Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017730.1 Corchorus olitorius cultivar O-4 contig17763, 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: 27769
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:2336 original size:18 final size:18
Alignment explanation
Indices: 2313--2348 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2303 AATTTTTTTC
*
2313 TTTTCTAATTTAGCCTCA
1 TTTTCTAATTTAGACTCA
*
2331 TTTTCTAGTTTAGACTCA
1 TTTTCTAATTTAGACTCA
2349 AGGTAATATT
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:0.22, C:0.19, G:0.08, T:0.50
Consensus pattern (18 bp):
TTTTCTAATTTAGACTCA
Found at i:5214 original size:21 final size:22
Alignment explanation
Indices: 5188--5260 Score: 96
Period size: 22 Copynumber: 3.4 Consensus size: 22
5178 CATATGCAAA
5188 TTTGATAA-TACATTGTGAAAT
1 TTTGATAACTACATTGTGAAAT
* *
5209 TTTGATAACCACATTATGAAAT
1 TTTGATAACTACATTGTGAAAT
*
5231 TTTGATAACCT-CAGTGTGAAAT
1 TTTGATAA-CTACATTGTGAAAT
5253 TTTGATAA
1 TTTGATAA
5261 TCTCTCTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
21 8 0.18
22 36 0.80
23 1 0.02
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.40
Consensus pattern (22 bp):
TTTGATAACTACATTGTGAAAT
Found at i:5228 original size:22 final size:22
Alignment explanation
Indices: 5203--5345 Score: 132
Period size: 22 Copynumber: 6.6 Consensus size: 22
5193 TAATACATTG
*
5203 TGAAATTTTGATAACCACATTA
1 TGAAATTTTGATAACCACACTA
* * *
5225 TGAAATTTTGATAACCTCAGTG
1 TGAAATTTTGATAACCACACTA
* * *
5247 TGAAATTTTGATAATCTCTCTA
1 TGAAATTTTGATAACCACACTA
* **
5269 TAAAATTTTGATAATAACACTA
1 TGAAATTTTGATAACCACACTA
*
5291 --AAA--TTGGTAACCACACTA
1 TGAAATTTTGATAACCACACTA
*
5309 TGAAAATTTTGATAACCACACCA
1 TG-AAATTTTGATAACCACACTA
*
5332 TGAAATTTAGATAA
1 TGAAATTTTGATAA
5346 TCTCCTTATA
Statistics
Matches: 99, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
18 12 0.12
20 3 0.03
21 3 0.03
22 66 0.67
23 15 0.15
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34
Consensus pattern (22 bp):
TGAAATTTTGATAACCACACTA
Found at i:5235 original size:43 final size:43
Alignment explanation
Indices: 5180--5284 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 43
5170 ATCATCTCCA
*
5180 TATGCAAA-TTTGATAATACATTGTGAAATTTTGATAACCACAT-
1 TATG-AAATTTTGATAATACAGTGTGAAATTTTGATAACCAC-TC
* *
5223 TATGAAATTTTGATAACCT-CAGTGTGAAATTTTGATAATCTCTC
1 TATGAAATTTTGATAA--TACAGTGTGAAATTTTGATAACCACTC
*
5267 TATAAAATTTTGATAATA
1 TATGAAATTTTGATAATA
5285 ACACTAAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
42 4 0.08
43 13 0.25
44 35 0.66
45 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.40
Consensus pattern (43 bp):
TATGAAATTTTGATAATACAGTGTGAAATTTTGATAACCACTC
Found at i:5316 original size:21 final size:22
Alignment explanation
Indices: 5290--5345 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
5280 TAATAACACT
* *
5290 AAAA-TTGGTAACCACACTATG
1 AAAATTTGATAACCACACCATG
5311 AAAATTTTGATAACCACACCATG
1 AAAA-TTTGATAACCACACCATG
5334 -AAATTTAGATAA
1 AAAATTT-GATAA
5346 TCTCCTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 7 0.23
22 8 0.27
23 15 0.50
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (22 bp):
AAAATTTGATAACCACACCATG
Found at i:5432 original size:21 final size:22
Alignment explanation
Indices: 5385--5433 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
5375 CTCTCTATGT
5385 AATTTTCATAATCTCTCCATAA
1 AATTTTCATAATCTCTCCATAA
*
5407 AATTTTCATAA-C-CTCCCTAGA
1 AATTTTCATAATCTCTCCATA-A
5428 AATTTT
1 AATTTT
5434 GATGACCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 6 0.24
21 8 0.32
22 11 0.44
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.41
Consensus pattern (22 bp):
AATTTTCATAATCTCTCCATAA
Found at i:5529 original size:22 final size:22
Alignment explanation
Indices: 5473--5551 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
5463 CCTCTGTATG
5473 AAATTTTGATAACTAAACTATA
1 AAATTTTGATAACTAAACTATA
* *
5495 AAGTATTGATAACTTAAA-TATA
1 AAATTTTGATAAC-TAAACTATA
* * * *
5517 AAATTTTGGTAACCACACTATG
1 AAATTTTGATAACTAAACTATA
*
5539 AATTTTTGATAAC
1 AAATTTTGATAAC
5552 CTTCCTATAT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 2 0.04
22 39 0.87
23 4 0.09
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAACTAAACTATA
Found at i:5944 original size:60 final size:60
Alignment explanation
Indices: 5773--6045 Score: 336
Period size: 60 Copynumber: 4.5 Consensus size: 60
5763 TTAATTGTTC
* * * * * * *
5773 AAAT-AGGTCCCTAATGTATG-AAAAACGCTCAATTTA-GAGTTCATACTTTTAATTTTGTT
1 AAATAAGG-CCCTAACGTATGTAAAAATGCTCAATTCACG-GTCCATGCTTTGAATTTGGTT
* * * *
5832 AAATAAGGCCCTAACTTATGAAAAAAATGCTCACTTCACGGTCCATGTTTTGAATTTGGTT
1 AAATAAGGCCCTAACGTATG-TAAAAATGCTCAATTCACGGTCCATGCTTTGAATTTGGTT
* * *
5893 AAATAAGGCCTTAACGTATGTAAAAATGTTCAATTCACGGTCCATGCTTTGAATTTAGTT
1 AAATAAGGCCCTAACGTATGTAAAAATGCTCAATTCACGGTCCATGCTTTGAATTTGGTT
* *
5953 AAATAAGGCCTTAACGTATGTAAAAATGTTCAATTCACGGTCCATGCTTTGAATTTGGTT
1 AAATAAGGCCCTAACGTATGTAAAAATGCTCAATTCACGGTCCATGCTTTGAATTTGGTT
* *
6013 AAATAAGGCCCTAATGTATGTGAAAATGCTCAA
1 AAATAAGGCCCTAACGTATGTAAAAATGCTCAA
6046 ATAAGGACTT
Statistics
Matches: 188, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
59 14 0.07
60 126 0.67
61 47 0.25
62 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (60 bp):
AAATAAGGCCCTAACGTATGTAAAAATGCTCAATTCACGGTCCATGCTTTGAATTTGGTT
Found at i:6208 original size:63 final size:63
Alignment explanation
Indices: 6100--6322 Score: 308
Period size: 63 Copynumber: 3.6 Consensus size: 63
6090 GCCATGCCTT
*
6100 TATTTGAGCATTTTCGCATACGTTAGGGCCCTATTCAACCAAATTAAAAATATGGGCTCTAAA
1 TATTTGAGCATTTTCGCATACGTTAGGGCCCTATTTAACCAAATTAAAAATATGGGCTCTAAA
* * *
6163 TATTTGAGCATTTTCGCATACGTTATGGCCCTATTTAACCTAATTAAAAGTATGGGCTCTAAA
1 TATTTGAGCATTTTCGCATACGTTAGGGCCCTATTTAACCAAATTAAAAATATGGGCTCTAAA
* * * * *
6226 TATTTGAGCATTTTCTCATACGTTAGGGCCCTATTTGACCAAATTAAAAAGCATAGGC-CTTAA
1 TATTTGAGCATTTTCGCATACGTTAGGGCCCTATTTAACCAAATTAAAAA-TATGGGCTCTAAA
* * *
6289 -A-TTGAGCATTTTCGCATATGTTAGAGACCTATTT
1 TATTTGAGCATTTTCGCATACGTTAGGGCCCTATTT
6323 GAACAATTAA
Statistics
Matches: 143, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
61 29 0.20
62 1 0.01
63 108 0.76
64 5 0.03
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (63 bp):
TATTTGAGCATTTTCGCATACGTTAGGGCCCTATTTAACCAAATTAAAAATATGGGCTCTAAA
Found at i:14073 original size:40 final size:39
Alignment explanation
Indices: 14020--14104 Score: 118
Period size: 40 Copynumber: 2.2 Consensus size: 39
14010 ATAAACAATA
*
14020 ATTAGGGGCTAAACCT-AGATTTAATTTCTTACCTTAATT
1 ATTAGGGGCTAAACCTGA-ATTTAATTTATTACCTTAATT
*
14059 ATTAGGGTGCTAAACCTGAATTTAATTTATTTCCTTAATT
1 ATTAGGG-GCTAAACCTGAATTTAATTTATTACCTTAATT
*
14099 CTTAGG
1 ATTAGG
14105 AGGGTCTAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
39 7 0.17
40 33 0.80
41 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.42
Consensus pattern (39 bp):
ATTAGGGGCTAAACCTGAATTTAATTTATTACCTTAATT
Found at i:18039 original size:14 final size:14
Alignment explanation
Indices: 18013--18043 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
18003 ATAGATATAG
18013 ATATATCTATATCT
1 ATATATCTATATCT
18027 ATATATCTATATCT
1 ATATATCTATATCT
18041 ATA
1 ATA
18044 CTATATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATATCTATATCT
Found at i:18847 original size:14 final size:14
Alignment explanation
Indices: 18823--18855 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
18813 AAAAATATTC
18823 AAAAT-ACCCTCTT
1 AAAATAACCCTCTT
18836 AAAATAACCCTCTT
1 AAAATAACCCTCTT
18850 AAAATA
1 AAAATA
18856 TTGAACCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATAACCCTCTT
Found at i:22103 original size:21 final size:21
Alignment explanation
Indices: 22058--22104 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
22048 ATTGATAGCA
* * *
22058 TTATAACTTTTTTGATAATCT
1 TTATAACTTCTTTGATAAACC
*
22079 TTATAACTTCTTTGGTAAACC
1 TTATAACTTCTTTGATAAACC
22100 TTATA
1 TTATA
22105 TGAAAAATGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.51
Consensus pattern (21 bp):
TTATAACTTCTTTGATAAACC
Found at i:22907 original size:13 final size:13
Alignment explanation
Indices: 22889--22914 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22879 ATACATCTGA
22889 TAACTTGTGTTAT
1 TAACTTGTGTTAT
22902 TAACTTGTGTTAT
1 TAACTTGTGTTAT
22915 ATAAATTTAA
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:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
TAACTTGTGTTAT
Found at i:24767 original size:4 final size:4
Alignment explanation
Indices: 24753--24911 Score: 54
Period size: 4 Copynumber: 42.2 Consensus size: 4
24743 TTTTTAACTA
* * * *
24753 TTAT CTAT TTAT TTA- CTAT TTAT CTAT TTAT TTA- TT-T TTAA TTA-
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * *
24797 TTAT CTAT TTAT TTA- CTAT TGAT CTAT TCAT TTA- TT-T TTAA TTA-
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * *
24841 TTAT CTAT TTAT TTA- CTAT TTAT CTT-T TTAGT GT-T TAAT TTAG CTA-
1 TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTA-T TTAT TTAT TTAT TTAT
* *
24887 TTAC CTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
24912 ATTATTATTA
Statistics
Matches: 109, Mismatches: 32, Indels: 28
0.64 0.19 0.17
Matches are distributed among these distances:
3 25 0.23
4 80 0.73
5 4 0.04
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.64
Consensus pattern (4 bp):
TTAT
Found at i:24771 original size:11 final size:11
Alignment explanation
Indices: 24757--24863 Score: 69
Period size: 11 Copynumber: 9.7 Consensus size: 11
24747 TAACTATTAT
24757 CTATTTATTTA
1 CTATTTATTTA
*
24768 CTATTTATCTA
1 CTATTTATTTA
*
24779 TTTATTTATTT-
1 -CTATTTATTTA
* *
24790 TTAATTA-TTA
1 CTATTTATTTA
24800 TCTATTTATTTA
1 -CTATTTATTTA
* *
24812 CTATTGATCTA
1 CTATTTATTTA
*
24823 TTCATTTATTT-
1 CT-ATTTATTTA
* *
24834 TTAATTA-TTA
1 CTATTTATTTA
24844 TCTATTTATTTA
1 -CTATTTATTTA
24856 CTATTTAT
1 CTATTTAT
24864 CTTTTTAGTG
Statistics
Matches: 74, Mismatches: 14, Indels: 16
0.71 0.13 0.15
Matches are distributed among these distances:
9 4 0.05
10 10 0.14
11 40 0.54
12 20 0.27
ACGTcount: A:0.27, C:0.08, G:0.01, T:0.64
Consensus pattern (11 bp):
CTATTTATTTA
Found at i:24799 original size:44 final size:44
Alignment explanation
Indices: 24738--24870 Score: 230
Period size: 44 Copynumber: 3.0 Consensus size: 44
24728 ATTTTTTAAA
*
24738 ATTTATTTTTAACTATTATCTATTTATTTACTATTTATCTATTT
1 ATTTATTTTTAATTATTATCTATTTATTTACTATTTATCTATTT
* *
24782 ATTTATTTTTAATTATTATCTATTTATTTACTATTGATCTATTC
1 ATTTATTTTTAATTATTATCTATTTATTTACTATTTATCTATTT
*
24826 ATTTATTTTTAATTATTATCTATTTATTTACTATTTATCTTTTT
1 ATTTATTTTTAATTATTATCTATTTATTTACTATTTATCTATTT
24870 A
1 A
24871 GTGTTTAATT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 83 1.00
ACGTcount: A:0.27, C:0.08, G:0.01, T:0.64
Consensus pattern (44 bp):
ATTTATTTTTAATTATTATCTATTTATTTACTATTTATCTATTT
Found at i:24913 original size:15 final size:15
Alignment explanation
Indices: 24751--24958 Score: 97
Period size: 15 Copynumber: 14.6 Consensus size: 15
24741 TATTTTTAAC
*
24751 TATTATCTATTTATT
1 TATTATTTATTTATT
* *
24766 TACTATTTATCTATT
1 TATTATTTATTTATT
*
24781 TATT-TATT-TTTAAT
1 TATTAT-TTATTTATT
*
24795 TATTATCTATTTATT
1 TATTATTTATTTATT
* * *
24810 TACTATTGATCTATT
1 TATTATTTATTTATT
* *
24825 CATT-TATT-TTTAAT
1 TATTAT-TTATTTATT
*
24839 TATTATCTATTTATT
1 TATTATTTATTTATT
*
24854 TACTATTTATCTT-TT
1 TATTATTTAT-TTATT
* * **
24869 TAGTGTTTAATTTAGC
1 TATTATTT-ATTTATT
**
24885 TATTACCTATTTATT
1 TATTATTTATTTATT
24900 TATTTATTTA-TTA-T
1 TA-TTATTTATTTATT
24914 TATTA-TTA-TTA-T
1 TATTATTTATTTATT
24926 TATTA-TTA-TTA-T
1 TATTATTTATTTATT
24938 TATTA-TTA-TTA-T
1 TATTATTTATTTATT
24950 TATTATTTA
1 TATTATTTA
24959 GCTACCTATT
Statistics
Matches: 148, Mismatches: 34, Indels: 24
0.72 0.17 0.12
Matches are distributed among these distances:
12 36 0.24
13 6 0.04
14 22 0.15
15 71 0.48
16 13 0.09
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (15 bp):
TATTATTTATTTATT
Found at i:24914 original size:19 final size:19
Alignment explanation
Indices: 24753--24944 Score: 72
Period size: 19 Copynumber: 10.4 Consensus size: 19
24743 TTTTTAACTA
*
24753 TTATCTATTTATTTA-CTAT
1 TTAT-TATTTATTTATTTAT
24772 TTATCTATTTATTTATTT-T
1 TTAT-TATTTATTTATTTAT
* *
24791 TAATTA-TTATCTATTTAT
1 TTATTATTTATTTATTTAT
* * * *
24809 TTACTATTGATCTATTCAT
1 TTATTATTTATTTATTTAT
*
24828 TTATT-TTTAATTA-TTAT
1 TTATTATTTATTTATTTAT
* *
24845 CTATTTATTTA-CTATTTAT
1 TTA-TTATTTATTTATTTAT
* * *
24864 CTTTTTAGTGT-TTAATTTAGCT
1 -TTATTA-TTTATTTATTTA--T
*
24886 ATTACCTATTTATTTATTTAT
1 -TTA-TTATTTATTTATTTAT
24907 TTATTA-TTA-TTA-TTA-
1 TTATTATTTATTTATTTAT
24922 TTATTA-TTA-TTA-TTA-
1 TTATTATTTATTTATTTAT
24937 TTATTATT
1 TTATTATT
24945 ATTATTATTA
Statistics
Matches: 134, Mismatches: 25, Indels: 31
0.71 0.13 0.16
Matches are distributed among these distances:
15 21 0.16
16 4 0.03
17 17 0.13
18 19 0.14
19 46 0.34
20 12 0.09
21 1 0.01
22 5 0.04
23 9 0.07
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (19 bp):
TTATTATTTATTTATTTAT
Found at i:24915 original size:3 final size:3
Alignment explanation
Indices: 24907--24956 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
24897 ATTTATTTAT
24907 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
24955 TT
1 TT
24957 TAGCTACCTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:24988 original size:24 final size:24
Alignment explanation
Indices: 24961--25021 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
24951 ATTATTTAGC
* *
24961 TACCTATTTATTTA-TTATTCTCTG
1 TACCTATTTATCTATTTA-TCTCTA
24985 TACCTATTTATCTATTTATCTCTA
1 TACCTATTTATCTATTTATCTCTA
25009 TACCTATTTATCT
1 TACCTATTTATCT
25022 TTTTTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 31 0.91
25 3 0.09
ACGTcount: A:0.23, C:0.20, G:0.02, T:0.56
Consensus pattern (24 bp):
TACCTATTTATCTATTTATCTCTA
Done.