Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001230.1 Kokia drynarioides strain JFW-HI SEQ_112591, 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: 12900
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Found at i:41 original size:25 final size:24
Alignment explanation
Indices: 2--50 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
1 T
2 TTATATATTTTAATATTAATATAA
1 TTATATATTTTAATATTAATATAA
*
26 TTATATTTATTTAATATTAATATAA
1 TTATATAT-TTTAATATTAATATAA
51 ATTTTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTATATATTTTAATATTAATATAA
Found at i:626 original size:26 final size:25
Alignment explanation
Indices: 587--641 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
577 GAAGTCTTTT
*
587 AACTCTTTCGCTTTATTTTTTAGGGA
1 AACTCTTTCGCTTTATCTTTT-GGGA
** *
613 AACTCTTTTTCTTTATCTTTTGGTA
1 AACTCTTTCGCTTTATCTTTTGGGA
638 AACT
1 AACT
642 ATCTAGTTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.20, C:0.16, G:0.11, T:0.53
Consensus pattern (25 bp):
AACTCTTTCGCTTTATCTTTTGGGA
Found at i:909 original size:29 final size:29
Alignment explanation
Indices: 852--909 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
842 AAAAAAAAAT
* *
852 GATTAAAGAGAAAAAGAGGTAAAATTAAG
1 GATTAAAGAGAAAAAGAGATAAAACTAAG
*
881 GATTAAAGCGAAAAA-AGATAGAAACTAAG
1 GATTAAAGAGAAAAAGAGATA-AAACTAAG
910 ATAATGCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.59, C:0.03, G:0.22, T:0.16
Consensus pattern (29 bp):
GATTAAAGAGAAAAAGAGATAAAACTAAG
Found at i:4218 original size:24 final size:24
Alignment explanation
Indices: 4186--4253 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
4176 CTCAAATAAC
*
4186 TAAACAGAGTTTAATTGAAACAAA
1 TAAATAGAGTTTAATTGAAACAAA
4210 TAAATAGAGTTTAATTGAAACAAA
1 TAAATAGAGTTTAATTGAAACAAA
*
4234 TAAATAGAGTTTAACTGAAA
1 TAAATAGAGTTTAATTGAAA
4254 GATTATTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.53, C:0.06, G:0.13, T:0.28
Consensus pattern (24 bp):
TAAATAGAGTTTAATTGAAACAAA
Found at i:4238 original size:28 final size:28
Alignment explanation
Indices: 4178--4239 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 28
4168 GAATTTGACT
*
4178 CAAATAACTAAACAGAGTTTAATTGAAA
1 CAAATAAATAAACAGAGTTTAATTGAAA
4206 CAAATAAAT----AGAGTTTAATTGAAA
1 CAAATAAATAAACAGAGTTTAATTGAAA
4230 CAAATAAATA
1 CAAATAAATA
4240 GAGTTTAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
24 24 0.75
28 8 0.25
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.26
Consensus pattern (28 bp):
CAAATAAATAAACAGAGTTTAATTGAAA
Found at i:5323 original size:18 final size:18
Alignment explanation
Indices: 5300--5335 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5290 GTTCTATACA
5300 ATGATCTGGAAATGAACT
1 ATGATCTGGAAATGAACT
5318 ATGATCTGGAAATGAACT
1 ATGATCTGGAAATGAACT
5336 TCAGATAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (18 bp):
ATGATCTGGAAATGAACT
Found at i:6945 original size:25 final size:25
Alignment explanation
Indices: 6894--6946 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
6884 TGTTTACTTC
* *
6894 TATACATTGGGTTGAATGCTAGTTG
1 TATACATTCGGTTAAATGCTAGTTG
*
6919 TATACATTTCGGTTAAATGTTAG-TG
1 TATACA-TTCGGTTAAATGCTAGTTG
6944 TAT
1 TAT
6947 TTTGATTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43
Consensus pattern (25 bp):
TATACATTCGGTTAAATGCTAGTTG
Found at i:7294 original size:43 final size:43
Alignment explanation
Indices: 7188--7295 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 43
7178 ATTTTAGCAA
* *
7188 CGTTTGTGGGAAAA-CGCCTCTAAAGAACATGTTCTATAGTGG
1 CGTTTGTGGAAAAAGCGCCGCTAAAGAACATGTTCTATAGTGG
* * * *
7230 CATTTGTGGTAAAAGCACCGCTAAAGAACATGGTT-TTTAGTGG
1 CGTTTGTGGAAAAAGCGCCGCTAAAGAACAT-GTTCTATAGTGG
* *
7273 TGTTTGTGGAAAAAGTGCCGCTA
1 CGTTTGTGGAAAAAGCGCCGCTA
7296 GTGGCGCTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 12 0.22
43 39 0.72
44 3 0.06
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (43 bp):
CGTTTGTGGAAAAAGCGCCGCTAAAGAACATGTTCTATAGTGG
Found at i:12288 original size:25 final size:26
Alignment explanation
Indices: 12260--12314 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
12250 CGAACTAGAT
*
12260 AGTTTACC-AAAAGATAAAGAAAAAG
1 AGTTTACCTAAAAAATAAAGAAAAAG
* **
12285 AGTTTCCCTAAAAAATAAAGCGAAAG
1 AGTTTACCTAAAAAATAAAGAAAAAG
12311 AGTT
1 AGTT
12315 AAAAGACTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.20
Consensus pattern (26 bp):
AGTTTACCTAAAAAATAAAGAAAAAG
Found at i:12882 original size:25 final size:24
Alignment explanation
Indices: 12851--12899 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
12841 AATTTAAAAT
12851 TTATATTAATATTAAATAAATATAA
1 TTATATTAATATTAAA-AAATATAA
*
12876 TTATATTAATATTAAAATATATAA
1 TTATATTAATATTAAAAAATATAA
12900 A
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTATATTAATATTAAAAAATATAA
Done.