Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011662.1 Corchorus capsularis cultivar CVL-1 contig11683, 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: 13881
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:4209 original size:13 final size:14
Alignment explanation
Indices: 4191--4220 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4181 ACTTTTGACC
4191 ATATATTATG-ATA
1 ATATATTATGTATA
4204 ATATATTATGTATA
1 ATATATTATGTATA
4218 ATA
1 ATA
4221 ATTTTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
ATATATTATGTATA
Found at i:12827 original size:28 final size:27
Alignment explanation
Indices: 12747--12827 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
12737 ATTTTTAATT
* *
12747 TCTTTTGCTACT-TTTATCATTT-TTAC
1 TCTTTTCCTACTCTTT-TTATTTATTAC
***
12773 TCTTTTCCTACTCTTTTTACCAATTAC
1 TCTTTTCCTACTCTTTTTATTTATTAC
*
12800 TCTTTTCTTACTCTCTTTTATTTATTAC
1 TCTTTTCCTACTCT-TTTTATTTATTAC
12828 CACTTTTTAC
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
26 13 0.30
27 20 0.47
28 10 0.23
ACGTcount: A:0.16, C:0.23, G:0.01, T:0.59
Consensus pattern (27 bp):
TCTTTTCCTACTCTTTTTATTTATTAC
Found at i:12968 original size:21 final size:20
Alignment explanation
Indices: 12892--12980 Score: 88
Period size: 21 Copynumber: 4.3 Consensus size: 20
12882 CTGATCACCC
12892 TTTACTCTTACTGATTACTAT
1 TTTACTCTTACTGATTA-TAT
* * *
12913 TTGACTCTTACTAATTATCAC
1 TTTACTCTTACTGATTAT-AT
* *
12934 TTTGCTCTTACTGGTTACTAT
1 TTTACTCTTACTGATTA-TAT
* *
12955 TTTACTCTTACTGGTTATCT
1 TTTACTCTTACTGATTATAT
12975 TTTACT
1 TTTACT
12981 GATTACTATT
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.16
21 46 0.82
22 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.08, T:0.52
Consensus pattern (20 bp):
TTTACTCTTACTGATTATAT
Found at i:13005 original size:22 final size:22
Alignment explanation
Indices: 12975--13242 Score: 185
Period size: 22 Copynumber: 12.0 Consensus size: 22
12965 CTGGTTATCT
12975 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
* * *
12997 TTTGCTGATTACCT-TCTTACTT
1 TTTACTGATTA-CTATTTTACTC
*
13019 TTTACTGATTACCATTTTACTC
1 TTTACTGATTACTATTTTACTC
* *
13041 TTTTACTGATTACCATTTTCTGCTCCC
1 -TTTACTGATTACTA-TTT-TACT--C
* *
13068 TTTTTTACTGATTACTCTTTTACTT
1 ---TTTACTGATTACTATTTTACTC
* * * *
13093 TTTACTGATT-GTCTTTTGCTT
1 TTTACTGATTACTATTTTACTC
13114 TTTACTGATTACCT-TTTTACTC
1 TTTACTGATTA-CTATTTTACTC
* *
13136 -TTATTGATTACTA-TTTACTT
1 TTTACTGATTACTATTTTACTC
*
13156 TTTACTGACTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
*
13178 TTGT--TGATTACCT-TCTTAC-C
1 TT-TACTGATTA-CTATTTTACTC
*
13198 TTTTACTGATTACTATTTTCCTC
1 -TTTACTGATTACTATTTTACTC
*
13221 TTTACTGATTTACCATTTTACT
1 TTTACTGA-TTACTATTTTACT
13243 GATTATTATT
Statistics
Matches: 196, Mismatches: 28, Indels: 43
0.73 0.10 0.16
Matches are distributed among these distances:
20 10 0.05
21 54 0.28
22 76 0.39
23 30 0.15
24 3 0.02
25 3 0.02
27 4 0.02
28 3 0.02
29 13 0.07
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.55
Consensus pattern (22 bp):
TTTACTGATTACTATTTTACTC
Found at i:13053 original size:15 final size:15
Alignment explanation
Indices: 13035--13091 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
13025 GATTACCATT
13035 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
13050 TTAC-CATTTT-CTGC
1 TTACTC-TTTTACTGA
** *
13064 TCCCTTTTTTACTGA
1 TTACTCTTTTACTGA
13079 TTACTCTTTTACT
1 TTACTCTTTTACT
13092 TTTTACTGAT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
14 10 0.32
15 21 0.68
ACGTcount: A:0.16, C:0.25, G:0.05, T:0.54
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:13094 original size:21 final size:21
Alignment explanation
Indices: 13070--13230 Score: 123
Period size: 21 Copynumber: 7.5 Consensus size: 21
13060 CTGCTCCCTT
13070 TTTTACTGATTACTCTTTTAC
1 TTTTACTGATTACTCTTTTAC
* *
13091 TTTTTACTGATT-GTCTTTTGC
1 -TTTTACTGATTACTCTTTTAC
13112 TTTTTACTGATTAC-CTTTTTAC
1 -TTTTACTGATTACTC-TTTTAC
* * *
13134 TCTTATTGATTACT-ATTTAC
1 TTTTACTGATTACTCTTTTAC
* *
13154 TTTTTACTGACTACTATTTTAC
1 -TTTTACTGATTACTCTTTTAC
* **
13176 TCTTGTTGATTAC-CTTCTTACC
1 TTTTACTGATTACTCTT-TTA-C
* *
13198 TTTTACTGATTACTATTTTCC
1 TTTTACTGATTACTCTTTTAC
13219 TCTTTACTGATT
1 T-TTTACTGATT
13231 TACCATTTTA
Statistics
Matches: 109, Mismatches: 21, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
20 7 0.06
21 56 0.51
22 44 0.40
23 2 0.02
ACGTcount: A:0.18, C:0.19, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTTACTGATTACTCTTTTAC
Found at i:13157 original size:42 final size:41
Alignment explanation
Indices: 13069--13222 Score: 166
Period size: 43 Copynumber: 3.6 Consensus size: 41
13059 TCTGCTCCCT
* * * * *
13069 TTTTTACTGATTACTCTTTTACTTTTTACTGATTGTCTTTTGC
1 TTTTTACTGATTACTATTTTAC-TCTTATTGATT-ACTTTTAC
13112 TTTTTACTGATTACCT-TTTTACTCTTATTGATTACTATTTAC
1 TTTTTACTGATTA-CTATTTTACTCTTATTGATTACT-TTTAC
* *
13154 TTTTTACTGACTACTATTTTACTCTTGTTGATTACCTTCTTAC
1 TTTTTACTGATTACTATTTTACTCTTATTGATTA-CTT-TTAC
* *
13197 CTTTTACTGATTACTATTTTCCTCTT
1 TTTTTACTGATTACTATTTTACTCTT
13223 TACTGATTTA
Statistics
Matches: 97, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
41 4 0.04
42 43 0.44
43 48 0.49
44 2 0.02
ACGTcount: A:0.18, C:0.19, G:0.06, T:0.57
Consensus pattern (41 bp):
TTTTTACTGATTACTATTTTACTCTTATTGATTACTTTTAC
Found at i:13298 original size:55 final size:55
Alignment explanation
Indices: 13237--13364 Score: 229
Period size: 55 Copynumber: 2.3 Consensus size: 55
13227 GATTTACCAT
*
13237 TTTACTGATTATTATTACCTTAACTCTGATTAATCTCTTTTCACTTAATTACTGA
1 TTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTCACTTAATTACTGA
* *
13292 TTTACTGATTACTATTACGTTGACTCTGATTAATCTCTTTTCACTTAATTACTGA
1 TTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTCACTTAATTACTGA
13347 TTTACTGATTACTATTAC
1 TTTACTGATTACTATTAC
13365 TCTTTACTGA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 70 1.00
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (55 bp):
TTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTCACTTAATTACTGA
Done.