Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024515.1 Corchorus olitorius cultivar O-4 contig24548, 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: 17390
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:3307 original size:45 final size:44
Alignment explanation
Indices: 3243--3367 Score: 128
Period size: 45 Copynumber: 2.7 Consensus size: 44
3233 AGGACTTGAC
*
3243 CTATACAAAATAAAGGCCTCTTCTAGATCATTGCAAGTT-AGTGAA
1 CTATACAAAATAAATGCCTCTTCTAGATCATTGCAAGTTAAG-G-A
* * * *
3288 CTATACAAAATAAATGCCTCCTCTAGATAATGGCAATTTAAGGA
1 CTATACAAAATAAATGCCTCTTCTAGATCATTGCAAGTTAAGGA
3332 CATATACAAAATAAGAGGCTGCCT-TTCTAGATCATT
1 C-TATACAAAATAA-A---TGCCTCTTCTAGATCATT
3368 TCCTACCCTA
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
44 2 0.03
45 47 0.71
46 3 0.05
48 9 0.14
49 5 0.08
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.29
Consensus pattern (44 bp):
CTATACAAAATAAATGCCTCTTCTAGATCATTGCAAGTTAAGGA
Found at i:6222 original size:22 final size:20
Alignment explanation
Indices: 6192--6240 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
6182 TAGATCTAGA
* *
6192 TTTAATTTATTTTGCTTTGTT
1 TTTAATTTA-ATTGCTTTCTT
6213 TTCTAATTTAATTGCTTTCTT
1 TT-TAATTTAATTGCTTTCTT
6234 TTTAATT
1 TTTAATT
6241 GTTATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.20
21 13 0.52
22 7 0.28
ACGTcount: A:0.18, C:0.08, G:0.06, T:0.67
Consensus pattern (20 bp):
TTTAATTTAATTGCTTTCTT
Found at i:10196 original size:21 final size:22
Alignment explanation
Indices: 10063--10211 Score: 137
Period size: 22 Copynumber: 6.9 Consensus size: 22
10053 TGATAAATAC
* *
10063 CCTATTAAATTTTGATAACCAT
1 CCTATGAAATTTTGATAACCTT
*
10085 CCTATGAAATTTTGGTAA--TT
1 CCTATGAAATTTTGATAACCTT
* *
10105 ACCTATGAAATTGTGATAAAC-T
1 -CCTATGAAATTTTGATAACCTT
* *
10127 CCATATGAAACTTTGATAACCTA
1 CC-TATGAAATTTTGATAACCTT
* *
10150 ACTATGAAATTTTAATAAACCTT
1 CCTATGAAATTTTGAT-AACCTT
*
10173 CCTATGAAATTTTG-TAATCTT
1 CCTATGAAATTTTGATAACCTT
*
10194 CCTATG-ATTTTTGATAAC
1 CCTATGAAATTTTGATAAC
10212 ATCCCTGTGA
Statistics
Matches: 102, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
20 7 0.07
21 32 0.31
22 45 0.44
23 18 0.18
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
CCTATGAAATTTTGATAACCTT
Found at i:10199 original size:44 final size:43
Alignment explanation
Indices: 10063--10210 Score: 151
Period size: 43 Copynumber: 3.4 Consensus size: 43
10053 TGATAAATAC
*
10063 CCTATTAAATTTTGAT-AACCATCCTATGAAATTTTGGTAAT-TA
1 CCTATGAAATTTTGATAAACC-TCCTATGAAATTTT-GTAATCTA
* * *
10106 CCTATGAAATTGTGATAAA-CTCCATATGAAACTTTGATAACCTA
1 CCTATGAAATTTTGATAAACCTCC-TATGAAATTTTG-TAATCTA
* * *
10150 ACTATGAAATTTTAATAAACCTTCCTATGAAATTTTGTAATCTT
1 CCTATGAAATTTTGATAAACC-TCCTATGAAATTTTGTAATCTA
*
10194 CCTATG-ATTTTTGATAA
1 CCTATGAAATTTTGATAA
10211 CATCCCTGTG
Statistics
Matches: 86, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
42 4 0.05
43 37 0.43
44 30 0.35
45 12 0.14
46 3 0.03
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (43 bp):
CCTATGAAATTTTGATAAACCTCCTATGAAATTTTGTAATCTA
Found at i:14733 original size:22 final size:22
Alignment explanation
Indices: 14703--14938 Score: 138
Period size: 22 Copynumber: 10.6 Consensus size: 22
14693 AAATTCCCTC
*
14703 CCTATGAAATTTTGTTAACCTT
1 CCTATGAAATTTTGATAACCTT
* *
14725 CTTATGAAATTTTGATAACC-A
1 CCTATGAAATTTTGATAACCTT
* * **
14746 CACTATAAAATTTCGATAATTTT
1 C-CTATGAAATTTTGATAACCTT
** * *
14769 TGTATGAAATTTTGTTAACCTC
1 CCTATGAAATTTTGATAACCTT
* *
14791 CCTAAGAAATTTTGATAACTTTT
1 CCTATGAAATTTTGATAAC-CTT
** *
14814 TTTAATGAAATTTTGGTAACCTCT
1 CCT-ATGAAATTTTGATAACCT-T
* *
14838 GC-ATGAAATTTTGATAA-CTA
1 CCTATGAAATTTTGATAACCTT
*
14858 CACTAT-AAAGTTTTGATAATCTT
1 C-CTATGAAA-TTTTGATAACCTT
* * * **
14881 CATATGAAAATTTGGTAACCAA
1 CCTATGAAATTTTGATAACCTT
* * *
14903 ACTATTAAATTTTGGTAACCTT
1 CCTATGAAATTTTGATAACCTT
*
14925 CCTATGTAATTTTG
1 CCTATGAAATTTTG
14939 GTTTGATTGT
Statistics
Matches: 155, Mismatches: 49, Indels: 20
0.69 0.22 0.09
Matches are distributed among these distances:
21 7 0.05
22 124 0.80
23 9 0.06
24 15 0.10
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (22 bp):
CCTATGAAATTTTGATAACCTT
Found at i:14828 original size:46 final size:45
Alignment explanation
Indices: 14699--14856 Score: 153
Period size: 44 Copynumber: 3.5 Consensus size: 45
14689 TGATAAATTC
* * * *
14699 CCTCCCTATGAAATTTTGTTAAC-CTTCTTATGAAATTTTGATAA
1 CCTCCCTAAGAAATTTTGATAACTTTTTTTATGAAATTTTGATAA
* * * * *
14743 CCACACTATA-AAATTTCGATAA-TTTTTGTATGAAATTTTGTTAA
1 CCTCCCTA-AGAAATTTTGATAACTTTTTTTATGAAATTTTGATAA
*
14787 CCTCCCTAAGAAATTTTGATAACTTTTTTTAATGAAATTTTGGTAA
1 CCTCCCTAAGAAATTTTGATAACTTTTTTT-ATGAAATTTTGATAA
* *
14833 CCTCTGC-ATGAAATTTTGATAACT
1 CCTC-CCTAAGAAATTTTGATAACT
14857 ACACTATAAA
Statistics
Matches: 92, Mismatches: 16, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
43 1 0.01
44 50 0.54
45 6 0.07
46 34 0.37
47 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.42
Consensus pattern (45 bp):
CCTCCCTAAGAAATTTTGATAACTTTTTTTATGAAATTTTGATAA
Found at i:14913 original size:112 final size:112
Alignment explanation
Indices: 14706--14921 Score: 272
Period size: 112 Copynumber: 1.9 Consensus size: 112
14696 TTCCCTCCCT
* * * **
14706 ATGAAATTTTGTTAACCTTCTTATGAAATTTTGATAACCACACTATAAAATTTCGATAATTTTTG
1 ATGAAATTTTGGTAACCTTCTCATGAAATTTTGATAACCACACTATAAAATTTCGATAATCTTCA
* * ***
14771 TATGAAATTTTGTTAACCTCCCTAAGAAATTTTGATAACTTTTTTTA
66 TATGAAAATTTGGTAACCAAACTAAGAAATTTTGATAACTTTTTTTA
* * *
14818 ATGAAATTTTGGTAACC-TCTGCATGAAATTTTGATAACTACACTATAAAGTTTTGATAATCTTC
1 ATGAAATTTTGGTAACCTTCT-CATGAAATTTTGATAACCACACTATAAAATTTCGATAATCTTC
** *
14882 ATATGAAAATTTGGTAACCAAACTATTAAATTTTGGTAAC
65 ATATGAAAATTTGGTAACCAAACTAAGAAATTTTGATAAC
14922 CTTCCTATGT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
111 3 0.03
112 84 0.97
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (112 bp):
ATGAAATTTTGGTAACCTTCTCATGAAATTTTGATAACCACACTATAAAATTTCGATAATCTTCA
TATGAAAATTTGGTAACCAAACTAAGAAATTTTGATAACTTTTTTTA
Found at i:15803 original size:29 final size:29
Alignment explanation
Indices: 15761--15823 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
15751 AAAAGCCTTG
*
15761 ATTTGGCCAAAATTGGTAG-TCATGGGCTT
1 ATTTGGCCAAAATT-GAAGTTCATGGGCTT
* *
15790 ATTTGGGCAAAATTGAAGTTCATGTGCTT
1 ATTTGGCCAAAATTGAAGTTCATGGGCTT
15819 ATTTG
1 ATTTG
15824 ACCATTGGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.38
Consensus pattern (29 bp):
ATTTGGCCAAAATTGAAGTTCATGGGCTT
Done.