Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017679.1 Corchorus olitorius cultivar O-4 contig17712, 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: 50550
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1605 original size:21 final size:21
Alignment explanation
Indices: 1581--1651 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
1571 TTTAGGCAAT
1581 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGAAACCTTC
*
1602 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGAAACCTTC
*
1623 TCCAATAAGCTTGAAA-CTTGC
1 TCCAATGAGCTTGAAACCTT-C
1644 TCCAATGA
1 TCCAATGA
1652 TCTCCTAGCA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 3 0.07
21 42 0.93
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGAAACCTTC
Found at i:7393 original size:27 final size:28
Alignment explanation
Indices: 7355--7428 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 28
7345 GTCATCTAGG
7355 GGGGCATTTTGGTCATTT-GCACATCCA
1 GGGGCATTTTGGTCATTTCGCACATCCA
* * *
7382 GGGGCACTTTGGTCATTTCCGCATATTCA
1 GGGGCATTTTGGTCATTT-CGCACATCCA
*
7411 GGGGTATTTTGGTCATTT
1 GGGGCATTTTGGTCATTT
7429 ACTAGTTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 17 0.43
29 23 0.57
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.38
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTCGCACATCCA
Found at i:9645 original size:17 final size:18
Alignment explanation
Indices: 9623--9664 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
9613 GGTTTCTGTC
9623 GAAGAAGATG-AGT-CGAG
1 GAAGAAGA-GAAGTGCGAG
9640 GAAGAA-AGAAGTGCGAG
1 GAAGAAGAGAAGTGCGAG
9657 GAAGAAGA
1 GAAGAAGA
9665 AGGCTTAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.05
16 4 0.18
17 16 0.73
18 1 0.05
ACGTcount: A:0.48, C:0.05, G:0.40, T:0.07
Consensus pattern (18 bp):
GAAGAAGAGAAGTGCGAG
Found at i:12188 original size:17 final size:17
Alignment explanation
Indices: 12149--12188 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
12139 ATTTAGAGAT
12149 AGAAAAAGGAAAAATCC
1 AGAAAAAGGAAAAATCC
*
12166 AAAAAAAGTGAAAAAT-C
1 AGAAAAAG-GAAAAATCC
12183 AGAAAA
1 AGAAAA
12189 TCAAGAGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.70, C:0.07, G:0.15, T:0.07
Consensus pattern (17 bp):
AGAAAAAGGAAAAATCC
Found at i:19849 original size:28 final size:28
Alignment explanation
Indices: 19818--19894 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
19808 TTAGGATCAA
*
19818 CTAGGGGCATTTCAGTCATTTTCAAAAT
1 CTAGGGGCATTTTAGTCATTTTCAAAAT
* * *
19846 CTAGGGGCATTTTAGTCATTTGCACATT
1 CTAGGGGCATTTTAGTCATTTTCAAAAT
*
19874 C-AGGGGCATTTTGGTCATTTT
1 CTAGGGGCATTTTAGTCATTTT
19895 AAGTTCAGGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 18 0.42
28 25 0.58
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (28 bp):
CTAGGGGCATTTTAGTCATTTTCAAAAT
Found at i:19913 original size:26 final size:26
Alignment explanation
Indices: 19872--19924 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
19862 CATTTGCACA
**
19872 TTCAGGGGCATTTTGGTCATTTTAAG
1 TTCAGGGGCACGTTGGTCATTTTAAG
19898 TTCAGGGGCACGTTGGTCATTTTAAG
1 TTCAGGGGCACGTTGGTCATTTTAAG
19924 T
1 T
19925 CCACTCTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40
Consensus pattern (26 bp):
TTCAGGGGCACGTTGGTCATTTTAAG
Found at i:25279 original size:78 final size:78
Alignment explanation
Indices: 25150--25310 Score: 322
Period size: 78 Copynumber: 2.1 Consensus size: 78
25140 TGTTCAAAAA
25150 GATGAAAATCTTCTTGAGAGTGATGACGGTCGGCCCAAGGGAGACCTAAACTATGGGGCCGACGT
1 GATGAAAATCTTCTTGAGAGTGATGACGGTCGGCCCAAGGGAGACCTAAACTATGGGGCCGACGT
25215 TACTGATTTCAAG
66 TACTGATTTCAAG
25228 GATGAAAATCTTCTTGAGAGTGATGACGGTCGGCCCAAGGGAGACCTAAACTATGGGGCCGACGT
1 GATGAAAATCTTCTTGAGAGTGATGACGGTCGGCCCAAGGGAGACCTAAACTATGGGGCCGACGT
25293 TACTGATTTCAAG
66 TACTGATTTCAAG
25306 GATGA
1 GATGA
25311 TCAACTTGAG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 83 1.00
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.23
Consensus pattern (78 bp):
GATGAAAATCTTCTTGAGAGTGATGACGGTCGGCCCAAGGGAGACCTAAACTATGGGGCCGACGT
TACTGATTTCAAG
Found at i:30543 original size:17 final size:18
Alignment explanation
Indices: 30521--30554 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30511 AAAGTTGCTT
30521 AAAATTATTT-CTATTTG
1 AAAATTATTTCCTATTTG
*
30538 AAAATTTTTTCCTATTT
1 AAAATTATTTCCTATTT
30555 TAATTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.56
Consensus pattern (18 bp):
AAAATTATTTCCTATTTG
Found at i:32041 original size:21 final size:21
Alignment explanation
Indices: 32015--32061 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
32005 CAACCTAGTG
*
32015 TACATAAT-TTCGTATGATATA
1 TACATAATATTC-TATGACATA
*
32036 TACATAATATTCTATGACATG
1 TACATAATATTCTATGACATA
32057 TACAT
1 TACAT
32062 GTACATGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (21 bp):
TACATAATATTCTATGACATA
Found at i:37072 original size:27 final size:27
Alignment explanation
Indices: 37012--37063 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
37002 AAGAAGCTCC
37012 ACAACATTATGATGTAGAGGAGATGCA
1 ACAACATTATGATGTAGAGGAGATGCA
37039 ACAACATTATGATGTAGAGGAGATG
1 ACAACATTATGATGTAGAGGAGATG
37064 TTGCAACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.10, G:0.27, T:0.23
Consensus pattern (27 bp):
ACAACATTATGATGTAGAGGAGATGCA
Found at i:45636 original size:17 final size:18
Alignment explanation
Indices: 45614--45649 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
45604 AATTAATACA
45614 ATCATATATTAT-CATAT
1 ATCATATATTATACATAT
45631 ATCATATATTATACATAT
1 ATCATATATTATACATAT
45649 A
1 A
45650 GTGATAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (18 bp):
ATCATATATTATACATAT
Found at i:46255 original size:43 final size:43
Alignment explanation
Indices: 46207--46296 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
46197 CTCAATTTCC
* * *
46207 GTAA-TTAACTTTGATATCCTCAATTTTGGCAATTAGTATTGAT
1 GTAATTTAACTAT-ATATCCTCAAATTTGGCAATTAGTATCGAT
*
46250 GTAATTTCACTATATATCCTCAAATTTGGCAATTAGTATCGAT
1 GTAATTTAACTATATATCCTCAAATTTGGCAATTAGTATCGAT
46293 GTAA
1 GTAA
46297 CTACACCCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 36 0.86
44 6 0.14
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (43 bp):
GTAATTTAACTATATATCCTCAAATTTGGCAATTAGTATCGAT
Found at i:47727 original size:20 final size:20
Alignment explanation
Indices: 47702--47741 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
47692 AATTACAAAC
*
47702 AAACTCATATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
47722 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
47742 TTGAACCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
AAACTCACATTCCGTGAGAG
Found at i:48012 original size:106 final size:107
Alignment explanation
Indices: 47826--48071 Score: 395
Period size: 106 Copynumber: 2.3 Consensus size: 107
47816 AAATAAAGAT
* * * *
47826 TTAGTTATATATTTTATTTATAAAACCCTATAACAATATATTATTAATTATGCAATTTACCCTAA
1 TTAGTTTTATATTTTATTTCTAAAACCCTATAAAAATATATTATTAATTATGAAATTTACCCTAA
*
47891 AAATAAAGATAAAATTTTAATTTGGGGCTAAACTTAGTGAAA
66 AAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAA
* * * *
47933 TTAGTTTTGTATTTTATTTCTAAAACCCTATAAAAATA-ATTATTAATTTTGAAATTTACCTTTA
1 TTAGTTTTATATTTTATTTCTAAAACCCTATAAAAATATATTATTAATTATGAAATTTACCCTAA
47997 AAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAA
66 AAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAA
*
48039 TTAGTTTTATATTTTATTTCTAAAACTCTATAA
1 TTAGTTTTATATTTTATTTCTAAAACCCTATAA
48072 TAAAACCTTT
Statistics
Matches: 128, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
106 94 0.73
107 34 0.27
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.43
Consensus pattern (107 bp):
TTAGTTTTATATTTTATTTCTAAAACCCTATAAAAATATATTATTAATTATGAAATTTACCCTAA
AAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAA
Found at i:48106 original size:106 final size:106
Alignment explanation
Indices: 47826--48106 Score: 372
Period size: 106 Copynumber: 2.6 Consensus size: 106
47816 AAATAAAGAT
* * * * * *
47826 TTAGTTATATATTTTATTTATAAAACCCTATAACAATATATTATTAATTATGC-AATTTACCCTA
1 TTAGTTTTATATTTTATTTCTAAAACCCTATAAAAATA-ACTATTAATT-TTCAAATTTACCTTA
*
47890 AAAATAAAGATAAAATTTTAATTTGGGGCTAAACTTAGTGAAA
64 AAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAA
* * * *
47933 TTAGTTTTGTATTTTATTTCTAAAACCCTATAAAAATAATTATTAATTTTGAAATTTACCTTTAA
1 TTAGTTTTATATTTTATTTCTAAAACCCTATAAAAATAACTATTAATTTTCAAATTTACCTTAAA
47998 AATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAA
66 AATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAA
* *
48039 TTAGTTTTATATTTTATTTCTAAAACTCTATAATAAA-ACCT-TTAA-TTTCATAATTTACTCTT
1 TTAGTTTTATATTTTATTTCTAAAACCCTATAA-AAATAACTATTAATTTTCA-AATTTAC-CTT
48101 AAAAAT
63 AAAAAT
48107 TAAATGTCTT
Statistics
Matches: 155, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
104 4 0.03
105 12 0.08
106 102 0.66
107 37 0.24
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (106 bp):
TTAGTTTTATATTTTATTTCTAAAACCCTATAAAAATAACTATTAATTTTCAAATTTACCTTAAA
AATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAA
Found at i:49087 original size:26 final size:26
Alignment explanation
Indices: 49051--49117 Score: 134
Period size: 26 Copynumber: 2.6 Consensus size: 26
49041 AGATAGGGGC
49051 TAAACATTTCTATATGTTTTTATGAA
1 TAAACATTTCTATATGTTTTTATGAA
49077 TAAACATTTCTATATGTTTTTATGAA
1 TAAACATTTCTATATGTTTTTATGAA
49103 TAAACATTTCTATAT
1 TAAACATTTCTATAT
49118 CACATCTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (26 bp):
TAAACATTTCTATATGTTTTTATGAA
Done.