Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001817.1 Kokia drynarioides strain JFW-HI SEQ_113557, 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: 14597
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Found at i:1334 original size:24 final size:24
Alignment explanation
Indices: 1293--1343 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1283 AATTTAAAAC
* *
1293 AAATTTAAATTAAAAAATGAATTT
1 AAATTTAAATTAAAAAATAAATCT
* *
1317 AAATTTAAATTTAGAAATAAATCT
1 AAATTTAAATTAAAAAATAAATCT
1341 AAA
1 AAA
1344 ATAATTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATTTAAATTAAAAAATAAATCT
Found at i:1338 original size:18 final size:17
Alignment explanation
Indices: 1251--1325 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 17
1241 AAGTTTAAGT
*
1251 TTTAAAAT-TATTTCAAA
1 TTTAAAATAAATTT-AAA
* *
1268 TTTAAACTAAATTGAAA
1 TTTAAAATAAATTTAAA
*
1285 TTTAAAACAAATTTAAA
1 TTTAAAATAAATTTAAA
* *
1302 TTAAAAAATGAATTTAAA
1 TT-TAAAATAAATTTAAA
1320 TTTAAA
1 TTTAAA
1326 TTTAGAAATA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
17 29 0.63
18 17 0.37
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.39
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:11462 original size:2 final size:2
Alignment explanation
Indices: 11457--11483 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11447 TTAAAAAATA
11457 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
11484 ACAAACATTT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11568 original size:31 final size:31
Alignment explanation
Indices: 11530--11592 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
11520 GTTGTAGAGG
*
11530 TGTGGTAGTTGGAGTATGATTGGTTAACTCC
1 TGTGGTAGTTGGAGTATAATTGGTTAACTCC
11561 TGTGGTAGTTGGAGTATAATTGGTTAACTCC
1 TGTGGTAGTTGGAGTATAATTGGTTAACTCC
11592 T
1 T
11593 ACTCAGGCCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.30, T:0.40
Consensus pattern (31 bp):
TGTGGTAGTTGGAGTATAATTGGTTAACTCC
Found at i:11804 original size:22 final size:22
Alignment explanation
Indices: 11742--11805 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
11732 ATTATTTAAA
*
11742 TATTATAAAAA-TATAAATTAT
1 TATTATAAAAATTATAATTTAT
** *
11763 TAAAATAAAAAATTAT-ATTTTT
1 TATTAT-AAAAATTATAATTTAT
11785 TATTATAAAAATTATAATTTA
1 TATTATAAAAATTATAATTTA
11806 ATTTTAACCG
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
21 13 0.39
22 17 0.52
23 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTATAAAAATTATAATTTAT
Found at i:13357 original size:30 final size:30
Alignment explanation
Indices: 13323--13388 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
13313 TAACATAATC
13323 TGCTGACATGACAGTCCAGATGTATTTAAA
1 TGCTGACATGACAGTCCAGATGTATTTAAA
*** *
13353 TGCTGACATGGTGGTCCAGATGTTTTTAAA
1 TGCTGACATGACAGTCCAGATGTATTTAAA
13383 TGCTGA
1 TGCTGA
13389 TGTGACATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (30 bp):
TGCTGACATGACAGTCCAGATGTATTTAAA
Found at i:13451 original size:20 final size:20
Alignment explanation
Indices: 13423--13477 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
13413 TCATGTCAGT
* *
13423 AAATGATTTTAAAATTATTG
1 AAATTATTTTAAAATTATTA
*
13443 AAATTATTTTAAAATTTTTA
1 AAATTATTTTAAAATTATTA
13463 AAATTATTTTAAAAT
1 AAATTATTTTAAAAT
13478 CATAATCATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:13461 original size:9 final size:10
Alignment explanation
Indices: 13423--13477 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
13413 TCATGTCAGT
13423 AAATGATTTTA
1 AAAT-ATTTTA
*
13434 AAAT-TATTGA
1 AAATAT-TTTA
*
13444 AATTATTTTA
1 AAATATTTTA
13454 AAAT-TTTTA
1 AAATATTTTA
13463 AAATTATTTTA
1 AAA-TATTTTA
13474 AAAT
1 AAAT
13478 CATAATCATC
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
9 9 0.25
10 14 0.39
11 13 0.36
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (10 bp):
AAATATTTTA
Found at i:13472 original size:11 final size:11
Alignment explanation
Indices: 13423--13477 Score: 64
Period size: 11 Copynumber: 5.4 Consensus size: 11
13413 TCATGTCAGT
*
13423 AAATGATTTTA
1 AAATTATTTTA
*
13434 AAATTA--TTG
1 AAATTATTTTA
13443 AAATTATTTTA
1 AAATTATTTTA
13454 AAA-T-TTTTA
1 AAATTATTTTA
13463 AAATTATTTTA
1 AAATTATTTTA
13474 AAAT
1 AAAT
13478 CATAATCATC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 16 0.43
10 2 0.05
11 19 0.51
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (11 bp):
AAATTATTTTA
Done.