Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016493.1 Corchorus capsularis cultivar CVL-1 contig16514, 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: 24953
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2081 original size:21 final size:21
Alignment explanation
Indices: 2043--2082 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2033 GTTTGGTATC
*
2043 GTTGCCAATTCTGTTTTTTTT
1 GTTGCCAATTCTGATTTTTTT
2064 GTTGCCAATT-TCGATTTTT
1 GTTGCCAATTCT-GATTTTT
2083 GAAAACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.57
Consensus pattern (21 bp):
GTTGCCAATTCTGATTTTTTT
Found at i:8958 original size:22 final size:22
Alignment explanation
Indices: 8921--8964 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
8911 ATCCCCTTCT
**
8921 TTAGGCTTGGTTTCGACCAAGA
1 TTAGGCTTGGCCTCGACCAAGA
*
8943 TTAGGCTTGGCCTCGATCAAGA
1 TTAGGCTTGGCCTCGACCAAGA
8965 CTTTCTCATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (22 bp):
TTAGGCTTGGCCTCGACCAAGA
Found at i:11272 original size:25 final size:24
Alignment explanation
Indices: 11218--11272 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
11208 TCATTAAGCT
****
11218 TAAAACTATATACTTTTTTTTTCA
1 TAAAACTATATACTTTTTGGAACA
11242 TCAAAACTATATACTGTTTTGGAACA
1 T-AAAACTATATACT-TTTTGGAACA
11268 TAAAA
1 TAAAA
11273 TTTAATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 17 0.68
26 7 0.28
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.42
Consensus pattern (24 bp):
TAAAACTATATACTTTTTGGAACA
Found at i:11703 original size:22 final size:22
Alignment explanation
Indices: 11678--11780 Score: 107
Period size: 22 Copynumber: 4.6 Consensus size: 22
11668 GCTCCCTATA
*
11678 AAATTTTAATAACCACCTAATG
1 AAATTTTGATAACCACCTAATG
* *
11700 AAATTTTGATAATCACCTTATG
1 AAATTTTGATAACCACCTAATG
* *
11722 AAATTTTGATAACCTCCCAATG
1 AAATTTTGATAACCACCTAATG
* * * *
11744 AAATATTGGTAAGCGCACATTATG
1 AAATTTTGATAA-C-CACCTAATG
11768 AAATTTTGATAAC
1 AAATTTTGATAAC
11781 TTTCTGGTAA
Statistics
Matches: 64, Mismatches: 15, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
22 47 0.73
23 2 0.03
24 15 0.23
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.34
Consensus pattern (22 bp):
AAATTTTGATAACCACCTAATG
Found at i:11744 original size:44 final size:45
Alignment explanation
Indices: 11678--11780 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 45
11668 GCTCCCTATA
* * * * *
11678 AAATTTTAATAACCACCTAATGAAATTTTGATAA-TCACCTTATG
1 AAATTTTGATAACCACCCAATGAAATATTGATAACGCACATTATG
* *
11722 AAATTTTGATAACCTCCCAATGAAATATTGGTAAGCGCACATTATG
1 AAATTTTGATAACCACCCAATGAAATATTGATAA-CGCACATTATG
11768 AAATTTTGATAAC
1 AAATTTTGATAAC
11781 TTTCTGGTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 29 0.58
46 21 0.42
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.34
Consensus pattern (45 bp):
AAATTTTGATAACCACCCAATGAAATATTGATAACGCACATTATG
Found at i:11826 original size:123 final size:120
Alignment explanation
Indices: 11674--11901 Score: 266
Period size: 123 Copynumber: 1.9 Consensus size: 120
11664 ATTGGCTCCC
* *
11674 TATAAAATTTTAATAACCACCTAATGAAATTTTGATA-ATCACCTTATGAAATT-TTGAT-AACC
1 TATAAAATTTTAATAACCACC-AATGAAATTGTGACACATCA-C-TATGAAATTCTT-ATAAACC
* * *
11736 TCCCAATGAAATATTGGTAAGCGCACATTATGAAATTTTGATAACTTTCTGGTAACCACAT
62 TCCCAATAAAATATTGATAACCGC-CATT-TGAAATTTTGATAACTTTCTGGTAACCACAT
* *
11797 TATAAAATTTTGATAACCATACC-ATGAAATTGTGACACCTCACTATGAAATTCTTATAAACCTC
1 TATAAAATTTTAATAACC--ACCAATGAAATTGTGACACATCACTATGAAATTCTTATAAACCTC
* * *
11861 CCTATAAAATTTTGATAACCTCCATTTGAAATTTTGATAAC
64 CCAATAAAATATTGATAACCGCCATTTGAAATTTTGATAAC
11902 CTCATGAAAT
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
121 15 0.17
122 15 0.17
123 54 0.60
124 3 0.03
125 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (120 bp):
TATAAAATTTTAATAACCACCAATGAAATTGTGACACATCACTATGAAATTCTTATAAACCTCCC
AATAAAATATTGATAACCGCCATTTGAAATTTTGATAACTTTCTGGTAACCACAT
Found at i:11865 original size:23 final size:22
Alignment explanation
Indices: 11801--12197 Score: 148
Period size: 22 Copynumber: 18.3 Consensus size: 22
11791 CCACATTATA
*
11801 AAATTTTGATAACCATACC-ATG
1 AAATTTTGATAACC-TCCCTATG
* * *
11823 AAATTGTGA-CACCTCACTATG
1 AAATTTTGATAACCTCCCTATG
*
11844 AAATTCTT-ATAAACCTCCCTATA
1 AAATT-TTGAT-AACCTCCCTATG
* *
11867 AAATTTTGATAACCTCCATTTG
1 AAATTTTGATAACCTCCCTATG
11889 AAATTTTGATAACCT--C-ATG
1 AAATTTTGATAACCTCCCTATG
*
11908 AAATTTTGCA-AA-CTACCTCATG
1 AAATTTTG-ATAACCTCCCT-ATG
* * *
11930 GAATTTCGATAACCAT-CTTATG
1 AAATTTTGATAACC-TCCCTATG
*
11952 AAATTTTGATAACATCCCTAT-
1 AAATTTTGATAACCTCCCTATG
* * *
11973 AAATTTTTTATTACCT--C-ATA
1 AAA-TTTTGATAACCTCCCTATG
* *
11993 AAATTTTGTTAACCT-CCTACG
1 AAATTTTGATAACCTCCCTATG
*** * *
12014 AAATTTTGATAAGAACACTATT
1 AAATTTTGATAACCTCCCTATG
** *
12036 AAATTTTGATAACC-CCAAAAG
1 AAATTTTGATAACCTCCCTATG
* *
12057 AAATTTGGATAACTAACTACACC-ATA
1 AAATTTTGATAAC---CT-C-CCTATG
** * *
12083 AAATTACGATAACTTACCTATG
1 AAATTTTGATAACCTCCCTATG
* *
12105 AAATTTTG-TGAATCTCCCTATA
1 AAATTTTGAT-AACCTCCCTATG
* * * * *
12127 AAATTTTTAGAACCACACTATC
1 AAATTTTGATAACCTCCCTATG
* * *
12149 AAATTTTGTTAATCTCACTAT-
1 AAATTTTGATAACCTCCCTATG
* **
12170 AAA-TTTGATAAACTCATTATG
1 AAATTTTGATAACCTCCCTATG
12191 AAATTTT
1 AAATTTT
12198 AAGTACCACA
Statistics
Matches: 274, Mismatches: 71, Indels: 60
0.68 0.18 0.15
Matches are distributed among these distances:
18 2 0.01
19 23 0.08
20 23 0.08
21 52 0.19
22 138 0.50
23 20 0.07
24 2 0.01
26 13 0.05
27 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:12185 original size:20 final size:21
Alignment explanation
Indices: 12142--12196 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
12132 TTTAGAACCA
* *
12142 CACTATCAAATTTTGTTAATCT
1 CACTATCAAA-TTTGATAAACT
12164 CACTAT-AAATTTGATAAACT
1 CACTATCAAATTTGATAAACT
* *
12184 CATTATGAAATTT
1 CACTATCAAATTT
12197 TAAGTACCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.48
21 9 0.31
22 6 0.21
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (21 bp):
CACTATCAAATTTGATAAACT
Found at i:13933 original size:22 final size:22
Alignment explanation
Indices: 13906--14015 Score: 82
Period size: 22 Copynumber: 5.0 Consensus size: 22
13896 GTGATAATTC
*
13906 CACTATAAAATTTTAATATCCT
1 CACTATAAAATTTTAATAACCT
* **
13928 -ACCTATGAAATTTTGGTAACCT
1 CA-CTATAAAATTTTAATAACCT
* * *
13950 CACTATAAAATTTTGAGAACCA
1 CACTATAAAATTTTAATAACCT
* *
13972 CACTATAAAATTTCAGTAA-CT
1 CACTATAAAATTTTAATAACCT
* *
13993 GCACGAT-AAATTTTGATAACCT
1 -CACTATAAAATTTTAATAACCT
14015 C
1 C
14016 CAAAATTAAA
Statistics
Matches: 67, Mismatches: 17, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
21 12 0.18
22 54 0.81
23 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (22 bp):
CACTATAAAATTTTAATAACCT
Found at i:13991 original size:44 final size:44
Alignment explanation
Indices: 13906--14014 Score: 116
Period size: 44 Copynumber: 2.5 Consensus size: 44
13896 GTGATAATTC
* * * **
13906 CACTATAAAATTTTAATATCCTACCTATGAAATTTTGGTAACCT-
1 CACTATAAAATTTTGATAACCTACCTATAAAATTTCAGTAA-CTG
*
13950 CACTATAAAATTTTGAGAACC-ACACTATAAAATTTCAGTAACTG
1 CACTATAAAATTTTGATAACCTAC-CTATAAAATTTCAGTAACTG
*
13994 CACGAT-AAATTTTGATAACCT
1 CACTATAAAATTTTGATAACCT
14015 CCAAAATTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
43 17 0.31
44 37 0.69
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (44 bp):
CACTATAAAATTTTGATAACCTACCTATAAAATTTCAGTAACTG
Found at i:14012 original size:21 final size:20
Alignment explanation
Indices: 13870--14012 Score: 65
Period size: 22 Copynumber: 6.7 Consensus size: 20
13860 ACTCCTTATG
*
13870 AAATTTTGATAACATC-CCAT
1 AAATTTTGATAAC-TCACTAT
* *
13890 GAAATTGTGATAATTCCACTAT
1 -AAATTTTGATAACT-CACTAT
* *
13912 AAAATTTTAATATC-CTACCTAT
1 -AAATTTTGATAACTC-A-CTAT
*
13934 GAAATTTTGGTAACCTCACTAT
1 -AAATTTTGATAA-CTCACTAT
* *
13956 AAAATTTTGAGAACCACACTAT
1 -AAATTTTGATAA-CTCACTAT
* * *
13978 AAAATTTCAGTAACTGCACGAT
1 AAATTTTGA-TAACT-CACTAT
14000 AAATTTTGATAAC
1 AAATTTTGATAAC
14013 CTCCAAAATT
Statistics
Matches: 91, Mismatches: 23, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
20 2 0.02
21 25 0.27
22 61 0.67
23 2 0.02
24 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (20 bp):
AAATTTTGATAACTCACTAT
Found at i:14636 original size:45 final size:45
Alignment explanation
Indices: 14585--14674 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
14575 TAATAGAGTA
*
14585 GTGGAATTACTAAAAGATCCCTACCCTGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTGG
14630 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTGG
14675 AGAAGTAATC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTGG
Found at i:15068 original size:2 final size:2
Alignment explanation
Indices: 15061--15130 Score: 69
Period size: 2 Copynumber: 36.5 Consensus size: 2
15051 TTTTAATTGA
* *
15061 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AA AT GA- AG A- AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
15100 AGT AT AT AT A- AT AT AT AT AT AT AT AT AT AT A
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15131 CACTACATAT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
1 5 0.08
2 51 0.86
3 3 0.05
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:15197 original size:13 final size:13
Alignment explanation
Indices: 15179--15204 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15169 AATTTTTACA
15179 TCTTTTCTCACTT
1 TCTTTTCTCACTT
15192 TCTTTTCTCACTT
1 TCTTTTCTCACTT
15205 GACAGATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.62
Consensus pattern (13 bp):
TCTTTTCTCACTT
Found at i:22676 original size:33 final size:33
Alignment explanation
Indices: 22579--22683 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 33
22569 TTGCAAAGAG
* * *
22579 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
** * *
22612 TAATTT-GAGTGTTGTTTGCAATGACACTAAATC
1 TGTTTTAG-GTGTTGTTTGCGATGAAACTAAATC
*
22645 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
22678 TGTTTT
1 TGTTTT
22684 GGATGCTAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 1 0.02
33 57 0.97
34 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.45
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
Found at i:22702 original size:33 final size:32
Alignment explanation
Indices: 22632--22719 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 32
22622 GTTGTTTGCA
* * ** *
22632 ATGACACTAAATCTGTTTTAGGTGTTGTTTGTG
1 ATGAAACTAAATCTGTTTT-GGTGCTAATTGTC
22665 ATGAAACTAAATCTGTTTTGGATGCTAATTGTC
1 ATGAAACTAAATCTGTTTTGG-TGCTAATTGTC
22698 ATGAAAAC-AAATCTGTTTTGGT
1 ATG-AAACTAAATCTGTTTTGGT
22720 TAATCATAGC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
32 3 0.06
33 41 0.85
34 4 0.08
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.41
Consensus pattern (32 bp):
ATGAAACTAAATCTGTTTTGGTGCTAATTGTC
Found at i:22787 original size:33 final size:32
Alignment explanation
Indices: 22709--22814 Score: 144
Period size: 33 Copynumber: 3.3 Consensus size: 32
22699 TGAAAACAAA
*
22709 TCTGTTTTGGTTAATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATC-TAGCATTGCAAATAAT
22742 TCTGTTTTGGTTGATCCTAGCATTGCAAATAAT
1 TCTGTTTTGGTTGAT-CTAGCATTGCAAATAAT
* *
22775 TCTGTTTTGGTTGA--TGGCATTGAAAATAAT
1 TCTGTTTTGGTTGATCTAGCATTGCAAATAAT
*
22805 TATGTTTTGG
1 TCTGTTTTGG
22815 GTGAAAAGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
30 23 0.34
33 44 0.65
34 1 0.01
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.44
Consensus pattern (32 bp):
TCTGTTTTGGTTGATCTAGCATTGCAAATAAT
Found at i:23225 original size:30 final size:30
Alignment explanation
Indices: 23189--23245 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
23179 TCTTCAAGGG
23189 GGAGGGAATGATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATGATGCG-CCAAGGACTTATCAT
23219 GGAGGGAATGATGCGCCAAGGACTTAT
1 GGAGGGAATGATGCGCCAAGGACTTAT
23246 TGTGGACTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.28, C:0.18, G:0.35, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGATGCGCCAAGGACTTATCAT
Done.