Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004864.1 Kokia drynarioides strain JFW-HI SEQ_118531, 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: 20716
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Found at i:6806 original size:39 final size:39
Alignment explanation
Indices: 6752--6834 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
6742 TTAACTCAGT
** *
6752 AAATTTAATAGTTACCGGTTAATGGAGACCAAAATTTTA
1 AAATTTAATAGTTACCACTTAATAGAGACCAAAATTTTA
** *
6791 AAATTTAATAGTTACCACTTGGTAGAGACTAAAATTTTA
1 AAATTTAATAGTTACCACTTAATAGAGACCAAAATTTTA
6830 AAATT
1 AAATT
6835 CGAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (39 bp):
AAATTTAATAGTTACCACTTAATAGAGACCAAAATTTTA
Found at i:16644 original size:14 final size:14
Alignment explanation
Indices: 16569--16645 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 14
16559 AAATTATAGA
16569 TTTAATTTTTATAT
1 TTTAATTTTTATAT
*
16583 TTTACTTTAATTA-AT
1 TTTAATTT--TTATAT
* *
16598 TTTAGTTATTGCATAT
1 TTTAATT-TT-TATAT
*
16614 TTTAAATTAGTTA-AT
1 TTT-AATT-TTTATAT
16629 TTTAATTTTTATAT
1 TTTAATTTTTATAT
16643 TTT
1 TTT
16646 TTGAAATTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
13 3 0.06
14 17 0.35
15 14 0.29
16 10 0.20
17 5 0.10
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.64
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:16813 original size:13 final size:13
Alignment explanation
Indices: 16797--16827 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
16787 GAAAAATCAT
16797 AAAAAAAATGTAA
1 AAAAAAAATGTAA
*
16810 AAAAAAAATGTAG
1 AAAAAAAATGTAA
16823 AAAAA
1 AAAAA
16828 TTATTAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (13 bp):
AAAAAAAATGTAA
Found at i:17379 original size:23 final size:22
Alignment explanation
Indices: 17349--17436 Score: 84
Period size: 23 Copynumber: 4.3 Consensus size: 22
17339 ATCTTAGCAC
17349 GCTCTCCGTTTAGCACT-TTGTGT
1 GCTCTCCGTTTAGCA-TGTT-TGT
17372 GCTCTCCGTTTAGCATGTTTGT
1 GCTCTCCGTTTAGCATGTTTGT
*
17394 GCTCTCAG-TT--CA--TTTGT
1 GCTCTCCGTTTAGCATGTTTGT
*
17411 GC-AT-CGTTTAGCATGTTTGT
1 GCTCTCCGTTTAGCATGTTTGT
17431 GCTCTC
1 GCTCTC
17437 TGTTCATTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
15 1 0.02
16 3 0.06
17 7 0.13
18 2 0.04
19 2 0.04
20 7 0.13
21 3 0.06
22 11 0.21
23 17 0.32
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (22 bp):
GCTCTCCGTTTAGCATGTTTGT
Found at i:17425 original size:37 final size:37
Alignment explanation
Indices: 17378--17451 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
17368 GTGTGCTCTC
17378 CGTTTAGCATGTTTGTGCTCTCAGTTCATTTGTGCAT
1 CGTTTAGCATGTTTGTGCTCTCAGTTCATTTGTGCAT
*
17415 CGTTTAGCATGTTTGTGCTCTCTGTTCATTTGTGCAT
1 CGTTTAGCATGTTTGTGCTCTCAGTTCATTTGTGCAT
17452 TGTTATGCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (37 bp):
CGTTTAGCATGTTTGTGCTCTCAGTTCATTTGTGCAT
Found at i:19501 original size:16 final size:16
Alignment explanation
Indices: 19482--19524 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
19472 ATTTATTATT
19482 TTAATAAATTATTCAA
1 TTAATAAATTATTCAA
*
19498 TTAATAAATTTAATCAA
1 TTAATAAA-TTATTCAA
19515 -TAAT-AATTAT
1 TTAATAAATTAT
19525 GTATTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 3 0.12
15 2 0.08
16 12 0.50
17 7 0.29
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAATAAATTATTCAA
Found at i:20317 original size:20 final size:20
Alignment explanation
Indices: 20292--20329 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20282 ACCATTACTA
*
20292 ATTAATTAGGTTTTAATTCC
1 ATTAATGAGGTTTTAATTCC
20312 ATTAATGAGGTTTTAATT
1 ATTAATGAGGTTTTAATT
20330 TAGTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (20 bp):
ATTAATGAGGTTTTAATTCC
Found at i:20470 original size:12 final size:12
Alignment explanation
Indices: 20453--20477 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20443 AAAAAGTTAT
20453 TTTAATTTTTCA
1 TTTAATTTTTCA
20465 TTTAATTTTTCA
1 TTTAATTTTTCA
20477 T
1 T
20478 CTCCTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTAATTTTTCA
Found at i:20674 original size:9 final size:9
Alignment explanation
Indices: 20618--20678 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
20608 AAAAAAGTTT
20618 TTTTTATAA
1 TTTTTATAA
*
20627 TTTTTTTATA
1 TTTTTATA-A
20637 TTTTTAATAA
1 TTTTT-ATAA
*
20647 -TGTTATAA
1 TTTTTATAA
20655 TTTTTATAA
1 TTTTTATAA
20664 TTTTT-TGAA
1 TTTTTAT-AA
20673 TTTTTA
1 TTTTTA
20679 AATATTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
8 5 0.12
9 29 0.67
10 7 0.16
11 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Done.