Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022914.1 Corchorus olitorius cultivar O-4 contig22947, 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: 28387
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:286 original size:23 final size:23
Alignment explanation
Indices: 256--302 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
246 GCACTGTGAG
256 AGTCTCATGTCAAGCCCTTAATT
1 AGTCTCATGTCAAGCCCTTAATT
*
279 AGTCTCATGTCAAGCTCTTAATT
1 AGTCTCATGTCAAGCCCTTAATT
302 A
1 A
303 AACTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (23 bp):
AGTCTCATGTCAAGCCCTTAATT
Found at i:5088 original size:28 final size:27
Alignment explanation
Indices: 5024--5088 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
5014 TGTGAAAAAT
*
5024 ATTTATATTCATTAAACTAACTTTTGAC
1 ATTTA-ATTCATTAAACTAACTTATGAC
**
5052 ATCAAAATTCATTAAACTAACTTAATGAC
1 AT-TTAATTCATTAAACTAACTT-ATGAC
*
5081 CTTTAATT
1 ATTTAATT
5089 TTTCTAACAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (27 bp):
ATTTAATTCATTAAACTAACTTATGAC
Found at i:5438 original size:21 final size:20
Alignment explanation
Indices: 5414--5458 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 20
5404 GTACATAAAG
5414 TAAATTATGTACTCTGGTACA
1 TAAATTA-GTACTCTGGTACA
5435 T-AA--AGTACTCTGGTACA
1 TAAATTAGTACTCTGGTACA
*
5452 TACATTA
1 TAAATTA
5459 ATTATTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 7
0.71 0.04 0.25
Matches are distributed among these distances:
17 14 0.70
18 2 0.10
20 3 0.15
21 1 0.05
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (20 bp):
TAAATTAGTACTCTGGTACA
Found at i:13768 original size:21 final size:21
Alignment explanation
Indices: 13754--13854 Score: 168
Period size: 21 Copynumber: 4.8 Consensus size: 21
13744 ATTGGATCAA
13754 GTTCCAAGCTCATTGGAGCAA-
1 GTTCCAAGCTCATTGGAG-AAG
*
13775 GTTCCAAGCTCATTAGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
13796 GTTCCAAGCTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
13817 GTTCCAAGCTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
*
13838 GTTTCAAGCTCATTGGA
1 GTTCCAAGCTCATTGGA
13855 ATTGCCTAAG
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
20 2 0.03
21 74 0.97
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (21 bp):
GTTCCAAGCTCATTGGAGAAG
Found at i:17991 original size:17 final size:17
Alignment explanation
Indices: 17969--18002 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17959 TAAAGGTAAT
*
17969 CTACTAAAACTAAATGC
1 CTACTAAAACAAAATGC
17986 CTACTAAAACAAAATGC
1 CTACTAAAACAAAATGC
18003 TAATCATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.24, G:0.06, T:0.21
Consensus pattern (17 bp):
CTACTAAAACAAAATGC
Found at i:18476 original size:39 final size:39
Alignment explanation
Indices: 18417--18492 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
18407 TTCTGATATT
* * *
18417 AACTGATAAAGTAATGATCCTAAATCAGGATCGAAATAA
1 AACTGACAAAGCAATAATCCTAAATCAGGATCGAAATAA
* *
18456 AACTGACAAAGCAATAATCCTAAATCATGATTGAAAT
1 AACTGACAAAGCAATAATCCTAAATCAGGATCGAAAT
18493 TGAATTATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.24
Consensus pattern (39 bp):
AACTGACAAAGCAATAATCCTAAATCAGGATCGAAATAA
Found at i:18848 original size:69 final size:69
Alignment explanation
Indices: 18776--19124 Score: 529
Period size: 69 Copynumber: 5.1 Consensus size: 69
18766 AAATCTATAT
* *
18776 GGCTTGGATGGAACCAAGGCTTAAACTGACCCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCT
1 GGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCT
*
18841 ATGT
66 ATGC
* * * * *
18845 GGCTTGGATGAAATCAAGGCTTAAACTAACTCGTATGGAAATGAGCTTGGCTTATGGAAAAGCCT
1 GGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCT
*
18910 GTGC
66 ATGC
* * *
18914 GGCTTGGATGAAACCAACGCTTAAACTGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAACCCT
1 GGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCT
18979 ATGC
66 ATGC
* *
18983 GGCTTGGATGGAACCAACGG-TTGAACTGACTCGTATGGAAACGAGGTTGGCTTGTGGAAAAGCC
1 GGCTTGGATGGAACCAA-GGCTTAAACTGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCC
19047 TATGC
65 TATGC
* * *
19052 GGCTTGGATGGAACCAAGGCTTGAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCT
1 GGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCT
19117 ATGC
66 ATGC
19121 GGCT
1 GGCT
19125 AACTAACTCG
Statistics
Matches: 255, Mismatches: 23, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
68 2 0.01
69 252 0.99
70 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.25
Consensus pattern (69 bp):
GGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCT
ATGC
Found at i:20679 original size:50 final size:50
Alignment explanation
Indices: 20620--20745 Score: 200
Period size: 50 Copynumber: 2.5 Consensus size: 50
20610 AATGCCCCTC
20620 GAAAAGCGAATTTTGATCTTGGACTCACAAATGG-AATGCAATCTTACTTT
1 GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAT-CAATCTTACTTT
* * *
20670 GAAAAGCGAATTTTGATCTTGGGCTCACAAATGGAAATCAATTTTATTTT
1 GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAATCAATCTTACTTT
*
20720 GAAAAGCGAATTTTGATCTTGAACTC
1 GAAAAGCGAATTTTGATCTTGGACTC
20746 TGATCTGTCA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 67 0.96
51 3 0.04
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (50 bp):
GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAATCAATCTTACTTT
Found at i:22286 original size:21 final size:21
Alignment explanation
Indices: 22262--22305 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
22252 GCGCCCACAA
* *
22262 GGTTTCCTTGAGCACCCATGT
1 GGTTTCCTTGAGAACCCAGGT
*
22283 GGTTTGCTTGAGAACCCAGGT
1 GGTTTCCTTGAGAACCCAGGT
22304 GG
1 GG
22306 GCAGTGTCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.32, T:0.30
Consensus pattern (21 bp):
GGTTTCCTTGAGAACCCAGGT
Done.