Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011156.1 Corchorus capsularis cultivar CVL-1 contig11177, 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: 68985
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:689 original size:31 final size:31
Alignment explanation
Indices: 623--760 Score: 141
Period size: 31 Copynumber: 4.5 Consensus size: 31
613 ACACGTGCAT
* ** **
623 GTGGCATGCCACGTGTCATTTTTTGAAACGT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAC
*
654 GTGGCATGCCATGTGTCACTTTTTGGTACAC
1 GTGGCATGCCACGTGTCACTTTTTGGTACAC
* * * *
685 GTGGCTTGACATGTGTCACTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAC
* * * *
716 GTGGCGTGCCACATATCACTTTTTTGTACAC
1 GTGGCATGCCACGTGTCACTTTTTGGTACAC
*
747 GTGGCGTGCCACGT
1 GTGGCATGCCACGT
761 TGGACACCGT
Statistics
Matches: 90, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 90 1.00
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.36
Consensus pattern (31 bp):
GTGGCATGCCACGTGTCACTTTTTGGTACAC
Found at i:2318 original size:15 final size:15
Alignment explanation
Indices: 2260--2324 Score: 64
Period size: 15 Copynumber: 4.5 Consensus size: 15
2250 GGCGTACTGC
*
2260 GGAGGATATCCCTGA
1 GGAGGATATCCCTGT
*
2275 GGAGGATAACCC--T
1 GGAGGATATCCCTGT
*
2288 -GAGGATATCCTTGT
1 GGAGGATATCCCTGT
*
2302 GGAGGATATCCCGGT
1 GGAGGATATCCCTGT
*
2317 GGTGGATA
1 GGAGGATA
2325 AGCATCCTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
12 9 0.22
14 1 0.03
15 30 0.75
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23
Consensus pattern (15 bp):
GGAGGATATCCCTGT
Found at i:19336 original size:17 final size:16
Alignment explanation
Indices: 19296--19346 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
19286 CATGTAATCT
*
19296 TTGATCACCAGTGATC
1 TTGATCACTAGTGATC
*
19312 TTGCATCACTGGTGATC
1 TTG-ATCACTAGTGATC
*
19329 TTAGATCACTAATGATC
1 TT-GATCACTAGTGATC
19346 T
1 T
19347 AGGGAGGTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (16 bp):
TTGATCACTAGTGATC
Found at i:20562 original size:2 final size:2
Alignment explanation
Indices: 20555--20588 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
20545 CCGGGTGTTA
*
20555 AT AT AT AT AT AT AT AT AT AT AT AT -T TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20589 ATCCAATCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:23281 original size:17 final size:19
Alignment explanation
Indices: 23259--23296 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
23249 GTGATTTTAA
23259 TTTTTTC-TTT-ATCCTTT
1 TTTTTTCGTTTCATCCTTT
*
23276 TTTTTTCGTTTCTTCCTTT
1 TTTTTTCGTTTCATCCTTT
23295 TT
1 TT
23297 CGTTGGGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (19 bp):
TTTTTTCGTTTCATCCTTT
Found at i:27722 original size:1 final size:1
Alignment explanation
Indices: 27716--27742 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
27706 GAAAGAGAAG
27716 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
27743 AAATAATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:30342 original size:2 final size:2
Alignment explanation
Indices: 30335--30361 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30325 TTTACTTTAC
30335 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
30362 GAGATGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33898 original size:2 final size:2
Alignment explanation
Indices: 33891--33917 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33881 TAAAAGTCCC
33891 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
33918 CCATTCTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35960 original size:2 final size:2
Alignment explanation
Indices: 35955--35983 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35945 CCCCTCTCTC
35955 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35984 TCTCTTTCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50270 original size:25 final size:24
Alignment explanation
Indices: 50236--50284 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
50226 CTATTTTCCA
* *
50236 TCAATCTTCAAACTTTTCAATTCTC
1 TCAAACTTCAAAC-TTTCAAATCTC
50261 TCAAACTTCAAACTTTCAAATCTC
1 TCAAACTTCAAACTTTCAAATCTC
50285 AATCATTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.33, C:0.29, G:0.00, T:0.39
Consensus pattern (24 bp):
TCAAACTTCAAACTTTCAAATCTC
Found at i:50757 original size:18 final size:20
Alignment explanation
Indices: 50723--50771 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
50713 AAGTTTTTTT
50723 TTTTCTTCTTCTTCTTTAAAG-
1 TTTTCTT-TT-TTCTTTAAAGA
*
50744 TTTT-TTTTTTCTTTTAAGA
1 TTTTCTTTTTTCTTTAAAGA
50763 TTTTCTTTT
1 TTTTCTTTT
50772 AATTTCCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 9 0.36
19 6 0.24
20 6 0.24
21 4 0.16
ACGTcount: A:0.12, C:0.12, G:0.04, T:0.71
Consensus pattern (20 bp):
TTTTCTTTTTTCTTTAAAGA
Found at i:50880 original size:24 final size:25
Alignment explanation
Indices: 50848--50896 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
50838 TTGAATGATT
*
50848 GAGATTTG-AAAGTTTGAAGGTTGA
1 GAGAATTGAAAAGTTTGAAGGTTGA
* *
50872 GAGAATTGAAAATTTTGAAGTTTGA
1 GAGAATTGAAAAGTTTGAAGGTTGA
50897 AGGAAAAGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.35
Consensus pattern (25 bp):
GAGAATTGAAAAGTTTGAAGGTTGA
Found at i:51500 original size:29 final size:30
Alignment explanation
Indices: 51460--51525 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
51450 TCTTGTAGCA
* * *
51460 TTTGGACGTTTTGTTCCTTAAACTTCAA-T
1 TTTGGACATTTTATTCCATAAACTTCAATT
* *
51489 TTTGGACATTTTATTCCATGAATTTCAATT
1 TTTGGACATTTTATTCCATAAACTTCAATT
51519 TTTGGAC
1 TTTGGAC
51526 GTTTAACCCC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.23, C:0.15, G:0.14, T:0.48
Consensus pattern (30 bp):
TTTGGACATTTTATTCCATAAACTTCAATT
Found at i:51759 original size:29 final size:29
Alignment explanation
Indices: 51712--51786 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
51702 TAGGTTGAGG
*
51712 GGGCAAAACGTTCCAAAATTGAAGTTCAAA
1 GGGCAAAATG-TCCAAAATTGAAGTTCAAA
*
51742 GGGCAAAATGTCCAAAATTGAAGTTCAGA
1 GGGCAAAATGTCCAAAATTGAAGTTCAAA
* *
51771 GGACAAAATTTCCAAA
1 GGGCAAAATGTCCAAA
51787 CACTACAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 32 0.78
30 9 0.22
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (29 bp):
GGGCAAAATGTCCAAAATTGAAGTTCAAA
Found at i:58190 original size:12 final size:13
Alignment explanation
Indices: 58166--58202 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 13
58156 AATCATTACA
58166 AAAATATAAATTTT
1 AAAATA-AAATTTT
58180 AAAA-AAAA-TTT
1 AAAATAAAATTTT
58191 AAAATAAAATTT
1 AAAATAAAATTT
58203 GGAAAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.33
12 7 0.33
13 3 0.14
14 4 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAATAAAATTTT
Done.