Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009731.1 Kokia drynarioides strain JFW-HI SEQ_124450, 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: 18165
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Found at i:389 original size:23 final size:22
Alignment explanation
Indices: 361--534 Score: 113
Period size: 23 Copynumber: 7.5 Consensus size: 22
351 ACACTAGTGC
361 GCTCTCTGTTTAGCACGTCTTGT
1 GCTCTCTGTTTAGCACGT-TTGT
* *
384 GCTCTCTGTTATTAACACTGTGTGT
1 GCTCTCTG-T-TTAGCAC-GTTTGT
* *
409 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACGTT-TGT
* *
432 GCTCTCTGATTAGTAC-TTTGT
1 GCTCTCTGTTTAGCACGTTTGT
*
453 GTACTCTCTGTTTAGCACTGTATGT
1 G--CTCTCTGTTTAGCAC-GTTTGT
*
478 GCTCTCTGTTGCCCAGCAC-TTATGT
1 GCTCTCTGTT---TAGCACGTT-TGT
*
503 GCTCTCTG-TTAGTAC-TTTGGT
1 GCTCTCTGTTTAGCACGTTT-GT
*
524 ACTCTCTGTTT
1 GCTCTCTGTTT
535 GTTCCGTATA
Statistics
Matches: 122, Mismatches: 15, Indels: 29
0.73 0.09 0.17
Matches are distributed among these distances:
20 1 0.01
21 19 0.16
22 5 0.04
23 54 0.44
24 3 0.02
25 33 0.27
26 7 0.06
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (22 bp):
GCTCTCTGTTTAGCACGTTTGT
Found at i:409 original size:25 final size:24
Alignment explanation
Indices: 361--486 Score: 136
Period size: 23 Copynumber: 5.4 Consensus size: 24
351 ACACTAGTGC
*
361 GCTCTCTGT-TTAGCAC-GTCTTGT
1 GCTCTCTGTATTAGCACTGT-GTGT
*
384 GCTCTCTGTTATTAACACTGTGTGT
1 GCTCTCTG-TATTAGCACTGTGTGT
*
409 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTGTGT
* *
432 GCTCTCTG-ATTAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTGTGTGT
* *
455 ACTCTCTGT-TTAGCACTGTATGT
1 GCTCTCTGTATTAGCACTGTGTGT
478 GCTCTCTGT
1 GCTCTCTGT
487 TGCCCAGCAC
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
23 69 0.78
24 1 0.01
25 17 0.19
26 2 0.02
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTGTGTGT
Found at i:422 original size:48 final size:47
Alignment explanation
Indices: 361--487 Score: 150
Period size: 46 Copynumber: 2.7 Consensus size: 47
351 ACACTAGTGC
361 GCTCTCTGTTTAGCACGTCTTGTGCTCTCTGTTATTAACACTGTGTGT
1 GCTCTCTGTTTAGCACGT-TTGTGCTCTCTGTTATTAACACTGTGTGT
* * ** *
409 GCTCTCTGATTAGCACTTTGTGTGCTCTCTG--ATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACGTT-TGTGCTCTCTGTTATTAACACTGTGTGT
* *
455 ACTCTCTGTTTAGCACTGTATGTGCTCTCTGTT
1 GCTCTCTGTTTAGCAC-GTTTGTGCTCTCTGTT
488 GCCCAGCACT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
46 37 0.56
47 2 0.03
48 27 0.41
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (47 bp):
GCTCTCTGTTTAGCACGTTTGTGCTCTCTGTTATTAACACTGTGTGT
Found at i:480 original size:69 final size:66
Alignment explanation
Indices: 385--534 Score: 185
Period size: 69 Copynumber: 2.2 Consensus size: 66
375 ACGTCTTGTG
* *
385 CTCTCTGTTATTAACACTGTGTGTGCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGTACT
1 CTCTCTG-T-TTAACACTGTATGTGCTCTCTG-TTCAGCAC-TTATGTGCTCTCTG-TTAGTACT
449 TTGTGTA
61 TTG-GTA
*
456 CTCTCTGTTTAGCACTGTATGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACTTT
1 CTCTCTGTTTAACACTGTATGTGCTCTCTGTT---CAGCACTTATGTGCTCTCTGTTAGTACTTT
521 GGTA
63 GGTA
525 CTCTCTGTTT
1 CTCTCTGTTT
535 GTTCCGTATA
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
68 2 0.03
69 33 0.46
70 12 0.17
71 20 0.28
72 5 0.07
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (66 bp):
CTCTCTGTTTAACACTGTATGTGCTCTCTGTTCAGCACTTATGTGCTCTCTGTTAGTACTTTGGT
A
Found at i:4225 original size:36 final size:36
Alignment explanation
Indices: 4178--4252 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
4168 GCACCATGGC
*
4178 CAAGGACAAGATCACGACATCTAAGAGAATCAGCAG
1 CAAGGAAAAGATCACGACATCTAAGAGAATCAGCAG
*
4214 CAAGGAAAAGATCATGACATCTAAGAGAATCAGCAG
1 CAAGGAAAAGATCACGACATCTAAGAGAATCAGCAG
4250 CAA
1 CAA
4253 TATTTCCCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.12
Consensus pattern (36 bp):
CAAGGAAAAGATCACGACATCTAAGAGAATCAGCAG
Found at i:8645 original size:21 final size:21
Alignment explanation
Indices: 8604--8645 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 21
8594 TTAATTTTAC
* *
8604 TTTATGATGTAAAATCAAAAT
1 TTTATGATCTAAAATAAAAAT
8625 TTTAT-ATCTAAAATAATAAAT
1 TTTATGATCTAAAATAA-AAAT
8646 AATGAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (21 bp):
TTTATGATCTAAAATAAAAAT
Found at i:14940 original size:20 final size:19
Alignment explanation
Indices: 14926--14973 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
14916 AAATTTATGT
14926 TTTTTTAAATTAATTTTTA
1 TTTTTTAAATTAATTTTTA
*
14945 TTTTTTAAAAT-ATTTTTA
1 TTTTTTAAATTAATTTTTA
*
14963 ATTTTTAAATT
1 TTTTTTAAATT
14974 TATGTCCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTAAATTAATTTTTA
Done.