Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007012.1 Corchorus capsularis cultivar CVL-1 contig07033, 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: 24058
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1117 original size:32 final size:32
Alignment explanation
Indices: 1050--1117 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
1040 TCAGGCTGTT
* * *
1050 TTCGGGTTCGGGTTAAATTTGGGTCGGATTGA
1 TTCGAGTTCGGGTCAAATTTGGGTCGGATTAA
*
1082 TTCGAGTTCGGGTCAATTTTGGGTCAGG-TTAA
1 TTCGAGTTCGGGTCAAATTTGGGTC-GGATTAA
1114 TTCG
1 TTCG
1118 GATTCGGACT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 29 0.94
33 2 0.06
ACGTcount: A:0.16, C:0.12, G:0.34, T:0.38
Consensus pattern (32 bp):
TTCGAGTTCGGGTCAAATTTGGGTCGGATTAA
Found at i:1300 original size:20 final size:20
Alignment explanation
Indices: 1267--1305 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1257 CATAGATGAA
*
1267 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
1287 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
1306 GAATTCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:3445 original size:23 final size:23
Alignment explanation
Indices: 3415--3461 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
3405 CGAAAATTTG
3415 TTCTTGATTTCATGTTATAATAA
1 TTCTTGATTTCATGTTATAATAA
*
3438 TTCTTGATTTTATGTTATAATAA
1 TTCTTGATTTCATGTTATAATAA
3461 T
1 T
3462 ATAAGTTGCA
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:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (23 bp):
TTCTTGATTTCATGTTATAATAA
Found at i:4019 original size:13 final size:12
Alignment explanation
Indices: 3995--4029 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
3985 GGCCGGGTTA
3995 AGTTTTTTTTTT
1 AGTTTTTTTTTT
*
4007 CGTTTTCTTTTTT
1 AGTTTT-TTTTTT
4020 AGTTTTTTTT
1 AGTTTTTTTT
4030 AGGGCTGGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.06, C:0.06, G:0.09, T:0.80
Consensus pattern (12 bp):
AGTTTTTTTTTT
Found at i:4876 original size:2 final size:2
Alignment explanation
Indices: 4869--4900 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4859 CCAAATCAAC
4869 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4901 ACTTTTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14017 original size:7 final size:7
Alignment explanation
Indices: 14005--14039 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
13995 CCACTTCTGT
14005 TTTGAGA
1 TTTGAGA
14012 TTTGAGA
1 TTTGAGA
*
14019 CTTGAGA
1 TTTGAGA
*
14026 ATTGAGA
1 TTTGAGA
14033 TTTGAGA
1 TTTGAGA
14040 GATGAGGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.37
Consensus pattern (7 bp):
TTTGAGA
Found at i:14045 original size:21 final size:21
Alignment explanation
Indices: 14006--14045 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13996 CACTTCTGTT
*
14006 TTGAGATTTGAGACTTGAGAA
1 TTGAGATTTGAGACATGAGAA
*
14027 TTGAGATTTGAGAGATGAG
1 TTGAGATTTGAGACATGAG
14046 GTTTCAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
TTGAGATTTGAGACATGAGAA
Found at i:19288 original size:29 final size:26
Alignment explanation
Indices: 19238--19297 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 26
19228 AAAAGAGTAA
19238 ATTTAAAAATAAAAAATAATTCAAAT
1 ATTTAAAAATAAAAAATAATTCAAAT
* *
19264 ATTTCAAAAATAAAGAAAATGATTCAATT
1 ATTT-AAAAAT-AA-AAAATAATTCAAAT
19293 ATTTA
1 ATTTA
19298 TTGACCCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 4 0.14
27 6 0.21
28 3 0.10
29 16 0.55
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.33
Consensus pattern (26 bp):
ATTTAAAAATAAAAAATAATTCAAAT
Found at i:20791 original size:51 final size:51
Alignment explanation
Indices: 20728--20841 Score: 201
Period size: 51 Copynumber: 2.2 Consensus size: 51
20718 AGCTATGATG
20728 CGTGTATAACACACGCTCTAACATGCTAAGTCAGAGCTGACATGGACAACA
1 CGTGTATAACACACGCTCTAACATGCTAAGTCAGAGCTGACATGGACAACA
* *
20779 CGTGTATGACACACGCTCTAACATGCTGAGTCAGAGCTGACATGGACAACA
1 CGTGTATAACACACGCTCTAACATGCTAAGTCAGAGCTGACATGGACAACA
*
20830 CGTATATAACAC
1 CGTGTATAACAC
20842 GTGGAATTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (51 bp):
CGTGTATAACACACGCTCTAACATGCTAAGTCAGAGCTGACATGGACAACA
Done.