Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016985.1 Corchorus olitorius cultivar O-4 contig17018, 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: 39761
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:1067 original size:27 final size:29
Alignment explanation
Indices: 1022--1084 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
1012 AAATTATCGA
* *
1022 TTTACCCTTGGAGTTGATAAA-TTACCA-T
1 TTTACCCTTAGAGTGGATAAAGTTA-CAGT
1050 TTTACCCTTAGAG-GGATAAAGTTACAGT
1 TTTACCCTTAGAGTGGATAAAGTTACAGT
1078 TTTACCC
1 TTTACCC
1085 CTTTAACCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 8 0.26
28 23 0.74
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (29 bp):
TTTACCCTTAGAGTGGATAAAGTTACAGT
Found at i:3839 original size:23 final size:23
Alignment explanation
Indices: 3788--3841 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
3778 AATTGTTGTG
* *
3788 TATATATATATCTATATCTATAA
1 TATATATATATCAATATCAATAA
*
3811 TCTATATATATCAATAT-AATAA
1 TATATATATATCAATATCAATAA
3833 TA-ATATATA
1 TATATATATA
3842 AAATGTGAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 7 0.26
22 5 0.19
23 15 0.56
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (23 bp):
TATATATATATCAATATCAATAA
Found at i:3872 original size:32 final size:32
Alignment explanation
Indices: 3836--3898 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
3826 ATAATAATAA
*
3836 TATATAAAATGTGAAGTAAATGTATCAAAAAG
1 TATATAAAACGTGAAGTAAATGTATCAAAAAG
*
3868 TATATAAAACGTTAAGTAAATGTATCAAAAA
1 TATATAAAACGTGAAGTAAATGTATCAAAAA
3899 ATCAGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.54, C:0.05, G:0.13, T:0.29
Consensus pattern (32 bp):
TATATAAAACGTGAAGTAAATGTATCAAAAAG
Found at i:9719 original size:22 final size:22
Alignment explanation
Indices: 9692--9779 Score: 93
Period size: 19 Copynumber: 4.3 Consensus size: 22
9682 GGGCTGAAAT
9692 TTATTAATTATT-A-AATAAATTA
1 TTATT-ATTATTCAGAAT-AATTA
*
9714 TTATTATTTTTCAGAATAATTA
1 TTATTATTATTCAGAATAATTA
9736 TTA-T-TT-TTCAGAATAATTA
1 TTATTATTATTCAGAATAATTA
9755 TTA-T-TT-TTCAGAATAATTA
1 TTATTATTATTCAGAATAATTA
9774 TTATTA
1 TTATTA
9780 AAATCATCAT
Statistics
Matches: 61, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
19 35 0.57
20 3 0.05
21 6 0.10
22 14 0.23
23 3 0.05
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (22 bp):
TTATTATTATTCAGAATAATTA
Found at i:9735 original size:19 final size:19
Alignment explanation
Indices: 9713--9778 Score: 132
Period size: 19 Copynumber: 3.5 Consensus size: 19
9703 TAAATAAATT
9713 ATTATTATTTTTCAGAATA
1 ATTATTATTTTTCAGAATA
9732 ATTATTATTTTTCAGAATA
1 ATTATTATTTTTCAGAATA
9751 ATTATTATTTTTCAGAATA
1 ATTATTATTTTTCAGAATA
9770 ATTATTATT
1 ATTATTATT
9779 AAAATCATCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTATTATTTTTCAGAATA
Found at i:11620 original size:76 final size:75
Alignment explanation
Indices: 11483--11634 Score: 173
Period size: 76 Copynumber: 2.0 Consensus size: 75
11473 ACAAGGACCC
* * *
11483 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCATACGGTTTGCTTGAGGACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCATA-GGTTTGCCTGAGCACCCAGAT
11548 GGGCGGTGTCA
65 GGGCGGTGTCA
* * * * *
11559 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAGACCCAT-GTGTTTCGCCTGATCACCCAG
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTGAACACCCATAG-GTTT-GCCTGAGCACCCAG
*
11622 ATGGGCTGTGTCA
63 ATGGGCGGTGTCA
11635 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
74 1 0.02
75 4 0.06
76 55 0.86
77 4 0.06
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24
Consensus pattern (75 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCATAGGTTTGCCTGAGCACCCAGATG
GGCGGTGTCA
Found at i:12576 original size:26 final size:26
Alignment explanation
Indices: 12534--12583 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
12524 ATGATTTAGG
*
12534 GGTTACTAACTCCCTTTTTCTTTTGA
1 GGTTACTAACACCCTTTTTCTTTTGA
* *
12560 GGTTACTAACACTCTTTTTTTTTT
1 GGTTACTAACACCCTTTTTCTTTT
12584 TCCAGAGGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.54
Consensus pattern (26 bp):
GGTTACTAACACCCTTTTTCTTTTGA
Found at i:14909 original size:17 final size:16
Alignment explanation
Indices: 14877--14910 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
14867 CAACTTCTCC
*
14877 AAAACTTGATAATTTG
1 AAAACTTGAGAATTTG
14893 AAAACTTGAGGAATTTG
1 AAAACTTGA-GAATTTG
14910 A
1 A
14911 TGGAAAAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (16 bp):
AAAACTTGAGAATTTG
Found at i:19420 original size:21 final size:21
Alignment explanation
Indices: 19387--19435 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
19377 AAGAATTTTA
**
19387 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
19407 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
19428 GCATTCCT
1 GC-TTCCT
19436 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:20560 original size:10 final size:9
Alignment explanation
Indices: 20517--20574 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
20507 TAAAAGTAAC
20517 TAAGAAAAA
1 TAAGAAAAA
*
20526 TAAACAAAAA
1 T-AAGAAAAA
20536 TAA-AAGAAA
1 TAAGAA-AAA
20545 -AAGAAAAA
1 TAAGAAAAA
20553 TAACGAAAAA
1 TAA-GAAAAA
*
20563 TAA-AAACA
1 TAAGAAAAA
20571 TAAG
1 TAAG
20575 GGTAAGAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 14 0.34
9 10 0.24
10 17 0.41
ACGTcount: A:0.76, C:0.05, G:0.09, T:0.10
Consensus pattern (9 bp):
TAAGAAAAA
Found at i:20560 original size:16 final size:17
Alignment explanation
Indices: 20531--20568 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
20521 AAAAATAAAC
20531 AAAAATAAAAGAAAAAG
1 AAAAATAAAAGAAAAAG
* *
20548 AAAAAT-AACGAAAAAT
1 AAAAATAAAAGAAAAAG
20564 AAAAA
1 AAAAA
20569 CATAAGGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAAATAAAAGAAAAAG
Found at i:37274 original size:17 final size:17
Alignment explanation
Indices: 37252--37285 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
37242 CTCTTATAAA
37252 TTTCTTAATTCTATTTG
1 TTTCTTAATTCTATTTG
*
37269 TTTCTTAATTTTATTTG
1 TTTCTTAATTCTATTTG
37286 GTTGGAGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.09, G:0.06, T:0.68
Consensus pattern (17 bp):
TTTCTTAATTCTATTTG
Done.