Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021239.1 Corchorus olitorius cultivar O-4 contig21272, 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: 19305
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:2467 original size:16 final size:16
Alignment explanation
Indices: 2446--2476 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2436 AGAGTACTCC
2446 AACACTCTACCAGCAG
1 AACACTCTACCAGCAG
2462 AACACTCTACCAGCA
1 AACACTCTACCAGCA
2477 CAGCAAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.39, G:0.10, T:0.13
Consensus pattern (16 bp):
AACACTCTACCAGCAG
Found at i:4061 original size:21 final size:22
Alignment explanation
Indices: 4036--4076 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4026 GTGTTCTGTG
4036 TTTTTCTC-TTTGATCTTTCTT
1 TTTTTCTCATTTGATCTTTCTT
*
4057 TTTTTCTCATTTTATCTTTC
1 TTTTTCTCATTTGATCTTTC
4077 ATTACTCTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTTCTCATTTGATCTTTCTT
Found at i:10726 original size:44 final size:44
Alignment explanation
Indices: 10676--10766 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
10666 TCCATTTTTA
10676 TATGCAATTATATATTATAAACAAATGTACATAATTATATATTC
1 TATGCAATTATATATTATAAACAAATGTACATAATTATATATTC
10720 TATGCAATTATATATTATAAACAAATGTACATAATTATATATTC
1 TATGCAATTATATATTATAAACAAATGTACATAATTATATATTC
10764 TAT
1 TAT
10767 ATACACTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (44 bp):
TATGCAATTATATATTATAAACAAATGTACATAATTATATATTC
Found at i:13928 original size:32 final size:32
Alignment explanation
Indices: 13892--13959 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
13882 CAAAACCCAA
* *
13892 CCGAACCCGAATTAACATGACCCAAATTTGAC
1 CCGAACCCGAATCAACATGACCCAAATTTAAC
*
13924 CCGAACCCGAATCAACCTGACCCAAATTTAAC
1 CCGAACCCGAATCAACATGACCCAAATTTAAC
13956 CCGA
1 CCGA
13960 CCTGACTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.35, G:0.12, T:0.16
Consensus pattern (32 bp):
CCGAACCCGAATCAACATGACCCAAATTTAAC
Found at i:13961 original size:16 final size:16
Alignment explanation
Indices: 13910--13961 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
13900 GAATTAACAT
*
13910 GACCCAAATTTGACCC
1 GACCCAAATTTAACCC
* * *
13926 GAACCCGAA-TCAACCT
1 G-ACCCAAATTTAACCC
13942 GACCCAAATTTAACCC
1 GACCCAAATTTAACCC
13958 GACC
1 GACC
13962 TGACTCAAGC
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
15 6 0.22
16 15 0.56
17 6 0.22
ACGTcount: A:0.35, C:0.38, G:0.12, T:0.15
Consensus pattern (16 bp):
GACCCAAATTTAACCC
Found at i:16096 original size:18 final size:18
Alignment explanation
Indices: 16075--16113 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
16065 CTAAAATTTA
16075 AAGTTAAATAAAAAGTTT
1 AAGTTAAATAAAAAGTTT
16093 AAGTTAAATAAAAAGTTT
1 AAGTTAAATAAAAAGTTT
16111 AAG
1 AAG
16114 AAGAAGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (18 bp):
AAGTTAAATAAAAAGTTT
Found at i:17910 original size:13 final size:13
Alignment explanation
Indices: 17892--17916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17882 GTTATCAAAT
17892 TTACAGTAATTAG
1 TTACAGTAATTAG
17905 TTACAGTAATTA
1 TTACAGTAATTA
17917 TCAAATTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
TTACAGTAATTAG
Found at i:18211 original size:36 final size:36
Alignment explanation
Indices: 18166--18237 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
18156 TTTACAATAC
18166 TTAATTACTCAAAAAGCTATAACGGTTATAAAAAAA
1 TTAATTACTCAAAAAGCTATAACGGTTATAAAAAAA
* *
18202 TTAATTACTCAAAAAGTTATAACGGTTATGAAAAAA
1 TTAATTACTCAAAAAGCTATAACGGTTATAAAAAAA
18238 GTTATATATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (36 bp):
TTAATTACTCAAAAAGCTATAACGGTTATAAAAAAA
Found at i:19189 original size:39 final size:39
Alignment explanation
Indices: 19154--19256 Score: 102
Period size: 41 Copynumber: 2.6 Consensus size: 39
19144 TATTGATCAC
** *
19154 CACACTATGAAATTC-ATAATGGTGTG-AAAATTTGATAA
1 CACACTATGAAATTCGATAA-CCTATGAAAAATTTGATAA
*
19192 CATCATTATGAAATTTCGATAACCTATGAAAAATTTGATAAA
1 CA-CACTATGAAA-TTCGATAACCTATGAAAAATTTGAT-AA
*
19234 CACACTATGAAATTTTGATAACC
1 CACACTATGAAA-TTCGATAACC
19257 ACATTATGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
38 2 0.04
39 9 0.17
40 6 0.11
41 33 0.61
42 4 0.07
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.32
Consensus pattern (39 bp):
CACACTATGAAATTCGATAACCTATGAAAAATTTGATAA
Found at i:19278 original size:22 final size:21
Alignment explanation
Indices: 19178--19277 Score: 107
Period size: 22 Copynumber: 4.7 Consensus size: 21
19168 CATAATGGTG
*
19178 TGAAAATTTGATAACATCATTA
1 TGAAATTTTGATAACA-CATTA
*
19200 TGAAATTTCGATAAC-C--TA
1 TGAAATTTTGATAACACATTA
* *
19218 TGAAAAATTTGATAAACACACTA
1 TG-AAATTTTGAT-AACACATTA
19241 TGAAATTTTGATAACCACATTA
1 TGAAATTTTGATAA-CACATTA
19263 TGAAATTTTGATAAC
1 TGAAATTTTGATAAC
19278 CTCAGTGTGA
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
18 4 0.06
19 8 0.12
20 4 0.06
21 4 0.06
22 42 0.64
23 4 0.06
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (21 bp):
TGAAATTTTGATAACACATTA
Found at i:19288 original size:22 final size:22
Alignment explanation
Indices: 19178--19291 Score: 92
Period size: 22 Copynumber: 5.3 Consensus size: 22
19168 CATAATGGTG
* * *
19178 TGAAAATTTGATAACATCATTA
1 TGAAATTTTGATAACCTCAGTA
*
19200 TGAAATTTCGATAA-C-C--TA
1 TGAAATTTTGATAACCTCAGTA
* * * *
19218 TGAAAAATTTGATAAACACACTA
1 TG-AAATTTTGATAACCTCAGTA
* *
19241 TGAAATTTTGATAACCACATTA
1 TGAAATTTTGATAACCTCAGTA
*
19263 TGAAATTTTGATAACCTCAGTG
1 TGAAATTTTGATAACCTCAGTA
19285 TGAAATT
1 TGAAATT
19292 GTAACAGCAT
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
18 4 0.05
19 10 0.13
20 2 0.03
21 1 0.01
22 55 0.72
23 4 0.05
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.34
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCAGTA
Done.