Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021403.1 Corchorus olitorius cultivar O-4 contig21436, 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: 13481
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:555 original size:18 final size:17
Alignment explanation
Indices: 523--601 Score: 88
Period size: 17 Copynumber: 4.6 Consensus size: 17
513 GGCCACCCTT
523 TTTTTTAATTGACTTATAA
1 TTTTTTAATT-ACTTA-AA
*
542 TTTTTTAATTACTTAAT
1 TTTTTTAATTACTTAAA
* **
559 TTTTTTAATTTCGAAAA
1 TTTTTTAATTACTTAAA
576 TTTTTTAATTACTT-AA
1 TTTTTTAATTACTTAAA
*
592 TTTTTGAATT
1 TTTTTTAATT
602 CTGAAATTCC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
16 11 0.22
17 25 0.49
18 5 0.10
19 10 0.20
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (17 bp):
TTTTTTAATTACTTAAA
Found at i:768 original size:30 final size:31
Alignment explanation
Indices: 732--808 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
722 TTTTTGTAAT
*
732 GTTATATCCTGAATTGTCA-CCTCA-TCAAAC
1 GTTATATCCTGAATTG-CATCCTCAGACAAAC
* * **
762 GTTATATCCTTAATTGGATTTTCAGACAAAC
1 GTTATATCCTGAATTGCATCCTCAGACAAAC
793 GTTATATCCTGAATTG
1 GTTATATCCTGAATTG
809 ATCATTTAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 1 0.03
30 18 0.46
31 20 0.51
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (31 bp):
GTTATATCCTGAATTGCATCCTCAGACAAAC
Found at i:1886 original size:47 final size:47
Alignment explanation
Indices: 1770--1988 Score: 357
Period size: 47 Copynumber: 4.6 Consensus size: 47
1760 ACGAGAGCTC
1770 TAGTAAATTTTAATTGACACCAGAAGTTGTCAAATTAAAATTTTACTTT
1 TAGTAAA-TTTAATTGACACCAGAAGTTGTCAAATTAAAATTTTAC-TT
*
1819 TAGTAAATTTAATTGACACTAGAAGTTGTCAAATTAAAATTTTACTT
1 TAGTAAATTTAATTGACACCAGAAGTTGTCAAATTAAAATTTTACTT
* * *
1866 TAGTAAATATAATTGACACTAGAAGTTGTTAAATTAAAATTTTACTT
1 TAGTAAATTTAATTGACACCAGAAGTTGTCAAATTAAAATTTTACTT
* **
1913 TAGTAAATTTAATTGACACCAGAAGTTGTCAAATTAAATTTTTGTTT
1 TAGTAAATTTAATTGACACCAGAAGTTGTCAAATTAAAATTTTACTT
1960 TAGTAAATTTAATTGACACCAGAAGTTGT
1 TAGTAAATTTAATTGACACCAGAAGTTGT
1989 TATCTTGGTA
Statistics
Matches: 161, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
47 117 0.73
48 37 0.23
49 7 0.04
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (47 bp):
TAGTAAATTTAATTGACACCAGAAGTTGTCAAATTAAAATTTTACTT
Found at i:4497 original size:22 final size:21
Alignment explanation
Indices: 4445--4498 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
4435 GCTTCTTGGA
4445 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
4466 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
4485 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
4499 CACGAATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:5009 original size:27 final size:27
Alignment explanation
Indices: 4979--5055 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
4969 AGGGTCATCC
4979 GGGGCATTTTGGTCATTTGCACACTCA
1 GGGGCATTTTGGTCATTTGCACACTCA
* * *
5006 GGGGTATTTTGGTCATTTACACACTTA
1 GGGGCATTTTGGTCATTTGCACACTCA
* *
5033 GGGACATTTTTGGTCATTCGCAC
1 GGGGCA-TTTTGGTCATTTGCAC
5056 TCAGGGTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 28 0.67
28 14 0.33
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTGCACACTCA
Found at i:9409 original size:15 final size:16
Alignment explanation
Indices: 9389--9433 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
9379 AAGTTGAAGA
9389 AAGAAATGAAAAAA-G
1 AAGAAATGAAAAAATG
*
9404 AAGAAAGGAAAAAATG
1 AAGAAATGAAAAAATG
*
9420 AA-AAATGGAAAAAT
1 AAGAAATGAAAAAAT
9434 CAGAAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 23 0.88
16 3 0.12
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (16 bp):
AAGAAATGAAAAAATG
Found at i:10241 original size:15 final size:14
Alignment explanation
Indices: 10221--10258 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
10211 AAATGGTTGC
10221 TTTGTTTTGTTTCG
1 TTTGTTTTGTTTCG
10235 ATTTGTTTTGTTTCG
1 -TTTGTTTTGTTTCG
*
10250 TTTGCTTTG
1 TTTGTTTTG
10259 ATATTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.03, C:0.08, G:0.21, T:0.68
Consensus pattern (14 bp):
TTTGTTTTGTTTCG
Found at i:12720 original size:28 final size:28
Alignment explanation
Indices: 12677--12858 Score: 274
Period size: 28 Copynumber: 6.5 Consensus size: 28
12667 TTTACTTCTT
12677 ATTTTGGTCATTTTGCATGTCCAGGGGC
1 ATTTTGGTCATTTTGCATGTCCAGGGGC
* *
12705 ATTTTGGTCATCTTGCATGTCCAGCGGC
1 ATTTTGGTCATTTTGCATGTCCAGGGGC
*
12733 ATTTAGGTCATTTTGCATGTCCAGGGGC
1 ATTTTGGTCATTTTGCATGTCCAGGGGC
* * *
12761 ATTTTGGTCATTTTACATGTCTATGGGC
1 ATTTTGGTCATTTTGCATGTCCAGGGGC
* *
12789 ATTTTGGTCATTTATGCATGTCCAGGAGT
1 ATTTTGGTCATTT-TGCATGTCCAGGGGC
12818 ATTTTGGTCATTTTGCATGTCCAGGGGC
1 ATTTTGGTCATTTTGCATGTCCAGGGGC
*
12846 ATTTTAGTCATTT
1 ATTTTGGTCATTT
12859 CAAGTACCTT
Statistics
Matches: 136, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
28 113 0.83
29 23 0.17
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.41
Consensus pattern (28 bp):
ATTTTGGTCATTTTGCATGTCCAGGGGC
Found at i:12846 original size:85 final size:84
Alignment explanation
Indices: 12677--12858 Score: 276
Period size: 85 Copynumber: 2.2 Consensus size: 84
12667 TTTACTTCTT
*
12677 ATTTTGGTCATTTTGCATGTCCAGGGGCATTTTGGTCATCTTGCATGTCCAGCGGCATTTAGGTC
1 ATTTTGGTCATTTTACATGTCCAGGGGCATTTTGGTCATCTTGCATGTCCAGCGGCATTTAGGTC
12742 ATTTTGCATGTCCAGGGGC
66 ATTTTGCATGTCCAGGGGC
* * * * *
12761 ATTTTGGTCATTTTACATGTCTATGGGCATTTTGGTCATTTATGCATGTCCAG-GAGTATTTTGG
1 ATTTTGGTCATTTTACATGTCCAGGGGCATTTTGGTCATCT-TGCATGTCCAGCG-GCATTTAGG
12825 TCATTTTGCATGTCCAGGGGC
64 TCATTTTGCATGTCCAGGGGC
*
12846 ATTTTAGTCATTT
1 ATTTTGGTCATTT
12859 CAAGTACCTT
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
84 38 0.43
85 51 0.57
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.41
Consensus pattern (84 bp):
ATTTTGGTCATTTTACATGTCCAGGGGCATTTTGGTCATCTTGCATGTCCAGCGGCATTTAGGTC
ATTTTGCATGTCCAGGGGC
Done.