Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013740.1 Corchorus capsularis cultivar CVL-1 contig13761, 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: 29063
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:5314 original size:15 final size:15
Alignment explanation
Indices: 5294--5323 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5284 CCGCGCACCC
5294 CCGGGAGTCTTCACG
1 CCGGGAGTCTTCACG
5309 CCGGGAGTCTTCACG
1 CCGGGAGTCTTCACG
5324 TTACTGGCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.33, G:0.33, T:0.20
Consensus pattern (15 bp):
CCGGGAGTCTTCACG
Found at i:5420 original size:48 final size:48
Alignment explanation
Indices: 5345--5441 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
5335 GCCATTAGAT
*
5345 GCCGATGAAGGTGGATTCTTTCGCTTTGAGCTTGATTCGGTGGCAACG
1 GCCGATGAAGGTGCATTCTTTCGCTTTGAGCTTGATTCGGTGGCAACG
*
5393 GCCGATGAAGGTGCATTCTTTCTCTTTGAGCTTGATTCGGTGGCAACG
1 GCCGATGAAGGTGCATTCTTTCGCTTTGAGCTTGATTCGGTGGCAACG
5441 G
1 G
5442 GCTTAGGATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.16, C:0.20, G:0.32, T:0.32
Consensus pattern (48 bp):
GCCGATGAAGGTGCATTCTTTCGCTTTGAGCTTGATTCGGTGGCAACG
Found at i:5625 original size:6 final size:6
Alignment explanation
Indices: 5618--5697 Score: 79
Period size: 6 Copynumber: 13.3 Consensus size: 6
5608 GGTTTTCTCC
* * * *
5618 TCCTCC TCCTCT TCCTCT TCCTCT TCCTCA TCCTCA TCCTCA TCCTCA
1 TCCTCA TCCTCA TCCTCA TCCTCA TCCTCA TCCTCA TCCTCA TCCTCA
* * * * *
5666 TCATCA TCATCA TCATCA TCATCA TCATCA TC
1 TCCTCA TCCTCA TCCTCA TCCTCA TCCTCA TC
5698 ATCACCGTCT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.17, C:0.45, G:0.00, T:0.38
Consensus pattern (6 bp):
TCCTCA
Found at i:5671 original size:3 final size:3
Alignment explanation
Indices: 5645--5701 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
5635 TTCCTCTTCC
* * *
5645 TCA TCC TCA TCC TCA TCC TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
5693 TCA TCA TCA
1 TCA TCA TCA
5702 CCGTCTTCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.28, C:0.39, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:6669 original size:53 final size:53
Alignment explanation
Indices: 6589--6695 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
6579 TTGTTATCAT
* *
6589 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAGAGAATTTATAAAA
1 TTCACAACAAAATTTGATTTCTTAACTGAATTTACTTAAAAGAATTTATAAAA
*
6642 TTCACAACAAAATTTGATTTCTTAACTGAATTTACTTAAAATAATTTATAAAA
1 TTCACAACAAAATTTGATTTCTTAACTGAATTTACTTAAAAGAATTTATAAAA
6695 T
1 T
6696 AAAACAGCCG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (53 bp):
TTCACAACAAAATTTGATTTCTTAACTGAATTTACTTAAAAGAATTTATAAAA
Found at i:7997 original size:438 final size:443
Alignment explanation
Indices: 7037--8052 Score: 1101
Period size: 438 Copynumber: 2.3 Consensus size: 443
7027 TTTCAAAAGT
* ** * * * *
7037 ATTTTCTAGAATTGAAACATAAAAATTAG-ATTTTGA-ATCTTTCATGAAAATTGTAGATTATAA
1 ATTTTTTAGAATCAAAACATAAAAATTGGCA-TTTGAGTTC-TTCATGAAAATTGTAGATCATGA
* * * *
7100 AATTACTTTTTAATAGACACCT-AAACTACCTTAATTGGACAAATAGAGAAAAAAAAATAAAAAT
64 AATTACATTTTAATAGACACATGAATC-ACCTTAATCGGACAAATAGAGAAAAAAAAATAAAAAT
* *
7164 AAATGAAGTGTTAAATCGAGTAAGATAGAATTTGTAAAGGACTAAATAGCATAAAATATAAAATA
128 AAATGAAATCTTAAATCGAGTAAGATAGAATTTGTAAAGGACT-AATAG-AT-AAATATAAAATA
* * * * *
7229 GAAAAGTATGAGATTCATTTGATAACTAATTCAAATAAGAAAATATTACTTAATGGATATCTTGA
190 GAAAAATATGAGAGTCATTTGATAAATAATCCAAATAAGAAAATATTACTTAATGGAGATCTTGA
* * * * * * *
7294 AACATAAAAATTCCCTTTTACACCATTCATGAAACTTGTAGATCAAATTAATTTTCTAGTTCTTC
255 AACATAAAAACTCCCTTTTACACCATTCATGAAACTCGTAGATCAAATTAACTTTCGAATCCTTA
** * * * * *
7359 ATAAAAGTTGTAGATCATACAGTAACCTTTTAACCAACACTTGAATAACTTTAATCGGACATGTG
320 ATAAAAGTCATAAATCATACAATAACCTTTGAACCAACACTTCAATAACTTCAATCGGACATGTG
** * * * * ** *
7424 GATCGAAAATTATATGGTATTAAATAGATCAACAACTGAAACGACCAAATTTAGGAAGT
385 GATAAAAAATTATACGATATTAAATAGATCAACAACTAAAACAAAAAAATTTAGGAAGC
* * * * * * *
7483 ATTTTTTTGAATTAGAACATAAAAATTTGCTTTTGAGTTCTTAATGAAAGTTGTAGATCATGAAA
1 ATTTTTTAGAATCAAAACATAAAAATTGGCATTTGAGTTCTTCATGAAAATTGTAGATCATGAAA
* ** *
7548 TTACATTTTAATAGACACATGAATCAACTTAATCGGACAAATA-A-AACGAATAAT-AAAA-AAA
66 TTACATTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAGAAAAAAAAATAAAAATAAA
*
7609 T-AAATCTTAAA-CGTTAGATTAAGATAGAATTTGTAAATGACT-A-AG-T-AATATAAAATAGA
131 TGAAATCTTAAATCG--AG--TAAGATAGAATTTGTAAAGGACTAATAGATAAATATAAAATAGA
* * * ** * *
7668 AAAATATGAGGGTCATTTGATAAATAATCCAAGTAAGAAAATGTTTGTTAGTGGAGATCTTGAAG
192 AAAATATGAGAGTCATTTGATAAATAATCCAAATAAGAAAATATTACTTAATGGAGATCTTGAAA
* * *
7733 CATAAAAACTCCCTTTTGA-ACCCTTTATGAAACTCGTAGATCAAATTTAGCTTTCGAATCCTTA
257 CATAAAAACTCCCTTTT-ACACCATTCATGAAACTCGTAGATCAAA-TTAACTTTCGAATCCTTA
* * *
7797 ATGAAAGTCATAAATCATGCAATAACCTTTGAACCGACACTTCAATAACTTCAATCGGACATGTG
320 ATAAAAGTCATAAATCATACAATAACCTTTGAACCAACACTTCAATAACTTCAATCGGACATGTG
* * *
7862 GATAAAAAATTATACGATATTAAATTGA-CTGACAA-TCAAAACAAAAAAATTTCGGAAGC
385 GATAAAAAATTATACGATATTAAATAGATC-AACAACT-AAAACAAAAAAATTTAGGAAGC
* *
7921 ATTTTTTAGAATCAAAACATTAAAATTGGCATTTGTGTTCTTCATGAAAATTGTAGATCATGAAA
1 ATTTTTTAGAATCAAAACATAAAAATTGGCATTTGAGTTCTTCATGAAAATTGTAGATCATGAAA
* * * * * *
7986 TTACCTTTTAATAGACACTTGAATCACCTTAATCAGACAAATAGGGAAAAAAATACAAAAATAAA
66 TTACATTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAGAAAAAAAAATAAAAATAAA
8051 TG
131 TG
8053 TGAGCGCGTT
Statistics
Matches: 469, Mismatches: 85, Indels: 35
0.80 0.14 0.06
Matches are distributed among these distances:
437 107 0.23
438 206 0.44
439 1 0.00
440 7 0.01
441 14 0.03
442 11 0.02
443 4 0.01
444 29 0.06
445 1 0.00
446 84 0.18
447 5 0.01
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (443 bp):
ATTTTTTAGAATCAAAACATAAAAATTGGCATTTGAGTTCTTCATGAAAATTGTAGATCATGAAA
TTACATTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAGAAAAAAAAATAAAAATAAA
TGAAATCTTAAATCGAGTAAGATAGAATTTGTAAAGGACTAATAGATAAATATAAAATAGAAAAA
TATGAGAGTCATTTGATAAATAATCCAAATAAGAAAATATTACTTAATGGAGATCTTGAAACATA
AAAACTCCCTTTTACACCATTCATGAAACTCGTAGATCAAATTAACTTTCGAATCCTTAATAAAA
GTCATAAATCATACAATAACCTTTGAACCAACACTTCAATAACTTCAATCGGACATGTGGATAAA
AAATTATACGATATTAAATAGATCAACAACTAAAACAAAAAAATTTAGGAAGC
Found at i:15290 original size:20 final size:21
Alignment explanation
Indices: 15265--15312 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
15255 AAATGAGTAG
15265 ACTCTCACT-AAGA-AGAGAAA
1 ACTCTCA-TGAAGAGAGAGAAA
15285 ACTCTCATGAAGAGAGAG-AA
1 ACTCTCATGAAGAGAGAGAAA
*
15305 GCTCTCAT
1 ACTCTCAT
15313 TTTAGAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 1 0.04
20 20 0.80
21 4 0.16
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.19
Consensus pattern (21 bp):
ACTCTCATGAAGAGAGAGAAA
Found at i:15724 original size:66 final size:66
Alignment explanation
Indices: 15643--15775 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
15633 ATAAATTAAT
*
15643 CACTCAATTGACAAGTTGGATGGATTAATACAGATCTAAATTAGTAATATTCCCCCTAAACTTAC
1 CACTCAATTGACAAGTAGGATGGATTAATACAGATCTAAATTAGTAATATTCCCCCTAAACTTAC
15708 C
66 C
* *
15709 CACTCAATTGACAAGTAGGATGGATTAATATAGATCTAAATTAGTACTATTCCCCCTAAACTTAC
1 CACTCAATTGACAAGTAGGATGGATTAATACAGATCTAAATTAGTAATATTCCCCCTAAACTTAC
15774 C
66 C
15775 C
1 C
15776 TATTCCGGTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (66 bp):
CACTCAATTGACAAGTAGGATGGATTAATACAGATCTAAATTAGTAATATTCCCCCTAAACTTAC
C
Found at i:16278 original size:3 final size:3
Alignment explanation
Indices: 16270--16295 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16260 AAATTAATAA
16270 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
16296 AGGGTTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:16751 original size:39 final size:39
Alignment explanation
Indices: 16678--16756 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 39
16668 ATTTATAACT
* *
16678 AGGGGCTAAATCTGGATTTAATTTCTTACCTTAATTATC
1 AGGGGCTAAACCTGAATTTAATTTCTTACCTTAATTATC
* *
16717 AGGGGACTAAACCTGAATTTAATTTGTT-CTTTAATTATC
1 AGGGG-CTAAACCTGAATTTAATTTCTTACCTTAATTATC
16756 A
1 A
16757 AGGAGAGACA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 16 0.46
40 19 0.54
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (39 bp):
AGGGGCTAAACCTGAATTTAATTTCTTACCTTAATTATC
Found at i:19750 original size:18 final size:18
Alignment explanation
Indices: 19727--19762 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19717 TCAGTTTCAT
*
19727 CTCCACAAGCAGAAGCAC
1 CTCCACAACCAGAAGCAC
*
19745 CTCCACTACCAGAAGCAC
1 CTCCACAACCAGAAGCAC
19763 TATTTCCTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.42, G:0.14, T:0.08
Consensus pattern (18 bp):
CTCCACAACCAGAAGCAC
Found at i:19891 original size:12 final size:12
Alignment explanation
Indices: 19873--19915 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
19863 AGGAGGAGGA
*
19873 GGAGGTGCTGCC
1 GGAGGTGCAGCC
* *
19885 GGTGGTGCAGCT
1 GGAGGTGCAGCC
19897 GGAGGTGCAGCC
1 GGAGGTGCAGCC
19909 GGAGGTG
1 GGAGGTG
19916 GAGGAGCAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.12, C:0.19, G:0.53, T:0.16
Consensus pattern (12 bp):
GGAGGTGCAGCC
Found at i:28727 original size:68 final size:67
Alignment explanation
Indices: 28618--28754 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 67
28608 AAAATACTAG
*
28618 ATCTATGGCACTCACTTTGTGAGTGTAGAAATAAAAAGGTAGTTTATAGTAGTTTTCTTTTTTGA
1 ATCTATGGCACTCACTTTGTGAGTATAGAAATAAAAAGGTAGTTTATAGTAGTTTTC-TTTTTGA
28683 CAC
65 CAC
28686 ATCTATGGCACTCACTTTGTGAGTATAGAAATAAAAAGGTAGTTTATAGTAGTTTTCTTTTTGAC
1 ATCTATGGCACTCACTTTGTGAGTATAGAAATAAAAAGGTAGTTTATAGTAGTTTTCTTTTTGAC
28751 AC
66 AC
28753 AT
1 AT
28755 TTAAATTGGT
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
67 12 0.18
68 56 0.82
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (67 bp):
ATCTATGGCACTCACTTTGTGAGTATAGAAATAAAAAGGTAGTTTATAGTAGTTTTCTTTTTGAC
AC
Done.