Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005754.1 Corchorus capsularis cultivar CVL-1 contig05772, 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: 9392
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Found at i:4163 original size:42 final size:42
Alignment explanation
Indices: 4115--4214 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
4105 CACCAACATC
** *
4115 ACATCTTTACCTTCAAAT-CTACCACCTTTATC-CCAAAATGTG
1 ACATCTTTACCACCAAATAC-ACCACCTTTA-CACAAAAATGTG
* *
4157 GCATCTTTACCACCAAATACGCCACCTTTACACAAAAATGTG
1 ACATCTTTACCACCAAATACACCACCTTTACACAAAAATGTG
4199 ACATCTTTA-CACCAAA
1 ACATCTTTACCACCAAA
4215 ATATGAATCC
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
41 8 0.16
42 41 0.82
43 1 0.02
ACGTcount: A:0.35, C:0.31, G:0.06, T:0.28
Consensus pattern (42 bp):
ACATCTTTACCACCAAATACACCACCTTTACACAAAAATGTG
Found at i:4215 original size:21 final size:21
Alignment explanation
Indices: 4147--4216 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
4137 CACCTTTATC
*
4147 CCAAAATGTGGCATCTTTACCA
1 CCAAAATGTGACATCTTTA-CA
** * *
4169 CC-AAATACGCCACCTTTACA
1 CCAAAATGTGACATCTTTACA
*
4189 CAAAAATGTGACATCTTTACA
1 CCAAAATGTGACATCTTTACA
4210 CCAAAAT
1 CCAAAAT
4217 ATGAATCCTC
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 3 0.08
21 32 0.86
22 2 0.05
ACGTcount: A:0.39, C:0.29, G:0.09, T:0.24
Consensus pattern (21 bp):
CCAAAATGTGACATCTTTACA
Found at i:4217 original size:42 final size:42
Alignment explanation
Indices: 4136--4214 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
4126 TTCAAATCTA
* *
4136 CCACCTTTATCCCAAAATGTGGCATCTTTACCACCAAATACG
1 CCACCTTTATCCAAAAATGTGACATCTTTACCACCAAATACG
4178 CCACCTTTA-CACAAAAATGTGACATCTTTA-CACCAAA
1 CCACCTTTATC-CAAAAATGTGACATCTTTACCACCAAA
4215 ATATGAATCC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
41 8 0.24
42 26 0.76
ACGTcount: A:0.35, C:0.32, G:0.08, T:0.25
Consensus pattern (42 bp):
CCACCTTTATCCAAAAATGTGACATCTTTACCACCAAATACG
Found at i:5123 original size:26 final size:26
Alignment explanation
Indices: 5065--5135 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 26
5055 TAAGAAAATA
*
5065 CCAGGGGCATTTTTGTCATTTTTGGC
1 CCAGGGGCATTTTAGTCATTTTTGGC
*
5091 CCTAGGGGTATTTTAGTCATTTTT-GC
1 CC-AGGGGCATTTTAGTCATTTTTGGC
* *
5117 TTCAGGGGCATTTTGGTCA
1 -CCAGGGGCATTTTAGTCA
5136 AAGTTTGTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
26 18 0.47
27 20 0.53
ACGTcount: A:0.14, C:0.17, G:0.27, T:0.42
Consensus pattern (26 bp):
CCAGGGGCATTTTAGTCATTTTTGGC
Found at i:6777 original size:20 final size:20
Alignment explanation
Indices: 6752--6791 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6742 TTACATCAAC
6752 CCAAAGATCAAATCTTTAAA
1 CCAAAGATCAAATCTTTAAA
* * *
6772 CCAAAGTTCTAATTTTTAAA
1 CCAAAGATCAAATCTTTAAA
6792 ATTAGGATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (20 bp):
CCAAAGATCAAATCTTTAAA
Found at i:8526 original size:30 final size:31
Alignment explanation
Indices: 8490--8551 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
8480 AATGTGCACG
8490 TTTGTTGAC-TCCTGATCCTGTAAATTTGCT
1 TTTGTTGACTTCCTGATCCTGTAAATTTGCT
** *
8520 TTTGTTGACTTTTTGATCCTGTGAATTTGCT
1 TTTGTTGACTTCCTGATCCTGTAAATTTGCT
8551 T
1 T
8552 AGTTCGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 9 0.32
31 19 0.68
ACGTcount: A:0.15, C:0.16, G:0.18, T:0.52
Consensus pattern (31 bp):
TTTGTTGACTTCCTGATCCTGTAAATTTGCT
Found at i:8569 original size:30 final size:30
Alignment explanation
Indices: 8502--8570 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
8492 TGTTGACTCC
*
8502 TGATCCTGTAAATTTGCTTTTGTTGACTTTT
1 TGATCCTGTAAATTTGCTTTAGTTGA-TTTT
*
8533 TGATCCTGTGAATTTGC-TTAGTTCG-TTTT
1 TGATCCTGTAAATTTGCTTTAGTT-GATTTT
8562 ATGATCCTG
1 -TGATCCTG
8571 CACTGCACAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 4 0.12
30 13 0.38
31 17 0.50
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (30 bp):
TGATCCTGTAAATTTGCTTTAGTTGATTTT
Found at i:9250 original size:14 final size:14
Alignment explanation
Indices: 9231--9275 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
9221 TGTCATTTGG
9231 TGCAAATGCACAAA
1 TGCAAATGCACAAA
*
9245 TGCAAATGCA-AGA
1 TGCAAATGCACAAA
*
9258 TGAAAATGC-C-AA
1 TGCAAATGCACAAA
9270 TGCAAA
1 TGCAAA
9276 ATGAAAGCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 6 0.23
13 10 0.38
14 10 0.38
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.16
Consensus pattern (14 bp):
TGCAAATGCACAAA
Found at i:9266 original size:19 final size:19
Alignment explanation
Indices: 9242--9281 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
9232 GCAAATGCAC
*
9242 AAATGCAAATGCAAGATGA
1 AAATGCAAATGCAAAATGA
*
9261 AAATGCCAATGCAAAATGA
1 AAATGCAAATGCAAAATGA
9280 AA
1 AA
9282 GCCATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.55, C:0.12, G:0.17, T:0.15
Consensus pattern (19 bp):
AAATGCAAATGCAAAATGA
Done.