Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018407.1 Corchorus olitorius cultivar O-4 contig18440, 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: 52813
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1893 original size:3 final size:3
Alignment explanation
Indices: 1867--1918 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
1857 ATGTCCCAAA
1867 AAT AA- AAT AA- AAT -AT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1911 AAT AAT AA
1 AAT AAT AA
1919 AATTAATTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 8 0.18
3 37 0.82
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1925 original size:12 final size:11
Alignment explanation
Indices: 1865--1921 Score: 68
Period size: 10 Copynumber: 5.5 Consensus size: 11
1855 AAATGTCCCA
1865 AAAATAA-AAT
1 AAAATAATAAT
1875 AAAAT-ATAAT
1 AAAATAATAAT
*
1885 ATAATAATAAT
1 AAAATAATAAT
1896 --AATAATAAT
1 AAAATAATAAT
1905 AATAATAATAAT
1 AA-AATAATAAT
1917 AAAAT
1 AAAAT
1922 TAATTAATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
9 10 0.24
10 12 0.29
11 8 0.20
12 11 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:6166 original size:24 final size:24
Alignment explanation
Indices: 6110--6176 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
6100 TATAAGTGGA
* *
6110 GCAGTGGCTGGTGTGGCAGCAGCT
1 GCAGCGGCTGGTGTGGCAGAAGCT
* *
6134 GCAGTGGCTGGTGTGGCGGAAGGCT
1 GCAGCGGCTGGTGTGGCAGAA-GCT
6159 -CAGCGGCTGGCT-TGGCAG
1 GCAGCGGCTGG-TGTGGCAG
6177 TGGGCTCAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 33 0.89
25 4 0.11
ACGTcount: A:0.12, C:0.21, G:0.48, T:0.19
Consensus pattern (24 bp):
GCAGCGGCTGGTGTGGCAGAAGCT
Found at i:6199 original size:24 final size:24
Alignment explanation
Indices: 6155--6200 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
6145 TGTGGCGGAA
*
6155 GGCTCAGCGGCTGGCTTGGCAGTG
1 GGCTCAGCGGCTGGCTGGGCAGTG
*
6179 GGCTCAGTGGCTGG-TAGGGCAG
1 GGCTCAGCGGCTGGCT-GGGCAG
6201 CTGCGCGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.11, C:0.22, G:0.48, T:0.20
Consensus pattern (24 bp):
GGCTCAGCGGCTGGCTGGGCAGTG
Found at i:10463 original size:31 final size:31
Alignment explanation
Indices: 10418--10556 Score: 251
Period size: 31 Copynumber: 4.5 Consensus size: 31
10408 AAGTATAGAA
*
10418 TTGGTCCCTTAAGTGGAGCGAATCTAGCATT
1 TTGGTCCCTCAAGTGGAGCGAATCTAGCATT
*
10449 TTGGTTCCTCAAGTGGAGCGAATCTAGCATT
1 TTGGTCCCTCAAGTGGAGCGAATCTAGCATT
10480 TTGGTCCCTCAAGTGGAGCGAATCTAGCATT
1 TTGGTCCCTCAAGTGGAGCGAATCTAGCATT
10511 TTGGTCCCTCAAGTGGAGCGAATCTAGCATT
1 TTGGTCCCTCAAGTGGAGCGAATCTAGCATT
*
10542 TTGGTCCCCCAAGTG
1 TTGGTCCCTCAAGTG
10557 AAAAATATGT
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (31 bp):
TTGGTCCCTCAAGTGGAGCGAATCTAGCATT
Found at i:10737 original size:15 final size:15
Alignment explanation
Indices: 10717--10746 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
10707 AAAAAATTAT
10717 TATTTTTTTTAAAAA
1 TATTTTTTTTAAAAA
10732 TATTTTTTTTAAAAA
1 TATTTTTTTTAAAAA
10747 AAATTTGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTTTTTTTAAAAA
Found at i:12018 original size:31 final size:29
Alignment explanation
Indices: 11952--12019 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 29
11942 TGTGCAAATG
*
11952 GGTCCCTGAAGTGAAGTTAGTGAGCAATT
1 GGTCCCTGAAGTGAAGTTAGTAAGCAATT
*
11981 GAGTCCCTGAAGTTG-AGTTGATTAAGCAATT
1 G-GTCCCTGAAG-TGAAGTT-AGTAAGCAATT
12012 AGGTCCCT
1 -GGTCCCT
12020 TACCCAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 1 0.03
30 14 0.42
31 17 0.52
32 1 0.03
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (29 bp):
GGTCCCTGAAGTGAAGTTAGTAAGCAATT
Found at i:14843 original size:21 final size:22
Alignment explanation
Indices: 14792--15002 Score: 101
Period size: 22 Copynumber: 9.4 Consensus size: 22
14782 TATGTAATTC
14792 TCAAAATTTCATATTGAG--GTTA
1 TCAAAATTTCATA--GAGTTGTTA
**
14814 TTGAAATTTCATAGAGTTGTTA
1 TCAAAATTTCATAGAGTTGTTA
*
14836 TC-AAATTTCATAGTATTATGTTA
1 TCAAAATTTCATAG-AGT-TGTTA
* *
14859 TCAAAATTTCATATGCGATGTTA
1 TCAAAATTTCATA-GAGTTGTTA
* ***
14882 TCAAAATTTCATAAAAAAAGTTA
1 TCAAAATTTCAT-AGAGTTGTTA
* * *
14905 TCACAATTTTATA-AGGTGATTA
1 TCAAAATTTCATAGAGTTG-TTA
* * *
14927 TCAAAATTTAATAGTGTGGTTA
1 TCAAAATTTCATAGAGTTGTTA
* ** *
14949 -CAAAAAATTTCAAAGAGAAGTTG
1 TC--AAAATTTCATAGAGTTGTTA
*
14972 TCAAAATTTCATAGTA-TGGTTA
1 TCAAAATTTCATAG-AGTTGTTA
*
14994 CCAAAATTT
1 TCAAAATTT
15003 TATTTTATTA
Statistics
Matches: 144, Mismatches: 32, Indels: 26
0.71 0.16 0.13
Matches are distributed among these distances:
20 3 0.02
21 14 0.10
22 58 0.40
23 56 0.39
24 12 0.08
25 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (22 bp):
TCAAAATTTCATAGAGTTGTTA
Found at i:14861 original size:23 final size:24
Alignment explanation
Indices: 14817--14894 Score: 92
Period size: 23 Copynumber: 3.4 Consensus size: 24
14807 GAGGTTATTG
*
14817 AAATTTCATAG-AGT-TGTTATC-
1 AAATTTCATAGTACTATGTTATCA
*
14838 AAATTTCATAGTATTATGTTATCA
1 AAATTTCATAGTACTATGTTATCA
* *
14862 AAATTTCATA-TGCGATGTTATCA
1 AAATTTCATAGTACTATGTTATCA
14885 AAATTTCATA
1 AAATTTCATA
14895 AAAAAAGTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.22
22 2 0.04
23 27 0.54
24 10 0.20
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (24 bp):
AAATTTCATAGTACTATGTTATCA
Found at i:14904 original size:23 final size:23
Alignment explanation
Indices: 14855--14918 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
14845 ATAGTATTAT
**** *
14855 GTTATCAAAATTTCATATGCGAT
1 GTTATCAAAATTTCATAAAAAAA
14878 GTTATCAAAATTTCATAAAAAAA
1 GTTATCAAAATTTCATAAAAAAA
* *
14901 GTTATCACAATTTTATAA
1 GTTATCAAAATTTCATAA
14919 GGTGATTATC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.38
Consensus pattern (23 bp):
GTTATCAAAATTTCATAAAAAAA
Found at i:26431 original size:45 final size:45
Alignment explanation
Indices: 26367--26497 Score: 235
Period size: 45 Copynumber: 2.9 Consensus size: 45
26357 TTTTCGAAGC
26367 AGTTGAATTTTTAAATGTATAATCATACTATAAGAACTAAACCGG
1 AGTTGAATTTTTAAATGTATAATCATACTATAAGAACTAAACCGG
*
26412 AGTTGAATTTTTAAATGTATAGTCATACTATAAGAACTAAACCGG
1 AGTTGAATTTTTAAATGTATAATCATACTATAAGAACTAAACCGG
* *
26457 AGTTGAATTTTTAAACGTATAATCATACTATAAGAGCTAAA
1 AGTTGAATTTTTAAATGTATAATCATACTATAAGAACTAAA
26498 TAGGATTAGA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (45 bp):
AGTTGAATTTTTAAATGTATAATCATACTATAAGAACTAAACCGG
Found at i:27369 original size:22 final size:21
Alignment explanation
Indices: 27343--27398 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
27333 ACTATGGTAT
27343 CAAAAAATTATAGGGAGATTA
1 CAAAAAATTATAGGGAGATTA
*
27364 -ACAAAATCCTATAGGGAGATTA
1 CAAAAAAT--TATAGGGAGATTA
* *
27386 TAAAAAATCATAG
1 CAAAAAATTATAG
27399 AAAGGTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 6 0.21
21 4 0.14
22 13 0.45
23 6 0.21
ACGTcount: A:0.52, C:0.09, G:0.16, T:0.23
Consensus pattern (21 bp):
CAAAAAATTATAGGGAGATTA
Found at i:27407 original size:21 final size:21
Alignment explanation
Indices: 27383--27425 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27373 TATAGGGAGA
27383 TTATAAAAAATCATAGAAAGG
1 TTATAAAAAATCATAGAAAGG
** *
27404 TTATAAAATTTCATAGGAAGG
1 TTATAAAAAATCATAGAAAGG
27425 T
1 T
27426 AAAATTTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (21 bp):
TTATAAAAAATCATAGAAAGG
Found at i:27451 original size:22 final size:22
Alignment explanation
Indices: 27426--27545 Score: 113
Period size: 22 Copynumber: 5.5 Consensus size: 22
27416 ATAGGAAGGT
* *
27426 AAAATTTCATAGTTAGGTTATC
1 AAAATTTCATAGGTAGATTATC
* *
27448 AAAAATTCATATGG-AGTTTATC
1 AAAATTTCATA-GGTAGATTATC
*
27470 ACAATTTCATAGGTA-ATTATC
1 AAAATTTCATAGGTAGATTATC
*
27491 AAAATTTCATAGCGT-GATTATT
1 AAAATTTCATAG-GTAGATTATC
* *
27513 AAAATTTAATAGGGTAG-TCATC
1 AAAATTTCATA-GGTAGATTATC
27535 AAAATTTCATA
1 AAAATTTCATA
27546 AAAATATTCT
Statistics
Matches: 80, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
21 18 0.22
22 59 0.74
23 3 0.04
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (22 bp):
AAAATTTCATAGGTAGATTATC
Found at i:31322 original size:52 final size:52
Alignment explanation
Indices: 31244--31348 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
31234 ATAAGCTGTT
31244 TAAATCTGTGTTCATCCTTATCACTATGTATCTTAATGTTGATACATAATAA
1 TAAATCTGTGTTCATCCTTATCACTATGTATCTTAATGTTGATACATAATAA
*
31296 TAAATCTGTGTTCATCCTTATCACTATGTATCTTAATGTTGATATATAATAA
1 TAAATCTGTGTTCATCCTTATCACTATGTATCTTAATGTTGATACATAATAA
31348 T
1 T
31349 GAACATACAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (52 bp):
TAAATCTGTGTTCATCCTTATCACTATGTATCTTAATGTTGATACATAATAA
Found at i:40151 original size:19 final size:19
Alignment explanation
Indices: 40127--40165 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40117 TCTTACTTGG
40127 TAGTCTGTAGATTTTGAGT
1 TAGTCTGTAGATTTTGAGT
40146 TAGTCTGTAGATTTTGAGT
1 TAGTCTGTAGATTTTGAGT
40165 T
1 T
40166 GCTTGGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.49
Consensus pattern (19 bp):
TAGTCTGTAGATTTTGAGT
Found at i:41932 original size:13 final size:13
Alignment explanation
Indices: 41914--41939 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41904 AACATTGAAG
41914 GTGGTAGGCATAT
1 GTGGTAGGCATAT
41927 GTGGTAGGCATAT
1 GTGGTAGGCATAT
41940 ATATACATCA
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:0.38, T:0.31
Consensus pattern (13 bp):
GTGGTAGGCATAT
Found at i:47191 original size:21 final size:18
Alignment explanation
Indices: 47143--47181 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
47133 TTGGTTACTG
*
47143 GTTGGGCTTAATACGTTA
1 GTTGGGCTTAATACATTA
47161 GTTGGGCTTAATACATTA
1 GTTGGGCTTAATACATTA
47179 GTT
1 GTT
47182 AGTGGGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.41
Consensus pattern (18 bp):
GTTGGGCTTAATACATTA
Done.