Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023768.1 Corchorus olitorius cultivar O-4 contig23801, 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: 93180
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1046 original size:12 final size:12
Alignment explanation
Indices: 1029--1058 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
1019 GTAACAAGCA
1029 TTTGCCTGATCT
1 TTTGCCTGATCT
1041 TTTGCCTGATCT
1 TTTGCCTGATCT
1053 TGTTGC
1 T-TTGC
1059 TTCTGTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.07, C:0.23, G:0.20, T:0.50
Consensus pattern (12 bp):
TTTGCCTGATCT
Found at i:21052 original size:60 final size:60
Alignment explanation
Indices: 20959--21083 Score: 241
Period size: 60 Copynumber: 2.1 Consensus size: 60
20949 TCACTGGGAC
20959 CCGTCATGTAGTGAGAATTACCTCTAAGAGCAGTGATAACAACCTACGCCACCGACTCGA
1 CCGTCATGTAGTGAGAATTACCTCTAAGAGCAGTGATAACAACCTACGCCACCGACTCGA
*
21019 CCGTCATGTAGTGAGAATTACCTCTAAGAGCAGTGATAACAACCTACGCCACCGACTTGA
1 CCGTCATGTAGTGAGAATTACCTCTAAGAGCAGTGATAACAACCTACGCCACCGACTCGA
21079 CCGTC
1 CCGTC
21084 CAAGAATGTG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (60 bp):
CCGTCATGTAGTGAGAATTACCTCTAAGAGCAGTGATAACAACCTACGCCACCGACTCGA
Found at i:26221 original size:16 final size:16
Alignment explanation
Indices: 26192--26225 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
26182 ATGCTAACCC
26192 TATATGCTGCTAAGAT
1 TATATGCTGCTAAGAT
26208 TATATGCTGCTAAGAT
1 TATATGCTGCTAAGAT
26224 TA
1 TA
26226 AGTATGCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (16 bp):
TATATGCTGCTAAGAT
Found at i:27171 original size:33 final size:33
Alignment explanation
Indices: 27124--27187 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
27114 AAATACTATA
* *
27124 TTAATGTGACTAGAATGGAACAAAAACATTTCC
1 TTAATGGGACTAGAATGAAACAAAAACATTTCC
* *
27157 TTAATGGGATTAGAATGAAACAAAAATATTT
1 TTAATGGGACTAGAATGAAACAAAAACATTT
27188 TTAGATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (33 bp):
TTAATGGGACTAGAATGAAACAAAAACATTTCC
Found at i:33131 original size:22 final size:25
Alignment explanation
Indices: 33097--33149 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 25
33087 TAAATGTTGA
* *
33097 TGATAA-TCTTCT-CTTTTATCTC-
1 TGATAATTCTTCTCCATTTATCACT
33119 TGATAATTC-TCTCCATTTATCACT
1 TGATAATTCTTCTCCATTTATCACT
33143 TGATAAT
1 TGATAAT
33150 ATCTAGACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 9 0.35
23 10 0.38
24 7 0.27
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.49
Consensus pattern (25 bp):
TGATAATTCTTCTCCATTTATCACT
Found at i:37366 original size:30 final size:30
Alignment explanation
Indices: 37210--37648 Score: 480
Period size: 30 Copynumber: 14.7 Consensus size: 30
37200 GAAAGGTAAA
*
37210 ATCATAACAACTTCTGGTGTCAATTG--A-
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
37237 ATTATGACAACTTCTGGTGTCAATTG--A-
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* * ** * * *
37264 ATTATGACATCTTCAAGTGTCTATTGGAAATTT
1 ATCATGACAACTTCTGGTGTCAATT-GCAA--G
*
37297 ATCATGACAACTTCT-G-GTCAATTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* * *
37325 ACCATTGACAACTTTTGGTGTCAATTGTAAG
1 ATCA-TGACAACTTCTGGTGTCAATTGCAAG
* *
37356 ATCATGACAACTTATGGTGTCAATTACAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* * *
37386 ATCATGACAACTTTTGGTGTCCATTGCAAT
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
37416 ATCATGACAACTTCTGGTGTCAATTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
37446 AGCATGACAACTTATGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
37476 AGCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
37506 ATCATAACAACTTCTAGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
37536 ATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* * *
37566 ACCATGACAACTTCTGGTGTCATTTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* * * *
37596 ATCATAACAACTTCTGGTGTCATTTGGAGATTT
1 ATCATGACAACTTCTGGTGTCAATTGCA-A--G
37629 ATCATGACAACTTCTGGTGT
1 ATCATGACAACTTCTGGTGT
37649 GTCATTTCGA
Statistics
Matches: 357, Mismatches: 43, Indels: 18
0.85 0.10 0.04
Matches are distributed among these distances:
27 46 0.13
28 4 0.01
29 10 0.03
30 243 0.68
31 22 0.06
32 1 0.00
33 31 0.09
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (30 bp):
ATCATGACAACTTCTGGTGTCAATTGCAAG
Found at i:45860 original size:42 final size:43
Alignment explanation
Indices: 45809--45902 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
45799 AGTGCATTAC
*
45809 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
45850 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
*
45895 CTCATATT
1 CTAATATT
45903 ATTTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:46210 original size:25 final size:25
Alignment explanation
Indices: 46181--46229 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
46171 TAATATACTA
46181 AATATAAGCAACTAATAGAAACCTC
1 AATATAAGCAACTAATAGAAACCTC
46206 AATATAAGCAACTAATAGAAACCT
1 AATATAAGCAACTAATAGAAACCT
46230 ATTAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.53, C:0.18, G:0.08, T:0.20
Consensus pattern (25 bp):
AATATAAGCAACTAATAGAAACCTC
Found at i:55825 original size:19 final size:20
Alignment explanation
Indices: 55801--55844 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
55791 TAGATAACTC
55801 CAAGTTGCATGCA-TGCATT
1 CAAGTTGCATGCAGTGCATT
55820 CAAGTTGCATGCATGTGCATT
1 CAAGTTGCATGCA-GTGCATT
55841 CAAG
1 CAAG
55845 AAGATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.57
21 10 0.43
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (20 bp):
CAAGTTGCATGCAGTGCATT
Found at i:61759 original size:25 final size:25
Alignment explanation
Indices: 61721--61769 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
61711 AGCCCGCCCA
* * *
61721 TATTTATTTTTTAATATAAAATAAT
1 TATTAATTTATTAATAAAAAATAAT
61746 TATTAATTTATTAATAAAAAATAA
1 TATTAATTTATTAATAAAAAATAA
61770 AATTTAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TATTAATTTATTAATAAAAAATAAT
Found at i:61776 original size:25 final size:26
Alignment explanation
Indices: 61722--61776 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
61712 GCCCGCCCAT
* * *
61722 ATTT-ATTTTTTAATATAAAATAATT
1 ATTTAATTTATTAATAAAAAATAATA
61747 A-TTAATTTATTAATAAAAAATAA-A
1 ATTTAATTTATTAATAAAAAATAATA
61771 ATTTAA
1 ATTTAA
61777 ACATTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTAATTTATTAATAAAAAATAATA
Found at i:73962 original size:17 final size:17
Alignment explanation
Indices: 73927--73969 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
73917 TATAACATCA
*
73927 ATTTTATTTGTTATATT
1 ATTTTATTAGTTATATT
* *
73944 ATTTTATTAGTTTTTTT
1 ATTTTATTAGTTATATT
73961 ATTTATATT
1 ATTT-TATT
73970 GTTGCTTAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (17 bp):
ATTTTATTAGTTATATT
Found at i:80692 original size:6 final size:6
Alignment explanation
Indices: 80681--80731 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
80671 ATTGTTAATA
80681 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
80729 ATA
1 ATA
80732 ATATAATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:80747 original size:13 final size:15
Alignment explanation
Indices: 80678--80754 Score: 77
Period size: 18 Copynumber: 4.8 Consensus size: 15
80668 TTTATTGTTA
80678 ATAATATACATATAC
1 ATAATATACATATAC
80693 ATATACATATACATATAC
1 --ATA-ATATACATATAC
80711 ATATACATATACATATAC
1 --ATA-ATATACATATAC
80729 ATAATATA-ATATA-
1 ATAATATACATATAC
80742 ATAATATATCATA
1 ATAATATA-CATA
80755 ATATTGTATT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.14
14 5 0.09
15 8 0.14
16 3 0.05
17 3 0.05
18 30 0.53
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAATATACATATAC
Found at i:92067 original size:12 final size:12
Alignment explanation
Indices: 92050--92086 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
92040 GTTTGGAAGA
92050 AAAATTTGGCCT
1 AAAATTTGGCCT
92062 AAAATTTGGCCT
1 AAAATTTGGCCT
92074 -AAATTTGGCCT
1 AAAATTTGGCCT
92085 AA
1 AA
92087 CAAGGTGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.46
12 13 0.54
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
AAAATTTGGCCT
Found at i:92079 original size:11 final size:11
Alignment explanation
Indices: 92051--92086 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
92041 TTTGGAAGAA
92051 AAATTTGGCCT
1 AAATTTGGCCT
92062 AAAATTTGGCCT
1 -AAATTTGGCCT
92074 AAATTTGGCCT
1 AAATTTGGCCT
92085 AA
1 AA
92087 CAAGGTGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (11 bp):
AAATTTGGCCT
Done.