Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003754.1 Kokia drynarioides strain JFW-HI SEQ_116718, 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: 17412
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.33
Warning! 146 characters in sequence are not A, C, G, or T
Found at i:603 original size:12 final size:12
Alignment explanation
Indices: 586--618 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
576 TTGCCCAGTA
586 GAAGTTCTGACT
1 GAAGTTCTGACT
598 GAAGTTCTGACT
1 GAAGTTCTGACT
610 GAAGTTCTG
1 GAAGTTCTG
619 TAGGCAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.33
Consensus pattern (12 bp):
GAAGTTCTGACT
Found at i:11368 original size:3 final size:3
Alignment explanation
Indices: 11362--11473 Score: 138
Period size: 3 Copynumber: 37.0 Consensus size: 3
11352 TTATTAATGA
* * * *
11362 TAT TATT TAT TAT TAT TAA TA- AAT TCAT TAC TGT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
*
11408 TAT TAT CA- TAT TCAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
11453 TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
11474 GAATTGTTTT
Statistics
Matches: 95, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
2 2 0.02
3 84 0.88
4 9 0.09
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:12043 original size:17 final size:17
Alignment explanation
Indices: 12021--12100 Score: 133
Period size: 17 Copynumber: 4.7 Consensus size: 17
12011 ATTAAACATT
*
12021 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
*
12038 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
12055 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
12072 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
12089 TAAATTCAAATT
1 TAAATTTAAATT
12101 CCATTAGACC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 61 1.00
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:12101 original size:6 final size:6
Alignment explanation
Indices: 12018--12100 Score: 79
Period size: 6 Copynumber: 14.5 Consensus size: 6
12008 TTAATTAAAC
12018 ATTTAA ATTTAA ATTTCAA A--TAA ATTTAA ATTTCAA A--TAA ATTTAA
1 ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA
* * *
12064 ATTTAA A-ATAA ATTTAA ATTTAA A-ATAA ATTCAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT
12101 CCATTAGACC
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
4 6 0.09
5 10 0.16
6 42 0.66
7 6 0.09
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:15100 original size:21 final size:21
Alignment explanation
Indices: 15031--15101 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 21
15021 AAAGTGGTGA
*
15031 AAATAA-TAAAAATTTATTA-
1 AAATAATTAAAAAATTATTAG
* *
15050 AAATCACT-AAAAATTA-TAG
1 AAATAATTAAAAAATTATTAG
15069 AAA-AATATAAAAAATTATTAG
1 AAATAAT-TAAAAAATTATTAG
*
15090 AAATTATTAAAA
1 AAATAATTAAAA
15102 TTAAAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
18 3 0.07
19 16 0.39
20 9 0.22
21 11 0.27
22 2 0.05
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (21 bp):
AAATAATTAAAAAATTATTAG
Found at i:15101 original size:20 final size:20
Alignment explanation
Indices: 15037--15101 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
15027 GTGAAAATAA
* *
15037 TAAAAATTTATTA-AAATCAC
1 TAAAAA-TTATTAGAAATTAT
*
15057 TAAAAATTA-TAGAAAAATAT
1 TAAAAATTATTAG-AAATTAT
*
15077 AAAAAATTATTAGAAATTAT
1 TAAAAATTATTAGAAATTAT
15097 TAAAA
1 TAAAA
15102 TTAAAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 2 0.06
19 3 0.08
20 28 0.78
21 3 0.08
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
TAAAAATTATTAGAAATTAT
Done.