Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001825.1 Kokia drynarioides strain JFW-HI SEQ_113569, 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: 22091
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.37
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:4636 original size:3 final size:3
Alignment explanation
Indices: 4628--4670 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
4618 CCTTTCCTAT
4628 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4671 AAAAGCATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5210 original size:18 final size:18
Alignment explanation
Indices: 5187--5224 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
5177 CCAAAGTCTT
5187 ATTTTAA-TTTATTTATAC
1 ATTTTAATTTTA-TTATAC
5205 ATTTTAATTTTATTATAC
1 ATTTTAATTTTATTATAC
5223 AT
1 AT
5225 ACTTTACTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTAATTTTATTATAC
Found at i:7013 original size:49 final size:50
Alignment explanation
Indices: 6939--7038 Score: 157
Period size: 49 Copynumber: 2.0 Consensus size: 50
6929 ACCCGTATAA
**
6939 ACTACACTTTTTCTATTTGACATTGATTAGAATAAGG-TTTTTCAACCTT
1 ACTACACTTCATCTATTTGACATTGATTAGAATAAGGTTTTTTCAACCTT
*
6988 ACTACACTTCATCTATTTGATATTGATTAGAATAAGGTTTTTTTCAACCTT
1 ACTACACTTCATCTATTTGACATTGATTAGAATAAGG-TTTTTTCAACCTT
7039 TAAATAGATG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 34 0.74
51 12 0.26
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (50 bp):
ACTACACTTCATCTATTTGACATTGATTAGAATAAGGTTTTTTCAACCTT
Found at i:8589 original size:15 final size:14
Alignment explanation
Indices: 8541--8591 Score: 52
Period size: 13 Copynumber: 3.7 Consensus size: 14
8531 ATATATTTAC
8541 AAATTATAT-AAAA
1 AAATTATATAAAAA
* *
8554 ACATT-TTTAAAAA
1 AAATTATATAAAAA
8567 AAATTATATAAAAA
1 AAATTATATAAAAA
*
8581 TAATATATATA
1 AAAT-TATATA
8592 TTTTTAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
12 2 0.07
13 12 0.40
14 10 0.33
15 6 0.20
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATTATATAAAAA
Found at i:8839 original size:19 final size:19
Alignment explanation
Indices: 8815--8851 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8805 TATATTAGAC
* *
8815 TAAAATTATTAGAAAAATA
1 TAAAATAATTAAAAAAATA
8834 TAAAATAATTAAAAAAAT
1 TAAAATAATTAAAAAAAT
8852 CACAATTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
TAAAATAATTAAAAAAATA
Found at i:9350 original size:16 final size:16
Alignment explanation
Indices: 9329--9359 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9319 GCTCTTTGAT
9329 AAATTTCAATTTTTTG
1 AAATTTCAATTTTTTG
*
9345 AAATTTGAATTTTTT
1 AAATTTCAATTTTTT
9360 TTTTCTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (16 bp):
AAATTTCAATTTTTTG
Found at i:10218 original size:34 final size:34
Alignment explanation
Indices: 10179--10250 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
10169 AATTTTTTTA
* *
10179 ATATTTACATTTTAATAATATTATATATTAC-T-AT
1 ATATTTA-ATTTTAAT-ATACTATAAATTACATAAT
*
10213 ATATTTAATTTTTATATACTATAAATTACATAAT
1 ATATTTAATTTTAATATACTATAAATTACATAAT
10247 ATAT
1 ATAT
10251 AAAAATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 12 0.36
33 8 0.24
34 13 0.39
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (34 bp):
ATATTTAATTTTAATATACTATAAATTACATAAT
Found at i:10230 original size:17 final size:16
Alignment explanation
Indices: 10164--10228 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 16
10154 TATAGACAGT
*
10164 TATTTAATTTTTTTAA
1 TATTTAATTTTTATAA
*
10180 TATTTACATTTTAATAA
1 TATTTA-ATTTTTATAA
**
10197 TATTATATATTACTAT-A
1 TATT-TA-ATTTTTATAA
10214 TATTTAATTTTTATA
1 TATTTAATTTTTATA
10229 TACTATAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
15 6 0.16
16 8 0.21
17 17 0.45
18 7 0.18
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTAATTTTTATAA
Found at i:16407 original size:16 final size:17
Alignment explanation
Indices: 16386--16431 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
16376 TAAGGATTTT
*
16386 TTTAAAAATAAAT-ATA
1 TTTAAAAATAAATAAAA
*
16402 TTTAAAAATATATAAAA
1 TTTAAAAATAAATAAAA
*
16419 TTTATAAATAAAT
1 TTTAAAAATAAAT
16432 TATAAATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTAAAAATAAATAAAA
Found at i:18021 original size:36 final size:36
Alignment explanation
Indices: 17974--18051 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
17964 CTAACATTAG
*
17974 ATTAAAATTTGATTTCACATTGTCTCGTTATTAATT
1 ATTAAAATTTGATTTCACATTCTCTCGTTATTAATT
* *
18010 ATTAAAATTTGATTTCATATTCTCTCTTTATTAATT
1 ATTAAAATTTGATTTCACATTCTCTCGTTATTAATT
18046 ATTAAA
1 ATTAAA
18052 TTTAACCCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (36 bp):
ATTAAAATTTGATTTCACATTCTCTCGTTATTAATT
Done.