Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010235.1 Corchorus capsularis cultivar CVL-1 contig10256, 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: 59046
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3307 original size:24 final size:24
Alignment explanation
Indices: 3275--3322 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
3265 AGTACATGTG
*
3275 TAGTGATTAAATCTCATTTAAATT
1 TAGTAATTAAATCTCATTTAAATT
*
3299 TAGTAATTAAATCTCATTTTAATT
1 TAGTAATTAAATCTCATTTAAATT
3323 AATTTGTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (24 bp):
TAGTAATTAAATCTCATTTAAATT
Found at i:4968 original size:20 final size:20
Alignment explanation
Indices: 4921--4980 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
4911 TTTAACCCAT
*
4921 CATATATTTATATTTTCATCA
1 CATATATCTATATTTTCA-CA
* *
4942 AATATATCTATATTTTCACC
1 CATATATCTATATTTTCACA
4962 CATATATCTATATTTTCAC
1 CATATATCTATATTTTCAC
4981 TTTTAACCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.48
Consensus pattern (20 bp):
CATATATCTATATTTTCACA
Found at i:6567 original size:17 final size:17
Alignment explanation
Indices: 6545--6583 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
6535 CTCATGGTAC
6545 CTAGGTAGTATGAGGTG
1 CTAGGTAGTATGAGGTG
6562 CTAGGTAGTATGAGGTG
1 CTAGGTAGTATGAGGTG
*
6579 ATAGG
1 CTAGG
6584 CTGCATCTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.41, T:0.28
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTG
Found at i:7236 original size:156 final size:155
Alignment explanation
Indices: 6932--7292 Score: 367
Period size: 156 Copynumber: 2.3 Consensus size: 155
6922 CTTCTCACCT
* *
6932 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGATGAAATTT
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGATG-AATTT
* * * *
6997 TTCCAAGGGTCTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAGCTCCCC
65 TTCCAAGAGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCAAACTCCCC
* * * *
7062 TTGATGGTGAACTAGGTTTCTCTCCC
130 TGGATAGAGAACTAGGTTTCACTCCC
* ** *
7088 TAAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGCTG-A-TT
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACG-AGATGAATTT
*
7150 TTCCACCAGTAGACTTAGATTAT-CACCATAA-AGCTATGGGAAAAAA-TCTAAGTAAAACCAAA
65 TTCCA--AG-AGACTTAGAATATCCA-CATAAGA-CTAT-GGAAAAAATTCTAAGTAAAACCAAA
* * * * *
7212 CT-CTCTAGGGTAGAGAAGTTGGTTTGACTCCC
124 CTCCCCT-GGATAGAGAACTAGGTTTCACTCCC
** * * *
7244 CAAACTGTGTTTAACTAAAAAACTAGCATAAGTTTTTCATGCTAAGTCT
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCT
7293 GTTTGAGATG
Statistics
Matches: 168, Mismatches: 28, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
153 7 0.04
154 1 0.01
155 11 0.07
156 141 0.84
157 8 0.05
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (155 bp):
CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGATGAATTTT
TCCAAGAGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCAAACTCCCCT
GGATAGAGAACTAGGTTTCACTCCC
Found at i:19166 original size:18 final size:18
Alignment explanation
Indices: 19145--19185 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
19135 TTTTTTGATT
19145 AAAAAATA-ATTTTTTTA
1 AAAAAATATATTTTTTTA
19162 AAAAAATATATTTTTTTA
1 AAAAAATATATTTTTTTA
19180 AAAAAA
1 AAAAAA
19186 AAAAATTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAAAATATATTTTTTTA
Found at i:19257 original size:30 final size:31
Alignment explanation
Indices: 19204--19263 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
19194 GTGAGGGATC
*
19204 CAATTGCTCAATTAACTCAACTTCAGGGACT
1 CAATTGCTCAATTAACTCAACTTCAAGGACT
*
19235 CAATTGCTC-ATTAAGTTC-ACTTCAAGGAC
1 CAATTGCTCAATTAA-CTCAACTTCAAGGAC
19264 CCATTTGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (31 bp):
CAATTGCTCAATTAACTCAACTTCAAGGACT
Found at i:19605 original size:13 final size:13
Alignment explanation
Indices: 19587--19613 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19577 ACTCACAACC
19587 TAATATATAATTT
1 TAATATATAATTT
19600 TAATATATAATTT
1 TAATATATAATTT
19613 T
1 T
19614 TAAGAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATATATAATTT
Found at i:37133 original size:30 final size:30
Alignment explanation
Indices: 37092--37152 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
37082 AACCTTTCAT
37092 GCTTCCAACCATCAATCTCCGATAAAACTC
1 GCTTCCAACCATCAATCTCCGATAAAACTC
*
37122 GCTTCCGACCATCAATCTCCGATAAAACTC
1 GCTTCCAACCATCAATCTCCGATAAAACTC
37152 G
1 G
37153 ATGATACCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.36, G:0.10, T:0.23
Consensus pattern (30 bp):
GCTTCCAACCATCAATCTCCGATAAAACTC
Found at i:49568 original size:43 final size:43
Alignment explanation
Indices: 49520--49638 Score: 202
Period size: 43 Copynumber: 2.8 Consensus size: 43
49510 TCTTTTGGGT
* *
49520 GGCAAAGCAGATGACAGAAAAACAGAGAGAACAGGGGTGGGGC
1 GGCAAAGCAAATGACAGAAAAACAGAGAGAACAGGGGTGGGGA
49563 GGCAAAGCAAATGACAGAAAAACAGAGAGAACAGGGGTGGGGA
1 GGCAAAGCAAATGACAGAAAAACAGAGAGAACAGGGGTGGGGA
* *
49606 GGCAGAGCAAATGATAGAAAAACAGAGAGAACA
1 GGCAAAGCAAATGACAGAAAAACAGAGAGAACA
49639 ATGATAGTGG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 72 1.00
ACGTcount: A:0.47, C:0.13, G:0.35, T:0.05
Consensus pattern (43 bp):
GGCAAAGCAAATGACAGAAAAACAGAGAGAACAGGGGTGGGGA
Found at i:51648 original size:20 final size:21
Alignment explanation
Indices: 51610--51648 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
51600 CCATTAAACC
51610 ATTAAACAATTCTTTCTTAGA
1 ATTAAACAATTCTTTCTTAGA
51631 ATTAAACAATTC-TTCTTA
1 ATTAAACAATTCTTTCTTA
51649 ATTTATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (21 bp):
ATTAAACAATTCTTTCTTAGA
Found at i:56033 original size:33 final size:35
Alignment explanation
Indices: 55968--56034 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
55958 GCTTTTTCCC
55968 TTGTAACTTTCAGAGGAGATATATATCCTATTTTT
1 TTGTAACTTTCAGAGGAGATATATATCCTATTTTT
*
56003 TTGTAACTTTCAGAGGA-A-ATTTATCCTATTTT
1 TTGTAACTTTCAGAGGAGATATATATCCTATTTT
56035 GTTTCAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 13 0.42
34 1 0.03
35 17 0.55
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.46
Consensus pattern (35 bp):
TTGTAACTTTCAGAGGAGATATATATCCTATTTTT
Done.