Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013796.1 Corchorus capsularis cultivar CVL-1 contig13817, 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: 15624
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Found at i:5198 original size:11 final size:11
Alignment explanation
Indices: 5184--5222 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
5174 GGGCCATGCG
5184 CTGGCCCGCGC
1 CTGGCCCGCGC
*
5195 CTGGCCATGCG-
1 CTGGCC-CGCGC
5206 CTGGCCCGCGC
1 CTGGCCCGCGC
5217 CTGGCC
1 CTGGCC
5223 TTGGCGCTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.03, C:0.49, G:0.36, T:0.13
Consensus pattern (11 bp):
CTGGCCCGCGC
Found at i:5203 original size:22 final size:22
Alignment explanation
Indices: 5175--5239 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
5165 CTAGGTGCTG
5175 GGCCATGCGCTGGCCCGCGCCT
1 GGCCATGCGCTGGCCCGCGCCT
5197 GGCCATGCGCTGGCCCGCGCCT
1 GGCCATGCGCTGGCCCGCGCCT
* *
5219 GGCCTTGGCGCTGGGCCGCGC
1 GGCCAT-GCGCTGGCCCGCGC
5240 AGGCCTGCGC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 27 0.68
23 13 0.32
ACGTcount: A:0.03, C:0.43, G:0.40, T:0.14
Consensus pattern (22 bp):
GGCCATGCGCTGGCCCGCGCCT
Found at i:6711 original size:131 final size:130
Alignment explanation
Indices: 6472--6743 Score: 510
Period size: 131 Copynumber: 2.1 Consensus size: 130
6462 TAGGTATATC
*
6472 TCTATTTGTAGTCTATTGTCGCTTTAACCTTTCGTATAACCTTTACTCCTTCATTCAACTCATCA
1 TCTACTTGTAGTCTATTGTCGCTTTAACCTTTCGTATAACCTTTACTCCTTCATTCAACTCATCA
6537 ATATATTTAGCTTTAAACGTTTTCTTCCACCAGCTCCATTCTACTTCTACAAAGTCTTAAATCCA
66 ATATATTTAGCTTTAAACGTTTTCTTCCACCAGCTCCATTCTACTTCTACAAAGTCTTAAATCC-
6602 T
130 T
6603 TCTACTTGTAGTCTATTGTCGCTTTAACCTTTCGTATAACCTTTACTCCTTCATTCAACTCATCA
1 TCTACTTGTAGTCTATTGTCGCTTTAACCTTTCGTATAACCTTTACTCCTTCATTCAACTCATCA
6668 ATATATTTAGCTTTAAACGTTTTCTTCCACCAGCTCCATTCTACTTCTACAAAGTCTTAAATCCT
66 ATATATTTAGCTTTAAACGTTTTCTTCCACCAGCTCCATTCTACTTCTACAAAGTCTTAAATCCT
*
6733 T-TACTTCTAGT
1 TCTACTTGTAGT
6744 GCTTCAATAG
Statistics
Matches: 139, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
129 9 0.06
130 2 0.01
131 128 0.92
ACGTcount: A:0.25, C:0.26, G:0.07, T:0.42
Consensus pattern (130 bp):
TCTACTTGTAGTCTATTGTCGCTTTAACCTTTCGTATAACCTTTACTCCTTCATTCAACTCATCA
ATATATTTAGCTTTAAACGTTTTCTTCCACCAGCTCCATTCTACTTCTACAAAGTCTTAAATCCT
Found at i:9402 original size:55 final size:55
Alignment explanation
Indices: 9251--9431 Score: 163
Period size: 55 Copynumber: 3.3 Consensus size: 55
9241 GACAAATAGC
* *
9251 TTGAACCTGATGGTGTTGCCTTCAACTTATCATTCAGATCATCTGGACCAAAAAA
1 TTGATCCTGATGGTGTTGCCTTCAATTTATCATTCAGATCATCTGGACCAAAAAA
* * * * * * ** *
9306 TTGGTCCTAATGGTGTTG---TCAATTAAAAATTACTCAAATCAT-TGGGACTGATAAA
1 TTGATCCTGATGGTGTTGCCTTCAATT---TATCATTCAGATCATCT-GGACCAAAAAA
**
9361 TTGATCCTGATGGTGTTGCCTTCAATTTATCATTCAGATCATCTGGACCAATTAA
1 TTGATCCTGATGGTGTTGCCTTCAATTTATCATTCAGATCATCTGGACCAAAAAA
* *
9416 TCGGTCCTGATGGTGT
1 TTGATCCTGATGGTGT
9432 AACAAAATAT
Statistics
Matches: 96, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
52 5 0.05
54 1 0.01
55 83 0.86
56 1 0.01
58 6 0.06
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (55 bp):
TTGATCCTGATGGTGTTGCCTTCAATTTATCATTCAGATCATCTGGACCAAAAAA
Found at i:9923 original size:54 final size:53
Alignment explanation
Indices: 9839--9940 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 53
9829 TCTTTCTTAA
*
9839 CCAGTACCAATGGCTCTCAGTCCCGCTAAGCCATCAA-TCTCATCATTATCATG
1 CCAGTACCAATAGCTCTCAGTCCCGCTAAGCCATCAACT-TCATCATTATCATG
*
9892 CCAGTCACCAATAGCTCTCAGTCCCGTTAAGCCATCAACTTCATCATTA
1 CCAGT-ACCAATAGCTCTCAGTCCCGCTAAGCCATCAACTTCATCATTA
9941 CCACTCCAGG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
53 5 0.11
54 39 0.87
55 1 0.02
ACGTcount: A:0.27, C:0.34, G:0.12, T:0.26
Consensus pattern (53 bp):
CCAGTACCAATAGCTCTCAGTCCCGCTAAGCCATCAACTTCATCATTATCATG
Found at i:13002 original size:55 final size:55
Alignment explanation
Indices: 12851--13031 Score: 179
Period size: 55 Copynumber: 3.3 Consensus size: 55
12841 GACAAATAGC
* * * *
12851 TTGAACCTGATGGTATTGCCTTCAACTTATCATTCAGATCATCTGGACCAAAAAA
1 TTGATCCTGATGGTGTTGCCTTCAATTTATCATTCAGATCATCTGGACCAATAAA
* * * * * * **
12906 TTGGTCCTGATGGTGTTG---TCAATTAAAAATTACTCAAATCATCGGGACTGATAAA
1 TTGATCCTGATGGTGTTGCCTTCAATT---TATCATTCAGATCATCTGGACCAATAAA
* *
12961 TTGATCCTGATGGTGTTGCCTTCAATTTATCATTCAGATCATCTAGACCAATTAA
1 TTGATCCTGATGGTGTTGCCTTCAATTTATCATTCAGATCATCTGGACCAATAAA
*
13016 TTGGTCCTGATGGTGT
1 TTGATCCTGATGGTGT
13032 AACAAAATAT
Statistics
Matches: 97, Mismatches: 23, Indels: 12
0.73 0.17 0.09
Matches are distributed among these distances:
52 5 0.05
55 86 0.89
58 6 0.06
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (55 bp):
TTGATCCTGATGGTGTTGCCTTCAATTTATCATTCAGATCATCTGGACCAATAAA
Found at i:15338 original size:14 final size:14
Alignment explanation
Indices: 15305--15343 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
15295 AAATTTCCTT
*
15305 AACCCGAAACTAACCT
1 AACCC-AAA-TAACCG
15321 AACCCAAATAACCG
1 AACCCAAATAACCG
15335 AACCCAAAT
1 AACCCAAAT
15344 CCAACCCGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.49, C:0.36, G:0.05, T:0.10
Consensus pattern (14 bp):
AACCCAAATAACCG
Done.