Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013416.1 Corchorus olitorius cultivar O-4 contig13449, 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: 46164
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:808 original size:17 final size:17
Alignment explanation
Indices: 788--824 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
778 GCTCTGGATT
788 TTATTTGTATAAGCATG
1 TTATTTGTATAAGCATG
805 TTATTTGTATAAGCATG
1 TTATTTGTATAAGCATG
822 TTA
1 TTA
825 ATAGTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (17 bp):
TTATTTGTATAAGCATG
Found at i:4652 original size:30 final size:29
Alignment explanation
Indices: 4609--4670 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
4599 GCAGCTAGCT
*
4609 ATTGAAGTTTAAGTTTTCTGACTTCAGTG
1 ATTGAAGTTTAAGTATTCTGACTTCAGTG
*
4638 ATTGAAGTTTTAAGTATTCTGATTTCAGTG
1 ATTGAAG-TTTAAGTATTCTGACTTCAGTG
4668 ATT
1 ATT
4671 TGTATGTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.26, C:0.08, G:0.19, T:0.47
Consensus pattern (29 bp):
ATTGAAGTTTAAGTATTCTGACTTCAGTG
Found at i:6714 original size:17 final size:19
Alignment explanation
Indices: 6680--6714 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
6670 AATTGTCTTT
6680 ATTAGATAAAATTTAATAA
1 ATTAGATAAAATTTAATAA
6699 ATTA-ATAAAA-TTAATA
1 ATTAGATAAAATTTAATA
6715 TACAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (19 bp):
ATTAGATAAAATTTAATAA
Found at i:8338 original size:25 final size:25
Alignment explanation
Indices: 8301--8349 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
8291 CAAAAACAAA
8301 AAAAAAATGAAAACAAGAGTTTGCC
1 AAAAAAATGAAAACAAGAGTTTGCC
*
8326 AAAAAAATTAAAACAAGAGTTTGC
1 AAAAAAATGAAAACAAGAGTTTGC
8350 TATGAAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.18
Consensus pattern (25 bp):
AAAAAAATGAAAACAAGAGTTTGCC
Found at i:8864 original size:140 final size:140
Alignment explanation
Indices: 8668--8931 Score: 458
Period size: 140 Copynumber: 1.9 Consensus size: 140
8658 GATAGATTCA
* *
8668 AGACATTCATAGATATAGAATCAACAACATGATTAGAAATTAAGGATAGATGAAAAAGTAACAAA
1 AGACATTCATAGATATAGAATCAACAACATAATTAGAAATTAAGGATAGATGAAAAAATAACAAA
*
8733 AACATAATTAGAAAATTAGAAAATAAGGATAAAAGATGAAAAAGATAACAAAGTTCATCTGTTAA
66 AAAATAATTAGAAAATTAGAAAATAAGGATAAAAGATGAAAAAGATAACAAAGTTCATCTGTTAA
8798 TCCATTATGT
131 TCCATTATGT
*
8808 AGACATTCATAGATATAGAATCAACAACATAATTAGAAA-TAAGGATATATGAAAAAAATAACAA
1 AGACATTCATAGATATAGAATCAACAACATAATTAGAAATTAAGGATAGATG-AAAAAATAACAA
* *
8872 AAAAATAATTAGAAAATTAGAAAATATGGATAAAAGATGAAAAGGATAACAAAGTTCATC
65 AAAAATAATTAGAAAATTAGAAAATAAGGATAAAAGATGAAAAAGATAACAAAGTTCATC
8932 CGTCATGAAT
Statistics
Matches: 117, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
139 11 0.09
140 106 0.91
ACGTcount: A:0.55, C:0.08, G:0.14, T:0.23
Consensus pattern (140 bp):
AGACATTCATAGATATAGAATCAACAACATAATTAGAAATTAAGGATAGATGAAAAAATAACAAA
AAAATAATTAGAAAATTAGAAAATAAGGATAAAAGATGAAAAAGATAACAAAGTTCATCTGTTAA
TCCATTATGT
Found at i:12886 original size:105 final size:106
Alignment explanation
Indices: 12708--12969 Score: 395
Period size: 107 Copynumber: 2.5 Consensus size: 106
12698 AATTTTTCTA
* ** * *
12708 ACCCTTAAAATAAAATTTTAATTTTAATTT-AGGCTAAATTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
12771 TTTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
* *
12811 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
12876 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
* *
12918 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAGCTTAGTGAGATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
12970 AGGCTAAACT
Statistics
Matches: 144, Mismatches: 11, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
103 27 0.19
104 13 0.09
105 37 0.26
107 67 0.47
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (106 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Found at i:20367 original size:28 final size:28
Alignment explanation
Indices: 20295--20468 Score: 179
Period size: 28 Copynumber: 5.7 Consensus size: 28
20285 CAATCTTGGG
*
20295 ATGACAACTTCTGGTGTCAATAATTTCCTCAGC
1 ATGACAACTTCTGGTGTCAAGAATTT--T---C
20328 ATGACAACTTCTGGTGTCAAGAATTTTC
1 ATGACAACTTCTGGTGTCAAGAATTTTC
*
20356 ATGACAACTTCTGGTGTCAAGATAATAATTTGAT
1 ATGACAACTTCTGGTGTCAAG--AAT--TTT--C
*
20390 ATGACAACTTCTGGTGTCAATAATTTTC
1 ATGACAACTTCTGGTGTCAAGAATTTTC
20418 ATGACAACTTCTGGTGTCAAGATAATTTAAT-
1 ATGACAACTTCTGGTGTCAAG--AATTT--TC
20449 ATGACAACTTCTGGTGTCAA
1 ATGACAACTTCTGGTGTCAA
20469 TTAAATTTAA
Statistics
Matches: 126, Mismatches: 5, Indels: 22
0.82 0.03 0.14
Matches are distributed among these distances:
28 42 0.33
30 11 0.09
31 21 0.17
32 7 0.06
33 25 0.20
34 20 0.16
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (28 bp):
ATGACAACTTCTGGTGTCAAGAATTTTC
Found at i:20409 original size:62 final size:59
Alignment explanation
Indices: 20328--20468 Score: 237
Period size: 62 Copynumber: 2.3 Consensus size: 59
20318 TTTCCTCAGC
*
20328 ATGACAACTTCTGGTGTCAAGAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGAT
1 ATGACAACTTCTGGTGTCAAGAATTTTCATGACAACTTCTGGTGTCAAG---ATAATTTAAT
*
20390 ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATTTAAT
1 ATGACAACTTCTGGTGTCAAGAATTTTCATGACAACTTCTGGTGTCAAGATAATTTAAT
20449 ATGACAACTTCTGGTGTCAA
1 ATGACAACTTCTGGTGTCAA
20469 TTAAATTTAA
Statistics
Matches: 77, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
59 29 0.38
62 48 0.62
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (59 bp):
ATGACAACTTCTGGTGTCAAGAATTTTCATGACAACTTCTGGTGTCAAGATAATTTAAT
Found at i:24989 original size:40 final size:40
Alignment explanation
Indices: 24934--25053 Score: 215
Period size: 40 Copynumber: 3.0 Consensus size: 40
24924 AAGAGATTAC
*
24934 AATTCTAGATAATTAAGGGGGATATGATTTATTATAACAT
1 AATTCTAGATGATTAAGGGGGATATGATTTATTATAACAT
24974 AATTCTAGATGATTAAGGGGGATATGATTTATTATAACAT
1 AATTCTAGATGATTAAGGGGGATATGATTTATTATAACAT
25014 AATTCTAGATGATTAAGGGGGATATGATTT-TTCATAACAT
1 AATTCTAGATGATTAAGGGGGATATGATTTATT-ATAACAT
25054 TTATGTGAAA
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
39 2 0.03
40 76 0.97
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (40 bp):
AATTCTAGATGATTAAGGGGGATATGATTTATTATAACAT
Found at i:25786 original size:29 final size:31
Alignment explanation
Indices: 25720--25786 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
25710 TCTAACTGAC
*
25720 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGATCGCTTTTCGTAACGT
*
25751 TATATCCTTAATTGATTG-TTTT-GTAACGT
1 TATATCCTTAATTGATCGCTTTTCGTAACGT
25780 TATATCC
1 TATATCC
25787 CAATTTGCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
30 4 0.12
31 16 0.47
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTGATCGCTTTTCGTAACGT
Found at i:30249 original size:35 final size:37
Alignment explanation
Indices: 30183--30255 Score: 132
Period size: 35 Copynumber: 2.0 Consensus size: 37
30173 GTTGCACTCC
30183 CACCAAAATGTTTTTTAAAGGGCAAGATCAAATTAAG
1 CACCAAAATGTTTTTTAAAGGGCAAGATCAAATTAAG
30220 CACCAAAATG-TTTTTAAA-GGCAAGATCAAATTAAG
1 CACCAAAATGTTTTTTAAAGGGCAAGATCAAATTAAG
30255 C
1 C
30256 TGATTGAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 18 0.50
36 8 0.22
37 10 0.28
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (37 bp):
CACCAAAATGTTTTTTAAAGGGCAAGATCAAATTAAG
Found at i:30406 original size:92 final size:92
Alignment explanation
Indices: 30249--30430 Score: 337
Period size: 92 Copynumber: 2.0 Consensus size: 92
30239 GCAAGATCAA
* *
30249 ATTAAGCTGATTGAATTCAATGTGTATGACCACAAACCATTAATAGTTCCTTGAATAAACCTATA
1 ATTAAGCTGATTGAATTCAATGTGTATGACCAAAAACCACTAATAGTTCCTTGAATAAACCTATA
30314 TATGCTATATGCTATAAGTTGAGAATC
66 TATGCTATATGCTATAAGTTGAGAATC
*
30341 ATTAAGCTGATTGAATTCAATGTGTATGACCAAAAACCACTAATAGTTCCTTGAATGAACCTATA
1 ATTAAGCTGATTGAATTCAATGTGTATGACCAAAAACCACTAATAGTTCCTTGAATAAACCTATA
30406 TATGCTATATGCTATAAGTTGAGAA
66 TATGCTATATGCTATAAGTTGAGAA
30431 ACATGTATTT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 87 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (92 bp):
ATTAAGCTGATTGAATTCAATGTGTATGACCAAAAACCACTAATAGTTCCTTGAATAAACCTATA
TATGCTATATGCTATAAGTTGAGAATC
Found at i:30566 original size:48 final size:49
Alignment explanation
Indices: 30473--30572 Score: 159
Period size: 49 Copynumber: 2.1 Consensus size: 49
30463 CCTGTTAATA
*
30473 TTTTTTTTTAATTTAAAATTAAAAAAATAACTTTAAAAATAATCAGATC
1 TTTTGTTTTAATTTAAAATTAAAAAAATAACTTTAAAAATAATCAGATC
*
30522 TTTTGTTTTAATTTCAAAATT-AAAAAATAAC-TTCAAAATAATCAGATC
1 TTTTGTTTTAATTT-AAAATTAAAAAAATAACTTTAAAAATAATCAGATC
30570 TTT
1 TTT
30573 ATCAATTAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
48 19 0.40
49 23 0.48
50 6 0.12
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (49 bp):
TTTTGTTTTAATTTAAAATTAAAAAAATAACTTTAAAAATAATCAGATC
Found at i:35122 original size:11 final size:11
Alignment explanation
Indices: 35106--35132 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
35096 GATAAGTTGT
35106 TACAATTTAAA
1 TACAATTTAAA
35117 TACAATTTAAA
1 TACAATTTAAA
35128 TACAA
1 TACAA
35133 ACTAACAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (11 bp):
TACAATTTAAA
Found at i:42429 original size:22 final size:22
Alignment explanation
Indices: 42404--42503 Score: 139
Period size: 22 Copynumber: 4.6 Consensus size: 22
42394 TATTTTTGTG
*
42404 AAATTTTGATAACTACCATATT
1 AAATTTTGATAACTACCATATA
42426 AAATTTTGATAACTACCATATA
1 AAATTTTGATAACTACCATATA
*
42448 AAATTTTGATAATTACC-TATA
1 AAATTTTGATAACTACCATATA
* * * *
42469 AAATTGTGATAAATTCCATAAA
1 AAATTTTGATAACTACCATATA
42491 AAATTTTGATAAC
1 AAATTTTGATAAC
42504 CTAACAATGA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
21 18 0.26
22 51 0.74
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACTACCATATA
Found at i:42488 original size:43 final size:44
Alignment explanation
Indices: 42404--42503 Score: 139
Period size: 43 Copynumber: 2.3 Consensus size: 44
42394 TATTTTTGTG
* * * *
42404 AAATTTTGATAACTACCATATTAAATTTTGATAACTACCATATA
1 AAATTTTGATAACTACCATATAAAATTGTGATAAATACCATAAA
* *
42448 AAATTTTGATAATTACC-TATAAAATTGTGATAAATTCCATAAA
1 AAATTTTGATAACTACCATATAAAATTGTGATAAATACCATAAA
42491 AAATTTTGATAAC
1 AAATTTTGATAAC
42504 CTAACAATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 33 0.67
44 16 0.33
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (44 bp):
AAATTTTGATAACTACCATATAAAATTGTGATAAATACCATAAA
Found at i:45409 original size:21 final size:22
Alignment explanation
Indices: 45369--45409 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
45359 GACAAACTCG
*
45369 TAACCCGAATAACCCGAGAAGA
1 TAACCCGAATAACCCAAGAAGA
*
45391 TAACCCG-ATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
45410 TATTATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.29, G:0.17, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Done.