Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012864.1 Corchorus olitorius cultivar O-4 contig12897, 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: 35835
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:5218 original size:16 final size:16
Alignment explanation
Indices: 5209--5240 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5199 ATAATAATTC
5209 ATTAATATAATATAAT
1 ATTAATATAATATAAT
5225 ATTAATATAATATAAT
1 ATTAATATAATATAAT
5241 TAGGAGACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTAATATAATATAAT
Found at i:5221 original size:5 final size:5
Alignment explanation
Indices: 5211--5240 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
5201 AATAATTCAT
5211 TAATA TAATA TAATA TTAATA TAATA TAAT
1 TAATA TAATA TAATA -TAATA TAATA TAAT
5241 TAGGAGACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TAATA
Found at i:5627 original size:45 final size:45
Alignment explanation
Indices: 5574--5703 Score: 215
Period size: 45 Copynumber: 2.9 Consensus size: 45
5564 CTAAATTCTA
*
5574 CTCCATCTCTAGGTAATTCATCAAAATAAAACTAATATTATACTC
1 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
* * * *
5619 CTCTATCTCTAGGTAAATCATCAAAATAAAGCTAATATTCTACTT
1 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
5664 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
1 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
5704 ATTGTTGCTT
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 77 1.00
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34
Consensus pattern (45 bp):
CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
Found at i:7630 original size:2 final size:2
Alignment explanation
Indices: 7619--7655 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
7609 TTCATTGATC
7619 AT AT -T AT AT AT AT 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 AT AT AT AT
7656 CGGCTCGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:8193 original size:24 final size:23
Alignment explanation
Indices: 8162--8213 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
8152 TATTTTTATA
8162 AATAATATATAT-TACTAATTACT
1 AATAATATATATATA-TAATTACT
8185 AATATATATATATATATAATTA--
1 AATA-ATATATATATATAATTACT
8207 AATAATA
1 AATAATA
8214 AACGAACGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 3 0.11
22 4 0.15
23 4 0.15
24 14 0.52
25 2 0.07
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
AATAATATATATATATAATTACT
Found at i:11982 original size:39 final size:39
Alignment explanation
Indices: 11921--11997 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
11911 CACCTTCTAC
*
11921 TTTCCCTTTCATCTCATTCAAAGTTCTTGGAATCCCTAT
1 TTTCCCTTTCATCTCATTCAAAGTTCTTGCAATCCCTAT
*
11960 TTTCTCTTTCATCTC-TTCCAAAGTTCTTGCAATCCCTA
1 TTTCCCTTTCATCTCATT-CAAAGTTCTTGCAATCCCTA
11998 AAATATCATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 2 0.06
39 33 0.94
ACGTcount: A:0.19, C:0.30, G:0.06, T:0.44
Consensus pattern (39 bp):
TTTCCCTTTCATCTCATTCAAAGTTCTTGCAATCCCTAT
Found at i:13943 original size:13 final size:13
Alignment explanation
Indices: 13925--13954 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
13915 CTCTTTATGT
*
13925 TTCTTATTATAAG
1 TTCTTATTATAAC
13938 TTCTTATTATAAC
1 TTCTTATTATAAC
13951 TTCT
1 TTCT
13955 ACTTAACTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.03, T:0.57
Consensus pattern (13 bp):
TTCTTATTATAAC
Found at i:18624 original size:26 final size:26
Alignment explanation
Indices: 18572--18628 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
18562 CAAGCGGCCC
* *
18572 TTTTCTTCTTTCTTTTTGTTTTCTTT
1 TTTTCTTCTTTCTTCTTCTTTTCTTT
18598 TTTTCTTCTTCTTCTTCTTCTTTT-TTT
1 TTTTCTTC-T-TTCTTCTTCTTTTCTTT
18625 TTTT
1 TTTT
18629 AAAGATTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 8 0.30
27 8 0.30
28 11 0.41
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.81
Consensus pattern (26 bp):
TTTTCTTCTTTCTTCTTCTTTTCTTT
Found at i:25004 original size:36 final size:36
Alignment explanation
Indices: 24957--25032 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
24947 GGCCTGCATG
* *
24957 GCGCGGCCCAAGCGCCTAGGCCAGGTGCGCGGGCCA
1 GCGCGGCCCAAGCGCCTAGGCCAGGCGCACGGGCCA
*
24993 GCGCGGCCCAAGCGCCTAGGCCAGGCGCATGGGCCA
1 GCGCGGCCCAAGCGCCTAGGCCAGGCGCACGGGCCA
25029 GCGC
1 GCGC
25033 CTAGGCTAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.14, C:0.39, G:0.41, T:0.05
Consensus pattern (36 bp):
GCGCGGCCCAAGCGCCTAGGCCAGGCGCACGGGCCA
Found at i:25159 original size:24 final size:26
Alignment explanation
Indices: 25118--25165 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
25108 GCCCAATGTG
25118 AAATAAAAGAAAGAAATAA-AAATAA
1 AAATAAAAGAAAGAAATAAGAAATAA
25143 AAAT-AAAGAAA-ATAATAAGAAAT
1 AAATAAAAGAAAGA-AATAAGAAAT
25166 TTTAGAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 1 0.05
24 12 0.57
25 8 0.38
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (26 bp):
AAATAAAAGAAAGAAATAAGAAATAA
Found at i:27885 original size:18 final size:17
Alignment explanation
Indices: 27862--27896 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
27852 CAAGCGGCCC
27862 TTTTCTTCTTTCTTTTTT
1 TTTTCTTCTTT-TTTTTT
27880 TTTTCTTCTTTTTTTTT
1 TTTTCTTCTTTTTTTTT
27897 AACCAGATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTCTTCTTTTTTTTT
Found at i:29945 original size:13 final size:13
Alignment explanation
Indices: 29927--29952 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29917 TATATAGTAT
29927 ATATGATTTATGA
1 ATATGATTTATGA
29940 ATATGATTTATGA
1 ATATGATTTATGA
29953 GGCTATACAA
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:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
ATATGATTTATGA
Found at i:32795 original size:48 final size:48
Alignment explanation
Indices: 32719--32858 Score: 180
Period size: 48 Copynumber: 2.9 Consensus size: 48
32709 CAAGCAATCC
*
32719 TTTACTTTTTAC-AGCACTTTTTCTCAATTTTTACA-ACAAAATTGAACT
1 TTTA-TTTTTACTTGCACTTTTTCTCAATTTTTA-AGACAAAATTGAACT
* *
32767 TTTATTTTTACTTGCATTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTATTTTTACTTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACT
* *
32815 TTTAATTTTTA-TTGCACTTTTTATCAATTTTT-GGACAAAATTGA
1 TTT-ATTTTTACTTGCACTTTTTCTCAATTTTTAAGACAAAATTGA
32859 TTGGCACGCT
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
47 19 0.23
48 57 0.69
49 7 0.08
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (48 bp):
TTTATTTTTACTTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACT
Found at i:35793 original size:21 final size:21
Alignment explanation
Indices: 35769--35835 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
35759 AATTCTCTGT
35769 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
35790 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
35811 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
35832 AAAT
1 AAAT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Done.