Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010440.1 Corchorus olitorius cultivar O-4 contig10472, 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: 4749
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Found at i:294 original size:22 final size:21
Alignment explanation
Indices: 226--524 Score: 118
Period size: 22 Copynumber: 13.6 Consensus size: 21
216 AATATTCAGA
* *
226 TATGAAATTGTGGTAATCTCCC
1 TATGAAATTTTGATAA-CTCCC
* * * * *
248 TATGACATTATAATAAGTACAC
1 TATGAAATTTTGATAACT-CCC
*
270 TATTAAGATTTTGATAACTCCC
1 TATGAA-ATTTTGATAACTCCC
* *
292 TATGAAAATTTGATAACCTTCC
1 TATGAAATTTTGATAA-CTCCC
* * **
314 TATGAAATTTTGGTAACGACAT
1 TATGAAATTTTGATAAC-TCCC
* * *
336 TATGGAATTTTGAGAACCATTCC
1 TATGAAATTTTGATAA-C-TCCC
*
359 -ATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAA-CTCCC
* * *
380 TATGGAATTTTGAAAACCTCAC
1 TATGAAATTTTGATAA-CTCCC
*
402 TATGAAATTTTGATCAACTCCA
1 TATGAAATTTTGAT-AACTCCC
* * *
424 TGTGAAATGTTTG-TAAACACAC
1 TATGAAAT-TTTGAT-AACTCCC
* * *
446 TATAAAATTTTAAAAACCTCCC
1 TATGAAATTTTGATAA-CTCCC
* * * *
468 TATAAAATGTTAATAA-TCACA
1 TATGAAATTTTGATAACTC-CC
* *
489 TCGTGAAATTTTGATAATCTCAC
1 T-ATGAAATTTTGATAA-CTCCC
*
512 TATAAAATTTTGA
1 TATGAAATTTTGA
525 CAAACCTTCC
Statistics
Matches: 200, Mismatches: 63, Indels: 28
0.69 0.22 0.10
Matches are distributed among these distances:
20 2 0.01
21 21 0.10
22 158 0.79
23 17 0.09
24 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (21 bp):
TATGAAATTTTGATAACTCCC
Found at i:364 original size:44 final size:44
Alignment explanation
Indices: 291--413 Score: 133
Period size: 44 Copynumber: 2.8 Consensus size: 44
281 TGATAACTCC
* * * *
291 CTATGAAAATTTGATAACCTTCCTATGAAATTTTGGTAACGACA
1 CTATGGAATTTTGAAAACCTTCCTATGAAATTTTGGTAACCACA
* * * * *
335 TTATGGAATTTTGAGAACCATTCC-ATGAAATTTTGTTAACCTCC
1 CTATGGAATTTTGAAAACC-TTCCTATGAAATTTTGGTAACCACA
379 CTATGGAATTTTGAAAACC-TCACTATGAAATTTTG
1 CTATGGAATTTTGAAAACCTTC-CTATGAAATTTTG
414 ATCAACTCCA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
42 2 0.03
43 1 0.02
44 59 0.89
45 4 0.06
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (44 bp):
CTATGGAATTTTGAAAACCTTCCTATGAAATTTTGGTAACCACA
Found at i:430 original size:66 final size:63
Alignment explanation
Indices: 360--549 Score: 177
Period size: 66 Copynumber: 2.9 Consensus size: 63
350 AACCATTCCA
* * **
360 TGAAATTTTGTTAACCTCCCTATGGAATTTTGAAAACCTCACTATGAAATTTTGATCAACTC-CA
1 TGAAATTTTG-TAAACTCACTATAAAATTTTGAAAACCTC-CTAT-AAATTTTGAT-AA-TCACA
424 T-G
61 TCG
* * * *
426 TGAAATGTTTGTAAACACACTATAAAATTTTAAAAACCTCCCTATAAAATGTTAATAATCACATC
1 TGAAAT-TTTGTAAACTCACTATAAAATTTTGAAAACCT-CCTAT-AAATTTTGATAATCACATC
491 G
63 G
* *
492 TGAAATTTTGATAATCTCACTATAAAATTTTGACAAACCTTCCTATAAACTTTGATAA
1 TGAAATTTTG-TAAACTCACTATAAAATTTTGA-AAACC-TCCTATAAATTTTGATAA
550 ATCTCTCTAT
Statistics
Matches: 102, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
64 2 0.02
65 9 0.09
66 75 0.74
67 15 0.15
68 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.35
Consensus pattern (63 bp):
TGAAATTTTGTAAACTCACTATAAAATTTTGAAAACCTCCTATAAATTTTGATAATCACATCG
Found at i:559 original size:22 final size:23
Alignment explanation
Indices: 498--559 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 23
488 ATCGTGAAAT
* *
498 TTTGAT-AATCTCACTATAAAAT
1 TTTGATAAATCTCTCTATAAAAC
* *
520 TTTGACAAACCT-TCCTAT-AAAC
1 TTTGATAAATCTCT-CTATAAAAC
542 TTTGATAAATCTCTCTAT
1 TTTGATAAATCTCTCTAT
560 TGTGGTCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
22 22 0.71
23 9 0.29
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.40
Consensus pattern (23 bp):
TTTGATAAATCTCTCTATAAAAC
Found at i:4441 original size:77 final size:77
Alignment explanation
Indices: 4166--4497 Score: 345
Period size: 78 Copynumber: 4.3 Consensus size: 77
4156 CGCACTGAGG
* * **
4166 GGGA-ACGTTCGTTTCATTT-GTTTTATACGGGGACACCAACT-TTGGTGTTCTACCGTTGTGAT
1 GGGAGACGTTCGTTTCATTTATTTTTATACGGGGACACCAA-TGTCGGTGTTCGGCCGTTGTGAT
4228 GAAACGGTCTCGA
65 GAAACGGTCTCGA
** * * * * * *
4241 TAGAGACGGTCGTTTCATCTAGTTCTTATACGGGGACACCAATTTTGGTTTTCGGCCGTTGTGAT
1 GGGAGACGTTCGTTTCATTTA-TTTTTATACGGGGACACCAATGTCGGTGTTCGGCCGTTGTGAT
*
4306 GAAACGGCCTCGA
65 GAAACGGTCTCGA
** * * *
4319 TAGAGACTTGTCGTTTCATTTATTTTCT-TATGGGGACACCGATGTCGGTGTTCGGCCGTTGTGA
1 GGGAGACGT-TCGTTTCATTTATTTT-TATACGGGGACACCAATGTCGGTGTTCGGCCGTTGTGA
* *
4383 TTAAACGGTCTCGG
64 TGAAACGGTCTCGA
*
4397 GGGAGACGTTCGTTGT-ATTTATTTTTATACGGGGACACCAATGTCGGTGTTTGGCCGTTGTGA-
1 GGGAGACGTTCGTT-TCATTTATTTTTATACGGGGACACCAATGTCGGTGTTCGGCCGTTGTGAT
* *
4460 CAGAATGGTCTCGA
65 GA-AACGGTCTCGA
4474 GGGAGACGTTCGTTGT-ATTTATTT
1 GGGAGACGTTCGTT-TCATTTATTT
4498 CAGAATTTCT
Statistics
Matches: 217, Mismatches: 31, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
75 2 0.01
76 15 0.07
77 81 0.37
78 107 0.49
79 12 0.06
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.35
Consensus pattern (77 bp):
GGGAGACGTTCGTTTCATTTATTTTTATACGGGGACACCAATGTCGGTGTTCGGCCGTTGTGATG
AAACGGTCTCGA
Found at i:4480 original size:155 final size:154
Alignment explanation
Indices: 4170--4497 Score: 353
Period size: 155 Copynumber: 2.1 Consensus size: 154
4160 CTGAGGGGGA
* * *
4170 ACGTTCGTTTCATTTGTTTTATACGGGGACACCAACTTTGGTGTTCTACCGTTGTGATGAAACGG
1 ACGTTCGTTTCATTTATTTTATACGGGGACACCAACTTCGGTGTTCGACCGTTGTGATGAAACGG
* * *
4235 TCTCGATAGAGACGGTCGTTTCATCTAGTTCTTATACGGGGACACCAATTTTGGTTTTCGGCCGT
66 TCTCGAGAGAGACGGTCGTTTCATCTAGTTCTTATACGGGGACACCAATGTCGGTTTTCGGCCGT
* *
4300 TGTGATGAAACGGCCTCGATAGAG
131 TGTGAAGAAACGGCCTCGAGAGAG
* * * * * *
4324 ACTTGTCGTTTCATTTATTTTCTTATGGGGACACCGA-TGTCGGTGTTCGGCCGTTGTGATTAAA
1 ACGT-TCGTTTCATTTATTTT-ATACGGGGACACCAACT-TCGGTGTTCGACCGTTGTGATGAAA
* * * * *
4388 CGGTCTCGGGGGAGACGTTCGTTGT-ATTTA-TTTTTATACGGGGACACCAATGTCGGTGTTT-G
63 CGGTCTCGAGAGAGACGGTCGTT-TCATCTAGTTCTTATACGGGGACACCAATGTCGGT-TTTCG
* * *
4450 GCCGTTGTGACAG-AATGGTCTCGAGGGAG
126 GCCGTTGTGA-AGAAACGGCCTCGAGAGAG
4479 ACGTTCGTTGT-ATTTATTT
1 ACGTTCGTT-TCATTTATTT
4498 CAGAATTTCT
Statistics
Matches: 144, Mismatches: 23, Indels: 14
0.80 0.13 0.08
Matches are distributed among these distances:
154 16 0.11
155 67 0.47
156 60 0.42
157 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.36
Consensus pattern (154 bp):
ACGTTCGTTTCATTTATTTTATACGGGGACACCAACTTCGGTGTTCGACCGTTGTGATGAAACGG
TCTCGAGAGAGACGGTCGTTTCATCTAGTTCTTATACGGGGACACCAATGTCGGTTTTCGGCCGT
TGTGAAGAAACGGCCTCGAGAGAG
Done.