Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014258.1 Corchorus capsularis cultivar CVL-1 contig14279, 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: 29478
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:682 original size:168 final size:167
Alignment explanation
Indices: 389--721 Score: 447
Period size: 168 Copynumber: 2.0 Consensus size: 167
379 AATGTCCCAA
* * * * ** *
389 ACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGGCTTACTTTTGGAGTTAGAGAAC
1 ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTACTGATGGAGATAGAGAAC
* * *
454 TTATTTTTTTCGTCTTTTCCTACTTGACAGATTACTTAAATGTCATAACTTTTGATTCTTGAGGG
66 TAATTTTTTCCGTCTTTACCTACTTGACAGATTACTTAAATGTCATAACTTTTGATTCTTGAGGG
**
519 GATTAAATAAGTAATTTTTTTTGGTCATTTCTCAATAT
131 GATTAAATAAGTAA-ACTTTTTGGTCATTTCTCAATAT
* *
557 ACTTGAATAGAGTAGTGGAATTAATAAATGATCCCCATCAAGGATTGA-TGAT-GAGATAGAGAA
1 ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATT-ACTGATGGAGATAGAGAA
* * *
620 CTAATATTTTTCCGTCTTTACCTACTTGCCAGATTACTTAAATGTTC-TAATTTTTTATTCTTGA
65 CTAAT-TTTTTCCGTCTTTACCTACTTGACAGATTACTTAAATG-TCATAACTTTTGATTCTTGA
*
684 GGGGATTAAATAATTAAACTTTTTGGTCATTTCTCAAT
128 GGGGATTAAATAAGTAAACTTTTTGGTCATTTCTCAAT
722 TGATAAATGA
Statistics
Matches: 144, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
167 33 0.23
168 108 0.75
169 3 0.02
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40
Consensus pattern (167 bp):
ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTACTGATGGAGATAGAGAAC
TAATTTTTTCCGTCTTTACCTACTTGACAGATTACTTAAATGTCATAACTTTTGATTCTTGAGGG
GATTAAATAAGTAAACTTTTTGGTCATTTCTCAATAT
Found at i:2567 original size:21 final size:21
Alignment explanation
Indices: 2535--2576 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2525 TATAGGTGTG
*
2535 TGTGATTGTTTGGTTTGATAGA
1 TGTGATTGTTTGATTTG-TAGA
2557 TGTGA-TGTTTGATTTGTAGA
1 TGTGATTGTTTGATTTGTAGA
2577 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (21 bp):
TGTGATTGTTTGATTTGTAGA
Found at i:7371 original size:14 final size:14
Alignment explanation
Indices: 7354--7387 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
7344 CCATCCATCT
7354 ACATATACATATAC
1 ACATATACATATAC
*
7368 ACATACACATATAC
1 ACATATACATATAC
*
7382 ATATAT
1 ACATAT
7388 CTAGTTAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (14 bp):
ACATATACATATAC
Found at i:17244 original size:15 final size:14
Alignment explanation
Indices: 17220--17259 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
17210 TTGACAATAA
17220 TAATAATTTTTATTT
1 TAATAATTTTTA-TT
*
17235 TAATATTTTTTATT
1 TAATAATTTTTATT
*
17249 TAATAAATTTT
1 TAATAATTTTT
17260 GGTCCATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TAATAATTTTTATT
Found at i:17259 original size:14 final size:15
Alignment explanation
Indices: 17220--17259 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
17210 TTGACAATAA
17220 TAATAATTTTTATTT
1 TAATAATTTTTATTT
*
17235 TAATATTTTTTA-TT
1 TAATAATTTTTATTT
17249 TAATAAATTTT
1 TAAT-AATTTT
17260 GGTCCATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TAATAATTTTTATTT
Found at i:24208 original size:23 final size:22
Alignment explanation
Indices: 24158--24205 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
24148 TTTTTTCTAC
*
24158 TTTTCTTTTGGCTGCTATTGGT
1 TTTTCTTTTGGCTGCTACTGGT
* *
24180 TTTTCTTTTTGTTGCTACTGGT
1 TTTTCTTTTGGCTGCTACTGGT
24202 TTTT
1 TTTT
24206 TCTACTTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.04, C:0.12, G:0.19, T:0.65
Consensus pattern (22 bp):
TTTTCTTTTGGCTGCTACTGGT
Found at i:28975 original size:14 final size:14
Alignment explanation
Indices: 28952--28985 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28942 TTAGGAGCTA
28952 GGTTTAGAGATTAG
1 GGTTTAGAGATTAG
* *
28966 GGTTTTGAGATTGG
1 GGTTTAGAGATTAG
28980 GGTTTA
1 GGTTTA
28986 AATGAGAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (14 bp):
GGTTTAGAGATTAG
Done.