Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019061.1 Corchorus olitorius cultivar O-4 contig19094, 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: 50146
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2699 original size:26 final size:25
Alignment explanation
Indices: 2653--2701 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
2643 TTAATGTTTA
*
2653 AATTTTATTTTTTATTGAAAAATTT
1 AATTTTATTTTTTATTAAAAAATTT
2678 AATTATTATTTTATT-TTAAAAAAT
1 AATT-TTATTTT-TTATTAAAAAAT
2702 AAATTTAGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 15 0.71
27 2 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
AATTTTATTTTTTATTAAAAAATTT
Found at i:2706 original size:25 final size:25
Alignment explanation
Indices: 2651--2707 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
2641 TTTTAATGTT
*
2651 TAAATTTTATTTTTTATTGAAAAAT
1 TAAATTTTATTTTTTATTGAAAAAA
*
2676 TTAATTATTATTTTATT-TT-AAAAAA
1 TAAATT-TTATTTT-TTATTGAAAAAA
2701 TAAATTT
1 TAAATTT
2708 AGACGGGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
24 1 0.04
25 15 0.56
26 9 0.33
27 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TAAATTTTATTTTTTATTGAAAAAA
Found at i:7853 original size:31 final size:32
Alignment explanation
Indices: 7818--7890 Score: 105
Period size: 31 Copynumber: 2.3 Consensus size: 32
7808 TCCAAATCAC
*
7818 GACAATTTACTTTTTGAA-TTTTTAAATTCAG
1 GACAATTTACTTTCTGAACTTTTTAAATTCAG
* *
7849 GACAATTTGC-TTCTGAACTTTTTAAATTTAG
1 GACAATTTACTTTCTGAACTTTTTAAATTCAG
7880 GACAATTTACT
1 GACAATTTACT
7891 CCTGATGTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 6 0.17
31 30 0.83
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (32 bp):
GACAATTTACTTTCTGAACTTTTTAAATTCAG
Found at i:25380 original size:48 final size:48
Alignment explanation
Indices: 25307--25403 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
25297 AGCATATTTT
*
25307 TAGTAGGATCACTAGGATAATATAGTAGGTAAATGTTTAGATTCGTGG
1 TAGTAGGATCACTAGGATAAAATAGTAGGTAAATGTTTAGATTCGTGG
25355 TAGTAGGATCACTAGGATAAAATAGTAGGTAAATGTTTAGATTCGTGG
1 TAGTAGGATCACTAGGATAAAATAGTAGGTAAATGTTTAGATTCGTGG
25403 T
1 T
25404 GAAAGATTGT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (48 bp):
TAGTAGGATCACTAGGATAAAATAGTAGGTAAATGTTTAGATTCGTGG
Found at i:26265 original size:65 final size:66
Alignment explanation
Indices: 26159--26292 Score: 225
Period size: 65 Copynumber: 2.0 Consensus size: 66
26149 TGTCCCTTTT
*
26159 TCAATTCTTTTCTTTTGTTCCTTTTTTTTTTATTGGGGTTATCATCATTTTACCAAGCATATTTT
1 TCAATTCTTTTCTTTTGTTCC--TTTTTTTTATCGGGGTTATCATCATTTTACCAAGCATATTTT
26224 TAG
64 TAG
*
26227 TCAATTTTTTTCTTTTGTTCC-TTTTTTTATCGGGGTTATCATCATTTTACCAAGCATATTTTTA
1 TCAATTCTTTTCTTTTGTTCCTTTTTTTTATCGGGGTTATCATCATTTTACCAAGCATATTTTTA
26291 G
66 G
26292 T
1 T
26293 AGGACTAGGA
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
65 44 0.69
68 20 0.31
ACGTcount: A:0.18, C:0.15, G:0.10, T:0.57
Consensus pattern (66 bp):
TCAATTCTTTTCTTTTGTTCCTTTTTTTTATCGGGGTTATCATCATTTTACCAAGCATATTTTTA
G
Found at i:31948 original size:29 final size:30
Alignment explanation
Indices: 31910--31968 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
31900 TTATTGTGTA
*
31910 AAGGACGTTTTGTCCCCTGAACTT-CAAAT
1 AAGGACGTTTTGCCCCCTGAACTTCCAAAT
31939 AAGGACGTTTTGCCCCCTGAACTTCCAAAT
1 AAGGACGTTTTGCCCCCTGAACTTCCAAAT
31969 TCGAACTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (30 bp):
AAGGACGTTTTGCCCCCTGAACTTCCAAAT
Found at i:31976 original size:14 final size:15
Alignment explanation
Indices: 31957--31985 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31947 TTTGCCCCCT
31957 GAACTTC-CAAATTC
1 GAACTTCTCAAATTC
31971 GAACTTCTCAAATTC
1 GAACTTCTCAAATTC
31986 AAGATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.28, G:0.07, T:0.31
Consensus pattern (15 bp):
GAACTTCTCAAATTC
Found at i:43732 original size:14 final size:15
Alignment explanation
Indices: 43690--43733 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
43680 CAGAATTCTG
*
43690 TCAATCCTGTTGATAT
1 TCAATCCT-TTGATCT
*
43706 TCAATCCTCTGATCT
1 TCAATCCTTTGATCT
43721 TC-ATCCTTTGATC
1 TCAATCCTTTGATC
43734 ACAAGTACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 10 0.40
15 7 0.28
16 8 0.32
ACGTcount: A:0.20, C:0.27, G:0.09, T:0.43
Consensus pattern (15 bp):
TCAATCCTTTGATCT
Found at i:46170 original size:2 final size:2
Alignment explanation
Indices: 46163--46192 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
46153 TACTATTTAG
46163 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46193 AATTCAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47984 original size:39 final size:40
Alignment explanation
Indices: 47925--48006 Score: 130
Period size: 39 Copynumber: 2.0 Consensus size: 40
47915 AAAAGTGGGA
*
47925 CTCTTTTGGGCCTTTCTAGTGTGTGT-GATGCATTGGGCC
1 CTCTCTTGGGCCTTTCTAGTGTGTGTAGATGCATTGGGCC
*
47964 CTCTCTTGGGCCTTTGTAGTGTGTGTGAGATGCATTGGGCC
1 CTCTCTTGGGCCTTTCTAGTGTGTGT-AGATGCATTGGGCC
48005 CT
1 CT
48007 TTTGATGTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
39 24 0.62
41 15 0.38
ACGTcount: A:0.09, C:0.21, G:0.32, T:0.39
Consensus pattern (40 bp):
CTCTCTTGGGCCTTTCTAGTGTGTGTAGATGCATTGGGCC
Found at i:47988 original size:41 final size:39
Alignment explanation
Indices: 47925--48006 Score: 119
Period size: 41 Copynumber: 2.1 Consensus size: 39
47915 AAAAGTGGGA
* *
47925 CTCTTTTGGGCCTTTCTAGTGTGTGTGATGCATTGGGCC
1 CTCTCTTGGGCCTTTCTAGTGTGTGAGATGCATTGGGCC
*
47964 CTCTCTTGGGCCTTTGTAGTGTGTGTGAGATGCATTGGGCC
1 CTCTCTTGGGCCTTTCTA--GTGTGTGAGATGCATTGGGCC
48005 CT
1 CT
48007 TTTGATGTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 16 0.42
41 22 0.58
ACGTcount: A:0.09, C:0.21, G:0.32, T:0.39
Consensus pattern (39 bp):
CTCTCTTGGGCCTTTCTAGTGTGTGAGATGCATTGGGCC
Found at i:49570 original size:28 final size:30
Alignment explanation
Indices: 49517--49572 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 30
49507 TGTAATAAAA
*
49517 TATAATTAAATTAAATAAATATATGTGTTC
1 TATAATTAAATTAAATAAATACATGTGTTC
*
49547 TATAA-TAAATTCAA-AAATACATGTGT
1 TATAATTAAATTAAATAAATACATGTGT
49573 ATGGATCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 11 0.46
29 8 0.33
30 5 0.21
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.39
Consensus pattern (30 bp):
TATAATTAAATTAAATAAATACATGTGTTC
Done.