Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015587.1 Corchorus olitorius cultivar O-4 contig15620, 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: 44546
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:309 original size:30 final size:29
Alignment explanation
Indices: 275--341 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 29
265 GGTTTGGTTG
**
275 TGGAAGGCCAGGGGGTCTT-GAGGAAGTGGA
1 TGGAAGG-CAGGGAATCTTGGA-GAAGTGGA
305 TGGAAGAGCAGGGAATCTTGGAGAAGTGGA
1 TGGAAG-GCAGGGAATCTTGGAGAAGTGGA
335 TGGAAGG
1 TGGAAGG
342 GTAGGGTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 1 0.03
30 29 0.88
31 3 0.09
ACGTcount: A:0.28, C:0.07, G:0.48, T:0.16
Consensus pattern (29 bp):
TGGAAGGCAGGGAATCTTGGAGAAGTGGA
Found at i:2438 original size:17 final size:17
Alignment explanation
Indices: 2411--2465 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
2401 AACCCATGTA
* *
2411 ATCTTTGATCACCAGTG
1 ATCTTAGATCACTAGTG
*
2428 ATCTT-GCATCACTGGTG
1 ATCTTAG-ATCACTAGTG
2445 ATCTTAGATCACTAGTG
1 ATCTTAGATCACTAGTG
2462 ATCT
1 ATCT
2466 GGGGGGTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (17 bp):
ATCTTAGATCACTAGTG
Found at i:3159 original size:13 final size:13
Alignment explanation
Indices: 3141--3166 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3131 AATGTAGCTA
3141 ATCATGTAGCGGT
1 ATCATGTAGCGGT
3154 ATCATGTAGCGGT
1 ATCATGTAGCGGT
3167 GTACGGGTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (13 bp):
ATCATGTAGCGGT
Found at i:3631 original size:2 final size:2
Alignment explanation
Indices: 3624--3648 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3614 AGTTATAGAG
3624 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3649 TTGTTCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4093 original size:231 final size:231
Alignment explanation
Indices: 3690--4149 Score: 839
Period size: 231 Copynumber: 2.0 Consensus size: 231
3680 AGAAAATTCG
* *
3690 ATATTTGGAGCATATCTTATAATTGAGGAACTAATCTGACAAAGTAAAATAGTAGTGCCTGAAAA
1 ATATTTGGAGCAGATCTTATAATTGAAGAACTAATCTGACAAAGTAAAATAGTAGTGCCTGAAAA
3755 CATGCTGTTGTAGAAAATAAAAGGTTTTGTAGTTGTCATACAATTTCCCCTTTTTTAGAGTTGTT
66 CATGCTGTTGTAGAAAATAAAAGGTTTTGTAGTTGTCATACAATTTCCCCTTTTTTAGAGTTGTT
3820 ATCGCTTAATTTATCGAATAAAGATAGAAGGATATATTGCAATATAAGTATGGAGAAAAAACCAT
131 ATCGCTTAATTTATCGAATAAAGATAGAAGGATATATTGCAATATAAGTATGGAGAAAAAACCAT
3885 CATTTCATGAATTTATAAGACTATAATCAATCTTAA
196 CATTTCATGAATTTATAAGACTATAATCAATCTTAA
* * * *
3921 ATATTTGGAGCAGATCTTATAATTGAAGAACTAATTTGGCAAGGTAAAATAGTAGTGCCTTAAAA
1 ATATTTGGAGCAGATCTTATAATTGAAGAACTAATCTGACAAAGTAAAATAGTAGTGCCTGAAAA
* *
3986 TATGCTGTTGTAGAAAATAAAAGTTTTTGTAGTTGTCATACAATTTCCCCTTTTTTAGAGTTGTT
66 CATGCTGTTGTAGAAAATAAAAGGTTTTGTAGTTGTCATACAATTTCCCCTTTTTTAGAGTTGTT
4051 ATCGCTTAATTTATCGAATAAAGATAGAAGGATATATTGCAATATAAGTATGGAGAAAAAACCAT
131 ATCGCTTAATTTATCGAATAAAGATAGAAGGATATATTGCAATATAAGTATGGAGAAAAAACCAT
*
4116 CATTTCATGAATTTATAAGACTATAATTAATCTT
196 CATTTCATGAATTTATAAGACTATAATCAATCTT
4150 TTTTTTTTTT
Statistics
Matches: 220, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
231 220 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (231 bp):
ATATTTGGAGCAGATCTTATAATTGAAGAACTAATCTGACAAAGTAAAATAGTAGTGCCTGAAAA
CATGCTGTTGTAGAAAATAAAAGGTTTTGTAGTTGTCATACAATTTCCCCTTTTTTAGAGTTGTT
ATCGCTTAATTTATCGAATAAAGATAGAAGGATATATTGCAATATAAGTATGGAGAAAAAACCAT
CATTTCATGAATTTATAAGACTATAATCAATCTTAA
Found at i:11133 original size:15 final size:15
Alignment explanation
Indices: 11109--11141 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
11099 TTTGTCCAAA
11109 TAACAACAAACATAG
1 TAACAACAAACATAG
*
11124 TAACATCAAACATAG
1 TAACAACAAACATAG
11139 TAA
1 TAA
11142 TCTTGATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.18, G:0.06, T:0.18
Consensus pattern (15 bp):
TAACAACAAACATAG
Found at i:14262 original size:2 final size:2
Alignment explanation
Indices: 14255--14316 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
14245 ACAACTTTAA
14255 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
14297 AC AC AC AC AC AC AC A- AC AC A
1 AC AC AC AC AC AC AC AC AC AC A
14317 TATATATTTA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:18723 original size:23 final size:23
Alignment explanation
Indices: 18666--18715 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
18656 AAGTGTTCGT
*
18666 TTATATAATAATCGAGCATTCAC
1 TTATATAATAATCGAACATTCAC
*
18689 TTATATAATAATCGAACATTCAT
1 TTATATAATAATCGAACATTCAC
18712 TTAT
1 TTAT
18716 TATTTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (23 bp):
TTATATAATAATCGAACATTCAC
Found at i:19446 original size:19 final size:20
Alignment explanation
Indices: 19422--19459 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
19412 TTTGCAGTTT
*
19422 GTGTCTTTATCT-TTCATTA
1 GTGTCTTTAACTGTTCATTA
19441 GTGTCTTTAACTGTTCATT
1 GTGTCTTTAACTGTTCATT
19460 CTGAACTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.55
Consensus pattern (20 bp):
GTGTCTTTAACTGTTCATTA
Found at i:22180 original size:38 final size:38
Alignment explanation
Indices: 22129--22206 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
22119 CATTATTTAC
22129 GTAGCCACTCTTATATTTTATGTTGTTTAGATGTTGAA
1 GTAGCCACTCTTATATTTTATGTTGTTTAGATGTTGAA
22167 GTAGCCACTCTTATATTTTATGTTGTTTAGATGTTGAA
1 GTAGCCACTCTTATATTTTATGTTGTTTAGATGTTGAA
22205 GT
1 GT
22207 CTCGGTTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.23, C:0.10, G:0.19, T:0.47
Consensus pattern (38 bp):
GTAGCCACTCTTATATTTTATGTTGTTTAGATGTTGAA
Found at i:23504 original size:29 final size:29
Alignment explanation
Indices: 23471--23533 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
23461 TACTTTCTTA
*
23471 AGAAAAACTATCTACCTTTTATTTTTTAT
1 AGAAAAACTATCTACCTTTTATTTTCTAT
** *
23500 AGAAAGGCTTTCTACCTTTTATTTTCTAT
1 AGAAAAACTATCTACCTTTTATTTTCTAT
23529 AGAAA
1 AGAAA
23534 CTTCCAAACG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.44
Consensus pattern (29 bp):
AGAAAAACTATCTACCTTTTATTTTCTAT
Found at i:26830 original size:49 final size:49
Alignment explanation
Indices: 26773--26872 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
26763 CGTTTCAATC
26773 TCAGGTTTTTCTTTCTCTAATTCAGCTAACTTTTTATTTGGTTTTACTT
1 TCAGGTTTTTCTTTCTCTAATTCAGCTAACTTTTTATTTGGTTTTACTT
26822 TCAGGTTTTTCTTTCTCTAATTCAGCTAACTTTTTATTTGGTTTTACTT
1 TCAGGTTTTTCTTTCTCTAATTCAGCTAACTTTTTATTTGGTTTTACTT
26871 TC
1 TC
26873 TTCATTAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.16, C:0.17, G:0.10, T:0.57
Consensus pattern (49 bp):
TCAGGTTTTTCTTTCTCTAATTCAGCTAACTTTTTATTTGGTTTTACTT
Found at i:29276 original size:18 final size:18
Alignment explanation
Indices: 29249--29286 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
29239 AAGCGACCAA
*
29249 TATACTATGATGAAGGGT
1 TATACAATGATGAAGGGT
29267 TATACAATGATGAAGGGT
1 TATACAATGATGAAGGGT
29285 TA
1 TA
29287 GAGGTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (18 bp):
TATACAATGATGAAGGGT
Found at i:30181 original size:84 final size:84
Alignment explanation
Indices: 30087--30256 Score: 331
Period size: 84 Copynumber: 2.0 Consensus size: 84
30077 ACATTATAAT
*
30087 TTAATTGTAAAAAATTCTTTAAGAATTGTAAAAGTTTGAAAATTTGGGAGAAAAGGGCCCAACCG
1 TTAATTGTAAAAAATTCTTTAAGAATTGTAAAAGTTTGAAAAATTGGGAGAAAAGGGCCCAACCG
30152 GGTTCGAACCGGTGACCTC
66 GGTTCGAACCGGTGACCTC
30171 TTAATTGTAAAAAATTCTTTAAGAATTGTAAAAGTTTGAAAAATTGGGAGAAAAGGGCCCAACCG
1 TTAATTGTAAAAAATTCTTTAAGAATTGTAAAAGTTTGAAAAATTGGGAGAAAAGGGCCCAACCG
30236 GGTTCGAACCGGTGACCTC
66 GGTTCGAACCGGTGACCTC
30255 TT
1 TT
30257 GATCTGCAGT
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (84 bp):
TTAATTGTAAAAAATTCTTTAAGAATTGTAAAAGTTTGAAAAATTGGGAGAAAAGGGCCCAACCG
GGTTCGAACCGGTGACCTC
Found at i:30730 original size:15 final size:15
Alignment explanation
Indices: 30710--30740 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30700 GATTAACATG
30710 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
30725 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
30740 T
1 T
30741 AATGTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Found at i:32220 original size:3 final size:3
Alignment explanation
Indices: 32207--32263 Score: 105
Period size: 3 Copynumber: 18.7 Consensus size: 3
32197 GACTTTTATG
32207 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
32253 TTA TTA TTA TT
1 TTA TTA TTA TT
32264 GGCCAACTCA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:32339 original size:2 final size:2
Alignment explanation
Indices: 32332--32366 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
32322 CTCAAACTAT
*
32332 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32367 TTTAACTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:40960 original size:16 final size:17
Alignment explanation
Indices: 40939--40973 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
40929 TTAAACGGAG
40939 AAGGATA-AGTTGAAAA
1 AAGGATAGAGTTGAAAA
40955 AAGGATATGAGTTGAAAA
1 AAGGATA-GAGTTGAAAA
40973 A
1 A
40974 GAATATGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
18 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.26, T:0.20
Consensus pattern (17 bp):
AAGGATAGAGTTGAAAA
Found at i:40974 original size:17 final size:18
Alignment explanation
Indices: 40946--40982 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
40936 GAGAAGGATA
*
40946 AGTTGAAAAAAGGATATG
1 AGTTGAAAAAAGAATATG
40964 AGTTG-AAAAAGAATATG
1 AGTTGAAAAAAGAATATG
40981 AG
1 AG
40983 AAATAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (18 bp):
AGTTGAAAAAAGAATATG
Found at i:42514 original size:2 final size:2
Alignment explanation
Indices: 42509--42539 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
42499 TGTGTGTGTG
42509 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42540 CTAAATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42547 original size:14 final size:13
Alignment explanation
Indices: 42509--42550 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
42499 TGTGTGTGTG
*
42509 TATATATATATA-
1 TATATATAAATAT
*
42521 TATATATATATAT
1 TATATATAAATAT
42534 TATATACTAAATAT
1 TATATA-TAAATAT
42548 TAT
1 TAT
42551 TCGAAACACC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 12 0.44
13 6 0.22
14 9 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (13 bp):
TATATATAAATAT
Done.