Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006312.1 Kokia drynarioides strain JFW-HI SEQ_120887, 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: 9095
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Found at i:4116 original size:41 final size:41
Alignment explanation
Indices: 4039--4218 Score: 202
Period size: 41 Copynumber: 4.4 Consensus size: 41
4029 AACAATATCA
* *
4039 GCGTTTATAAGAAAAACGTCGCTAAATA-TCAAAGCATTAGTG
1 GCGTTTATGAG-AAAACGTCGCTAAA-AGTCAGAGCATTAGTG
*
4081 GCGTTTATGAGAAAACGTCGTTAAAAGTCAGAGCATTAGTG
1 GCGTTTATGAGAAAACGTCGCTAAAAGTCAGAGCATTAGTG
* * **
4122 GCGTTTATGAGAAAACGCCGCTAAATGTCAGAGCATTAGAA
1 GCGTTTATGAGAAAACGTCGCTAAAAGTCAGAGCATTAGTG
* * * *
4163 GCGTTTATTAGAAAACGCCGCT-AAAGATAAGAGCATTAGCG
1 GCGTTTATGAGAAAACGTCGCTAAAAG-TCAGAGCATTAGTG
* *
4204 ACGTTTATGGGAAAA
1 GCGTTTATGAGAAAA
4219 ATGTCGTTAA
Statistics
Matches: 120, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
40 4 0.03
41 106 0.88
42 10 0.08
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (41 bp):
GCGTTTATGAGAAAACGTCGCTAAAAGTCAGAGCATTAGTG
Found at i:4249 original size:82 final size:82
Alignment explanation
Indices: 4040--4250 Score: 192
Period size: 82 Copynumber: 2.6 Consensus size: 82
4030 ACAATATCAG
* * * * * * * *
4040 CGTTTATAAGAAAAACGTCGCTAAATATCAAAGCATTAGTGGCGTTTATGAGAAAACGTCGTTAA
1 CGTTTATGAG-AAAACGCCGCTAAATGTCAGAGAAATAGTGGCGTTTATGAGAAAACGCCGCTAA
* * *
4105 AAGTCAGAGCATTAGTGG
65 AAGTAAGAGCATTAGCGA
* * ** *
4123 CGTTTATGAGAAAACGCCGCTAAATGTCAGAGCATTAGAAGCGTTTATTAGAAAACGCCGCT-AA
1 CGTTTATGAGAAAACGCCGCTAAATGTCAGAGAAATAGTGGCGTTTATGAGAAAACGCCGCTAAA
4187 AGATAAGAGCATTAGCGA
66 AG-TAAGAGCATTAGCGA
* * * * *
4205 CGTTTATGGGAAAAATGTCGTTAAATGTTA-AGAAATAGTGGCGTTT
1 CGTTTATGAG-AAAACGCCGCTAAATGTCAGAGAAATAGTGGCGTTT
4251 TCCTATAAAT
Statistics
Matches: 105, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
81 4 0.04
82 77 0.73
83 24 0.23
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (82 bp):
CGTTTATGAGAAAACGCCGCTAAATGTCAGAGAAATAGTGGCGTTTATGAGAAAACGCCGCTAAA
AGTAAGAGCATTAGCGA
Found at i:5105 original size:22 final size:22
Alignment explanation
Indices: 5073--5114 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5063 TTGCATATGA
*
5073 ATTAATCAATTTTGTGGTTTCT
1 ATTAATCAATTTTATGGTTTCT
*
5095 ATTAATTAATTTTATGGTTT
1 ATTAATCAATTTTATGGTTT
5115 TAGAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57
Consensus pattern (22 bp):
ATTAATCAATTTTATGGTTTCT
Found at i:5830 original size:42 final size:40
Alignment explanation
Indices: 5760--5838 Score: 104
Period size: 42 Copynumber: 1.9 Consensus size: 40
5750 TCATAAACGT
*
5760 CGCAAAAGGTAAAGAAATAGCAGTGTTTATGGGAAAATGC
1 CGCAAAAGGTAAAGAAATAGCAGCGTTTATGGGAAAATGC
* * *
5800 CGCAAAAGGTTCAGAGAAATAGCGGCGTTTATTGGAAAA
1 CGCAAAAGG-T-AAAGAAATAGCAGCGTTTATGGGAAAA
5839 CGCTACAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 9 0.27
41 1 0.03
42 23 0.70
ACGTcount: A:0.41, C:0.11, G:0.28, T:0.20
Consensus pattern (40 bp):
CGCAAAAGGTAAAGAAATAGCAGCGTTTATGGGAAAATGC
Found at i:5848 original size:42 final size:42
Alignment explanation
Indices: 5772--5851 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
5762 CAAAAGGTAA
* * *
5772 AGAAATAGCAGTGTTTATGGGAAAATGCCGCAAAAGGTTCAG
1 AGAAATAGCAGCGTTTATGGGAAAACGCCACAAAAGGTTCAG
* * *
5814 AGAAATAGCGGCGTTTATTGGAAAACGCTACAAAAGGT
1 AGAAATAGCAGCGTTTATGGGAAAACGCCACAAAAGGT
5852 CTAGGTCATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.21
Consensus pattern (42 bp):
AGAAATAGCAGCGTTTATGGGAAAACGCCACAAAAGGTTCAG
Found at i:6092 original size:34 final size:34
Alignment explanation
Indices: 6047--6139 Score: 116
Period size: 34 Copynumber: 2.7 Consensus size: 34
6037 TAATTACTCT
*
6047 CACCCTTCTCTTCTTCACGCCCGATTCTCCTTCA
1 CACCCTTCTCTTCTTCACGCCCGAATCTCCTTCA
* * * *
6081 CTCCCTTCTCTT-TTGGACGCCGGAATCTTCTTCA
1 CACCCTTCTCTTCTT-CACGCCCGAATCTCCTTCA
*
6115 CACCATTCTCTTCTTCACGCCCGAA
1 CACCCTTCTCTTCTTCACGCCCGAA
6140 CCTCGTACCA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
33 2 0.04
34 44 0.92
35 2 0.04
ACGTcount: A:0.14, C:0.42, G:0.10, T:0.34
Consensus pattern (34 bp):
CACCCTTCTCTTCTTCACGCCCGAATCTCCTTCA
Found at i:7927 original size:39 final size:41
Alignment explanation
Indices: 7849--7928 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 41
7839 CTTGAAATTA
* *
7849 CAAGTATTTTCTATAGATAAAGGTTACTGTCCAATGTAACT
1 CAAGTATTTTCTATAGATAAAGCTTACTGTCCAAAGTAACT
*
7890 CAAGTATTTTCTATTGA-AAA-CTTACTGTCCAAAGTAACT
1 CAAGTATTTTCTATAGATAAAGCTTACTGTCCAAAGTAACT
7929 TAAAACAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 17 0.47
40 3 0.08
41 16 0.44
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.36
Consensus pattern (41 bp):
CAAGTATTTTCTATAGATAAAGCTTACTGTCCAAAGTAACT
Found at i:9005 original size:8 final size:8
Alignment explanation
Indices: 8992--9038 Score: 76
Period size: 8 Copynumber: 5.6 Consensus size: 8
8982 AAAATAACCC
8992 AAATATTT
1 AAATATTT
9000 AAATATTT
1 AAATATTT
9008 AAATATTT
1 AAATATTT
9016 AAATATTT
1 AAATATTT
9024 AATTATATTT
1 AA--ATATTT
9034 AAATA
1 AAATA
9039 AATATTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
8 29 0.78
10 8 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
AAATATTT
Found at i:9031 original size:72 final size:72
Alignment explanation
Indices: 8954--9095 Score: 239
Period size: 72 Copynumber: 2.0 Consensus size: 72
8944 ATTAATTCCT
*
8954 TTATATTTAAATAAATATTTAATAATTAAAAATAACCCAAATATTTAAATATTTAAATATTTAAA
1 TTATATTTAAATAAATATTTAATAATTAAAAACAACCCAAATATTTAAATATTTAAATATTTAAA
9019 TATTTAA
66 TATTTAA
* * * *
9026 TTATATTTAAATAAATATTTAATTATTACAAACAACCCAAATATTTAATTATTTAAATATTTAAT
1 TTATATTTAAATAAATATTTAATAATTAAAAACAACCCAAATATTTAAATATTTAAATATTTAAA
9091 TATTT
66 TATTT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (72 bp):
TTATATTTAAATAAATATTTAATAATTAAAAACAACCCAAATATTTAAATATTTAAATATTTAAA
TATTTAA
Found at i:9085 original size:16 final size:16
Alignment explanation
Indices: 9064--9095 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
9054 CAAACAACCC
9064 AAATATTTAATTATTT
1 AAATATTTAATTATTT
9080 AAATATTTAATTATTT
1 AAATATTTAATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATATTTAATTATTT
Done.