Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002694.1 Kokia drynarioides strain JFW-HI SEQ_114970, 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: 30886
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3302 original size:27 final size:27
Alignment explanation
Indices: 3244--3302 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
3234 TTGTATATAT
** * * *
3244 ATTTTTATTAATTGGTAAAATAGGTTT
1 ATTTTTAAGAATTAGTAAAATAGGATG
*
3271 TTTTTTAAGAATTAGTAAAATAGGATG
1 ATTTTTAAGAATTAGTAAAATAGGATG
3298 ATTTT
1 ATTTT
3303 GGAGAAAAAG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (27 bp):
ATTTTTAAGAATTAGTAAAATAGGATG
Found at i:3906 original size:12 final size:12
Alignment explanation
Indices: 3883--3916 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3873 TTAGAGGATA
3883 AATTATTAATATT
1 AATTA-TAATATT
*
3896 TATTATAATATT
1 AATTATAATATT
3908 AATTATAAT
1 AATTATAAT
3917 TGCTGTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTATAATATT
Found at i:11485 original size:9 final size:10
Alignment explanation
Indices: 11442--11482 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
11432 AAAATTCAAA
*
11442 TTATATTTTT
1 TTATAATTTT
11452 TTATAATTTT
1 TTATAATTTT
*
11462 TTGTAATTTT
1 TTATAATTTT
11472 TTATAATTTT
1 TTATAATTTT
11482 T
1 T
11483 ATATTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (10 bp):
TTATAATTTT
Found at i:14389 original size:27 final size:27
Alignment explanation
Indices: 14359--14412 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
14349 AACTAGTGTG
14359 ATTGATGAAATAACAAGAAAGTGACGC
1 ATTGATGAAATAACAAGAAAGTGACGC
14386 ATTGATGAAATAACAAGAAAGTGACGC
1 ATTGATGAAATAACAAGAAAGTGACGC
14413 GTAGCGTGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.11, G:0.22, T:0.19
Consensus pattern (27 bp):
ATTGATGAAATAACAAGAAAGTGACGC
Found at i:18532 original size:3 final size:3
Alignment explanation
Indices: 18526--18556 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
18516 TTTTCCTTAG
18526 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
18557 GCGGATTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:25830 original size:18 final size:19
Alignment explanation
Indices: 25797--25833 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
25787 ATTGGATGAC
*
25797 TAAATTAAATAATTAAATT
1 TAAAGTAAATAATTAAATT
25816 TAAAGTAAA-AATTAAATT
1 TAAAGTAAATAATTAAATT
25834 AGATCTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TAAAGTAAATAATTAAATT
Found at i:27222 original size:2 final size:2
Alignment explanation
Indices: 27217--27241 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27207 TGTTTGTTTT
27217 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
27242 TTTGTTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:30672 original size:42 final size:42
Alignment explanation
Indices: 30625--30730 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 42
30615 CATGAATCTG
* *
30625 ATTCAACCATGGGAACTGAGCAGCTCAATATCCAGGGGACTC
1 ATTCAACCCTGGGAACTGAGCAGCTCAATATCCAGGAGACTC
* * * *
30667 ATTCAACCCTGGGAACTCAGCATCTCCATATTCAGGAGACTC
1 ATTCAACCCTGGGAACTGAGCAGCTCAATATCCAGGAGACTC
* *
30709 ATTCAACCCTCGCAACTGAGCA
1 ATTCAACCCTGGGAACTGAGCA
30731 ACTCCCTGGA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (42 bp):
ATTCAACCCTGGGAACTGAGCAGCTCAATATCCAGGAGACTC
Done.