Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015210.1 Kokia drynarioides strain JFW-HI SEQ_130254, 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: 42373
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 208 characters in sequence are not A, C, G, or T
Found at i:7008 original size:100 final size:100
Alignment explanation
Indices: 6846--7045 Score: 391
Period size: 100 Copynumber: 2.0 Consensus size: 100
6836 TTTATATAAA
*
6846 ATTTTTTCAGTTTTAAAAGAAAATGGTCCATTCTTTTTATTAAAGTTAAAGAAGATTATGTTTAT
1 ATTTTTTCAGTTTTAAAAGAAAATGGTCCATCCTTTTTATTAAAGTTAAAGAAGATTATGTTTAT
6911 GAAAATAAATCCATTAATCAATAAATAAATGGATT
66 GAAAATAAATCCATTAATCAATAAATAAATGGATT
6946 ATTTTTTCAGTTTTAAAAGAAAATGGTCCATCCTTTTTATTAAAGTTAAAGAAGATTATGTTTAT
1 ATTTTTTCAGTTTTAAAAGAAAATGGTCCATCCTTTTTATTAAAGTTAAAGAAGATTATGTTTAT
7011 GAAAATAAATCCATTAATCAATAAATAAATGGATT
66 GAAAATAAATCCATTAATCAATAAATAAATGGATT
7046 TGTTATTGCA
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 99 1.00
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (100 bp):
ATTTTTTCAGTTTTAAAAGAAAATGGTCCATCCTTTTTATTAAAGTTAAAGAAGATTATGTTTAT
GAAAATAAATCCATTAATCAATAAATAAATGGATT
Found at i:11067 original size:2 final size:2
Alignment explanation
Indices: 11060--11086 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11050 ACGAAGAAAC
11060 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
11087 AGGGTGTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13642 original size:22 final size:21
Alignment explanation
Indices: 13599--13646 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
13589 ATTTCATACT
13599 ATTTTTTTTTTAATTTTATGA
1 ATTTTTTTTTTAATTTTATGA
13620 ACTTTTTATTTTT-ATATTT-TGA
1 A-TTTTT-TTTTTAAT-TTTATGA
13642 ATTTT
1 ATTTT
13647 GAAAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
21 5 0.21
22 11 0.46
23 8 0.33
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (21 bp):
ATTTTTTTTTTAATTTTATGA
Found at i:14289 original size:26 final size:25
Alignment explanation
Indices: 14247--14306 Score: 59
Period size: 26 Copynumber: 2.3 Consensus size: 25
14237 TTAAGATTGC
14247 TATATAAAAACTTTTAATAAATAAAAA
1 TATAT-AAAACTTTTAA-AAATAAAAA
* *
14274 TATATAAAA-TTATTAAATATTAAAA
1 TATATAAAACTT-TTAAAAATAAAAA
14299 TAATATAA
1 T-ATATAA
14307 TATAAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 10 0.34
26 14 0.48
27 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
TATATAAAACTTTTAAAAATAAAAA
Found at i:24334 original size:17 final size:18
Alignment explanation
Indices: 24307--24340 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
24297 CTACAAAAAA
24307 ACCCAATAACCATTAAAG
1 ACCCAATAACCATTAAAG
*
24325 ACCC-ATAACCTTTAAA
1 ACCCAATAACCATTAAA
24341 TTCACCATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.47, C:0.29, G:0.03, T:0.21
Consensus pattern (18 bp):
ACCCAATAACCATTAAAG
Found at i:33691 original size:16 final size:16
Alignment explanation
Indices: 33667--33707 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
33657 AACCCTTTAA
33667 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
33682 AAATTAATAAAAATAAT
1 AAATT-ATAAAAATAAT
33699 AAAATTATA
1 -AAATTATA
33708 TTTTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.22
16 8 0.35
17 5 0.22
18 5 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Done.