Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009989.1 Corchorus capsularis cultivar CVL-1 contig10010, 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: 29984
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Found at i:3564 original size:16 final size:17
Alignment explanation
Indices: 3540--3573 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3530 CCACTTTCCC
*
3540 AAAACTTGAT-AATTTG
1 AAAAATTGATGAATTTG
3556 AAAAATTGATGAATTTG
1 AAAAATTGATGAATTTG
3573 A
1 A
3574 TGGAAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.35
Consensus pattern (17 bp):
AAAAATTGATGAATTTG
Found at i:3899 original size:21 final size:21
Alignment explanation
Indices: 3873--3918 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3863 CCAGGGCACA
*
3873 TGGGTGCCCAGGCAAACCGGC
1 TGGGTGCCCAGGCAAACCGCC
* *
3894 TGGGTGCGCAGGCAAAGCGCC
1 TGGGTGCCCAGGCAAACCGCC
3915 TGGG
1 TGGG
3919 CGCACAGCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.17, C:0.28, G:0.43, T:0.11
Consensus pattern (21 bp):
TGGGTGCCCAGGCAAACCGCC
Found at i:6220 original size:21 final size:21
Alignment explanation
Indices: 6187--6235 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
6177 AAGAATTGTA
**
6187 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
6207 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
6228 GCATTCCT
1 GC-TTCCT
6236 AGAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:9162 original size:22 final size:20
Alignment explanation
Indices: 9120--9163 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
9110 AGGCATAATC
*
9120 AAGCATAAAAAATACCCTAA
1 AAGCATAAAAAATACCATAA
*
9140 AAGCATAGGAAAATGACCATAA
1 AAGCATA-AAAAAT-ACCATAA
9162 AA
1 AA
9164 AGATGCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 8 0.40
ACGTcount: A:0.59, C:0.16, G:0.11, T:0.14
Consensus pattern (20 bp):
AAGCATAAAAAATACCATAA
Found at i:9386 original size:23 final size:23
Alignment explanation
Indices: 9360--9412 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
9350 CGGGATGCAG
9360 CCATGCGCGCGCCAAGCATGCCA
1 CCATGCGCGCGCCAAGCATGCCA
*
9383 CCATTCGCGCGCCAAGCATGCCA
1 CCATGCGCGCGCCAAGCATGCCA
9406 CCATGCG
1 CCATGCG
9413 TGGCTTCACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.43, G:0.25, T:0.11
Consensus pattern (23 bp):
CCATGCGCGCGCCAAGCATGCCA
Found at i:17037 original size:24 final size:24
Alignment explanation
Indices: 17005--17056 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
16995 CCATAATACT
17005 AGTTTATTGCGCTCATCTAAAACC
1 AGTTTATTGCGCTCATCTAAAACC
*
17029 AGTTTATTGCGCTCATTTAAAACC
1 AGTTTATTGCGCTCATCTAAAACC
17053 AGTT
1 AGTT
17057 CAATGGCTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (24 bp):
AGTTTATTGCGCTCATCTAAAACC
Found at i:19088 original size:33 final size:33
Alignment explanation
Indices: 19051--19286 Score: 276
Period size: 33 Copynumber: 6.9 Consensus size: 33
19041 CTCTTTTTAG
19051 ATTAAGTTCTTTTATTCTACTTAATTACCCTGA
1 ATTAAGTTCTTTTATTCTACTTAATTACCCTGA
** * * *
19084 ATTAAGCCACTTATTAACTCCACTTAATCACCCTGA
1 ATTAAG-TTCTT-TT-ATTCTACTTAATTACCCTGA
19120 ATTAAGTTCTTTTATTCTACTTAATTACCCTGA
1 ATTAAGTTCTTTTATTCTACTTAATTACCCTGA
** * * *
19153 ATTAAGCCACTTACTAACTCTACTTAATTACCATGA
1 ATTAAG-TTCTT--TTATTCTACTTAATTACCCTGA
*
19189 ATTGAGTTCTTTTATTCTACTTAATTACCCTGA
1 ATTAAGTTCTTTTATTCTACTTAATTACCCTGA
* *
19222 ATTAAGTGCTTATTAACTCTACTTAATTACCCTGA
1 ATTAAGTTCTT-TT-ATTCTACTTAATTACCCTGA
19257 ATTAAGTTCTTTTATTCTACTTAATT-CCCT
1 ATTAAGTTCTTTTATTCTACTTAATTACCCT
19287 TCCCTGAAAT
Statistics
Matches: 169, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
32 4 0.02
33 69 0.41
34 12 0.07
35 37 0.22
36 47 0.28
ACGTcount: A:0.29, C:0.22, G:0.06, T:0.43
Consensus pattern (33 bp):
ATTAAGTTCTTTTATTCTACTTAATTACCCTGA
Found at i:19135 original size:69 final size:69
Alignment explanation
Indices: 19051--19286 Score: 395
Period size: 69 Copynumber: 3.4 Consensus size: 69
19041 CTCTTTTTAG
* *
19051 ATTAAGTTCTTTTATTCTACTTAATTACCCTGAATTAAGCCACTTATTAACTCCACTTAATCACC
1 ATTAAGTTCTTTTATTCTACTTAATTACCCTGAATTAAGCCACTTATTAACTCTACTTAATTACC
19116 CTGA
66 CTGA
*
19120 ATTAAGTTCTTTTATTCTACTTAATTACCCTGAATTAAGCCACTTACTAACTCTACTTAATTACC
1 ATTAAGTTCTTTTATTCTACTTAATTACCCTGAATTAAGCCACTTATTAACTCTACTTAATTACC
*
19185 ATGA
66 CTGA
* **
19189 ATTGAGTTCTTTTATTCTACTTAATTACCCTGAATTAAG-TGCTTATTAACTCTACTTAATTACC
1 ATTAAGTTCTTTTATTCTACTTAATTACCCTGAATTAAGCCACTTATTAACTCTACTTAATTACC
19253 CTGA
66 CTGA
19257 ATTAAGTTCTTTTATTCTACTTAATT-CCCT
1 ATTAAGTTCTTTTATTCTACTTAATTACCCT
19287 TCCCTGAAAT
Statistics
Matches: 157, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
67 4 0.03
68 50 0.32
69 103 0.66
ACGTcount: A:0.29, C:0.22, G:0.06, T:0.43
Consensus pattern (69 bp):
ATTAAGTTCTTTTATTCTACTTAATTACCCTGAATTAAGCCACTTATTAACTCTACTTAATTACC
CTGA
Found at i:19367 original size:39 final size:39
Alignment explanation
Indices: 19309--19768 Score: 659
Period size: 39 Copynumber: 12.2 Consensus size: 39
19299 AGCATGTGCC
* *
19309 TCAGTCATTCTTTACCTAATTTCCTTCCTCGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
* *
19348 TAAGTCTTTCTTTGCCTAATTTCCTTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
*
19387 TCAGTCTATCTTTACCTAATTTCCTTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
19426 TCAGTCTTTCTTTACCTAATTTCCTT-CTTCGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTT-GAAATTAAG
* * *
19465 TCAGTCTTTCATTAACTAATTTCCTTCTTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
19504 TCAGTCTTTCTTTACCTAA--T--TTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
19539 TCAGTCTATT-TTTACCTAATTTCCTTCCTTGAAATTAAG
1 TCAGTCT-TTCTTTACCTAATTTCCTTCCTTGAAATTAAG
*
19578 TCAGTCTATCTTTACCTAA--T--TTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
*
19613 TCAGTCTATCTTTACCTAATTTCCTTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
*
19652 TCAGTCTATCTTTACCTAATTTCCTTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
*
19691 TCAGTCTTTCTTTATCTAA-TT--TT-CTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
*
19726 TCAGTCTATCTTTACCTAA--T--TTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
19761 TCAGTCTT
1 TCAGTCTT
19769 CTAATGTTTT
Statistics
Matches: 388, Mismatches: 20, Indels: 30
0.89 0.05 0.07
Matches are distributed among these distances:
34 3 0.01
35 112 0.29
36 4 0.01
37 4 0.01
38 6 0.02
39 257 0.66
40 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (39 bp):
TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
Found at i:19450 original size:74 final size:74
Alignment explanation
Indices: 19309--19767 Score: 649
Period size: 74 Copynumber: 6.1 Consensus size: 74
19299 AGCATGTGCC
* * * *
19309 TCAGTC-ATTCTTTACCTAATTTCCTTCCTCGAAATTAAGTAAGTCTTTCTTTGCCTAATTTCCT
1 TCAGTCTA-TCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTATCTTTACCTAA--T--T
19373 TCCTTGAAATTAAG
61 TCCTTGAAATTAAG
*
19387 TCAGTCTATCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTCTTTACCTAATTTCCTT
1 TCAGTCTATCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTATCTTTACCTAATTT-C--
19452 CTTCGAAATTAAG
63 CTT-GAAATTAAG
* * * * *
19465 TCAGTCTTTCATTAACTAATTTCCTTCTTTGAAATTAAGTCAGTCTTTCTTTACCTAATTTCCTT
1 TCAGTCTATCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTATCTTTACCTAATTTCCTT
19530 GAAATTAAG
66 GAAATTAAG
*
19539 TCAGTCTATTTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTATCTTTACCTAATTTCCTT
1 TCAGTCTATCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTATCTTTACCTAATTTCCTT
19604 GAAATTAAG
66 GAAATTAAG
19613 TCAGTCTATCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTATCTTTACCTAATTTCCTT
1 TCAGTCTATCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTATCTTTACCTAA--T--TT
19678 CCTTGAAATTAAG
62 CCTTGAAATTAAG
* *
19691 TCAGTCTTTCTTTATCTAA-TT--TT-CTTGAAATTAAGTCAGTCTATCTTTACCTAATTTCCTT
1 TCAGTCTATCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTATCTTTACCTAATTTCCTT
19752 GAAATTAAG
66 GAAATTAAG
19761 TCAGTCT
1 TCAGTCT
19768 TCTAATGTTT
Statistics
Matches: 356, Mismatches: 16, Indels: 26
0.89 0.04 0.07
Matches are distributed among these distances:
70 22 0.06
72 1 0.00
74 167 0.47
75 6 0.02
76 2 0.01
77 6 0.02
78 151 0.42
79 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (74 bp):
TCAGTCTATCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTATCTTTACCTAATTTCCTT
GAAATTAAG
Found at i:19531 original size:113 final size:113
Alignment explanation
Indices: 19309--19768 Score: 670
Period size: 113 Copynumber: 4.1 Consensus size: 113
19299 AGCATGTGCC
* * * *
19309 TCAGTCATTCTTTACCTAATTTCCTTCCTCGAAATTAAGTAAGTCTTTCTTTGCCTAATTTCCTT
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTCTTTACCTAATTT-CTT
19374 CCTTGAAATTAAGTCAGTCTATCTTTACCTAATTTCCTTCCTTGAAATTAAG
65 -CTTGAAATTAAGTCAGTCTATCTTTACCTAA-TT-CTTCCTTGAAATTAAG
* *
19426 TCAGTCTTTCTTTACCTAATTTCCTT-CTTCGAAATTAAGTCAGTCTTTCATTAACTAATTTCCT
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTT-GAAATTAAGTCAGTCTTTCTTTACCTAATTT-CT
*
19490 TCTTTGAAATTAAGTCAGTCTTTCTTTACCTAA-T-TTCCTTGAAATTAAG
64 TC-TTGAAATTAAGTCAGTCTATCTTTACCTAATTCTTCCTTGAAATTAAG
*
19539 TCAGTCTATT-TTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTATCTTTACCTAATTTC--
1 TCAGTCT-TTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTCTTTACCTAATTTCTT
19601 CTTGAAATTAAGTCAGTCTATCTTTACCTAATTTCCTTCCTTGAAATTAAG
65 CTTGAAATTAAGTCAGTCTATCTTTACCTAA-TT-CTTCCTTGAAATTAAG
* *
19652 TCAGTCTATCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTCTTTATCTAA-TT-TTC
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTCTTTACCTAATTTCTTC
19715 TTGAAATTAAGTCAGTCTATCTTTACCTAA-T-TTCCTTGAAATTAAG
66 TTGAAATTAAGTCAGTCTATCTTTACCTAATTCTTCCTTGAAATTAAG
19761 TCAGTCTT
1 TCAGTCTT
19769 CTAATGTTTT
Statistics
Matches: 317, Mismatches: 15, Indels: 30
0.88 0.04 0.08
Matches are distributed among these distances:
109 51 0.16
110 1 0.00
111 2 0.01
112 4 0.01
113 165 0.52
114 5 0.02
115 1 0.00
116 3 0.01
117 85 0.27
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (113 bp):
TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTCTTTACCTAATTTCTTC
TTGAAATTAAGTCAGTCTATCTTTACCTAATTCTTCCTTGAAATTAAG
Found at i:19817 original size:40 final size:40
Alignment explanation
Indices: 19773--19940 Score: 300
Period size: 40 Copynumber: 4.2 Consensus size: 40
19763 AGTCTTCTAA
* *
19773 TGTTTTTACTTAATTACTATGAATTAAGTCTTTTGCCTAC
1 TGTTTTTACTTAATTTCTATGAATTAAGTCTTTTGACTAC
19813 TGTTTTTACTTAATTTCTATGAATTAAGTCTTTTGACTAC
1 TGTTTTTACTTAATTTCTATGAATTAAGTCTTTTGACTAC
*
19853 TGTTTTTACTTAATTTCTATGAATTAAGTCTTTTGACTGC
1 TGTTTTTACTTAATTTCTATGAATTAAGTCTTTTGACTAC
*
19893 TGTTTTTACTTCATTTCTATGAATTAAGTCTTTTGACTAC
1 TGTTTTTACTTAATTTCTATGAATTAAGTCTTTTGACTAC
19933 TGTTTTTA
1 TGTTTTTA
19941 TCTATGAATT
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 123 1.00
ACGTcount: A:0.23, C:0.13, G:0.11, T:0.53
Consensus pattern (40 bp):
TGTTTTTACTTAATTTCTATGAATTAAGTCTTTTGACTAC
Found at i:23469 original size:27 final size:26
Alignment explanation
Indices: 23432--23482 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
23422 ATTGCCCCCA
*
23432 AAAGTGACCAAAATATCCCTGAAACG
1 AAAGTGACCAAAATACCCCTGAAACG
23458 AAAGATGACCAAAATACCCCTGAAA
1 AAAG-TGACCAAAATACCCCTGAAA
23483 TGACCAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.49, C:0.24, G:0.14, T:0.14
Consensus pattern (26 bp):
AAAGTGACCAAAATACCCCTGAAACG
Found at i:28587 original size:21 final size:22
Alignment explanation
Indices: 28563--28615 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
28553 CCCGCGGCAC
*
28563 CTGGGTGCCCAAGCCAACG-GG
1 CTGGGTGCCCAAGCCAAAGCGG
* *
28584 CTGGGTGCTC-AGGCAAAGCGG
1 CTGGGTGCCCAAGCCAAAGCGG
28605 CTGGGTGCCCA
1 CTGGGTGCCCA
28616 CCCACGAGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.17, C:0.30, G:0.40, T:0.13
Consensus pattern (22 bp):
CTGGGTGCCCAAGCCAAAGCGG
Done.