Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018001.1 Corchorus olitorius cultivar O-4 contig18034, 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: 18748
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:1554 original size:26 final size:26
Alignment explanation
Indices: 1506--1557 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1496 AAAATAGACA
*
1506 AATTAAACTAGAAAACAATAAAATAG
1 AATTAAACTAGAAAACAAGAAAATAG
*
1532 AATTAAACTA-AAAATTAAGAAAATAG
1 AATTAAACTAGAAAA-CAAGAAAATAG
1558 TTTGAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.21
Consensus pattern (26 bp):
AATTAAACTAGAAAACAAGAAAATAG
Found at i:2943 original size:76 final size:76
Alignment explanation
Indices: 2797--2944 Score: 174
Period size: 76 Copynumber: 1.9 Consensus size: 76
2787 GGACCCCGAC
* *
2797 TCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCATGTGGTTTGCTTGAGAACCCAGGTGCGC
1 TCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCATGTGGTTTGCCTGAGAACCCAGATGCGC
2862 AGTGTCACGAG
66 AGTGTCACGAG
* * * * ** *
2873 TCCAGCTGGGTGCCCACATGGTTTGTC-TGAAGACCCATGT-GTTTCGCCTGATCACCCAGATGG
1 TCCACCTGGGCGCCCACATGG-TTGCCTTGAACACCCATGTGGTTT-GCCTGAGAACCCAGATGC
*
2936 GCTGTGTCA
64 GCAGTGTCA
2945 TAGCTCATCA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
75 4 0.07
76 52 0.87
77 4 0.07
ACGTcount: A:0.18, C:0.29, G:0.28, T:0.25
Consensus pattern (76 bp):
TCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCATGTGGTTTGCCTGAGAACCCAGATGCGC
AGTGTCACGAG
Found at i:3929 original size:28 final size:26
Alignment explanation
Indices: 3874--3923 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3864 ATGATTTAGG
*
3874 GGTTACTAACTCCCTTTTTCTTTTGA
1 GGTTACTAACGCCCTTTTTCTTTTGA
* *
3900 GGTTACTAACGCTCTTTTTTTTTT
1 GGTTACTAACGCCCTTTTTCTTTT
3924 CAGAGGGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.14, C:0.20, G:0.12, T:0.54
Consensus pattern (26 bp):
GGTTACTAACGCCCTTTTTCTTTTGA
Found at i:3997 original size:4 final size:4
Alignment explanation
Indices: 3988--4013 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3978 ACCTTTTCTT
3988 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
4014 TTTTTCAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:6348 original size:21 final size:21
Alignment explanation
Indices: 6324--6368 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
6314 GTAAGTGATG
*
6324 AAGT-AGTGAAATTGATGATTA
1 AAGTGAGTG-AATTGATGAATA
*
6345 AAGTGAGTGAATTTATGAATA
1 AAGTGAGTGAATTGATGAATA
6366 AAG
1 AAG
6369 GTAATAGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.31
Consensus pattern (21 bp):
AAGTGAGTGAATTGATGAATA
Found at i:10935 original size:20 final size:20
Alignment explanation
Indices: 10894--10935 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
10884 TGATATGATG
*
10894 AATTAATTACTAGCAAATGA
1 AATTAATTACTAGCAAAAGA
10914 AATTAATTACTAG-AAGAAGA
1 AATTAATTACTAGCAA-AAGA
10934 AA
1 AA
10936 AAAAATGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.26
Consensus pattern (20 bp):
AATTAATTACTAGCAAAAGA
Found at i:13213 original size:21 final size:21
Alignment explanation
Indices: 13180--13228 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
13170 AAGAATTGTA
*
13180 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCGCTCTT
* *
13200 GCTTCCTTTGAAATCTCTCTT
1 GCTTCCTTGGAAATCGCTCTT
13221 GCATTCCT
1 GC-TTCCT
13229 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.27, G:0.16, T:0.43
Consensus pattern (21 bp):
GCTTCCTTGGAAATCGCTCTT
Found at i:14396 original size:10 final size:9
Alignment explanation
Indices: 14353--14411 Score: 52
Period size: 10 Copynumber: 6.4 Consensus size: 9
14343 TAAAAGTAAC
14353 TAAGAAAAA
1 TAAGAAAAA
*
14362 TAAACAAAAA
1 T-AAGAAAAA
14372 TAA-AAGAAA
1 TAAGAA-AAA
14381 -AAGAAAAA
1 TAAGAAAAA
14389 TAACGAAAAA
1 TAA-GAAAAA
14399 TAA-AAAGAA
1 TAAGAAA-AA
14408 TAAG
1 TAAG
14412 GGTAAGAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
8 10 0.24
9 15 0.36
10 17 0.40
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10
Consensus pattern (9 bp):
TAAGAAAAA
Found at i:14396 original size:16 final size:17
Alignment explanation
Indices: 14367--14404 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
14357 AAAAATAAAC
14367 AAAAATAAAAGAAAAAG
1 AAAAATAAAAGAAAAAG
* *
14384 AAAAAT-AACGAAAAAT
1 AAAAATAAAAGAAAAAG
14400 AAAAA
1 AAAAA
14405 GAATAAGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAAATAAAAGAAAAAG
Found at i:16004 original size:12 final size:12
Alignment explanation
Indices: 15989--16015 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
15979 CCACCTGGGC
15989 GCCCACATGGTT
1 GCCCACATGGTT
16001 GCCCACATGGTT
1 GCCCACATGGTT
16013 GCC
1 GCC
16016 TTGAACACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.37, G:0.26, T:0.22
Consensus pattern (12 bp):
GCCCACATGGTT
Found at i:16851 original size:29 final size:29
Alignment explanation
Indices: 16817--17070 Score: 334
Period size: 29 Copynumber: 8.7 Consensus size: 29
16807 TTGCGAACCC
*
16817 AAGGGCATTCTGGTCATTTTTGCACATCT
1 AAGGGCATTTTGGTCATTTTTGCACATCT
* *
16846 AGGGGCATTTTGGTCATTTTTGCACATCC
1 AAGGGCATTTTGGTCATTTTTGCACATCT
* *
16875 AAGGGCATTTTGGTCATTTTACGCATAT-T
1 AAGGGCATTTTGGTCATTTT-TGCACATCT
* * *
16904 CAAGGGCATTTTGGTCATTTTCGCATATCC
1 -AAGGGCATTTTGGTCATTTTTGCACATCT
16934 AAGGGCATTTTGGTCATTTTTGCACATCT
1 AAGGGCATTTTGGTCATTTTTGCACATCT
* * *
16963 AGGGGCATTTCGGTCA-TTTTGCACATCC
1 AAGGGCATTTTGGTCATTTTTGCACATCT
16991 AAGGGCATTTTGGTCATTTTTGCACAAT-T
1 AAGGGCATTTTGGTCATTTTTGCAC-ATCT
*
17020 CAAGGGCATTCTGGTCATTTTTGCACATCT
1 -AAGGGCATTTTGGTCATTTTTGCACATCT
*
17050 AGGGGCATTTTGGTCATTTTT
1 AAGGGCATTTTGGTCATTTTT
17071 ACATACTCTG
Statistics
Matches: 198, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
28 25 0.13
29 121 0.61
30 52 0.26
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (29 bp):
AAGGGCATTTTGGTCATTTTTGCACATCT
Found at i:16934 original size:59 final size:58
Alignment explanation
Indices: 16815--17070 Score: 356
Period size: 59 Copynumber: 4.4 Consensus size: 58
16805 TTTTGCGAAC
* *
16815 CCAAGGGCATTCTGGTCATTTTTGCACATCTAGGGGCATTTTGGTCATTTTTGCACAT
1 CCAAGGGCATTTTGGTCATTTTTGCACATCTAAGGGCATTTTGGTCATTTTTGCACAT
* * * *
16873 CCAAGGGCATTTTGGTCATTTTACGCATAT-TCAAGGGCATTTTGGTCATTTTCGCATAT
1 CCAAGGGCATTTTGGTCATTTT-TGCACATCT-AAGGGCATTTTGGTCATTTTTGCACAT
* *
16932 CCAAGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTCGGTCA-TTTTGCACAT
1 CCAAGGGCATTTTGGTCATTTTTGCACATCTAAGGGCATTTTGGTCATTTTTGCACAT
*
16989 CCAAGGGCATTTTGGTCATTTTTGCACAAT-TCAAGGGCATTCTGGTCATTTTTGCACAT
1 CCAAGGGCATTTTGGTCATTTTTGCAC-ATCT-AAGGGCATTTTGGTCATTTTTGCACAT
* *
17048 CTAGGGGCATTTTGGTCATTTTT
1 CCAAGGGCATTTTGGTCATTTTT
17071 ACATACTCTG
Statistics
Matches: 175, Mismatches: 17, Indels: 11
0.86 0.08 0.05
Matches are distributed among these distances:
57 36 0.21
58 56 0.32
59 83 0.47
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (58 bp):
CCAAGGGCATTTTGGTCATTTTTGCACATCTAAGGGCATTTTGGTCATTTTTGCACAT
Found at i:17035 original size:116 final size:117
Alignment explanation
Indices: 16815--17070 Score: 408
Period size: 116 Copynumber: 2.2 Consensus size: 117
16805 TTTTGCGAAC
* *
16815 CCAAGGGCATTCTGGTCATTTTTGCACATCTAGGGGCATTTTGGTCATTTTTGCACATCCAAGGG
1 CCAAGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTCGGTCATTTTTGCACATCCAAGGG
* * *
16880 CATTTTGGTCATTTTACGCATATTCAAGGGCATTTTGGTCATTTTCGCATAT
66 CATTTTGGTCATTTTACGCAAATTCAAGGGCATTCTGGTCATTTTCGCACAT
16932 CCAAGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTCGGTCA-TTTTGCACATCCAAGGG
1 CCAAGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTCGGTCATTTTTGCACATCCAAGGG
* *
16996 CATTTTGGTCATTTT-TGCACAATTCAAGGGCATTCTGGTCATTTTTGCACAT
66 CATTTTGGTCATTTTACGCA-AATTCAAGGGCATTCTGGTCATTTTCGCACAT
* *
17048 CTAGGGGCATTTTGGTCATTTTT
1 CCAAGGGCATTTTGGTCATTTTT
17071 ACATACTCTG
Statistics
Matches: 129, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
115 3 0.02
116 81 0.63
117 45 0.35
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (117 bp):
CCAAGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTCGGTCATTTTTGCACATCCAAGGG
CATTTTGGTCATTTTACGCAAATTCAAGGGCATTCTGGTCATTTTCGCACAT
Done.