Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015524.1 Corchorus olitorius cultivar O-4 contig15557, 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: 15426
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:155 original size:2 final size:2
Alignment explanation
Indices: 148--227 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
138 TCTTAATATT
148 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
190 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
228 TATATATATA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:232 original size:2 final size:2
Alignment explanation
Indices: 227--258 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
217 ACACACACAC
227 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
259 GTACTAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:632 original size:42 final size:42
Alignment explanation
Indices: 573--652 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
563 TAGGAATCAG
* *
573 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTCAGTTGAGTATTTCTTAATTGACAAAGAATTTTCTAT
*
615 GATTTCAGTTGAGTATTTCTTAATTGACAGAGAATTTT
1 GATTTCAGTTGAGTATTTCTTAATTGACAAAGAATTTT
653 TAAGACTTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.46
Consensus pattern (42 bp):
GATTTCAGTTGAGTATTTCTTAATTGACAAAGAATTTTCTAT
Found at i:4588 original size:22 final size:22
Alignment explanation
Indices: 4539--4590 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
4529 GACGAAATCG
*
4539 CGGAGATTTCAGAGAAAAAGCA
1 CGGAGCTTTCAGAGAAAAAGCA
* *
4561 CGGAGCTTTGAGAGAATAAGCA
1 CGGAGCTTTCAGAGAAAAAGCA
4583 CGGAGCTT
1 CGGAGCTT
4591 GATTTTTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.31, T:0.17
Consensus pattern (22 bp):
CGGAGCTTTCAGAGAAAAAGCA
Found at i:13313 original size:19 final size:19
Alignment explanation
Indices: 13289--13325 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
13279 AGGGATCCAG
13289 TAGATAATTATTTGAATAA
1 TAGATAATTATTTGAATAA
13308 TAGATAATTATTTGAATA
1 TAGATAATTATTTGAATA
13326 GACATTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (19 bp):
TAGATAATTATTTGAATAA
Found at i:14814 original size:22 final size:22
Alignment explanation
Indices: 14784--14983 Score: 97
Period size: 22 Copynumber: 8.8 Consensus size: 22
14774 TCCAACGTAG
*
14784 AAATATTGATAACTACACTGCGA
1 AAAT-TTGATAACTACACTGTGA
* *
14807 AAATTTGATAACTTCATTGTG-
1 AAATTTGATAACTACACTGTGA
* *
14828 AAATTTCGATAACCT-CCCTATGA
1 AAATTT-GATAA-CTACACTGTGA
* *
14851 AAATTTTGATAACCACAATGTGA
1 AAA-TTTGATAACTACACTGTGA
* * *
14874 AATTTTGAATTGATAACCACACTGCGA
1 AA-----ATTTGATAACTACACTGTGA
*
14901 AAATTTGATAACCT-CATTGTG-
1 AAATTTGATAA-CTACACTGTGA
* *
14922 AAATTTCGATAACCT-CCCTATGA
1 AAATTT-GATAA-CTACACTGTGA
* *
14945 AATTTTGATAACCACACTGTG-
1 AAATTTGATAACTACACTGTGA
*
14966 AAATTCTGATAACCACAC
1 AAATT-TGATAACTACAC
14984 AATGAAGTTT
Statistics
Matches: 137, Mismatches: 25, Indels: 31
0.71 0.13 0.16
Matches are distributed among these distances:
21 17 0.12
22 71 0.52
23 27 0.20
24 3 0.02
27 18 0.13
28 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.32
Consensus pattern (22 bp):
AAATTTGATAACTACACTGTGA
Found at i:14853 original size:44 final size:44
Alignment explanation
Indices: 14783--15092 Score: 196
Period size: 44 Copynumber: 6.8 Consensus size: 44
14773 CTCCAACGTA
* ** *
14783 GAAATATT-GATAACTACACTGCGAAAATTTGATAACTTCATTGT
1 GAAAT-TTCGATAACCACACTATGAAAATTTGATAACCTCATTGT
* * * *
14827 GAAATTTCGATAACCTCCCTATGAAAATTTTGATAACCACAATGT
1 GAAATTTCGATAACCACACTATGAAAA-TTTGATAACCTCATTGT
* **
14872 GAAATTTTGAATTGATAACCACACTGCGAAAATTTGATAACCTCATTGT
1 GAAA--TT---TCGATAACCACACTATGAAAATTTGATAACCTCATTGT
* * * * *
14921 GAAATTTCGATAACCTCCCTATGAAATTTTGATAACCACACTGT
1 GAAATTTCGATAACCACACTATGAAAATTTGATAACCTCATTGT
* **
14965 GAAA-TTCTGATAACCACACAATGAAGTTTTGATAACCTCATTGTCTAT
1 GAAATTTC-GATAACCACACTATGAAAATTTGATAACCTCATTG----T
* * * * * * * *
15013 GAAATTTTGATAATCACATTAT-AAAA-TTGGTAATCGCACTAT
1 GAAATTTCGATAACCACACTATGAAAATTTGATAACCTCATTGT
* * *
15055 GAAAATTTTGATAACCACACCATGAAATTTTCGATAAC
1 G-AAATTTCGATAACCACACTATGAAAATTT-GATAAC
15093 TTCCCTATAA
Statistics
Matches: 203, Mismatches: 46, Indels: 32
0.72 0.16 0.11
Matches are distributed among these distances:
42 2 0.01
43 23 0.11
44 85 0.42
45 20 0.10
46 14 0.07
47 6 0.03
48 16 0.08
49 21 0.10
50 16 0.08
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (44 bp):
GAAATTTCGATAACCACACTATGAAAATTTGATAACCTCATTGT
Found at i:14892 original size:27 final size:27
Alignment explanation
Indices: 14856--14908 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
14846 TATGAAAATT
* *
14856 TTGATAACCACAATGTGAAATTTTGAA
1 TTGATAACCACAATGCGAAAATTTGAA
*
14883 TTGATAACCACACTGCGAAAATTTGA
1 TTGATAACCACAATGCGAAAATTTGA
14909 TAACCTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (27 bp):
TTGATAACCACAATGCGAAAATTTGAA
Found at i:14989 original size:22 final size:22
Alignment explanation
Indices: 14883--15092 Score: 109
Period size: 22 Copynumber: 9.4 Consensus size: 22
14873 AAATTTTGAA
*** *
14883 TTGATAACCACACTGCGAAAAT
1 TTGATAACCACACAATGAAATT
* ***
14905 TTGATAACCTCATTGTGAAATT
1 TTGATAACCACACAATGAAATT
* * * *
14927 TCGATAACCTCCCTATGAAATT
1 TTGATAACCACACAATGAAATT
**
14949 TTGATAACCACACTGTGAAATT
1 TTGATAACCACACAATGAAATT
* *
14971 CTGATAACCACACAATGAAGTT
1 TTGATAACCACACAATGAAATT
* *
14993 TTGATAACCTCATTGTCTATGAAATT
1 TTGATAACCACA----CAATGAAATT
* ** *
15019 TTGATAATCACATTAT-AAA-A
1 TTGATAACCACACAATGAAATT
* * * *
15039 TTGGTAATCGCACTATGAAAATT
1 TTGATAACCACACAATG-AAATT
*
15062 TTGATAACCACACCATGAAATT
1 TTGATAACCACACAATGAAATT
15084 TTCGATAAC
1 TT-GATAAC
15093 TTCCCTATAA
Statistics
Matches: 148, Mismatches: 32, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
20 13 0.09
21 3 0.02
22 95 0.64
23 19 0.13
26 18 0.12
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (22 bp):
TTGATAACCACACAATGAAATT
Found at i:14999 original size:66 final size:67
Alignment explanation
Indices: 14883--15030 Score: 165
Period size: 66 Copynumber: 2.2 Consensus size: 67
14873 AAATTTTGAA
* ***
14883 TTGATAACCACACTGCGAAAATTTGATAACCTCATTGTGAAATTTCGATAACCTC-CCTATGAAA
1 TTGATAACCACACTGCGAAAATTTGATAACCACACAATGAAATTTCGATAACCTCTCCTATGAAA
14947 TT
66 TT
* * * *
14949 TTGATAACCACACTGTG-AAATTCTGATAACCACACAATGAAGTTTTGATAACCTCATTGTCTAT
1 TTGATAACCACACTGCGAAAATT-TGATAACCACACAATGAAATTTCGATAACCTC--T-CCTAT
15013 GAAATT
62 GAAATT
*
15019 TTGATAATCACA
1 TTGATAACCACA
15031 TTATAAAATT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
65 5 0.07
66 42 0.62
70 21 0.31
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (67 bp):
TTGATAACCACACTGCGAAAATTTGATAACCACACAATGAAATTTCGATAACCTCTCCTATGAAA
TT
Found at i:15259 original size:22 final size:23
Alignment explanation
Indices: 15234--15290 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
15224 CGTTCTAATT
15234 AATTTTGATAATCAC-TC-TATAA
1 AATTTTGATAATC-CTTCGTATAA
** *
15256 AATTTCAATAA-CCTTCGTATGA
1 AATTTTGATAATCCTTCGTATAA
15278 AATTTTGATAATC
1 AATTTTGATAATC
15291 TCCATAAGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
20 1 0.04
21 3 0.11
22 22 0.81
23 1 0.04
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (23 bp):
AATTTTGATAATCCTTCGTATAA
Found at i:15347 original size:22 final size:22
Alignment explanation
Indices: 15319--15425 Score: 101
Period size: 22 Copynumber: 4.9 Consensus size: 22
15309 AACCTTTTTT
* **
15319 TATGAAATTTTGGTAACCTCTG
1 TATGAAATTTTGATAACCTCAC
*
15341 TATGAAATTTTGATAA-TTACAC
1 TATGAAATTTTGATAACCT-CAC
* *
15363 TACGAAGTTTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
15384 ATATGAAATTTTGGTAACCACAC
1 -TATGAAATTTTGATAACCTCAC
*
15407 TATGAAATTTTAATAACCT
1 TATGAAATTTTGATAACCT
15426 T
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
21 2 0.03
22 63 0.94
23 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:15374 original size:68 final size:66
Alignment explanation
Indices: 15264--15422 Score: 171
Period size: 68 Copynumber: 2.4 Consensus size: 66
15254 AAAATTTCAA
* ***
15264 TAACCT-TCGTATGAAATTTTGATAATCTCCATAAGAGATTTTGATAACCTTTTTTTATGAAATT
1 TAACCTCT-GTATGAAATTTTGATAATCTACATAAGAGATTTTGATAACC--TCCATATGAAATT
15328 TTGG
63 TTGG
*
15332 TAACCTCTGTATGAAATTTTGATAAT-TACACTACGA-AGTTTTGATAACCTCCATATGAAATTT
1 TAACCTCTGTATGAAATTTTGATAATCTACA-TAAGAGA-TTTTGATAACCTCCATATGAAATTT
15395 TGG
64 TGG
* ** *
15398 TAACCACACTATGAAATTTTAATAA
1 TAACCTCTGTATGAAATTTTGATAA
15423 CCTT
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
66 35 0.44
67 4 0.05
68 39 0.49
69 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (66 bp):
TAACCTCTGTATGAAATTTTGATAATCTACATAAGAGATTTTGATAACCTCCATATGAAATTTTG
G
Found at i:15380 original size:44 final size:44
Alignment explanation
Indices: 15276--15425 Score: 129
Period size: 44 Copynumber: 3.4 Consensus size: 44
15266 ACCTTCGTAT
* * * **** *
15276 GAAATTTTGATAATCTCCATAAGAGATTTTGATAACCTTTTTTTAT
1 GAAATTTTGATAACCTCCATATGAAATTTTGATAACC--ACACTAC
* ** **
15322 GAAATTTTGGTAACCTCTGTATGAAATTTTGATAATTACACTAC
1 GAAATTTTGATAACCTCCATATGAAATTTTGATAACCACACTAC
* * *
15366 GAAGTTTTGATAACCTCCATATGAAATTTTGGTAACCACACTAT
1 GAAATTTTGATAACCTCCATATGAAATTTTGATAACCACACTAC
*
15410 GAAATTTTAATAACCT
1 GAAATTTTGATAACCT
15426 T
Statistics
Matches: 81, Mismatches: 23, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
44 52 0.64
46 29 0.36
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (44 bp):
GAAATTTTGATAACCTCCATATGAAATTTTGATAACCACACTAC
Done.