Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006297.1 Kokia drynarioides strain JFW-HI SEQ_120871, 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: 44500
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:6649 original size:20 final size:20
Alignment explanation
Indices: 6620--6662 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
6610 TAGTTCTAAT
6620 TTTAAAAATTA-TAAAATATA
1 TTTAAAAATTATTAAAA-ATA
*
6640 TTTAACAATTATTAAAAATA
1 TTTAAAAATTATTAAAAATA
6660 TTT
1 TTT
6663 TTGTATTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTAAAAATTATTAAAAATA
Found at i:15668 original size:33 final size:33
Alignment explanation
Indices: 15592--15668 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 33
15582 CCTATTTACT
* * * ** *
15592 TAAAATAAATAATTTTAGTCAAAATGAAATTAG
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
*
15625 GAAAAT-AACAAATTTAATCAAAACAAAATTAA
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
15657 TAAAATAAACAA
1 TAAAATAAACAA
15669 CTTTGACTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 25 0.71
33 10 0.29
ACGTcount: A:0.62, C:0.06, G:0.05, T:0.26
Consensus pattern (33 bp):
TAAAATAAACAAATTTAATCAAAACAAAATTAA
Found at i:20813 original size:6 final size:7
Alignment explanation
Indices: 20800--20832 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
20790 TTTATTTTTT
20800 ATTAAAA
1 ATTAAAA
20807 ATT-AAA
1 ATTAAAA
20813 ATTAAAA
1 ATTAAAA
20820 ATTAAAA
1 ATTAAAA
20827 ATTAAA
1 ATTAAA
20833 TTGAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
ATTAAAA
Found at i:20818 original size:13 final size:14
Alignment explanation
Indices: 20800--20832 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
20790 TTTATTTTTT
20800 ATTAAAAATT-AAA
1 ATTAAAAATTAAAA
20813 ATTAAAAATTAAAA
1 ATTAAAAATTAAAA
20827 ATTAAA
1 ATTAAA
20833 TTGAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATTAAAAATTAAAA
Found at i:26314 original size:16 final size:17
Alignment explanation
Indices: 26279--26317 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
26269 GGGTTTAGAG
*
26279 ATAAAACATCAAACTAAA
1 ATAAAACA-CAAAATAAA
26297 ATAAAACA-AAAATAAA
1 ATAAAACACAAAATAAA
26313 ATAAA
1 ATAAA
26318 TAAGTGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
18 8 0.40
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.15
Consensus pattern (17 bp):
ATAAAACACAAAATAAA
Found at i:27318 original size:33 final size:33
Alignment explanation
Indices: 27242--27318 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 33
27232 CCTATTTACT
* * * **
27242 TAAAATAAATAATTTTAGTCAAAATGAAATTAA
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
*
27275 GAAAAT-AACAAATTTAATCAAAACAAAATTAA
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
27307 TAAAATAAACAA
1 TAAAATAAACAA
27319 CTTTGACTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 26 0.72
33 10 0.28
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (33 bp):
TAAAATAAACAAATTTAATCAAAACAAAATTAA
Found at i:36608 original size:22 final size:22
Alignment explanation
Indices: 36576--36620 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
36566 TAGCAATTAT
*
36576 AAAAAATATGGTATAAAATATA
1 AAAAAACATGGTATAAAATATA
36598 AAAAAACATGGTATAAAATATA
1 AAAAAACATGGTATAAAATATA
36620 A
1 A
36621 GTATATGTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.24
Consensus pattern (22 bp):
AAAAAACATGGTATAAAATATA
Found at i:37371 original size:6 final size:6
Alignment explanation
Indices: 37354--37399 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
37344 GAGGGTTTTG
* *
37354 AAATTAA AAATTA AAATTA AAATTA AAATTA AAACTA AAACTA AAA
1 AAATT-A AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAA
37400 GTATGTAAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
6 33 0.87
7 5 0.13
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (6 bp):
AAATTA
Found at i:40139 original size:20 final size:22
Alignment explanation
Indices: 40100--40139 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
40090 TTAATATTTA
*
40100 TATATTTTATCAATTTAATTAT
1 TATATTTTATCAATTAAATTAT
40122 TATATTTT-T-AATTAAATT
1 TATATTTTATCAATTAAATT
40140 TGAACTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 1 0.06
22 8 0.47
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (22 bp):
TATATTTTATCAATTAAATTAT
Found at i:40455 original size:25 final size:23
Alignment explanation
Indices: 40395--40455 Score: 59
Period size: 28 Copynumber: 2.4 Consensus size: 23
40385 ATATCAAGTT
40395 TTAATTATAATATATATTTATAA
1 TTAATTATAATATATATTTATAA
*
40418 TTCAATAAATATAATATATTATTTTTATA
1 TT-AAT---TATAATATA-TATTTATA-A
40447 TTAATTATA
1 TTAATTATA
40456 TATTATCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
23 2 0.06
24 3 0.10
25 4 0.13
27 9 0.29
28 10 0.32
29 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAATTATAATATATATTTATAA
Done.