Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006361.1 Kokia drynarioides strain JFW-HI SEQ_120937, 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: 18190
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:8478 original size:34 final size:34
Alignment explanation
Indices: 8440--8505 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
8430 GTAAAAACAA
* * *
8440 CAATGATGGTGAAATTAAATGTTGTAACGATACG
1 CAATGATGATGAAATTAAATGCTATAACGATACG
* *
8474 CAATGGTGATGAGATTAAATGCTATAACGATA
1 CAATGATGATGAAATTAAATGCTATAACGATA
8506 TTGTAACATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (34 bp):
CAATGATGATGAAATTAAATGCTATAACGATACG
Found at i:14193 original size:28 final size:28
Alignment explanation
Indices: 14160--14270 Score: 123
Period size: 28 Copynumber: 3.7 Consensus size: 28
14150 ACCCAAATTA
*
14160 TGGTTTATTTACATATAATTGATTAAAT
1 TGGTTTATTTACCTATAATTGATTAAAT
**
14188 TGGTTTATTTACCTATAATTTTTTAAACTCAATT
1 TGGTTTATTTACCTATAATTGATT--A---AA-T
14222 ATGGTTTATTTACCTATAATTGATTAAAT
1 -TGGTTTATTTACCTATAATTGATTAAAT
*
14251 TGGTTTATTTATCTATAATT
1 TGGTTTATTTACCTATAATT
14271 TTTTAACTCA
Statistics
Matches: 70, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
28 40 0.57
29 1 0.01
30 3 0.04
33 3 0.04
34 1 0.01
35 22 0.31
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52
Consensus pattern (28 bp):
TGGTTTATTTACCTATAATTGATTAAAT
Found at i:14227 original size:63 final size:62
Alignment explanation
Indices: 14155--14294 Score: 246
Period size: 63 Copynumber: 2.3 Consensus size: 62
14145 ACTAAACCCA
14155 AATTATGGTTTATTTACATATAATTGATTAAATTGGTTTATTTACCTATAATTTTTTAAACTC
1 AATTATGGTTTATTTACATATAATTGATTAAATTGGTTTATTTACCTATAATTTTTT-AACTC
* *
14218 AATTATGGTTTATTTACCTATAATTGATTAAATTGGTTTATTTATCTATAATTTTTTAACTC
1 AATTATGGTTTATTTACATATAATTGATTAAATTGGTTTATTTACCTATAATTTTTTAACTC
14280 AATTATGGTTT-TTTA
1 AATTATGGTTTATTTA
14295 AATTTGATTG
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
61 4 0.05
62 16 0.21
63 55 0.73
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.53
Consensus pattern (62 bp):
AATTATGGTTTATTTACATATAATTGATTAAATTGGTTTATTTACCTATAATTTTTTAACTC
Found at i:14234 original size:35 final size:34
Alignment explanation
Indices: 14188--14294 Score: 129
Period size: 35 Copynumber: 3.3 Consensus size: 34
14178 TTGATTAAAT
14188 TGGTTTATTTACCTATAATTTTTTAAACTCAATTA
1 TGGTTTATTTACCTATAATTTTTT-AACTCAATTA
**
14223 TGGTTTATTTACCTATAATTGATT-A---AA-T-
1 TGGTTTATTTACCTATAATTTTTTAACTCAATTA
*
14251 TGGTTTATTTATCTATAATTTTTTAACTCAATTA
1 TGGTTTATTTACCTATAATTTTTTAACTCAATTA
14285 TGGTTT-TTTA
1 TGGTTTATTTA
14295 AATTTGATTG
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
28 21 0.34
29 2 0.03
30 2 0.03
32 2 0.03
33 6 0.10
34 6 0.10
35 22 0.36
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.54
Consensus pattern (34 bp):
TGGTTTATTTACCTATAATTTTTTAACTCAATTA
Found at i:17604 original size:21 final size:20
Alignment explanation
Indices: 17567--17620 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
17557 TTAAAACCCC
* *
17567 AAATTAAAAAAATATTATTT
1 AAATTAATAAAATATTACTT
*
17587 TAATTAATAAAATAATTACTT
1 AAATTAATAAAAT-ATTACTT
*
17608 AAATAAATAAAAT
1 AAATTAATAAAAT
17621 TAAAAGTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATTAATAAAATATTACTT
Found at i:17831 original size:58 final size:58
Alignment explanation
Indices: 17768--17911 Score: 152
Period size: 58 Copynumber: 2.5 Consensus size: 58
17758 ATCGAACAAA
* * *
17768 AAAAAAGATTAAGTACCAAATTAGGAAAAAA-GTCAAGTTCAAATACTAAACTGAACCC
1 AAAAAA-ATTAAGTACCAAATTAAGAAAAAACATCAAGTTCAAATACCAAACTGAACCC
* * * * *
17826 AAAAAAATTAAGTACTAACTTAAGAAAAAACATCAAGTTTAAATACCAAATTGAA--G
1 AAAAAAATTAAGTACCAAATTAAGAAAAAACATCAAGTTCAAATACCAAACTGAACCC
*
17882 AAAAACAATTTAAATACCAAATTAA-AAAAA
1 AAAAA-AA-TTAAGTACCAAATTAAGAAAAA
17912 TATAAAATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
56 5 0.07
57 28 0.39
58 39 0.54
ACGTcount: A:0.58, C:0.12, G:0.08, T:0.21
Consensus pattern (58 bp):
AAAAAAATTAAGTACCAAATTAAGAAAAAACATCAAGTTCAAATACCAAACTGAACCC
Done.