Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010823.1 Corchorus capsularis cultivar CVL-1 contig10844, 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: 11198
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:40 original size:6 final size:6
Alignment explanation
Indices: 1--169 Score: 239
Period size: 6 Copynumber: 26.3 Consensus size: 6
1 AACCCT AGACCCT AAACCCT AAACCCT AAACCCT AACCCT AAACCCT AATCCCT
1 AACCCT A-ACCCT -AACCCT -AACCCT -AACCCT AACCCT -AACCCT AA-CCCT
55 AACCCT AAACCCT AACCCT AACCCT AACCCT AAACCCT AACCCT AACCCT
1 AACCCT -AACCCT AACCCT AACCCT AACCCT -AACCCT AACCCT AACCCT
105 AACCCT AAACCCT AAACCCT AACCCT AACCCT AACCCT AACCCT AACCCT
1 AACCCT -AACCCT -AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT
155 AAACCCT AACCCT AA
1 -AACCCT AACCCT AA
170 AATAGTCCTG
Statistics
Matches: 155, Mismatches: 0, Indels: 16
0.91 0.00 0.09
Matches are distributed among these distances:
6 87 0.56
7 67 0.43
8 1 0.01
ACGTcount: A:0.37, C:0.46, G:0.01, T:0.16
Consensus pattern (6 bp):
AACCCT
Found at i:170 original size:13 final size:12
Alignment explanation
Indices: 1--169 Score: 239
Period size: 13 Copynumber: 13.2 Consensus size: 12
1 AACCCTAGACCCT
1 AACCCTA-ACCCT
14 AAACCCTAAACCCT
1 -AACCCT-AACCCT
28 AAACCCTAACCCT
1 -AACCCTAACCCT
41 AAACCCTAATCCCT
1 -AACCCTAA-CCCT
55 AACCCTAAACCCT
1 AACCCT-AACCCT
68 AACCCTAACCCT
1 AACCCTAACCCT
80 AACCCTAAACCCT
1 AACCCT-AACCCT
93 AACCCTAACCCT
1 AACCCTAACCCT
105 AACCCTAAACCCT
1 AACCCT-AACCCT
118 AAACCCTAACCCT
1 -AACCCTAACCCT
131 AACCCTAACCCT
1 AACCCTAACCCT
143 AACCCTAACCCT
1 AACCCTAACCCT
155 AAACCCTAACCCT
1 -AACCCTAACCCT
168 AA
1 AA
170 AATAGTCCTG
Statistics
Matches: 148, Mismatches: 0, Indels: 16
0.90 0.00 0.10
Matches are distributed among these distances:
12 50 0.34
13 67 0.45
14 30 0.20
15 1 0.01
ACGTcount: A:0.37, C:0.46, G:0.01, T:0.16
Consensus pattern (12 bp):
AACCCTAACCCT
Found at i:716 original size:134 final size:134
Alignment explanation
Indices: 470--738 Score: 398
Period size: 134 Copynumber: 2.0 Consensus size: 134
460 TTACAGTTTG
* * * *
470 GGGTTTTGTGTTTTATGGCCAGGGTGTACGGTTTTAATGACTATAGTGGTTTCTAACCCTAGGTT
1 GGGTTTTGTGTTTTAGGGCCAAGGTGTACGGTTTTAAGGACTATAGTGGTTTCTAACCCTAGGCT
* *
535 CTCTCTCCTTGATCCATGTAGCTTCCGTTCCGGCCTCTTACCCTAAATTCTCTCTCTTCGACCAT
66 CTCTCTCCTTGATCCATGTAGCTTCCGTTCCGGCCTCTAACCCTAAATTCTCTCTCCTCGACCAT
600 TTTA
131 TTTA
* **
604 GGGTTTTGTGTTTTAGGGTCAAGGTGTACGGTTTTAAGGACTATAGTGGTCTT-TAACTTTAGGC
1 GGGTTTTGTGTTTTAGGGCCAAGGTGTACGGTTTTAAGGACTATAGTGGT-TTCTAACCCTAGGC
* *
668 TCTCTCTCCTTGATCCTTGTAGCTGT-CGTTCCGGCCTCTAACCGTAAATTCTCTCTCCTCGACC
65 TCTCTCTCCTTGATCCATGTAGCT-TCCGTTCCGGCCTCTAACCCTAAATTCTCTCTCCTCGACC
*
732 GTTTTA
129 ATTTTA
738 G
1 G
739 AGTTATGGTT
Statistics
Matches: 121, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
134 118 0.98
135 3 0.02
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.40
Consensus pattern (134 bp):
GGGTTTTGTGTTTTAGGGCCAAGGTGTACGGTTTTAAGGACTATAGTGGTTTCTAACCCTAGGCT
CTCTCTCCTTGATCCATGTAGCTTCCGTTCCGGCCTCTAACCCTAAATTCTCTCTCCTCGACCAT
TTTA
Found at i:6055 original size:134 final size:134
Alignment explanation
Indices: 5815--6082 Score: 518
Period size: 134 Copynumber: 2.0 Consensus size: 134
5805 GCCAATAGAC
*
5815 TGAAGAAATGTCTTCCCTCAGTTATCAGCTCAAACCAAACTGCTTTTATAGACGGTAGTAGTATG
1 TGAAGAAATGTCTTCCCTCAGTTATCAGCTCAAACCAAACTGCTTTTATAGACGGTAGAAGTATG
5880 TTAGAAAATGTTATACTTGCCCAAGAACTTGTTGCTGGGTATCAAAGAAAGTCCAAGTCCCCTAG
66 TTAGAAAATGTTATACTTGCCCAAGAACTTGTTGCTGGGTATCAAAGAAAGTCCAAGTCCCCTAG
5945 ATGT
131 ATGT
*
5949 TGAAGAAATGTCTTCCCTCAGTTATCAGCTCAAACCAAACTGCTTTTATAGAGGGTAGAAGTATG
1 TGAAGAAATGTCTTCCCTCAGTTATCAGCTCAAACCAAACTGCTTTTATAGACGGTAGAAGTATG
6014 TTAGAAAATGTTATACTTGCCCAAGAACTTGTTGCTGGGTATCAAAGAAAGTCCAAGTCCCCTAG
66 TTAGAAAATGTTATACTTGCCCAAGAACTTGTTGCTGGGTATCAAAGAAAGTCCAAGTCCCCTAG
6079 ATGT
131 ATGT
6083 GCACTAAAGA
Statistics
Matches: 132, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 132 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (134 bp):
TGAAGAAATGTCTTCCCTCAGTTATCAGCTCAAACCAAACTGCTTTTATAGACGGTAGAAGTATG
TTAGAAAATGTTATACTTGCCCAAGAACTTGTTGCTGGGTATCAAAGAAAGTCCAAGTCCCCTAG
ATGT
Found at i:10800 original size:3 final size:3
Alignment explanation
Indices: 10792--10822 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
10782 AAAGGGATGG
10792 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10823 AAGGATTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Done.