Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023013.1 Corchorus olitorius cultivar O-4 contig23046, 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: 64524
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:8505 original size:11 final size:11
Alignment explanation
Indices: 8468--8505 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
8458 TTCCTATATA
*
8468 AAATAAATTAT
1 AAATTAATTAT
8479 CAAA-TAATTAT
1 -AAATTAATTAT
8490 AAATTAATTAT
1 AAATTAATTAT
8501 AAATT
1 AAATT
8506 TGTTGTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:8884 original size:28 final size:31
Alignment explanation
Indices: 8827--8887 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
8817 CAATATTTAT
* *
8827 TTTTTTGTGTATTATTAGTATGTAACATTAA
1 TTTTTTGTGTATTATTAATATATAACATTAA
8858 TTTTTTGTGTATTA-TAATA-ATAA-ATTAA
1 TTTTTTGTGTATTATTAATATATAACATTAA
8886 TT
1 TT
8888 ATAGTTTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 3 0.11
30 4 0.14
31 14 0.50
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.56
Consensus pattern (31 bp):
TTTTTTGTGTATTATTAATATATAACATTAA
Found at i:9262 original size:29 final size:28
Alignment explanation
Indices: 9204--9275 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 28
9194 CTTGAGTCTT
* * * *
9204 AAAACCATCCAAT-TTTTTTTTTAAAGA
1 AAAAGCATCCAATAATTTTTTTGAAACA
9231 AAAAGCATCCAATAATTTTTTTGAAATCA
1 AAAAGCATCCAATAATTTTTTTGAAA-CA
9260 AAAAGCATCCAATAAT
1 AAAAGCATCCAATAAT
9276 GATTGATTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 12 0.31
28 10 0.26
29 17 0.44
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (28 bp):
AAAAGCATCCAATAATTTTTTTGAAACA
Found at i:17385 original size:14 final size:15
Alignment explanation
Indices: 17359--17387 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17349 AAAAAAAAAA
17359 CTGCTCGAAATTTTG
1 CTGCTCGAAATTTTG
17374 CTGCTC-AAATTTTG
1 CTGCTCGAAATTTTG
17388 TCAACGTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (15 bp):
CTGCTCGAAATTTTG
Found at i:17707 original size:12 final size:13
Alignment explanation
Indices: 17684--17708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17674 TAAATAATGA
17684 TTACCAAAAAAAT
1 TTACCAAAAAAAT
17697 TTACCAAAAAAA
1 TTACCAAAAAAA
17709 CTCACCAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (13 bp):
TTACCAAAAAAAT
Found at i:22056 original size:36 final size:36
Alignment explanation
Indices: 22009--22078 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
21999 TTCAATAACC
* * *
22009 TTACATCTTTTGTGATTTTGGTTATCATATTTCTAA
1 TTACATCTTTTGTAATCTTGATTATCATATTTCTAA
*
22045 TTACATTTTTTGTAATCTTGATTATCATATTTCT
1 TTACATCTTTTGTAATCTTGATTATCATATTTCT
22079 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (36 bp):
TTACATCTTTTGTAATCTTGATTATCATATTTCTAA
Found at i:22966 original size:203 final size:200
Alignment explanation
Indices: 22589--22993 Score: 738
Period size: 203 Copynumber: 2.0 Consensus size: 200
22579 CTTAATAACT
22589 TTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
1 TTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
*
22654 ATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGA
66 ATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGA
*
22719 TTTATTAAATTAAATTTGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
131 TTTATTAAATTAAATTGGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCC
22784 AATTTA
195 AATTTA
22790 TTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
1 TTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
*
22855 ATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTT
66 ATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTT
*
22920 GATTTATTAAATTAAATTGGATCAATGTCAAATAAAATTTCAAAATTATAAAAGATATTAAGATC
129 GATTTATTAAATTAAATTGGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATC
*
22985 CGATTTA
194 CAATTTA
22992 TT
1 TT
22994 TATTATTAAG
Statistics
Matches: 197, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
201 89 0.45
202 15 0.08
203 93 0.47
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (200 bp):
TTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
ATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGA
TTTATTAAATTAAATTGGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCA
ATTTA
Found at i:23420 original size:6 final size:6
Alignment explanation
Indices: 23402--23458 Score: 78
Period size: 6 Copynumber: 9.0 Consensus size: 6
23392 GTTTAGACTT
*
23402 ATATAG TATATAG ATATAG ATATAG ATATAG ATATAG ATATATAG ATATAA
1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATAG --ATATAG ATATAG
23453 ATATAG
1 ATATAG
23459 GGAGACATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
6 34 0.74
7 6 0.13
8 6 0.13
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (6 bp):
ATATAG
Found at i:23444 original size:20 final size:19
Alignment explanation
Indices: 23401--23458 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 19
23391 AGTTTAGACT
23401 TATATAGTATATAGATATAG
1 TATATAG-ATATAGATATAG
23421 -ATATAGATATAGATATAG
1 TATATAGATATAGATATAG
*
23439 ATATATAGATATAAATATAG
1 -TATATAGATATAGATATAG
23459 GGAGACATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 12 0.34
19 6 0.17
20 17 0.49
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (19 bp):
TATATAGATATAGATATAG
Found at i:23468 original size:26 final size:26
Alignment explanation
Indices: 23415--23468 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
23405 TAGTATATAG
* * * *
23415 ATATAGATATAGATATAGATATAGAT
1 ATATAGATATAAATATAGAGAGACAT
*
23441 ATATAGATATAAATATAGGGAGACAT
1 ATATAGATATAAATATAGAGAGACAT
23467 AT
1 AT
23469 TCACTTGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.31
Consensus pattern (26 bp):
ATATAGATATAAATATAGAGAGACAT
Found at i:26831 original size:33 final size:33
Alignment explanation
Indices: 26793--26861 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
26783 AAAGATGGAA
26793 ATGAAATTCTGTATACAACATAACTAAAAAGGT
1 ATGAAATTCTGTATACAACATAACTAAAAAGGT
*
26826 ATGAAATTCTGTATACAACATAACTAAGAAGGT
1 ATGAAATTCTGTATACAACATAACTAAAAAGGT
26859 ATG
1 ATG
26862 TGGCTATGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGAAATTCTGTATACAACATAACTAAAAAGGT
Found at i:30096 original size:46 final size:46
Alignment explanation
Indices: 30039--30127 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
30029 CGGTAAACCG
* * *
30039 GCTGATTCAATCGTAGTTGAACCGGGTCAACGTTGGTACGTTGTAA
1 GCTGATTCAATCGCAGTTGAACCGGGTCAACATCGGTACGTTGTAA
*
30085 GCTGGTTCAATCGCAGTTGAACCGGGTCAACATCGGTACGTTG
1 GCTGATTCAATCGCAGTTGAACCGGGTCAACATCGGTACGTTG
30128 ACTTACAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (46 bp):
GCTGATTCAATCGCAGTTGAACCGGGTCAACATCGGTACGTTGTAA
Found at i:44217 original size:17 final size:17
Alignment explanation
Indices: 44195--44228 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
44185 GATTAGGTTG
44195 TGTTATCATGTTATGTA
1 TGTTATCATGTTATGTA
44212 TGTTATCATGTTATGTA
1 TGTTATCATGTTATGTA
44229 CAATGATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.53
Consensus pattern (17 bp):
TGTTATCATGTTATGTA
Found at i:48425 original size:49 final size:49
Alignment explanation
Indices: 48368--48468 Score: 159
Period size: 49 Copynumber: 2.1 Consensus size: 49
48358 TGAAGATTTT
* * *
48368 CAATCAAATAAGTTAATCATCCTATTACAATGTTTCTGCCTA-TAAATAA
1 CAATCAAATAAGTTAATCATACTATTACAATATTTCAG-CTAGTAAATAA
48417 CAATCAAATAAGTTAATCATACTATTACAATATTTCAGCTAGTAAATAA
1 CAATCAAATAAGTTAATCATACTATTACAATATTTCAGCTAGTAAATAA
48466 CAA
1 CAA
48469 ACAATGGCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
48 3 0.06
49 45 0.94
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.33
Consensus pattern (49 bp):
CAATCAAATAAGTTAATCATACTATTACAATATTTCAGCTAGTAAATAA
Found at i:51727 original size:20 final size:20
Alignment explanation
Indices: 51702--51741 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
51692 GCCTCTAATC
*
51702 TATAAAGATTAATCAGCTTT
1 TATAAAGATTAACCAGCTTT
51722 TATAAAGATTAACCAGCTTT
1 TATAAAGATTAACCAGCTTT
51742 ATTATCATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (20 bp):
TATAAAGATTAACCAGCTTT
Found at i:53024 original size:22 final size:22
Alignment explanation
Indices: 52999--53171 Score: 131
Period size: 22 Copynumber: 7.8 Consensus size: 22
52989 ACAATCAAAC
*
52999 CAAAATTACATAGAAAGGTTAT
1 CAAAATTTCATAGAAAGGTTAT
53021 CAAAATTTCATATGAAA-GTTAT
1 CAAAATTTCATA-GAAAGGTTAT
* *
53043 CAAAACTTT-ATAGTATA-GTCAT
1 CAAAA-TTTCATAG-AAAGGTTAT
* * *
53065 CAAAATTTCATATAGAGGTTAC
1 CAAAATTTCATAGAAAGGTTAT
*
53087 CAAAATTTCATAAAAAGGTTAT
1 CAAAATTTCATAGAAAGGTTAT
* * *
53109 CAAAATTTCTTATG-GAGGTTAA
1 CAAAATTTCATA-GAAAGGTTAT
* * * *
53131 CATAATTTCCTATGAAA-CTTAA
1 CAAAATTTCATA-GAAAGGTTAT
53153 CAAAATTTCATAGAGAAGG
1 CAAAATTTCATAGA-AAGG
53172 AGGTTACCAA
Statistics
Matches: 121, Mismatches: 21, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
21 8 0.07
22 105 0.87
23 8 0.07
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAGAAAGGTTAT
Found at i:55278 original size:4 final size:4
Alignment explanation
Indices: 55269--55307 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
55259 TTTTATGCCC
*
55269 TTTA TTTA TTTA TTTA TTTA TTT- TACTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTT
55308 TTGATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 1 0.03
4 29 0.94
5 1 0.03
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:56752 original size:11 final size:11
Alignment explanation
Indices: 56732--56764 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
56722 GTTCATGGGT
56732 CGGG-TCGGGC
1 CGGGTTCGGGC
56742 CGGGTTCGGGC
1 CGGGTTCGGGC
56753 CGGGTTCGGGC
1 CGGGTTCGGGC
56764 C
1 C
56765 AGGCTCAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.00, C:0.30, G:0.55, T:0.15
Consensus pattern (11 bp):
CGGGTTCGGGC
Found at i:56965 original size:21 final size:24
Alignment explanation
Indices: 56936--56986 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
56926 TTTTGAACTC
56936 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
56959 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
56982 ATTAT
1 ATTAT
56987 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:56981 original size:25 final size:25
Alignment explanation
Indices: 56936--56984 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
56926 TTTTGAACTC
*
56936 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
56961 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
56985 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:57357 original size:5 final size:5
Alignment explanation
Indices: 57349--57376 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
57339 TTCTTTTTAT
57349 TTTCC TTTCC TTTCC TTTCC TTTCC TTT
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTT
57377 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTCC
Found at i:58693 original size:85 final size:85
Alignment explanation
Indices: 58576--58832 Score: 505
Period size: 85 Copynumber: 3.0 Consensus size: 85
58566 GGAAGGCCTA
*
58576 ATTTTTTGTAGTCAAGGAGCATGTATAGTTGTCGTAGGAAAATTGAATTAGTTGAGAACATTTGT
1 ATTTTTTGTAGTCAAGGAGCATGTATAGTTGTCGTAGGAAAATTGAATTAGGTGAGAACATTTGT
58641 AGGAGCATATTACACAATGC
66 AGGAGCATATTACACAATGC
58661 ATTTTTTGTAGTCAAGGAGCATGTATAGTTGTCGTAGGAAAATTGAATTAGGTGAGAACATTTGT
1 ATTTTTTGTAGTCAAGGAGCATGTATAGTTGTCGTAGGAAAATTGAATTAGGTGAGAACATTTGT
58726 AGGAGCATATTACACAATGC
66 AGGAGCATATTACACAATGC
58746 ATTTTTTGTAGTCAAGGAGCATGTATAGTTGTCGTAGGAAAATTGAATTAGGTGAGAACATTTGT
1 ATTTTTTGTAGTCAAGGAGCATGTATAGTTGTCGTAGGAAAATTGAATTAGGTGAGAACATTTGT
58811 AGGAGCATATTACACAATGC
66 AGGAGCATATTACACAATGC
58831 AT
1 AT
58833 CACAAAATGA
Statistics
Matches: 171, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 171 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (85 bp):
ATTTTTTGTAGTCAAGGAGCATGTATAGTTGTCGTAGGAAAATTGAATTAGGTGAGAACATTTGT
AGGAGCATATTACACAATGC
Found at i:64507 original size:2 final size:2
Alignment explanation
Indices: 64500--64524 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
64490 TTATGATGAA
64500 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.