Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004347.1 Kokia drynarioides strain JFW-HI SEQ_117686, 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: 9357
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Found at i:7615 original size:19 final size:20
Alignment explanation
Indices: 7548--7617 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 20
7538 TCAACAAAAA
*
7548 TTATAAAAAAATCAAAATAAT
1 TTAT-AAAAATTCAAAATAAT
* ** *
7569 TTTTAAATTTTTAAAATAAT
1 TTATAAAAATTCAAAATAAT
*
7589 TT-TTAAAATTCAAAAT-AT
1 TTATAAAAATTCAAAATAAT
7607 TTATAAAAATT
1 TTATAAAAATT
7618 TTGAATTTTA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
18 4 0.11
19 17 0.45
20 14 0.37
21 3 0.08
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (20 bp):
TTATAAAAATTCAAAATAAT
Found at i:7904 original size:23 final size:25
Alignment explanation
Indices: 7860--7909 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
7850 TCAAGTGAAT
*
7860 TTTACTATTTAAAATAATAATAATA
1 TTTACTATTTAAAATAAAAATAATA
*
7885 TTTACTA-TT-AAATAAAAATATTA
1 TTTACTATTTAAAATAAAAATAATA
7908 TT
1 TT
7910 AAATATGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 14 0.61
24 2 0.09
25 7 0.30
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (25 bp):
TTTACTATTTAAAATAAAAATAATA
Found at i:8451 original size:30 final size:30
Alignment explanation
Indices: 8393--8451 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
8383 CCATAATAAA
8393 ATTCTTTCCTTCCTAAAAAATTAATATTAAG
1 ATTCTTTCCTTCCTAAAAAA-TAATATTAAG
*
8424 ATTCTTTCCTTCCTCAAAAGA-AATATTA
1 ATTCTTTCCTTCCT-AAAAAATAATATTA
8452 TTATTTCCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 7 0.27
31 14 0.54
32 5 0.19
ACGTcount: A:0.37, C:0.19, G:0.03, T:0.41
Consensus pattern (30 bp):
ATTCTTTCCTTCCTAAAAAATAATATTAAG
Found at i:9071 original size:25 final size:24
Alignment explanation
Indices: 9026--9073 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
9016 TTAAAAAAAT
* *
9026 ATATTTAAAATATTTAAAATTTTC
1 ATATTCAAAATATATAAAATTTTC
*
9050 ATATTCAAATATATATATAATTTT
1 ATATTCAAA-ATATATAAAATTTT
9074 ATAAAAACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
ATATTCAAAATATATAAAATTTTC
Found at i:9232 original size:11 final size:11
Alignment explanation
Indices: 9218--9255 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
9208 AATTTTATTA
9218 TTTTTTATATG
1 TTTTTTATATG
*
9229 TTTTTTTTA-G
1 TTTTTTATATG
9239 TATTTTTATATG
1 T-TTTTTATATG
9251 TTTTT
1 TTTTT
9256 ATAAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 2 0.09
11 19 0.83
12 2 0.09
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTTATATG
Found at i:9236 original size:23 final size:22
Alignment explanation
Indices: 9210--9255 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
9200 TTTAATGAAA
*
9210 TTTTATTATTTTTTATATGTTTT
1 TTTTAGTA-TTTTTATATGTTTT
9233 TTTTAGTATTTTTATATGTTTT
1 TTTTAGTATTTTTATATGTTTT
9255 T
1 T
9256 ATAAAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (22 bp):
TTTTAGTATTTTTATATGTTTT
Found at i:9301 original size:87 final size:86
Alignment explanation
Indices: 9166--9354 Score: 299
Period size: 87 Copynumber: 2.2 Consensus size: 86
9156 ATATAAAAAA
** *
9166 TTATAAAATTAATATTTTTTATATTTTTATGATTTTTAATGAAATTTTATTATTTTTTATATGTT
1 TTATAAAATTAATATTTTCCATATTTTTATGATTTTTAATGAAATTTTATTATTTTTTATAAG--
*
9231 TTTTTTAGTATTTTTATATGTTT
64 TTTTTTAGAATTTTTATATGTTT
9254 TTATAAAATTAATATTTTCCATA-TTTTATGATTTTTAATGAAATTTTATTATTTTTTATAAGTT
1 TTATAAAATTAATATTTTCCATATTTTTATGATTTTTAATGAAATTTTATTATTTTTTATAAGTT
9318 TTTTAGAATTTTTATATGTTT
66 TTTTAGAATTTTTATATGTTT
*
9339 TTATAATATTATATAT
1 TTATAAAATTA-ATAT
9355 ATA
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
85 32 0.34
86 4 0.04
87 38 0.40
88 21 0.22
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.62
Consensus pattern (86 bp):
TTATAAAATTAATATTTTCCATATTTTTATGATTTTTAATGAAATTTTATTATTTTTTATAAGTT
TTTTAGAATTTTTATATGTTT
Done.