Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013987.1 Kokia drynarioides strain JFW-HI SEQ_129018, 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: 33644
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1856 original size:16 final size:16
Alignment explanation
Indices: 1835--1865 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1825 AGTGTAATGA
1835 TAAAATATGAAAAAAT
1 TAAAATATGAAAAAAT
*
1851 TAAAATATTAAAAAA
1 TAAAATATGAAAAAA
1866 AAATAACAAC
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:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
TAAAATATGAAAAAAT
Found at i:6421 original size:16 final size:16
Alignment explanation
Indices: 6400--6432 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6390 CAACAATACT
6400 ATAATATTA-TTTTAAA
1 ATAATA-TAGTTTTAAA
6416 ATAATATAGTTTTAAA
1 ATAATATAGTTTTAAA
6432 A
1 A
6433 CAAAAAGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
ATAATATAGTTTTAAA
Found at i:19344 original size:55 final size:55
Alignment explanation
Indices: 19278--19388 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
19268 GCCTGTGCAA
19278 AAAGTAAAACCAATAAAACAATCATTGGCACCCTGTTAAGCACTAGAGCAATACC
1 AAAGTAAAACCAATAAAACAATCATTGGCACCCTGTTAAGCACTAGAGCAATACC
*
19333 AAAGTAAAACCAATAAAACAATCATTGGCACCGTGTTAAGCACTAGAGCAATACC
1 AAAGTAAAACCAATAAAACAATCATTGGCACCCTGTTAAGCACTAGAGCAATACC
19388 A
1 A
19389 GTGTCAAATT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.46, C:0.23, G:0.14, T:0.18
Consensus pattern (55 bp):
AAAGTAAAACCAATAAAACAATCATTGGCACCCTGTTAAGCACTAGAGCAATACC
Found at i:22101 original size:24 final size:25
Alignment explanation
Indices: 22074--22127 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 25
22064 TGAATACTTT
22074 TCTCTTGATCTTGATG-CTTGAA-TA
1 TCTCTTGATCTTGA-GCCTTGAAGTA
22098 TCTCTT--TCTTGAGCCTTGAAGTA
1 TCTCTTGATCTTGAGCCTTGAAGTA
22121 T-TCTTGA
1 TCTCTTGA
22128 AGTGTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
21 1 0.04
22 16 0.62
23 3 0.12
24 6 0.23
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.46
Consensus pattern (25 bp):
TCTCTTGATCTTGAGCCTTGAAGTA
Found at i:23686 original size:20 final size:20
Alignment explanation
Indices: 23633--23690 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
23623 ATATCATTTT
* *
23633 TATATTTTAAAATTTTTAAC
1 TATATTTTACAATTTTTAAA
* *
23653 GATCCTTTT-C-ATTTTTAAA
1 TAT-ATTTTACAATTTTTAAA
23672 TATATTTTACAATTTTTAA
1 TATATTTTACAATTTTTAA
23691 TTATTTCTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
18 4 0.14
19 11 0.38
20 10 0.34
21 4 0.14
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (20 bp):
TATATTTTACAATTTTTAAA
Found at i:25334 original size:23 final size:23
Alignment explanation
Indices: 25272--25424 Score: 148
Period size: 23 Copynumber: 6.5 Consensus size: 23
25262 TATACGGAAC
**
25272 AAACAGAGAGCACTTA-AGTGCT
1 AAACAGAGAGCACACACAGTGCT
25294 GGATAACAGAGAGCACACACAGTGCT
1 --A-AACAGAGAGCACACACAGTGCT
* * * *
25320 AAAAAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
* *
25343 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
25366 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
25389 AATAACAGAGAGCACGAGAC-GTGCT
1 -A-AACAGAGAGCAC-ACACAGTGCT
25414 AAACAGAGAGC
1 AAACAGAGAGC
25425 GCGCTAGTGT
Statistics
Matches: 111, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
23 69 0.62
24 4 0.04
25 29 0.26
26 9 0.08
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Found at i:32538 original size:23 final size:23
Alignment explanation
Indices: 32496--32585 Score: 117
Period size: 23 Copynumber: 3.9 Consensus size: 23
32486 GCACATAAGT
* * *
32496 GAGAGCATACACAGTGCTAAACA
1 GAGAGCACACAAAGTGCTAATCA
* *
32519 GAGAGTACACAAAGTACTAATCA
1 GAGAGCACACAAAGTGCTAATCA
*
32542 GAGAGCACACATAGTGCTAATCA
1 GAGAGCACACAAAGTGCTAATCA
*
32565 GAGAGCACACACAGTGCTAAT
1 GAGAGCACACAAAGTGCTAAT
32586 AACAGAGCGC
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.16
Consensus pattern (23 bp):
GAGAGCACACAAAGTGCTAATCA
Done.