Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014262.1 Corchorus capsularis cultivar CVL-1 contig14283, 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: 78916
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2523 original size:1 final size:1
Alignment explanation
Indices: 2519--2561 Score: 86
Period size: 1 Copynumber: 43.0 Consensus size: 1
2509 CCACATTTGG
2519 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2562 CTTTCATTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:6319 original size:15 final size:16
Alignment explanation
Indices: 6284--6322 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
6274 AAGAGAGATG
6284 CCGCCACCGGGATGGGGA
1 CCGCCACCGGGA--GGGA
6302 CCGCCACCGGGA-GGA
1 CCGCCACCGGGAGGGA
6317 CCGCCA
1 CCGCCA
6323 GGGCCTCCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
18 12 0.57
ACGTcount: A:0.18, C:0.41, G:0.38, T:0.03
Consensus pattern (16 bp):
CCGCCACCGGGAGGGA
Found at i:6439 original size:21 final size:21
Alignment explanation
Indices: 6414--6455 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
6404 TCATTGACAT
6414 GTTATTTATCAATCATCATTC
1 GTTATTTATCAATCATCATTC
6435 GTTATTTATCAATCATCATTC
1 GTTATTTATCAATCATCATTC
6456 ATCACCCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.48
Consensus pattern (21 bp):
GTTATTTATCAATCATCATTC
Found at i:17738 original size:15 final size:15
Alignment explanation
Indices: 17720--17750 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17710 AACAATTATA
17720 ATAGCAACAAAATTC
1 ATAGCAACAAAATTC
17735 ATAGCAACAAAATTC
1 ATAGCAACAAAATTC
17750 A
1 A
17751 GAGCTGTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (15 bp):
ATAGCAACAAAATTC
Found at i:21683 original size:23 final size:23
Alignment explanation
Indices: 21657--21710 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
21647 AAATCTGTTT
21657 ATATTATAT-ATATTCATATATAA
1 ATATTATATCATATT-ATATATAA
*
21680 ATATGATATATCATATTATTTATAA
1 ATAT--TATATCATATTATATATAA
21705 ATATTA
1 ATATTA
21711 AAATTTTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 6 0.22
25 16 0.59
26 5 0.19
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATTATATCATATTATATATAA
Found at i:21689 original size:25 final size:25
Alignment explanation
Indices: 21661--21708 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
21651 CTGTTTATAT
21661 TATAT-ATATTCATATATAAATATGA
1 TATATCATATT-ATATATAAATATGA
*
21686 TATATCATATTATTTATAAATAT
1 TATATCATATTATATATAAATAT
21709 TAAAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (25 bp):
TATATCATATTATATATAAATATGA
Found at i:21995 original size:26 final size:26
Alignment explanation
Indices: 21959--22009 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
21949 TATCTGAATA
21959 TAAATACATAGGAAATAGATAGAGCC
1 TAAATACATAGGAAATAGATAGAGCC
21985 TAAATACATAGGAAATAGATAGAGC
1 TAAATACATAGGAAATAGATAGAGC
22010 GGCATGTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.20
Consensus pattern (26 bp):
TAAATACATAGGAAATAGATAGAGCC
Found at i:23604 original size:2 final size:2
Alignment explanation
Indices: 23593--23621 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
23583 ATTACTATTA
23593 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23622 CTCTTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:33630 original size:29 final size:30
Alignment explanation
Indices: 33564--33622 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
33554 GAGTTTTTGA
33564 CCAAACCATTATACCTTTTAAAAATAATTC
1 CCAAACCATTATACCTTTTAAAAATAATTC
* *
33594 CCAAACCATTGTA-CTTTTAAAATTAATTC
1 CCAAACCATTATACCTTTTAAAAATAATTC
33623 TCATACCACC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.41, C:0.22, G:0.02, T:0.36
Consensus pattern (30 bp):
CCAAACCATTATACCTTTTAAAAATAATTC
Found at i:34130 original size:13 final size:13
Alignment explanation
Indices: 34112--34137 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34102 TCAAATGATT
34112 TGTTTAATTTTGA
1 TGTTTAATTTTGA
34125 TGTTTAATTTTGA
1 TGTTTAATTTTGA
34138 AGTCAAATTT
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:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (13 bp):
TGTTTAATTTTGA
Found at i:35541 original size:29 final size:29
Alignment explanation
Indices: 35495--35552 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
35485 GTTGTCTAAT
*
35495 TATAAACGTCAACTATTCCATTTTTTTTC
1 TATAAACGTCAACCATTCCATTTTTTTTC
35524 TATAAACGTCAACCATTCCATTTTTTTTC
1 TATAAACGTCAACCATTCCATTTTTTTTC
35553 AATGCATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.22, G:0.03, T:0.47
Consensus pattern (29 bp):
TATAAACGTCAACCATTCCATTTTTTTTC
Found at i:35779 original size:76 final size:75
Alignment explanation
Indices: 35699--35853 Score: 256
Period size: 76 Copynumber: 2.1 Consensus size: 75
35689 TTTCTTGGGA
* * * *
35699 ATTTCCAAAATTTTAGTAAGTCAGAAAATATGAAGAATATACAAAAAAATGTTGTATATATATGT
1 ATTTCCAAAATTTTAGTAAGTCAGAAAATACGAAAAATATACAAAAAAATGTTATATATATATAT
35764 AAAAAAAGATT
66 -AAAAAAGATT
35775 ATTTCCAAAATTTTAGTAAGTCAGAAAATACGAAAAATATACAAAAAAATGTTATATATATATAT
1 ATTTCCAAAATTTTAGTAAGTCAGAAAATACGAAAAATATACAAAAAAATGTTATATATATATAT
*
35840 ATAAAAGATT
66 AAAAAAGATT
35850 ATTT
1 ATTT
35854 ATATATATAT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
75 13 0.18
76 61 0.82
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.33
Consensus pattern (75 bp):
ATTTCCAAAATTTTAGTAAGTCAGAAAATACGAAAAATATACAAAAAAATGTTATATATATATAT
AAAAAAGATT
Found at i:38637 original size:7 final size:7
Alignment explanation
Indices: 38617--38658 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
38607 CTGAATTATT
38617 AGAAAAA
1 AGAAAAA
* *
38624 GGGAAAA
1 AGAAAAA
38631 AGAAAAA
1 AGAAAAA
38638 AG-AAAA
1 AGAAAAA
38644 AGAAAAA
1 AGAAAAA
38651 AGAAAAA
1 AGAAAAA
38658 A
1 A
38659 ATCGAACTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:38642 original size:13 final size:13
Alignment explanation
Indices: 38626--38657 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
38616 TAGAAAAAGG
38626 GAAAAAGAAAAAA
1 GAAAAAGAAAAAA
38639 GAAAAAGAAAAAA
1 GAAAAAGAAAAAA
38652 GAAAAA
1 GAAAAA
38658 AATCGAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
GAAAAAGAAAAAA
Found at i:38659 original size:21 final size:21
Alignment explanation
Indices: 38617--38658 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
38607 CTGAATTATT
*
38617 AGAAAAAGGGAAAAAGAAAAA
1 AGAAAAAGGAAAAAAGAAAAA
38638 AGAAAAA-GAAAAAAGAAAAA
1 AGAAAAAGGAAAAAAGAAAAA
38658 A
1 A
38659 ATCGAACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (21 bp):
AGAAAAAGGAAAAAAGAAAAA
Found at i:39143 original size:3 final size:3
Alignment explanation
Indices: 39135--39170 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
39125 TTCTCATTAT
39135 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39171 TATTCAATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:41989 original size:31 final size:31
Alignment explanation
Indices: 41921--42082 Score: 139
Period size: 31 Copynumber: 5.5 Consensus size: 31
41911 TCCTTTTGTG
* **
41921 CACGTGGCATGCCACGTG-C-CTTTTTTGAAA
1 CACGTGGCGTGCCACGTGTCAC-TTTTTGGTA
* *
41951 CATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
41982 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
*
42013 CA--T---GTGGCAC--G--ACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* * *
42035 CATGTGACGTGCCACATGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
42066 CACGTGGCGTGCCACGT
1 CACGTGGCGTGCCACGT
42083 CGGACACCGT
Statistics
Matches: 108, Mismatches: 13, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
22 13 0.12
24 2 0.02
26 5 0.05
27 6 0.06
29 2 0.02
30 17 0.16
31 62 0.57
32 1 0.01
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33
Consensus pattern (31 bp):
CACGTGGCGTGCCACGTGTCACTTTTTGGTA
Found at i:42033 original size:53 final size:53
Alignment explanation
Indices: 41971--42073 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
41961 GCCACGTGTC
* ** *
41971 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGACGTGACACATGTCACTTTTTGGTACACGTGGCACG
* *
42024 ACTTTTTGGTACATGTGACGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGACGTGACACATGTCACTTTTTGGTACACGTGGC
42074 GTGCCACGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.36
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGACGTGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:58775 original size:427 final size:427
Alignment explanation
Indices: 57980--58833 Score: 1708
Period size: 427 Copynumber: 2.0 Consensus size: 427
57970 TCATTGCCTA
57980 ATGCCAAGTCCATTACAATTAACAAAGCAAAAACTTCCTTAGCTAGCTGCAACAGCAGATTCAAC
1 ATGCCAAGTCCATTACAATTAACAAAGCAAAAACTTCCTTAGCTAGCTGCAACAGCAGATTCAAC
58045 AATCCTTCTTCAGTTTTGCTTGATTATTCATGATTCATCCCAAACAAAAATTCCAAAATACCAAC
66 AATCCTTCTTCAGTTTTGCTTGATTATTCATGATTCATCCCAAACAAAAATTCCAAAATACCAAC
58110 TCCCAAGGAAACAAAGAGTGACAAAGACGAAATGGAACGAATGAATTCAAGCTCAAAGAGAAGTA
131 TCCCAAGGAAACAAAGAGTGACAAAGACGAAATGGAACGAATGAATTCAAGCTCAAAGAGAAGTA
58175 CAAGTAGAGTGTATGCAAACATAGATTGATTACAAATTCAAGCTGTCTTTCAACAAATGTTACAA
196 CAAGTAGAGTGTATGCAAACATAGATTGATTACAAATTCAAGCTGTCTTTCAACAAATGTTACAA
58240 ATTAAGGTTATAATCACACTCACACAATAACATCAAAGCCAATATATATGAAGCAAACAAAGTAC
261 ATTAAGGTTATAATCACACTCACACAATAACATCAAAGCCAATATATATGAAGCAAACAAAGTAC
58305 GAAGTTCTCAAATTTATTCAAACAATAATCCATGTCATGAAGAACGCACCGCAGGGACTCTGAAC
326 GAAGTTCTCAAATTTATTCAAACAATAATCCATGTCATGAAGAACGCACCGCAGGGACTCTGAAC
58370 TCTGAATCAAACAAAGCAAAGGAAAAGCTTCCGTAGG
391 TCTGAATCAAACAAAGCAAAGGAAAAGCTTCCGTAGG
58407 ATGCCAAGTCCATTACAATTAACAAAGCAAAAACTTCCTTAGCTAGCTGCAACAGCAGATTCAAC
1 ATGCCAAGTCCATTACAATTAACAAAGCAAAAACTTCCTTAGCTAGCTGCAACAGCAGATTCAAC
58472 AATCCTTCTTCAGTTTTGCTTGATTATTCATGATTCATCCCAAACAAAAATTCCAAAATACCAAC
66 AATCCTTCTTCAGTTTTGCTTGATTATTCATGATTCATCCCAAACAAAAATTCCAAAATACCAAC
58537 TCCCAAGGAAACAAAGAGTGACAAAGACGAAATGGAACGAATGAATTCAAGCTCAAAGAGAAGTA
131 TCCCAAGGAAACAAAGAGTGACAAAGACGAAATGGAACGAATGAATTCAAGCTCAAAGAGAAGTA
58602 CAAGTAGAGTGTATGCAAACATAGATTGATTACAAATTCAAGCTGTCTTTCAACAAATGTTACAA
196 CAAGTAGAGTGTATGCAAACATAGATTGATTACAAATTCAAGCTGTCTTTCAACAAATGTTACAA
58667 ATTAAGGTTATAATCACACTCACACAATAACATCAAAGCCAATATATATGAAGCAAACAAAGTAC
261 ATTAAGGTTATAATCACACTCACACAATAACATCAAAGCCAATATATATGAAGCAAACAAAGTAC
58732 GAAGTTCTCAAATTTATTCAAACAATAATCCATGTCATGAAGAACGCACCGCAGGGACTCTGAAC
326 GAAGTTCTCAAATTTATTCAAACAATAATCCATGTCATGAAGAACGCACCGCAGGGACTCTGAAC
58797 TCTGAATCAAACAAAGCAAAGGAAAAGCTTCCGTAGG
391 TCTGAATCAAACAAAGCAAAGGAAAAGCTTCCGTAGG
58834 TTGACAGGCT
Statistics
Matches: 427, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
427 427 1.00
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.23
Consensus pattern (427 bp):
ATGCCAAGTCCATTACAATTAACAAAGCAAAAACTTCCTTAGCTAGCTGCAACAGCAGATTCAAC
AATCCTTCTTCAGTTTTGCTTGATTATTCATGATTCATCCCAAACAAAAATTCCAAAATACCAAC
TCCCAAGGAAACAAAGAGTGACAAAGACGAAATGGAACGAATGAATTCAAGCTCAAAGAGAAGTA
CAAGTAGAGTGTATGCAAACATAGATTGATTACAAATTCAAGCTGTCTTTCAACAAATGTTACAA
ATTAAGGTTATAATCACACTCACACAATAACATCAAAGCCAATATATATGAAGCAAACAAAGTAC
GAAGTTCTCAAATTTATTCAAACAATAATCCATGTCATGAAGAACGCACCGCAGGGACTCTGAAC
TCTGAATCAAACAAAGCAAAGGAAAAGCTTCCGTAGG
Found at i:63794 original size:65 final size:64
Alignment explanation
Indices: 63688--63831 Score: 225
Period size: 65 Copynumber: 2.2 Consensus size: 64
63678 TTCAGTCAAC
* * *
63688 CAAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGATAGAG
1 CAAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGAAAAGGACGACTTAGGCAAAACATAGAG
*
63752 CAAAAAAAAAAAAAGGCTCGCTAAGTTGAAAATCCTGAAAAGGACGACTTAGGCAAAACTTAGAG
1 CAAAAAAAAAAAAA-GCTCGCTAAGTTGAAAATCCTGAAAAGGACGACTTAGGCAAAACATAGAG
*
63817 CACCAAAAAAAAAAA
1 CA-AAAAAAAAAAAA
63832 TGAACTACGT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
64 14 0.19
65 48 0.66
66 11 0.15
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (64 bp):
CAAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGAAAAGGACGACTTAGGCAAAACATAGAG
Found at i:64597 original size:16 final size:16
Alignment explanation
Indices: 64576--64610 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
64566 ACAATTCAGA
*
64576 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAACTCTG
64592 AAGCAGAAAAACTCTG
1 AAGCAGAAAAACTCTG
64608 AAG
1 AAG
64611 AATTTCAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAACTCTG
Found at i:66465 original size:21 final size:21
Alignment explanation
Indices: 66431--66470 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
66421 TGCCCTTATA
*
66431 TAAAAAATAATTATTATATTC
1 TAAAAAATAATTATAATATTC
**
66452 TAAAAAATGTTTATAATAT
1 TAAAAAATAATTATAATAT
66471 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (21 bp):
TAAAAAATAATTATAATATTC
Found at i:75956 original size:20 final size:20
Alignment explanation
Indices: 75931--75972 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
75921 TTAATTAATT
75931 AAGAAAATTCATATTATCAG
1 AAGAAAATTCATATTATCAG
*
75951 AAGAAAATTGATATTATCAG
1 AAGAAAATTCATATTATCAG
75971 AA
1 AA
75973 TCCGGGGCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (20 bp):
AAGAAAATTCATATTATCAG
Done.