Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015207.1 Corchorus capsularis cultivar CVL-1 contig15228, 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: 10250
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Found at i:4802 original size:31 final size:31
Alignment explanation
Indices: 4754--4812 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
4744 TGTTTTGAGA
* * *
4754 AACTTTTGAAATGCCTATTGTACCCTTATTT
1 AACTTTTAAAATACCTATTATACCCTTATTT
*
4785 AACTTTTAAAATACCTATTATATCCTTA
1 AACTTTTAAAATACCTATTATACCCTTA
4813 CTTATCTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (31 bp):
AACTTTTAAAATACCTATTATACCCTTATTT
Found at i:5712 original size:109 final size:104
Alignment explanation
Indices: 5550--5761 Score: 289
Period size: 109 Copynumber: 2.0 Consensus size: 104
5540 AATGTAAAAT
* * * * *
5550 TTAATTAACAATATTCTTATCAATTTTTTTGTTTTTTTTTCGAATATCTCAACCTTATAATTTAT
1 TTAATTAAAAATATCCTTATCAATTTTTTGGTTTTTTTTTCGAATATCCCAACCTTAAAATTTAT
* * * *
5615 AATGTAAAGTCGGATTATTTTGTTCAAGAATTACTATAA
66 AATATAAAATCGGATTATTTTATTCAAGAATTAATATAA
5654 TTAATTAAAAATATCCTTAAATCAATTTTTTGGTTTTCTTTTTTCCGAATATCCCAACCTTAAAA
1 TTAATTAAAAATATCCTT--ATCAATTTTTTGG-TTT-TTTTTT-CGAATATCCCAACCTTAAAA
*
5719 TTTATAATATAAAATCGGATTATTTTATTGAAGAATTAATATA
61 TTTATAATATAAAATCGGATTATTTTATTCAAGAATTAATATA
5762 TCCGATTAAT
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
104 16 0.17
106 12 0.13
107 3 0.03
108 6 0.06
109 56 0.60
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (104 bp):
TTAATTAAAAATATCCTTATCAATTTTTTGGTTTTTTTTTCGAATATCCCAACCTTAAAATTTAT
AATATAAAATCGGATTATTTTATTCAAGAATTAATATAA
Found at i:6761 original size:11 final size:11
Alignment explanation
Indices: 6747--6784 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6737 ATTCATAACA
6747 AATTTATAATT
1 AATTTATAATT
6758 AATTTATAATT
1 AATTTATAATT
6769 -ATTTGATAATT
1 AATTT-ATAATT
*
6780 TATTT
1 AATTT
6785 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:7121 original size:18 final size:18
Alignment explanation
Indices: 7100--7134 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7090 TCGATATTTA
* *
7100 TCGATATCTCGATAAATC
1 TCGATATATCCATAAATC
7118 TCGATATATCCATAAAT
1 TCGATATATCCATAAAT
7135 ATCCGTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (18 bp):
TCGATATATCCATAAATC
Found at i:8003 original size:12 final size:11
Alignment explanation
Indices: 7974--8001 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
7964 TTCGCAGTAC
7974 AAAAAATTAAA
1 AAAAAATTAAA
7985 AAAAAATTAAA
1 AAAAAATTAAA
7996 AAAAAA
1 AAAAAA
8002 ATGTCTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAATTAAA
Found at i:8205 original size:13 final size:12
Alignment explanation
Indices: 8163--8217 Score: 83
Period size: 12 Copynumber: 4.5 Consensus size: 12
8153 CATCGATACC
**
8163 TCGATATATCAA
1 TCGATATATCCG
8175 TCGATATATCCG
1 TCGATATATCCG
8187 TCGATATATCCG
1 TCGATATATCCG
8199 TTCGATATATCCG
1 -TCGATATATCCG
8212 TCGATA
1 TCGATA
8218 CCTGTATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
12 28 0.70
13 12 0.30
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:8666 original size:17 final size:17
Alignment explanation
Indices: 8644--8678 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
8634 TTTATTATAT
8644 TGGATTGCTAAATACCG
1 TGGATTGCTAAATACCG
*
8661 TGGATTTCTAAATACCG
1 TGGATTGCTAAATACCG
8678 T
1 T
8679 CCCCTTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (17 bp):
TGGATTGCTAAATACCG
Found at i:8693 original size:20 final size:21
Alignment explanation
Indices: 8668--8707 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
8658 CCGTGGATTT
8668 CTAAATACCGT-CCCCTTTTG
1 CTAAATACCGTCCCCCTTTTG
*
8688 CTAAATATCGTCCCCCTTTT
1 CTAAATACCGTCCCCCTTTT
8708 TACACTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.20, C:0.35, G:0.07, T:0.38
Consensus pattern (21 bp):
CTAAATACCGTCCCCCTTTTG
Found at i:8812 original size:25 final size:25
Alignment explanation
Indices: 8778--8834 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
8768 TTCAAACCCT
* *
8778 AAACTTCATTCCTAATAACTTCTTC
1 AAACTTCATTCCTAACAACTTCTCC
*
8803 AAACTTCATTTCTAACAACTTCTCC
1 AAACTTCATTCCTAACAACTTCTCC
*
8828 AGACTTC
1 AAACTTC
8835 TTAAAGGAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.30, G:0.02, T:0.37
Consensus pattern (25 bp):
AAACTTCATTCCTAACAACTTCTCC
Done.