Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015854.1 Corchorus olitorius cultivar O-4 contig15887, 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: 37700
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2356 original size:2 final size:2
Alignment explanation
Indices: 2349--2381 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2339 AAATTACTAG
2349 TA TA TA TA TA TA TA TA TA 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 T
2382 TATTGATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5304 original size:30 final size:29
Alignment explanation
Indices: 5231--5315 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 29
5221 AAATTTAATT
5231 ATTTTGCCCCATAAACTTCTAAAATCTTGAC
1 ATTTTGCCCC-TAAACTT-TAAAATCTTGAC
* **
5262 GTTTTGTTCCTAAACATTTAAAATCTTGAC
1 ATTTTGCCCCTAAAC-TTTAAAATCTTGAC
* *
5292 ATTTTACCCCTAAATTTTTAAAAT
1 ATTTTGCCCCTAAA-CTTTAAAAT
5316 TTTGTTGACA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
30 35 0.80
31 9 0.20
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (29 bp):
ATTTTGCCCCTAAACTTTAAAATCTTGAC
Found at i:5913 original size:112 final size:109
Alignment explanation
Indices: 5705--5919 Score: 378
Period size: 112 Copynumber: 1.9 Consensus size: 109
5695 AAATCTTAAT
5705 CTATTATATTTTTCCACATATTGCATTTTCCACATTAGGAATGCCAAATCTTAATATATAATTGA
1 CTATTATATTTTTCCACATATTGCATTTTCCACATTAGGAATGCCAAATCTTAATATATAATTGA
5770 TTCATTTCTAAATTTAACTTGGTACATGCATCACTATATATATA
66 TTCATTTCTAAATTTAACTTGGTACATGCATCACTATATATATA
*
5814 CTATTATATTTTTCCACATATTGCATTTTCCCCATTAGCTAGGAATGCCAAATCTTAATATAT-A
1 CTATTATATTTTTCCACATATTGCATTTTCCACA-T---TAGGAATGCCAAATCTTAATATATAA
5878 TTGATTCATTTCTAAATTTAACTTGGTACATGCATCACTATA
62 TTGATTCATTTCTAAATTTAACTTGGTACATGCATCACTATA
5920 CACTACTATA
Statistics
Matches: 101, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
109 33 0.33
110 1 0.01
112 43 0.43
113 24 0.24
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.42
Consensus pattern (109 bp):
CTATTATATTTTTCCACATATTGCATTTTCCACATTAGGAATGCCAAATCTTAATATATAATTGA
TTCATTTCTAAATTTAACTTGGTACATGCATCACTATATATATA
Found at i:7678 original size:15 final size:15
Alignment explanation
Indices: 7658--7686 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
7648 TTCAATGTTC
7658 TAAATATTATATTTA
1 TAAATATTATATTTA
7673 TAAATATTATATTT
1 TAAATATTATATTT
7687 GGAATTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAATATTATATTTA
Found at i:24023 original size:1 final size:1
Alignment explanation
Indices: 24019--24062 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
24009 CTTGAAATCC
* * * *
24019 AAAAAAAAAAAAAGAAAAAAAAGAAAGAAAACAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
24063 TTTCTGTTTG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.02, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:24038 original size:13 final size:13
Alignment explanation
Indices: 24020--24062 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
24010 TTGAAATCCA
24020 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
*
24033 AAAAAAAAGAAAG
1 AAAAAAAAAAAAG
24046 AAAACAAAAAAAA-
1 AAAA-AAAAAAAAG
24059 AAAA
1 AAAA
24063 TTTCTGTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 20 0.74
14 7 0.26
ACGTcount: A:0.91, C:0.02, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:32816 original size:34 final size:34
Alignment explanation
Indices: 32771--32837 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
32761 AACTAACTAG
*
32771 CCATCAGGCATCTATCCTGGTGTTAAATTGCTGT
1 CCATCAAGCATCTATCCTGGTGTTAAATTGCTGT
*
32805 CCATCAAGCATCTATCCTGGTGTTATATTGCTG
1 CCATCAAGCATCTATCCTGGTGTTAAATTGCTG
32838 GACTCTGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (34 bp):
CCATCAAGCATCTATCCTGGTGTTAAATTGCTGT
Found at i:32909 original size:20 final size:20
Alignment explanation
Indices: 32884--32923 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
32874 TCAATTACAA
32884 AAAAAAAGTGCAAGATATGG
1 AAAAAAAGTGCAAGATATGG
32904 AAAAAAAGTGCAAGATATGG
1 AAAAAAAGTGCAAGATATGG
32924 TTTTAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.25, T:0.15
Consensus pattern (20 bp):
AAAAAAAGTGCAAGATATGG
Found at i:33292 original size:78 final size:78
Alignment explanation
Indices: 33202--33362 Score: 286
Period size: 78 Copynumber: 2.1 Consensus size: 78
33192 AGATTTATAG
* *
33202 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
*
33267 TACCATTTTACTA
66 TACCATTTAACTA
*
33280 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATTTAATATCTTTATAACTATTTCAGTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
33345 TACCATTTAACTA
66 TACCATTTAACTA
33358 TTTTA
1 TTTTA
33363 ACTAGAAAAC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.35, C:0.14, G:0.01, T:0.51
Consensus pattern (78 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
TACCATTTAACTA
Found at i:33942 original size:25 final size:23
Alignment explanation
Indices: 33897--33943 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
33887 GTCGAGTCAA
*
33897 TTGGATTTTTCGTCATTTGGGTT
1 TTGGATTTTTCGTCAATTGGGTT
33920 TTGGATTTTTCGAGTCAATTGGGT
1 TTGGATTTTTC--GTCAATTGGGT
33944 CATACTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.52
25 10 0.48
ACGTcount: A:0.13, C:0.09, G:0.28, T:0.51
Consensus pattern (23 bp):
TTGGATTTTTCGTCAATTGGGTT
Found at i:37612 original size:2 final size:2
Alignment explanation
Indices: 37605--37642 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
37595 AGGTGGGATA
37605 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37643 GATTGTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.