Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000915.1 Kokia drynarioides strain JFW-HI SEQ_112057, 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: 22328
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:2601 original size:21 final size:21
Alignment explanation
Indices: 2570--2613 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2560 CCATTTACTT
*
2570 TCCCTCAAAACTCTTTATTTTC
1 TCCCTCAAAACT-TTTATTCTC
2592 TCCC-CAAAACTTTTATTCTC
1 TCCCTCAAAACTTTTATTCTC
2612 TC
1 TC
2614 TCATTTTCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 7 0.33
22 4 0.19
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.43
Consensus pattern (21 bp):
TCCCTCAAAACTTTTATTCTC
Found at i:2864 original size:24 final size:24
Alignment explanation
Indices: 2832--2877 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2822 TTATTTAACT
*
2832 TAATCGAACATGTTCATGAACATA
1 TAATCGAACATGTTCACGAACATA
*
2856 TAATTGAACATGTTCACGAACA
1 TAATCGAACATGTTCACGAACA
2878 ATGTTAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (24 bp):
TAATCGAACATGTTCACGAACATA
Found at i:4694 original size:29 final size:29
Alignment explanation
Indices: 4639--4694 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
4629 AGTAAAAATC
* * **
4639 ATAGGTTAAGGGTTTATTTAATTACAAAA
1 ATAGGTTAAAGGCTTATTTAAACACAAAA
*
4668 ATAGGTTAAAGGCTTGTTTAAACACAA
1 ATAGGTTAAAGGCTTATTTAAACACAA
4695 TATAGAGAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (29 bp):
ATAGGTTAAAGGCTTATTTAAACACAAAA
Found at i:8450 original size:12 final size:12
Alignment explanation
Indices: 8435--8460 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8425 ATACACTTAA
8435 AAATATTAAAAC
1 AAATATTAAAAC
8447 AAATATTAAAAC
1 AAATATTAAAAC
8459 AA
1 AA
8461 CAAACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:9848 original size:3 final size:3
Alignment explanation
Indices: 9840--9864 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9830 GAAGCAGAAG
9840 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
9865 AAGAAAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:18890 original size:14 final size:14
Alignment explanation
Indices: 18871--18897 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18861 TTAAAAAAGG
18871 AATAAAAAACAAAA
1 AATAAAAAACAAAA
18885 AATAAAAAACAAA
1 AATAAAAAACAAA
18898 GAAGACCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.85, C:0.07, G:0.00, T:0.07
Consensus pattern (14 bp):
AATAAAAAACAAAA
Found at i:19840 original size:7 final size:7
Alignment explanation
Indices: 19828--19852 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19818 AAAGGGAGTG
19828 TGTGGTT
1 TGTGGTT
19835 TGTGGTT
1 TGTGGTT
19842 TGTGGTT
1 TGTGGTT
19849 TGTG
1 TGTG
19853 ATTAGTGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.44, T:0.56
Consensus pattern (7 bp):
TGTGGTT
Done.