Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012777.1 Corchorus capsularis cultivar CVL-1 contig12798, 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: 43805
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:272 original size:30 final size:29
Alignment explanation
Indices: 236--297 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
226 TCTTCAAGGG
236 GGAGGGAATGATGCGCCCAAAG-CTTATCAT
1 GGAGGGAATGAT--GCCCAAAGACTTATCAT
*
266 GGAGGGAATGATGCCCAAGGACTTATCAT
1 GGAGGGAATGATGCCCAAAGACTTATCAT
295 GGA
1 GGA
298 CTTGAAGACA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 7 0.23
29 11 0.37
30 12 0.40
ACGTcount: A:0.31, C:0.18, G:0.32, T:0.19
Consensus pattern (29 bp):
GGAGGGAATGATGCCCAAAGACTTATCAT
Found at i:10381 original size:6 final size:6
Alignment explanation
Indices: 10372--10405 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
10362 CACTAAAACG
10372 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
10406 TAACGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:10386 original size:18 final size:18
Alignment explanation
Indices: 10365--10405 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
10355 ATTATAACAC
*
10365 TAAAACGAAAAATAAAAA
1 TAAAAAGAAAAATAAAAA
*
10383 TAAAAATAAAAATAAAAA
1 TAAAAAGAAAAATAAAAA
10401 TAAAA
1 TAAAA
10406 TAACGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.15
Consensus pattern (18 bp):
TAAAAAGAAAAATAAAAA
Found at i:13071 original size:33 final size:34
Alignment explanation
Indices: 12994--13072 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 34
12984 TGCAAAGAGT
* * *
12994 GTTTTAGATGTTGTTTGCAATGATACTAAATCTA
1 GTTTTAGGTGTTGTTTGCAACGACACTAAATCTA
* * *
13028 ATTTGA-GTGTTGTTTGCGACGACACTAAATC-A
1 GTTTTAGGTGTTGTTTGCAACGACACTAAATCTA
13060 GTTTTAGGTGTTG
1 GTTTTAGGTGTTG
13073 CTTGTGATGA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
32 5 0.14
33 27 0.75
34 4 0.11
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (34 bp):
GTTTTAGGTGTTGTTTGCAACGACACTAAATCTA
Found at i:13574 original size:30 final size:30
Alignment explanation
Indices: 13538--13600 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
13528 TCTTCAAGGG
13538 GGAGGGAATGATGCGCCCAAAG-CTTATCAT
1 GGAGGGAATGATGC-CCCAAAGACTTATCAT
* *
13568 GGAGGGATTGATGCCCCAAGGACTTATCAT
1 GGAGGGAATGATGCCCCAAAGACTTATCAT
13598 GGA
1 GGA
13601 CTTGAAGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.29, C:0.19, G:0.32, T:0.21
Consensus pattern (30 bp):
GGAGGGAATGATGCCCCAAAGACTTATCAT
Found at i:21196 original size:11 final size:11
Alignment explanation
Indices: 21180--21209 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21170 TGTGTTCAAT
*
21180 TCTTCAAATTA
1 TCTTCAAATAA
21191 TCTTCAAATAA
1 TCTTCAAATAA
21202 TCTTCAAA
1 TCTTCAAA
21210 CACGAACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:21196 original size:19 final size:18
Alignment explanation
Indices: 21159--21197 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
21149 TTCTTGAAAT
* *
21159 AATTCTTCAATTGTGTTC
1 AATTCTTCAATTATCTTC
21177 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATTATCTTC
21196 AA
1 AA
21198 ATAATCTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (18 bp):
AATTCTTCAATTATCTTC
Found at i:24182 original size:15 final size:15
Alignment explanation
Indices: 24162--24201 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
24152 TATCCAAGTT
*
24162 GCTCATCTTCTTGTG
1 GCTCATCTTCTGGTG
24177 GCTCATCTTCTGGTG
1 GCTCATCTTCTGGTG
24192 GCTCATCTTC
1 GCTCATCTTC
24202 AGGCTTAGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.07, C:0.30, G:0.20, T:0.42
Consensus pattern (15 bp):
GCTCATCTTCTGGTG
Found at i:25307 original size:16 final size:17
Alignment explanation
Indices: 25286--25323 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
25276 CCTAAATTTA
*
25286 TTTTCGA-CACATTTTT
1 TTTTCGACCAAATTTTT
25302 TTTTCGACGCAAATTTTT
1 TTTTCGAC-CAAATTTTT
25320 TTTT
1 TTTT
25324 TTTTTAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
18 12 0.63
ACGTcount: A:0.18, C:0.16, G:0.08, T:0.58
Consensus pattern (17 bp):
TTTTCGACCAAATTTTT
Found at i:25665 original size:18 final size:17
Alignment explanation
Indices: 25637--25673 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
25627 CTAAGCAAAG
*
25637 TAAATTAAATCTGAATC
1 TAAATTAAATCTAAATC
25654 TAAATATAAATCTAAATC
1 TAAAT-TAAATCTAAATC
25672 TA
1 TA
25674 TGGCAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.35
Consensus pattern (17 bp):
TAAATTAAATCTAAATC
Found at i:28589 original size:11 final size:10
Alignment explanation
Indices: 28571--28604 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
28561 AATTGTCTTC
28571 AAATCTTCAA
1 AAATCTTCAA
28581 AATATCTTCAA
1 AA-ATCTTCAA
28592 GAAATCTTCAA
1 -AAATCTTCAA
28603 AA
1 AA
28605 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:31872 original size:18 final size:19
Alignment explanation
Indices: 31835--31872 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
31825 TATTTTTATA
*
31835 GCTATTTTTATATACTTGTT
1 GCTATTTTTATATA-GTGTT
31855 GCTATTTTTATAT-GTGTT
1 GCTATTTTTATATAGTGTT
31873 TTTACCCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
20 13 0.76
ACGTcount: A:0.18, C:0.08, G:0.13, T:0.61
Consensus pattern (19 bp):
GCTATTTTTATATAGTGTT
Found at i:37078 original size:21 final size:21
Alignment explanation
Indices: 37054--37113 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
37044 CGAGACACCA
37054 CCGCGCCATGCCCGGCC-TTG
1 CCGCGCCATGCCCGGCCTTTG
*
37074 TCCGCGCACCATGTCCGGCCTTTG
1 -CCGCG--CCATGCCCGGCCTTTG
**
37098 CCATGCCATGCCCGGC
1 CCGCGCCATGCCCGGC
37114 TAATGCCCGG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 15 0.47
23 14 0.44
24 3 0.09
ACGTcount: A:0.08, C:0.47, G:0.27, T:0.18
Consensus pattern (21 bp):
CCGCGCCATGCCCGGCCTTTG
Found at i:37595 original size:9 final size:9
Alignment explanation
Indices: 37581--37611 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
37571 ATTCATATAG
37581 ATATAGGTT
1 ATATAGGTT
37590 ATATAGGTT
1 ATATAGGTT
37599 ATATAGGATT
1 ATATAGG-TT
37609 ATA
1 ATA
37612 AAGATGCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (9 bp):
ATATAGGTT
Done.