Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018327.1 Corchorus olitorius cultivar O-4 contig18360, 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: 75477
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1904 original size:15 final size:16
Alignment explanation
Indices: 1875--1906 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1865 CCAGAATGTC
1875 CCAAACTACAGCAATT
1 CCAAACTACAGCAATT
1891 CCAAACTA-AGCAATT
1 CCAAACTACAGCAATT
1906 C
1 C
1907 ATTGCTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.44, C:0.31, G:0.06, T:0.19
Consensus pattern (16 bp):
CCAAACTACAGCAATT
Found at i:3354 original size:16 final size:15
Alignment explanation
Indices: 3331--3375 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
3321 TTTAAAGTTT
*
3331 AAATTCAGTACTTATG
1 AAATTCAGTACTTA-A
*
3347 AGATTCAGTA-TTAA
1 AAATTCAGTACTTAA
3361 AAATTCAGTACTTAA
1 AAATTCAGTACTTAA
3376 TCTTTCAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 9 0.36
15 7 0.28
16 9 0.36
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (15 bp):
AAATTCAGTACTTAA
Found at i:3397 original size:14 final size:15
Alignment explanation
Indices: 3364--3397 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3354 GTATTAAAAA
*
3364 TTCAGTACTTAATCT
1 TTCAGCACTTAATCT
3379 TTCAGCACTTAAT-T
1 TTCAGCACTTAATCT
3393 TTCAG
1 TTCAG
3398 TTTTATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (15 bp):
TTCAGCACTTAATCT
Found at i:6071 original size:106 final size:106
Alignment explanation
Indices: 5886--6102 Score: 434
Period size: 106 Copynumber: 2.0 Consensus size: 106
5876 ATATGCGTTG
5886 AACACCCAAGAATCCCATAATGTCAAACTTTGCCACTTCTGGAATATTGCTACTAAACATGATTG
1 AACACCCAAGAATCCCATAATGTCAAACTTTGCCACTTCTGGAATATTGCTACTAAACATGATTG
5951 ATGACTTCTCAATATTTATTTGCTGCCCTGATGCCAGCTCA
66 ATGACTTCTCAATATTTATTTGCTGCCCTGATGCCAGCTCA
5992 AACACCCAAGAATCCCATAATGTCAAACTTTGCCACTTCTGGAATATTGCTACTAAACATGATTG
1 AACACCCAAGAATCCCATAATGTCAAACTTTGCCACTTCTGGAATATTGCTACTAAACATGATTG
6057 ATGACTTCTCAATATTTATTTGCTGCCCTGATGCCAGCTCA
66 ATGACTTCTCAATATTTATTTGCTGCCCTGATGCCAGCTCA
6098 AACAC
1 AACAC
6103 TTTTAACACA
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 111 1.00
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (106 bp):
AACACCCAAGAATCCCATAATGTCAAACTTTGCCACTTCTGGAATATTGCTACTAAACATGATTG
ATGACTTCTCAATATTTATTTGCTGCCCTGATGCCAGCTCA
Found at i:11839 original size:28 final size:28
Alignment explanation
Indices: 11800--11859 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
11790 GCTCATAAGA
11800 TTAA-TAGTAGGTATATAATATGAAATT
1 TTAATTAGTAGGTATATAATATGAAATT
11827 TTAATTAGTAGGTATATAATATGAAATT
1 TTAATTAGTAGGTATATAATATGAAATT
11855 TTAAT
1 TTAAT
11860 AACTACTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 4 0.12
28 28 0.88
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (28 bp):
TTAATTAGTAGGTATATAATATGAAATT
Found at i:12141 original size:98 final size:104
Alignment explanation
Indices: 11938--12148 Score: 290
Period size: 107 Copynumber: 2.1 Consensus size: 104
11928 GTCATTGTTT
* * *
11938 AAACATTTATAGTTTTACTCAATTAAATACTCTATTTTTATTTAATTAAATCTAATATCCTTATC
1 AAACTTTTATAGTTTTACTCAACTAAAAACTCTA--TTTATTTAATTAAATCTAATATCCTTATC
* *
12003 AGTACTATTTTATTTTTTTTCCATTTTACTATTTTAATTAAA
64 AG-ACTATTTTATTTTTTATCCATTTTACTAATTTAATTAAA
*
12045 ATACTTTTATAGTTTTACTCAACTAAAAACTCTA-TT-TTTAATTAAATCTAATATCCTTAT-A-
1 AAACTTTTATAGTTTTACTCAACTAAAAACTCTATTTATTTAATTAAATCTAATATCCTTATCAG
*
12106 CCTATTTTA-TTTTTAT-CATTTTACTAATTTAATTAAA
66 ACTATTTTATTTTTTATCCATTTTACTAATTTAATTAAA
12143 AAACTT
1 AAACTT
12149 AGATATATTA
Statistics
Matches: 96, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
98 25 0.26
99 6 0.06
100 8 0.08
102 1 0.01
103 24 0.25
104 2 0.02
107 30 0.31
ACGTcount: A:0.35, C:0.13, G:0.01, T:0.51
Consensus pattern (104 bp):
AAACTTTTATAGTTTTACTCAACTAAAAACTCTATTTATTTAATTAAATCTAATATCCTTATCAG
ACTATTTTATTTTTTATCCATTTTACTAATTTAATTAAA
Found at i:12170 original size:98 final size:101
Alignment explanation
Indices: 11978--12158 Score: 246
Period size: 98 Copynumber: 1.8 Consensus size: 101
11968 TCTATTTTTA
* *
11978 TTTAATTAAATCTAATATCCTTATCAGTACTATTTTATTTTTTTTCCATTTTACTATTTTAATTA
1 TTTAATTAAATCTAATATCCTTATCAG-ACTATTTTATTTTTTATCCATTTTACTAATTTAATTA
* ** *
12043 AAATACTTTTATAGTTTTACTCAACTAAAAACTCTATT
65 AAAAACTTAGATAGTATTAC-CAACTAAAAACTCTATT
*
12081 TTTAATTAAATCTAATATCCTTAT-A-CCTATTTTA-TTTTTAT-CATTTTACTAATTTAATTAA
1 TTTAATTAAATCTAATATCCTTATCAGACTATTTTATTTTTTATCCATTTTACTAATTTAATTAA
12142 AAAACTTAGATA-TATTA
66 AAAACTTAGATAGTATTA
12159 GAATTTTTAA
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
97 4 0.06
98 28 0.39
99 6 0.08
100 8 0.11
102 1 0.01
103 24 0.34
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (101 bp):
TTTAATTAAATCTAATATCCTTATCAGACTATTTTATTTTTTATCCATTTTACTAATTTAATTAA
AAAACTTAGATAGTATTACCAACTAAAAACTCTATT
Found at i:21136 original size:29 final size:29
Alignment explanation
Indices: 21104--21165 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
21094 GTAAATTTGA
* *
21104 ATTAATTCATAGCTATTTCCATTTTGCTT
1 ATTAATTAATAGCTATTTCCATATTGCTT
21133 ATTAATTAATAGCTATTTCCATATTGCTT
1 ATTAATTAATAGCTATTTCCATATTGCTT
21162 ATTA
1 ATTA
21166 TAATCAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (29 bp):
ATTAATTAATAGCTATTTCCATATTGCTT
Found at i:21470 original size:16 final size:18
Alignment explanation
Indices: 21451--21489 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
21441 TTTTTATTTG
21451 AGTTTG-TTTTT-GAGTC
1 AGTTTGTTTTTTCGAGTC
*
21467 AGTTAGTTTTTTCGAGTC
1 AGTTTGTTTTTTCGAGTC
21485 AGTTT
1 AGTTT
21490 CAAATCTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 5 0.26
17 5 0.26
18 9 0.47
ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (18 bp):
AGTTTGTTTTTTCGAGTC
Found at i:24014 original size:26 final size:27
Alignment explanation
Indices: 23985--24043 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
23975 TTAGGGTTTG
*
23985 TTATAATGAAATTGTTAACAAAATTA-
1 TTATAATGAAATAGTTAACAAAATTAC
* **
24011 TTATAATGAAGTAGTTATTAAAATTAC
1 TTATAATGAAATAGTTAACAAAATTAC
24038 TTATAA
1 TTATAA
24044 CTGGATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 22 0.79
27 6 0.21
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.41
Consensus pattern (27 bp):
TTATAATGAAATAGTTAACAAAATTAC
Found at i:26809 original size:16 final size:17
Alignment explanation
Indices: 26781--26817 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
26771 TGAGCCTCCA
26781 ATTTTCAGGTTCAGGT-
1 ATTTTCAGGTTCAGGTC
26797 ATTTT-AGGATTCAGGTC
1 ATTTTCAGG-TTCAGGTC
26814 ATTT
1 ATTT
26818 AAATATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.16
16 12 0.63
17 4 0.21
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.46
Consensus pattern (17 bp):
ATTTTCAGGTTCAGGTC
Found at i:40016 original size:28 final size:27
Alignment explanation
Indices: 39973--40029 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
39963 TTGTGCCTAA
39973 AGTATTCTAACTAGCTCACTATCCACAG
1 AGTATTCTAACTAGCTCACTAT-CACAG
40001 AGTATTCTAA-TCAGCTCACTATCACAG
1 AGTATTCTAACT-AGCTCACTATCACAG
40028 AG
1 AG
40030 GGATCCTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.28
Consensus pattern (27 bp):
AGTATTCTAACTAGCTCACTATCACAG
Found at i:57455 original size:116 final size:117
Alignment explanation
Indices: 57281--57493 Score: 290
Period size: 116 Copynumber: 1.8 Consensus size: 117
57271 TAGATTATAT
* * *
57281 ATATAAGAGAAAATCCAGCTTTTTCCAGCTTATTTTCCCCAAAATTTCACCTTTGCTTTAACC-C
1 ATATAAGAGAAAATCCAACTTTTTCCAGCTTATTTTCACCAAAATTTCACCTTAGCTTTAACCAC
* *
57345 ATGTTGTTAACCCTTTTTAACAAACTTTGAGTGATTGCAAATATGAACTCTAG
66 -TGTTGATAACCCTTTTTAACAAAATTTGAGTGATTGCAAATATGAACTCTAG
*
57398 ATAT-AGAGAAAA-CCAACTTTTTTCCCAGCTTATTTTCACCAAAA-TTCACCTTAGCTTTAACT
1 ATATAAGAGAAAATCCAAC-TTTTT-CCAGCTTATTTTCACCAAAATTTCACCTTAGCTTTAACC
* * *
57460 ACTTTTGATATCCCTTTTTGACAAAATTTGAGTG
64 ACTGTTGATAACCCTTTTTAACAAAATTTGAGTG
57494 GTTTTAAACA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
115 4 0.05
116 56 0.67
117 24 0.29
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (117 bp):
ATATAAGAGAAAATCCAACTTTTTCCAGCTTATTTTCACCAAAATTTCACCTTAGCTTTAACCAC
TGTTGATAACCCTTTTTAACAAAATTTGAGTGATTGCAAATATGAACTCTAG
Found at i:58764 original size:3 final size:3
Alignment explanation
Indices: 58756--58794 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
58746 TTTTATGATG
*
58756 TAT TAT TA- TAT TAT TAT TAT TAT TAT ATAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
58795 ATGATACTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:58772 original size:11 final size:10
Alignment explanation
Indices: 58756--58796 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
58746 TTTTATGATG
58756 TATTATTATA
1 TATTATTATA
58766 TTATTATTAT-
1 -TATTATTATA
58776 TATTA-TATA
1 TATTATTATA
58785 TCATTATTATA
1 T-ATTATTATA
58796 T
1 T
58797 GATACTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 3 0.11
9 6 0.22
10 4 0.15
11 14 0.52
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTATTATA
Found at i:58790 original size:19 final size:17
Alignment explanation
Indices: 58756--58794 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
58746 TTTTATGATG
58756 TATTATTATATTATTAT
1 TATTATTATATTATTAT
*
58773 TATTATTATA-TATCAT
1 TATTATTATATTATTAT
58789 TATTAT
1 TATTAT
58795 ATGATACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATTATATTATTAT
Found at i:58792 original size:13 final size:13
Alignment explanation
Indices: 58764--58796 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
58754 TGTATTATTA
*
58764 TATTAT-TATTAT
1 TATTATATATCAT
58776 TATTATATATCAT
1 TATTATATATCAT
58789 TATTATAT
1 TATTATAT
58797 GATACTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTATATATCAT
Found at i:67672 original size:7 final size:7
Alignment explanation
Indices: 67660--67684 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
67650 TCCTAAATCT
67660 AATTTTA
1 AATTTTA
67667 AATTTTA
1 AATTTTA
67674 AATTTTA
1 AATTTTA
67681 AATT
1 AATT
67685 CAATAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:74793 original size:36 final size:36
Alignment explanation
Indices: 74746--74815 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
74736 TTCAATAACC
* *
74746 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
74782 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
74816 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Done.