Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000909.1 Kokia drynarioides strain JFW-HI SEQ_112046, 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: 33891
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:4906 original size:7 final size:7
Alignment explanation
Indices: 4890--4918 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
4880 CAAAAACCAC
4890 AAAA-AA
1 AAAAGAA
4896 AAAAGAA
1 AAAAGAA
4903 AAAAGAA
1 AAAAGAA
4910 AAAAGAA
1 AAAAGAA
4917 AA
1 AA
4919 GAAAAGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:4911 original size:14 final size:13
Alignment explanation
Indices: 4890--4923 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
4880 CAAAAACCAC
4890 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
4903 AAAAGAAAAAAGAA
1 AAAA-AAAAAAGAA
4917 AAGAAAA
1 AA-AAAA
4924 GAAATCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 13 0.68
15 2 0.11
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:12859 original size:4 final size:4
Alignment explanation
Indices: 12850--12890 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
12840 ACGCAGCATG
* * *
12850 TACA TACA TATA TACA TGCA TACA TACA CACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T
12891 CCATGCATGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:12897 original size:88 final size:88
Alignment explanation
Indices: 12782--12954 Score: 283
Period size: 88 Copynumber: 2.0 Consensus size: 88
12772 CAACCAATAT
* * * *
12782 TACATACATACATACGTTCATATATGCATGGCAATACCATATGAAAATGGTGTAATAAACGCAGC
1 TACATACACACATACATACATACATGCATGGCAATACCATATGAAAATGGTGTAATAAACGCAGC
*
12847 ATGTACATACATATATACATGCA
66 ATGTACATACATACATACATGCA
* *
12870 TACATACACACATACATACATCCATGCATGGCAATACCATATGAAAATGGTGTAATAAACGTAGC
1 TACATACACACATACATACATACATGCATGGCAATACCATATGAAAATGGTGTAATAAACGCAGC
12935 ATGTACATACATACATACAT
66 ATGTACATACATACATACAT
12955 ACATGCATGG
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 78 1.00
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.26
Consensus pattern (88 bp):
TACATACACACATACATACATACATGCATGGCAATACCATATGAAAATGGTGTAATAAACGCAGC
ATGTACATACATACATACATGCA
Found at i:15788 original size:18 final size:18
Alignment explanation
Indices: 15765--15801 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
15755 AAGAAAGTCC
15765 TGATTCTCCTTACTGAAA
1 TGATTCTCCTTACTGAAA
15783 TGATTCTCCTTACTGAAA
1 TGATTCTCCTTACTGAAA
15801 T
1 T
15802 CTGTTGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (18 bp):
TGATTCTCCTTACTGAAA
Found at i:16011 original size:21 final size:19
Alignment explanation
Indices: 15971--16012 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
15961 ACATCATAAT
*
15971 CAAATAAGTTAACAAGTTA
1 CAAATAAATTAACAAGTTA
15990 CAAACTAAATTAACATAGTTA
1 CAAA-TAAATTAACA-AGTTA
16011 CA
1 CA
16013 TTGAAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.26
Consensus pattern (19 bp):
CAAATAAATTAACAAGTTA
Found at i:19140 original size:20 final size:20
Alignment explanation
Indices: 19111--19149 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19101 TGTAATGAAA
*
19111 GAAAGGAAAACAGAACAAAC
1 GAAAGAAAAACAGAACAAAC
*
19131 GAAAGAAAAACTGAACAAA
1 GAAAGAAAAACAGAACAAA
19150 AGAACTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.67, C:0.13, G:0.18, T:0.03
Consensus pattern (20 bp):
GAAAGAAAAACAGAACAAAC
Found at i:19409 original size:21 final size:19
Alignment explanation
Indices: 19369--19409 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
19359 ACATCATAAC
*
19369 CAAATAAGTTAACAAGTTA
1 CAAATAAATTAACAAGTTA
19388 CAAACTAAATTAACATAGTTA
1 CAAA-TAAATTAACA-AGTTA
19409 C
1 C
19410 TTTGAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.51, C:0.15, G:0.07, T:0.27
Consensus pattern (19 bp):
CAAATAAATTAACAAGTTA
Found at i:21405 original size:23 final size:22
Alignment explanation
Indices: 21355--21418 Score: 83
Period size: 23 Copynumber: 2.9 Consensus size: 22
21345 TAAAAATAAT
* **
21355 AAAATTTTAATTTTATTTTTTA
1 AAAATTATAATTTTATTTCATA
21377 AAAATTATAATTTTATTATCATA
1 AAAATTATAATTTTATT-TCATA
*
21400 AAAATTATAATTTAATTTC
1 AAAATTATAATTTTATTTC
21419 GATCCCCTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 18 0.49
23 19 0.51
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (22 bp):
AAAATTATAATTTTATTTCATA
Found at i:29104 original size:3 final size:3
Alignment explanation
Indices: 29096--29120 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29086 GCCCGTTGCG
29096 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
29121 GTTGAATCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:30069 original size:31 final size:31
Alignment explanation
Indices: 30034--30097 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
30024 TTTAAGAATA
30034 ACTTAAATAAAAAC-TTTGAGATAGTTCAGTG
1 ACTTAAATAAAAACTTTTGA-ATAGTTCAGTG
30065 ACTTAAATAAAAACTTTTGAATAGTTCAGTG
1 ACTTAAATAAAAACTTTTGAATAGTTCAGTG
30096 AC
1 AC
30098 CAAATTGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 27 0.84
32 5 0.16
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTTGAATAGTTCAGTG
Done.