Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014914.1 Kokia drynarioides strain JFW-HI SEQ_129957, 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: 52131
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7903 original size:51 final size:51
Alignment explanation
Indices: 7830--7942 Score: 210
Period size: 51 Copynumber: 2.2 Consensus size: 51
7820 TTTTTTTTTT
7830 AAAAAT-AAAAATAAAACATCAGAGTGCAACTAATTGAATTAATTAAGGAA
1 AAAAATAAAAAATAAAACATCAGAGTGCAACTAATTGAATTAATTAAGGAA
7880 AAAAATAAAAAATAAAACATCAGAGTGCAACTAATTGAATTAATTAAGGAA
1 AAAAATAAAAAATAAAACATCAGAGTGCAACTAATTGAATTAATTAAGGAA
*
7931 AAAAAAAAAAAA
1 AAAAATAAAAAA
7943 AAGTCTAAGT
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
50 6 0.10
51 55 0.90
ACGTcount: A:0.63, C:0.07, G:0.11, T:0.19
Consensus pattern (51 bp):
AAAAATAAAAAATAAAACATCAGAGTGCAACTAATTGAATTAATTAAGGAA
Found at i:10089 original size:6 final size:6
Alignment explanation
Indices: 10078--10112 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
10068 TTCCTCATCT
10078 TTCTCA TTCTCA TTCTCA TTCTCA TTCTCA TTCTC
1 TTCTCA TTCTCA TTCTCA TTCTCA TTCTCA TTCTC
10113 CTTTCTTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.51
Consensus pattern (6 bp):
TTCTCA
Found at i:14689 original size:17 final size:17
Alignment explanation
Indices: 14667--14700 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
14657 AAAAAAATTC
*
14667 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
14684 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
14701 TCATGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:15136 original size:32 final size:35
Alignment explanation
Indices: 15095--15161 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 35
15085 ATATAATAAT
*
15095 ATTTAGAAAT-AAATATATTTTT-AAATATTAAAA
1 ATTTAGAAATAAAAAATATTTTTAAAATATTAAAA
*
15128 ATTT-GAAATAAAAAATATTTTTAAAATTTTAAAA
1 ATTTAGAAATAAAAAATATTTTTAAAATATTAAAA
15162 TGACAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 5 0.17
33 15 0.50
34 10 0.33
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (35 bp):
ATTTAGAAATAAAAAATATTTTTAAAATATTAAAA
Found at i:24324 original size:13 final size:13
Alignment explanation
Indices: 24306--24331 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24296 ATGATGGGTC
24306 CTATGATCTTGTA
1 CTATGATCTTGTA
24319 CTATGATCTTGTA
1 CTATGATCTTGTA
24332 GGCATGCATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
CTATGATCTTGTA
Found at i:28116 original size:27 final size:27
Alignment explanation
Indices: 28086--28143 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
28076 TTTTTTGAGC
28086 TAAAAAAGTTCACTTTCGAACAAATAA
1 TAAAAAAGTTCACTTTCGAACAAATAA
*
28113 TAAAAAAGTTCACTTTTGAACAAATAA
1 TAAAAAAGTTCACTTTCGAACAAATAA
28140 TAAA
1 TAAA
28144 TAGATGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (27 bp):
TAAAAAAGTTCACTTTCGAACAAATAA
Found at i:44943 original size:18 final size:18
Alignment explanation
Indices: 44920--44956 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
44910 AATTTTATTT
44920 AATAAAGAAAAGTTTATG
1 AATAAAGAAAAGTTTATG
**
44938 AATAAAGAATTGTTTATG
1 AATAAAGAAAAGTTTATG
44956 A
1 A
44957 TATTTTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.32
Consensus pattern (18 bp):
AATAAAGAAAAGTTTATG
Found at i:52051 original size:23 final size:23
Alignment explanation
Indices: 52019--52078 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
52009 ACGCTAGCGC
*
52019 GCTTACTGTTTTGCACTTTGTGT
1 GCTTACTGTTTTGCACTTCGTGT
* *
52042 GCTTATTGTTTCGCACTTCGTGT
1 GCTTACTGTTTTGCACTTCGTGT
*
52065 GCTTACTGATTTGC
1 GCTTACTGTTTTGC
52079 GCTATGTGCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.48
Consensus pattern (23 bp):
GCTTACTGTTTTGCACTTCGTGT
Found at i:52125 original size:23 final size:22
Alignment explanation
Indices: 52029--52131 Score: 91
Period size: 23 Copynumber: 4.5 Consensus size: 22
52019 GCTTACTGTT
* * * *
52029 TTGCACTTTGTGTGCTTATTGT
1 TTGCACTGTGTGTGCCTACTGA
*
52051 TTCGCACT-TCGTGTGCTTACTGA
1 TT-GCACTGT-GTGTGCCTACTGA
* * *
52074 TTTGCGCTATGTGCGCCTACTGA
1 -TTGCACTGTGTGTGCCTACTGA
52097 TTGCACTGTGTGTGCCTACTGGA
1 TTGCACTGTGTGTGCCTACT-GA
52120 TTGCACTGTGTG
1 TTGCACTGTGTG
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
22 20 0.29
23 45 0.66
24 3 0.04
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.41
Consensus pattern (22 bp):
TTGCACTGTGTGTGCCTACTGA
Done.