Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016146.1 Corchorus capsularis cultivar CVL-1 contig16167, 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: 12546
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1281 original size:1 final size:1
Alignment explanation
Indices: 1275--1299 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1265 ACATGTATTG
1275 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1300 ACAAGTACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:6625 original size:19 final size:20
Alignment explanation
Indices: 6598--6635 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
6588 TACTATTATT
6598 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
6618 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
6636 AATATCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:6936 original size:44 final size:44
Alignment explanation
Indices: 6855--6944 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 44
6845 AGGTTATCAA
* * *
6855 AGTGTGGTTAGCAAAATTTCATATGAAAGTTATCAAAATTTTAT
1 AGTGTGGTTACCAAAATTTCATATGAAAGTTACCAAAATTTCAT
***
6899 AGTGTGGTTACCAAAATTTCATA-GCGTGGTTACCAAAATTTCAT
1 AGTGTGGTTACCAAAATTTCATATG-AAAGTTACCAAAATTTCAT
6943 AG
1 AG
6945 GATCAGGTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 1 0.03
44 38 0.97
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (44 bp):
AGTGTGGTTACCAAAATTTCATATGAAAGTTACCAAAATTTCAT
Found at i:6960 original size:24 final size:22
Alignment explanation
Indices: 6867--6991 Score: 92
Period size: 22 Copynumber: 5.6 Consensus size: 22
6857 TGTGGTTAGC
* * * *
6867 AAAATTTCATATGAAAGTTATC
1 AAAATTTCATAGGTAGGTTATT
* **
6889 AAAATTTTATAGTGT-GGTTACC
1 AAAATTTCATAG-GTAGGTTATT
**
6911 AAAATTTCATAGCGT-GGTTACC
1 AAAATTTCATAG-GTAGGTTATT
6933 AAAATTTCATAGGATCAGGTTATT
1 AAAATTTCATAGG-T-AGGTTATT
* *
6957 AAAATTTCTTAGGTTGGTTATT
1 AAAATTTCATAGGTAGGTTATT
*
6979 GAAATTTCATAGG
1 AAAATTTCATAGG
6992 GTGGTTAATT
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
21 1 0.01
22 66 0.77
23 2 0.02
24 17 0.20
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
AAAATTTCATAGGTAGGTTATT
Found at i:6978 original size:22 final size:22
Alignment explanation
Indices: 6883--6998 Score: 106
Period size: 22 Copynumber: 5.2 Consensus size: 22
6873 TCATATGAAA
* * *
6883 GTTATCAAAATTTTATAGTGTG
1 GTTATTAAAATTTCATAGGGTG
** *
6905 GTTACCAAAATTTCATAGCGTG
1 GTTATTAAAATTTCATAGGGTG
** *
6927 GTTACCAAAATTTCATAGGATCAG
1 GTTATTAAAATTTCATAGGGT--G
* *
6951 GTTATTAAAATTTCTTAGGTTG
1 GTTATTAAAATTTCATAGGGTG
*
6973 GTTATTGAAATTTCATAGGGTG
1 GTTATTAAAATTTCATAGGGTG
6995 GTTA
1 GTTA
6999 ATTATCACAA
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
22 62 0.77
24 18 0.22
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (22 bp):
GTTATTAAAATTTCATAGGGTG
Found at i:7144 original size:22 final size:21
Alignment explanation
Indices: 7034--7376 Score: 108
Period size: 22 Copynumber: 15.4 Consensus size: 21
7024 ATCAAAGAGA
* * *
7034 TTATCATAATGTCATAACAAGG
1 TTATCAAAATTTCAT-AGAAGG
*
7056 TTAT-AAGAATTTCATAG-TGTG
1 TTATCAA-AATTTCATAGAAG-G
* *
7077 ATTAACAAAATTTCATTAGGAGG
1 -TTATCAAAATTTCA-TAGAAGG
* * *
7100 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGAAGG
7122 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GAAGG
* * *
7144 TTATAAAAATCTCAATTTCATAAGG
1 TTATCAAAATTTC-A--T-AGAAGG
* * *
7169 AGTACCAAAATTTTATAGAAGG
1 -TTATCAAAATTTCATAGAAGG
* *
7191 TTATC-AAATCTCATAG-AGT
1 TTATCAAAATTTCATAGAAGG
* *
7210 TATAATCGAAATTTCATAGAGATCAGA
1 T-T-ATCAAAATTTCAT--AGA--AGG
* *
7237 TTATAAAAATTTCATAG-TGTTG
1 TTATCAAAATTTCATAGAAG--G
* *
7259 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-AAGG
*
7281 TTATCAAAA--TCATATAATGTG
1 TTATCAAAATTTCATAGAA-G-G
*
7302 ATTATCAGAATTTCATAGAAGGG
1 -TTATCAAAATTTCATAGAA-GG
* * * *
7325 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGA-AGG
*
7347 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGA-AGG
7369 TTATCAAA
1 TTATCAAA
7377 TGTTCAAAAT
Statistics
Matches: 240, Mismatches: 48, Indels: 66
0.68 0.14 0.19
Matches are distributed among these distances:
19 4 0.02
20 17 0.07
21 12 0.05
22 152 0.63
23 13 0.05
24 12 0.05
25 17 0.07
26 10 0.04
27 3 0.01
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCATAGAAGG
Found at i:7382 original size:22 final size:22
Alignment explanation
Indices: 7258--7376 Score: 111
Period size: 22 Copynumber: 5.4 Consensus size: 22
7248 TCATAGTGTT
*
7258 GTTATCAAAATTTCA-AAGCGAG
1 GTTATCAAAATTTCATAA-AGAG
*
7280 GTTATCAAAA--TCATATAATGTG
1 GTTATCAAAATTTCATA-AA-GAG
* *
7302 ATTATCAGAATTTCATAGAAG-G
1 GTTATCAAAATTTCATA-AAGAG
* * *
7324 GTCAACAAAATTTTATAAAGAG
1 GTTATCAAAATTTCATAAAGAG
7346 GTTATCAAAATTTCATAAAGAG
1 GTTATCAAAATTTCATAAAGAG
7368 GTTATCAAA
1 GTTATCAAA
7377 TGTTCAAAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 12
0.76 0.13 0.12
Matches are distributed among these distances:
20 3 0.04
21 4 0.05
22 63 0.81
23 1 0.01
24 7 0.09
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAAGAG
Found at i:7615 original size:11 final size:11
Alignment explanation
Indices: 7577--7617 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
7567 GGAGATTAAC
7577 AAAATTTCATAA
1 AAAATTT-ATAA
**
7589 AAAGGTTATAA
1 AAAATTTATAA
7600 AAAATTTATAA
1 AAAATTTATAA
7611 AAAATTT
1 AAAATTT
7618 CATAGGACGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 20 0.80
12 5 0.20
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (11 bp):
AAAATTTATAA
Found at i:7682 original size:40 final size:40
Alignment explanation
Indices: 7631--7758 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 40
7621 AGGACGAAGG
7631 TTATCAAAATTTCATAATGGGATCATAAAAAATAGTGTAA
1 TTATCAAAATTTCATAATGGGATCATAAAAAATAGTGTAA
* * * * * *
7671 TTATCATAATTTAATAGA-GAGATTAT-CATAAT--T-TAA
1 TTATCAAAATTTCATA-ATGGGATCATAAAAAATAGTGTAA
7707 TTATCAAAATTTCATAATGGGATCATAAAAAATAGTGTAA
1 TTATCAAAATTTCATAATGGGATCATAAAAAATAGTGTAA
*
7747 TTATCATAATTT
1 TTATCAAAATTT
7759 AATAGAGAGA
Statistics
Matches: 69, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
35 1 0.01
36 23 0.33
37 5 0.07
39 5 0.07
40 34 0.49
41 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (40 bp):
TTATCAAAATTTCATAATGGGATCATAAAAAATAGTGTAA
Found at i:7714 original size:76 final size:76
Alignment explanation
Indices: 7631--7780 Score: 300
Period size: 76 Copynumber: 2.0 Consensus size: 76
7621 AGGACGAAGG
7631 TTATCAAAATTTCATAATGGGATCATAAAAAATAGTGTAATTATCATAATTTAATAGAGAGATTA
1 TTATCAAAATTTCATAATGGGATCATAAAAAATAGTGTAATTATCATAATTTAATAGAGAGATTA
7696 TCATAATTTAA
66 TCATAATTTAA
7707 TTATCAAAATTTCATAATGGGATCATAAAAAATAGTGTAATTATCATAATTTAATAGAGAGATTA
1 TTATCAAAATTTCATAATGGGATCATAAAAAATAGTGTAATTATCATAATTTAATAGAGAGATTA
7772 TCATAATTT
66 TCATAATTT
7781 CATATGAATA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (76 bp):
TTATCAAAATTTCATAATGGGATCATAAAAAATAGTGTAATTATCATAATTTAATAGAGAGATTA
TCATAATTTAA
Found at i:9535 original size:27 final size:27
Alignment explanation
Indices: 9497--9570 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
9487 ACGGTCAAAT
9497 AGGGGCATTTTGGTCATTTTCACATTC
1 AGGGGCATTTTGGTCATTTTCACATTC
* ** *
9524 AGGGGCATTTTGGTAATTTTTGCATTT
1 AGGGGCATTTTGGTCATTTTCACATTC
*
9551 AGGGGTATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
9571 AATTTCACTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.18, C:0.11, G:0.26, T:0.46
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTCACATTC
Found at i:9678 original size:17 final size:18
Alignment explanation
Indices: 9652--9693 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
9642 CACCTTTGGC
* *
9652 ATTTTTACTT-ATTTCGT
1 ATTTTAACTTCATTTAGT
9669 ATTTTAACTTCATTTAGT
1 ATTTTAACTTCATTTAGT
*
9687 AATTTAA
1 ATTTTAA
9694 TTAGCATTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.57
Consensus pattern (18 bp):
ATTTTAACTTCATTTAGT
Found at i:9915 original size:14 final size:14
Alignment explanation
Indices: 9896--9928 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
9886 TATATTAACT
*
9896 TTAGTCCATTTAGC
1 TTAGTCCATTTAGA
9910 TTAGTCCATTTAGA
1 TTAGTCCATTTAGA
9924 TTAGT
1 TTAGT
9929 ATCGTAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (14 bp):
TTAGTCCATTTAGA
Found at i:10095 original size:21 final size:21
Alignment explanation
Indices: 10069--10108 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10059 AAATACAAGG
*
10069 CATTTGATTTACGAATTGGAA
1 CATTTGATTTACAAATTGGAA
*
10090 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
10109 TGCTCTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (21 bp):
CATTTGATTTACAAATTGGAA
Done.