Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007522.1 Corchorus capsularis cultivar CVL-1 contig07543, 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: 18210
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:6998 original size:155 final size:154
Alignment explanation
Indices: 6714--7068 Score: 358
Period size: 155 Copynumber: 2.3 Consensus size: 154
6704 TCATCTCAAA
* * * * ** *
6714 CAGACTTAGGATGAAAAATTTATGCTAGTTTTTCAGTTAAGGACAGTTTGGGGTGACAAACCAAC
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTCAGGGAGACAAACCAAC
* * * * * *
6779 TTCTCTATGATAGAGAGTTTGGTTTTACTTAGATTTTTCCCATAGATTTACGGAGATAATCTAAG
66 TTCACCATGATAGAGAGCTCGGTTTTACTTAGAATTTTCCCATAGATTTACGGAGAGAATCTAAG
* *
6844 ACTATTGGTGGAAA-ATCAGCTTC-AT
131 ACCATT-G-GCAAAGATCAGC-TCGAT
** * * * * *
6869 TGGACTTAGAATGAAAAACTTATGCTAGATTTTCATTTAAAGACAATTCAGGGAGAGAAACCTAG
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTCAGGGAGACAAACCAAC
* * **
6934 TTCACCATGA-AGGAGAGCTCGGTTTTACTTTGAAATTTT-CCATAGTTTTGTGGAGAGAATCTA
66 TTCACCATGATA-GAGAGCTCGGTTTTACTTAG-AATTTTCCCATAGATTTACGGAGAGAATCTA
* * * *
6997 AGTCCCTTGGCAAAGTTTCATCTCGAT
129 AGACCATTGGCAAAG-ATCAGCTCGAT
7024 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA
7069 GTTTGAGGTG
Statistics
Matches: 161, Mismatches: 34, Indels: 10
0.79 0.17 0.05
Matches are distributed among these distances:
153 4 0.02
154 4 0.02
155 148 0.92
156 5 0.03
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (154 bp):
CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTCAGGGAGACAAACCAAC
TTCACCATGATAGAGAGCTCGGTTTTACTTAGAATTTTCCCATAGATTTACGGAGAGAATCTAAG
ACCATTGGCAAAGATCAGCTCGAT
Found at i:7448 original size:17 final size:17
Alignment explanation
Indices: 7426--7459 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
7416 GATATTATCC
7426 AGTGCCTCATGCTACCT
1 AGTGCCTCATGCTACCT
7443 AGTGCCTCATGCTACCT
1 AGTGCCTCATGCTACCT
7460 GGTACCATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.35, G:0.18, T:0.29
Consensus pattern (17 bp):
AGTGCCTCATGCTACCT
Found at i:10598 original size:23 final size:26
Alignment explanation
Indices: 10572--10632 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 26
10562 AATAATTGGC
10572 AAATTTGTAATTTG-CTCCC-CTAA-
1 AAATTTGTAATTTGACTCCCTCTAAG
* * *
10595 AAATTTATAAATTGATTCCCTCTAAG
1 AAATTTGTAATTTGACTCCCTCTAAG
10621 AAATCTTGTAAT
1 AAAT-TTGTAAT
10633 AAAATGGAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
23 12 0.41
24 4 0.14
25 4 0.14
26 4 0.14
27 5 0.17
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.39
Consensus pattern (26 bp):
AAATTTGTAATTTGACTCCCTCTAAG
Found at i:17731 original size:54 final size:52
Alignment explanation
Indices: 17672--17795 Score: 212
Period size: 54 Copynumber: 2.3 Consensus size: 52
17662 GTAACAAATG
*
17672 TTTAACGTCTTGAGACGATGCTGAAAGAGAAGAAAAACTCGCGGAGAGTTGTTT
1 TTTAACGTCTTGAGACGATGCTGAAAGAGAAGAAAAACTCGCGGAGAG-T-TAT
17726 TTTAACGTCTTGAGACGATGCTGAAAGAGAAGAAAAACTCGCGGAGAGTTAT
1 TTTAACGTCTTGAGACGATGCTGAAAGAGAAGAAAAACTCGCGGAGAGTTAT
*
17778 TTTAACGTCCTGAGACGA
1 TTTAACGTCTTGAGACGA
17796 AATTAATGTA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
52 19 0.28
53 1 0.01
54 48 0.71
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.25
Consensus pattern (52 bp):
TTTAACGTCTTGAGACGATGCTGAAAGAGAAGAAAAACTCGCGGAGAGTTAT
Found at i:17860 original size:2 final size:2
Alignment explanation
Indices: 17853--17878 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17843 AGAGTTTTCA
17853 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
17879 GTGTGTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.