Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006988.1 Corchorus capsularis cultivar CVL-1 contig07009, 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: 17751
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:176 original size:19 final size:19
Alignment explanation
Indices: 136--173 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
126 GATTTATCCT
136 ATCTATCTGTTGAATTTGA
1 ATCTATCTGTTGAATTTGA
*
155 ATCT-TCTGTTGGATTTGA
1 ATCTATCTGTTGAATTTGA
173 A
1 A
174 ATCCTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (19 bp):
ATCTATCTGTTGAATTTGA
Found at i:4682 original size:19 final size:19
Alignment explanation
Indices: 4642--4679 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
4632 GATTTATCCT
4642 ATCTATCTGTTGAATTTGA
1 ATCTATCTGTTGAATTTGA
*
4661 ATCT-TCTGTTGGATTTGA
1 ATCTATCTGTTGAATTTGA
4679 A
1 A
4680 ATCCTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (19 bp):
ATCTATCTGTTGAATTTGA
Found at i:5014 original size:23 final size:23
Alignment explanation
Indices: 4984--5030 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4974 GTAGATATAA
**
4984 GGGATAACAGGAAAGAGGAATTG
1 GGGATAACACAAAAGAGGAATTG
*
5007 GGGATAACACAAAAGAGGGATTG
1 GGGATAACACAAAAGAGGAATTG
5030 G
1 G
5031 AAGTAGGGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.06, G:0.38, T:0.13
Consensus pattern (23 bp):
GGGATAACACAAAAGAGGAATTG
Found at i:5065 original size:2 final size:2
Alignment explanation
Indices: 5058--5088 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5048 GGATGGTTGG
5058 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 T
5089 TTACAAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5762 original size:105 final size:104
Alignment explanation
Indices: 5584--5842 Score: 371
Period size: 105 Copynumber: 2.5 Consensus size: 104
5574 AATTTAGCCT
* * * *
5584 TAATTTTACTAAGTTTACCCCAAATTAAAATTTTATTTT-TATTAAGGGTAAATTTCAAAATTAA
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTATTTTAAGGGTAAATTCCAAAATTAA
5648 TAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 TAA-TTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
5688 TAATTTCACTAAGTTTAGCTCCAAATTAAAATTTTATTTTCATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGC-CCAAATTAAAATTTTATTTT-ATTTTAAGGGTAAATTCCAAAATT
* * *
5753 AATAA-TATTGTTATAGGGTTTTAGAAATAAAATATATAAT
64 AATAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
**
5793 TAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATT-TTATTTTATTTTAAGGGT
5843 TAGAAAAATT
Statistics
Matches: 141, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
103 24 0.17
104 37 0.26
105 55 0.39
107 25 0.18
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (104 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTATTTTAAGGGTAAATTCCAAAATTAA
TAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:8928 original size:23 final size:23
Alignment explanation
Indices: 8879--8933 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
8869 GTTTCTGTTT
** *
8879 AAAAAAAAAACCCTTCGATAGAC
1 AAAAAAAAAACCCTGAGAGAGAC
* *
8902 AAAAAAAAAACGCTGAGAGAGAG
1 AAAAAAAAAACCCTGAGAGAGAC
8925 AAAAAAAAA
1 AAAAAAAAA
8934 CCCCAAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.65, C:0.13, G:0.15, T:0.07
Consensus pattern (23 bp):
AAAAAAAAAACCCTGAGAGAGAC
Found at i:9619 original size:2 final size:2
Alignment explanation
Indices: 9612--9643 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9602 ACATGCATGA
9612 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
9644 TACCTTCTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15211 original size:17 final size:17
Alignment explanation
Indices: 15191--15223 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
15181 ATATTGCCCC
15191 TTTTGCTATATAATTTT
1 TTTTGCTATATAATTTT
15208 TTTTGCTATATAATTT
1 TTTTGCTATATAATTT
15224 CTCCACTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (17 bp):
TTTTGCTATATAATTTT
Found at i:16150 original size:14 final size:15
Alignment explanation
Indices: 16131--16160 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16121 GCCTAATTGG
16131 TTTTTC-TTTTTCTT
1 TTTTTCTTTTTTCTT
16145 TTTTTCTTTTTTCTT
1 TTTTTCTTTTTTCTT
16160 T
1 T
16161 CCCCTCTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTCTTTTTTCTT
Done.