Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024235.1 Corchorus olitorius cultivar O-4 contig24268, 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: 4485
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:1668 original size:32 final size:32
Alignment explanation
Indices: 1627--1693 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
1617 TGAACTTTTG
1627 GATTTCTCTCTTGTTGATGTGGAATTGCGAAA
1 GATTTCTCTCTTGTTGATGTGGAATTGCGAAA
1659 GATTTCTCTCTTGTTGATGTGGAATTGCGAAA
1 GATTTCTCTCTTGTTGATGTGGAATTGCGAAA
1691 GAT
1 GAT
1694 AGAAAACAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.40
Consensus pattern (32 bp):
GATTTCTCTCTTGTTGATGTGGAATTGCGAAA
Found at i:1838 original size:17 final size:16
Alignment explanation
Indices: 1826--1879 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 16
1816 GTTTTTTTCT
1826 GTATCTCTGTTTTTTG
1 GTATCTCTGTTTTTTG
* *
1842 GTATCCACTATTTTTTG
1 GTAT-CTCTGTTTTTTG
1859 GTATCTCTGTTTTTTTG
1 GTATCTCTG-TTTTTTG
1876 GTAT
1 GTAT
1880 TTTTTTTGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 7 0.22
17 25 0.78
ACGTcount: A:0.11, C:0.13, G:0.17, T:0.59
Consensus pattern (16 bp):
GTATCTCTGTTTTTTG
Found at i:1885 original size:12 final size:12
Alignment explanation
Indices: 1868--1908 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1858 GGTATCTCTG
1868 TTTTTTTGGTAT
1 TTTTTTTGGTAT
1880 TTTTTTTGGTA-
1 TTTTTTTGGTAT
* *
1891 TCTTTCT-GTAT
1 TTTTTTTGGTAT
1902 TTTTTTT
1 TTTTTTT
1909 CTCCCCCCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
10 3 0.12
11 10 0.42
12 11 0.46
ACGTcount: A:0.07, C:0.05, G:0.12, T:0.76
Consensus pattern (12 bp):
TTTTTTTGGTAT
Found at i:2950 original size:25 final size:25
Alignment explanation
Indices: 2921--2972 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
2911 CAAATGATAG
2921 CAAGATGAAGCTAAAAGCAAATAAC
1 CAAGATGAAGCTAAAAGCAAATAAC
2946 CAAGATGAAGCTAAAAGCAAATAAC
1 CAAGATGAAGCTAAAAGCAAATAAC
2971 CA
1 CA
2973 GGAGGGCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.56, C:0.17, G:0.15, T:0.12
Consensus pattern (25 bp):
CAAGATGAAGCTAAAAGCAAATAAC
Found at i:3650 original size:39 final size:40
Alignment explanation
Indices: 3609--4117 Score: 464
Period size: 40 Copynumber: 13.2 Consensus size: 40
3599 AGACCCTAAA
* * * *
3609 TAGGACTTTGAAATTAA-CTGAAAAAGCAATGACCCTGAA
1 TAGGATTTTGAAATTAATCTGATAAAGCAATGATCCTGAG
* * *
3648 TAGGATTTTGAGATTAA-CCGATAAAGAAATGATCCTG-G
1 TAGGATTTTGAAATTAATCTGATAAAGCAATGATCCTGAG
** * * *
3686 ATAGGATAATG--ATTGA-CTGGTAAAGAAATGATCCTGAG
1 -TAGGATTTTGAAATTAATCTGATAAAGCAATGATCCTGAG
* *
3724 TAGGATTGTG--ATTAATTTGATAAAGCAATGATCCTGAG
1 TAGGATTTTGAAATTAATCTGATAAAGCAATGATCCTGAG
* *
3762 TAGGATTTTGAAATTAATTTGGTAAAGCAATGATCCTGAG
1 TAGGATTTTGAAATTAATCTGATAAAGCAATGATCCTGAG
* * *
3802 CAGGATTTTGAAATTAATTTGGTAAAGCAATGATCCTGAG
1 TAGGATTTTGAAATTAATCTGATAAAGCAATGATCCTGAG
* * * *
3842 CAGGATTTTGAAATTAATTTGGTAAAGCCATGATCCTGAG
1 TAGGATTTTGAAATTAATCTGATAAAGCAATGATCCTGAG
* *
3882 CAGGA--TT--AA-T--T-TGGTAAAGCAATGATCCTGAG
1 TAGGATTTTGAAATTAATCTGATAAAGCAATGATCCTGAG
* * * *
3914 CAGGATTTTGAAATTAATTTGGTAAAGCCATGATCCTGAG
1 TAGGATTTTGAAATTAATCTGATAAAGCAATGATCCTGAG
* * * *
3954 CAAGATTTTGAAATTAATTTGGTAAAGCAATGATCCTGAG
1 TAGGATTTTGAAATTAATCTGATAAAGCAATGATCCTGAG
* * * *
3994 CAGGATTTTGAAATTAATTTGGTAAAACAATGATCCTGAG
1 TAGGATTTTGAAATTAATCTGATAAAGCAATGATCCTGAG
* * * *
4034 CAGGATTTTGAAATTAATTTGGTAAACCAATGATCCTGAG
1 TAGGATTTTGAAATTAATCTGATAAAGCAATGATCCTGAG
* *
4074 CAGGA--TTGAAATTAA-CT-AGTAAAGAAATGATCCTGAG
1 TAGGATTTTGAAATTAATCTGA-TAAAGCAATGATCCTGAG
*
4111 CAGGATT
1 TAGGATT
4118 AAAACCCATA
Statistics
Matches: 421, Mismatches: 33, Indels: 32
0.87 0.07 0.07
Matches are distributed among these distances:
32 25 0.06
33 1 0.00
34 2 0.00
35 1 0.00
36 4 0.01
37 57 0.14
38 41 0.10
39 40 0.10
40 250 0.59
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (40 bp):
TAGGATTTTGAAATTAATCTGATAAAGCAATGATCCTGAG
Found at i:3789 original size:40 final size:40
Alignment explanation
Indices: 3703--4117 Score: 622
Period size: 40 Copynumber: 10.7 Consensus size: 40
3693 AATGATTGAC
* * *
3703 TGGTAAAGAAATGATCCTGAGTAGGATTGTG--ATTAATT
1 TGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
* *
3741 TGATAAAGCAATGATCCTGAGTAGGATTTTGAAATTAATT
1 TGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
3781 TGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
1 TGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
3821 TGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
1 TGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
*
3861 TGGTAAAGCCATGATCCTGAGCA-G-----G--ATTAATT
1 TGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
3893 TGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
1 TGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
* *
3933 TGGTAAAGCCATGATCCTGAGCAAGATTTTGAAATTAATT
1 TGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
3973 TGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
1 TGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
*
4013 TGGTAAAACAATGATCCTGAGCAGGATTTTGAAATTAATT
1 TGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
* *
4053 TGGTAAACCAATGATCCTGAGCAGGA--TTGAAATTAA-C
1 TGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
* *
4090 TAGTAAAGAAATGATCCTGAGCAGGATT
1 TGGTAAAGCAATGATCCTGAGCAGGATT
4118 AAAACCCATA
Statistics
Matches: 348, Mismatches: 17, Indels: 23
0.90 0.04 0.06
Matches are distributed among these distances:
32 29 0.08
33 1 0.00
34 1 0.00
37 23 0.07
38 39 0.11
39 1 0.00
40 254 0.73
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (40 bp):
TGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
Found at i:3911 original size:112 final size:112
Alignment explanation
Indices: 3774--4119 Score: 527
Period size: 112 Copynumber: 3.0 Consensus size: 112
3764 GGATTTTGAA
3774 ATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGGTAAAGCAATGATCCT
1 ATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGGTAAAGCAATGATCCT
*
3839 GAGCAGGATTTTGAAATTAATTTGGTAAAGCCATGATCCTGAGCAGG
66 GAGCAGGATTTTGAAATTAATTTGGTAAAGCAATGATCCTGAGCAGG
*
3886 ATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGGTAAAGCCATGATCCT
1 ATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGGTAAAGCAATGATCCT
*
3951 GAGCAAGATTTTGAAATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTG
66 GAGCAGGATTTTGAAATTAATTTGGTAAAGCAATGATCCTGAGCA-G-----G
* *
4004 AAATTAATTTGGTAAAACAATGATCCTGAGCAGGATTTTGAAATTAATTTGGTAAACCAATGATC
1 --ATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGGTAAAGCAATGATC
* * *
4069 CTGAGCAGGA--TTGAAATTAA-CTAGTAAAGAAATGATCCTGAGCAGG
64 CTGAGCAGGATTTTGAAATTAATTTGGTAAAGCAATGATCCTGAGCAGG
4115 ATTAA
1 ATTAA
4120 AACCCATATT
Statistics
Matches: 216, Mismatches: 10, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
109 5 0.02
111 1 0.00
112 107 0.50
113 1 0.00
116 1 0.00
117 21 0.10
118 11 0.05
120 69 0.32
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (112 bp):
ATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGGTAAAGCAATGATCCT
GAGCAGGATTTTGAAATTAATTTGGTAAAGCAATGATCCTGAGCAGG
Found at i:3919 original size:152 final size:154
Alignment explanation
Indices: 3731--4117 Score: 595
Period size: 152 Copynumber: 2.5 Consensus size: 154
3721 GAGTAGGATT
* *
3731 GTGATTAATTTGATAAAGCAATGATCCTGAGTAGGATTTTGAAATTAATTTGGTAAAGCAATGAT
1 GTGATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGGTAAAGCAATGAT
3796 CCTGAGCAGGATTTTGAAATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
66 CCTGAGCAGGATTTTGAAATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
* *
3861 TGGTAAAGCCATGATCCTGAGCA-
131 TGGTAAAACAATGATCCTGAGCAG
*
3884 G-GATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGGTAAAGCCATGAT
1 GTGATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGGTAAAGCAATGAT
*
3948 CCTGAGCAAGATTTTGAAATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
66 CCTGAGCAGGATTTTGAAATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
4013 TGGTAAAACAATGATCCTGAGCAG
131 TGGTAAAACAATGATCCTGAGCAG
* * * *
4037 GATTTTGAAATTAATTTGGTAAACCAATGATCCTGAGCAGGA--TTGAAATTAA-CTAGTAAAGA
1 G----TG--ATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGGTAAAGC
4099 AATGATCCTGAGCAGGATT
60 AATGATCCTGAGCAGGATT
4118 AAAACCCATA
Statistics
Matches: 214, Mismatches: 12, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
152 145 0.68
153 2 0.01
157 24 0.11
158 11 0.05
160 32 0.15
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.32
Consensus pattern (154 bp):
GTGATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGGTAAAGCAATGAT
CCTGAGCAGGATTTTGAAATTAATTTGGTAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
TGGTAAAACAATGATCCTGAGCAG
Done.