Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007014.1 Corchorus capsularis cultivar CVL-1 contig07035, 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: 19792
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:3017 original size:33 final size:33
Alignment explanation
Indices: 2945--3017 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
2935 AAAATTGCTC
* * *
2945 ATGCCGCCCTAGGGGGGCGGCTGAGCCATGGTA
1 ATGCCGCCCCAGGGGAGAGGCTGAGCCATGGTA
**
2978 GGGCCGCCCCAGGGGAGAGGCCTG-GCCATGGTA
1 ATGCCGCCCCAGGGGAGAGG-CTGAGCCATGGTA
3011 ATGCCGC
1 ATGCCGC
3018 ACCCCTGGGA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.15, C:0.30, G:0.42, T:0.12
Consensus pattern (33 bp):
ATGCCGCCCCAGGGGAGAGGCTGAGCCATGGTA
Found at i:3222 original size:33 final size:33
Alignment explanation
Indices: 3069--3228 Score: 225
Period size: 33 Copynumber: 4.9 Consensus size: 33
3059 AAAAAGTCTT
* * *
3069 GCCGCTCTAGTGGGGCGGCT-AGCCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* *
3101 GCCGCCCTAGTGGGGCGGCTCCACCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* *
3134 GCCGCCCTAGTGGGGAGGCTCCACTGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
*
3167 GCCGCCCTAGTGGGGAGGCTCCGCTGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
*
3200 GCCGTCCTAGTGGGGAGGCTCCG-CGTGGC
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGC
3229 TAAGGGCAAA
Statistics
Matches: 119, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
32 24 0.20
33 95 0.80
ACGTcount: A:0.12, C:0.31, G:0.42, T:0.15
Consensus pattern (33 bp):
GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
Found at i:4694 original size:15 final size:15
Alignment explanation
Indices: 4676--4723 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
4666 CTATTTTTTC
4676 TTCGAAAATTTCCCT
1 TTCGAAAATTTCCCT
**
4691 TTCGAAAATCCTTTTC-
1 TTCGAAAAT--TTCCCT
4707 TTCGAAAATTTCCCT
1 TTCGAAAATTTCCCT
4722 TT
1 TT
4724 TTTTTTTGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
14 3 0.12
15 11 0.42
16 9 0.35
17 3 0.12
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (15 bp):
TTCGAAAATTTCCCT
Found at i:5994 original size:12 final size:12
Alignment explanation
Indices: 5977--6008 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
5967 TGATTTGTGG
5977 GTTGCATTTCTT
1 GTTGCATTTCTT
5989 GTTGCATTTCTT
1 GTTGCATTTCTT
*
6001 ATTGCATT
1 GTTGCATT
6009 CATATTGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.12, C:0.16, G:0.16, T:0.56
Consensus pattern (12 bp):
GTTGCATTTCTT
Found at i:7279 original size:29 final size:29
Alignment explanation
Indices: 7236--7319 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 29
7226 TAAACGCCTC
*
7236 TAAATAGCGGTGTCTAGACGCCGCTACTA
1 TAAATAGCGGCGTCTAGACGCCGCTACTA
* *
7265 TAAATCGCGGCGTCTAGACGCCGCTACTC
1 TAAATAGCGGCGTCTAGACGCCGCTACTA
*
7294 TAAATAGCGGCGTCTAGATGCCGCTA
1 TAAATAGCGGCGTCTAGACGCCGCTA
7320 TTTATAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (29 bp):
TAAATAGCGGCGTCTAGACGCCGCTACTA
Found at i:13240 original size:8 final size:8
Alignment explanation
Indices: 13227--13261 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
13217 TAAAGAAAAC
13227 AAAAAAGA
1 AAAAAAGA
13235 AAAAAAGA
1 AAAAAAGA
*
13243 GAAAAAGA
1 AAAAAAGA
*
13251 AAAAGAGA
1 AAAAAAGA
13259 AAA
1 AAA
13262 TAAATTGATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:13246 original size:22 final size:22
Alignment explanation
Indices: 13220--13261 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
13210 CATCATCTAA
13220 AGAAAACA-AAAAAGAAAAAAAG
1 AGAAAA-AGAAAAAGAAAAAAAG
*
13242 AGAAAAAGAAAAAGAGAAAA
1 AGAAAAAGAAAAAGAAAAAA
13262 TAAATTGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (22 bp):
AGAAAAAGAAAAAGAAAAAAAG
Done.