACTACGATAACTACTGAAAAATGACATGTTTCTAGTCGA
* *
6375 TTTTGATAACTTCTAAAAGATGACCTGTTTCTAGTCAACTTCGATAACTGCAGAATGATGACCTG
129 TTTTGATAACTTCTAAAAGATGACCTGTTTCCAGTCAACTTCGATAACTGCAGAAAGATGACCTG
*
6440 TTTCCAGTCAACTTTGATAACT
194 TTTCCAGTCAACTTCGATAACT
6462 TCTTTGAGTT
Statistics
Matches: 187, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
228 2 0.01
229 182 0.97
230 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (229 bp):
TGTTTCCAGTCAATTCTGATAACTGCTAAAAGATGACCTATCTTGAGTCAACTTCGATAAACTTC
TGAAAAATGACATGCTTCCAGTCAACTACGATAACTACTGAAAAATGACATGTTTCTAGTCGATT
TTGATAACTTCTAAAAGATGACCTGTTTCCAGTCAACTTCGATAACTGCAGAAAGATGACCTGTT
TCCAGTCAACTTCGATAACTGCTGAAAGATGACC
Done.