Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012695.1 Kokia drynarioides strain JFW-HI SEQ_127706, 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: 21546
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:3214 original size:22 final size:21
Alignment explanation
Indices: 3173--3358 Score: 70
Period size: 23 Copynumber: 8.7 Consensus size: 21
3163 ATAAACGGAA
* *
3173 TAAACAGAGAGTACCGAAGTAC
1 TAAACAGAGAGCA-CAAAGTAC
*
3195 TAAACAGAGAGCACATAAGTGC
1 TAAACAGAGAGCACA-AAGTAC
* *
3217 TAGGCAACAAAGAGCATACAAAGTGC
1 TA---AACAGAGAGC--ACAAAGTAC
3243 TAAACAGAGAGTACACAAAGTAC
1 TAAACAGAGAG--CACAAAGTAC
* * *
3266 T--A-AG-CA-CACAATGTGC
1 TAAACAGAGAGCACAAAGTAC
3282 TAAACAGAGAGTACACAAAGTAC
1 TAAACAGAGAG--CACAAAGTAC
*
3305 T-----GAGCA-CACAAAGTGC
1 TAAACAGAG-AGCACAAAGTAC
* *
3321 TAATCAGAGAGCACACACAGTGC
1 TAAACAGAGAGCACA-A-AGTAC
3344 TAAACAGAGAGCACA
1 TAAACAGAGAGCACA
3359 CACTGTGCTA
Statistics
Matches: 126, Mismatches: 14, Indels: 47
0.67 0.07 0.25
Matches are distributed among these distances:
16 19 0.15
18 4 0.03
19 4 0.03
20 4 0.03
21 9 0.07
22 20 0.16
23 45 0.36
25 10 0.08
26 8 0.06
27 3 0.02
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (21 bp):
TAAACAGAGAGCACAAAGTAC
Found at i:3293 original size:39 final size:39
Alignment explanation
Indices: 3229--3346 Score: 173
Period size: 39 Copynumber: 3.0 Consensus size: 39
3219 GGCAACAAAG
*
3229 AGCATACAAAGTGCTAAACAGAGAGTACACAAAGTACTA
1 AGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACTA
* *
3268 AGCACACAATGTGCTAAACAGAGAGTACACAAAGTACTG
1 AGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACTA
* * * *
3307 AGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTA
1 AGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACTA
3346 A
1 A
3347 ACAGAGAGCA
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.14
Consensus pattern (39 bp):
AGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACTA
Found at i:3336 original size:23 final size:23
Alignment explanation
Indices: 3306--3380 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
3296 ACAAAGTACT
* *
3306 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAAACAGA
3329 GAGCACACACAGTGCTAAACAGA
1 GAGCACACACAGTGCTAAACAGA
*
3352 GAGCACACACTGTGCTAAACA-A
1 GAGCACACACAGTGCTAAACAGA
3374 GGAGCAC
1 -GAGCAC
3381 GCTAGTGTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
22 1 0.02
23 47 0.98
ACGTcount: A:0.41, C:0.25, G:0.23, T:0.11
Consensus pattern (23 bp):
GAGCACACACAGTGCTAAACAGA
Found at i:8556 original size:18 final size:18
Alignment explanation
Indices: 8529--8586 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
8519 CTTGGGTTAG
*
8529 GCTCGAGATCGGGCTCAA
1 GCTCGGGATCGGGCTCAA
* ** *
8547 GCTCTGGATCCTGCTCGA
1 GCTCGGGATCGGGCTCAA
*
8565 GCTCGGGCTCGGGCTCAA
1 GCTCGGGATCGGGCTCAA
8583 GCTC
1 GCTC
8587 AGCCGGTTGA
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.14, C:0.33, G:0.33, T:0.21
Consensus pattern (18 bp):
GCTCGGGATCGGGCTCAA
Found at i:12230 original size:25 final size:26
Alignment explanation
Indices: 12202--12276 Score: 100
Period size: 25 Copynumber: 3.0 Consensus size: 26
12192 CCGAAGTACT
* * **
12202 TAACAGAGGGCACA-TAAGTGCTGGG
1 TAACAGAGGACACACAAAGTGCTGAA
12227 TAACAGAGGACACACAAAGTGCT-AA
1 TAACAGAGGACACACAAAGTGCTGAA
12252 TAACAGAGGACACACAAAGTGCTGA
1 TAACAGAGGACACACAAAGTGCTGA
12277 TCAGTAAGCG
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
25 36 0.82
26 8 0.18
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.13
Consensus pattern (26 bp):
TAACAGAGGACACACAAAGTGCTGAA
Found at i:14017 original size:13 final size:13
Alignment explanation
Indices: 13999--14034 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
13989 TTTTCTCACA
13999 TTTACTA-ATACAT
1 TTTACTAGA-ACAT
14012 TTTACTAGAACAT
1 TTTACTAGAACAT
14025 TTTACTAGAA
1 TTTACTAGAA
14035 AACACTCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 21 0.95
14 1 0.05
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.42
Consensus pattern (13 bp):
TTTACTAGAACAT
Done.