Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001863.1 Kokia drynarioides strain JFW-HI SEQ_113626, 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, 619
Length: 1032
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Found at i:16 original size:11 final size:11
Alignment explanation
Indices: 1--52 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
1 AATTTATTTTA
1 AATTTATTTTA
*
12 AATTTAAATTT-
1 AATTT-ATTTTA
*
23 AATTTAAGTTTA
1 AATTT-ATTTTA
35 AATTTATTTTCA
1 AATTTATTTT-A
47 AATTTA
1 AATTTA
53 AAATTACTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 19 0.54
12 16 0.46
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
AATTTATTTTA
Found at i:18 original size:6 final size:6
Alignment explanation
Indices: 8--54 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
1 AATTTAT
* *
8 TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA TTT-AT TTTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
55 ATTACTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 9 0.26
6 21 0.62
7 4 0.12
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:23 original size:17 final size:17
Alignment explanation
Indices: 1--54 Score: 81
Period size: 17 Copynumber: 3.1 Consensus size: 17
1 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
18 AATTTAATTTAAGTTTA
1 AATTTATTTTAAATTTA
35 AATTTATTTTCAAATTTA
1 AATTTATTTT-AAATTTA
53 AA
1 AA
55 ATTACTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 24 0.75
18 8 0.25
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:38 original size:12 final size:12
Alignment explanation
Indices: 8--54 Score: 53
Period size: 11 Copynumber: 4.0 Consensus size: 12
1 AATTTAT
8 TTTAAATTTAAA
1 TTTAAATTTAAA
*
20 TTT-AATTTAAG
1 TTTAAATTTAAA
*
31 TTTAAATTT-AT
1 TTTAAATTTAAA
42 TTTCAAATTTAAA
1 TTT-AAATTTAAA
55 ATTACTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 14 0.48
12 14 0.48
13 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:70 original size:35 final size:34
Alignment explanation
Indices: 1--72 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 34
* ** *
1 AATTTATTTTAAATTTAAATTTAATTTAAGTTTA
1 AATTTATTTTAAATTTAAAATTAATAAAAATTTA
*
35 AATTTATTTTCAAATTTAAAATTACTAAAAATTTA
1 AATTTATTTT-AAATTTAAAATTAATAAAAATTTA
70 AAT
1 AAT
73 AAAGTTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
34 10 0.31
35 22 0.69
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (34 bp):
AATTTATTTTAAATTTAAAATTAATAAAAATTTA
Found at i:246 original size:29 final size:30
Alignment explanation
Indices: 211--335 Score: 141
Period size: 29 Copynumber: 4.2 Consensus size: 30
201 CTAAAAATCT
*
211 CATTTTTGACCCTGAAACTT-TCAAAATTC
1 CATTTTTGACCCTGAAACTTCCCAAAATTC
* * **
240 TATTTTTAACCCTGAAACTTCTAAAAATTC
1 CATTTTTGACCCTGAAACTTCCCAAAATTC
270 CATTTTT-AGCCCTG-AACTTCCCAAAATTC
1 CATTTTTGA-CCCTGAAACTTCCCAAAATTC
*
299 CATTTTTGACTCC-GAAACTTCCTAAAATTAC
1 CATTTTTGAC-CCTGAAACTTCCCAAAATT-C
330 CATTTT
1 CATTTT
336 ACCCCTGGAT
Statistics
Matches: 83, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
29 41 0.49
30 35 0.42
31 7 0.08
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (30 bp):
CATTTTTGACCCTGAAACTTCCCAAAATTC
Found at i:295 original size:59 final size:60
Alignment explanation
Indices: 200--335 Score: 158
Period size: 59 Copynumber: 2.3 Consensus size: 60
190 GCCTAAATTG
* *
200 CCTAAAAA-TCTCATTTTTGACCCTGAAACTTTCAAAATTCTATTTTTAAC-CCTGAAACTT
1 CCTAAAAATTC-CATTTTTGACCCTGAAACTTCCAAAATTCCATTTTTAACTCC-GAAACTT
*
260 -CTAAAAATTCCATTTTT-AGCCCTG-AACTTCCCAAAATTCCATTTTTGACTCCGAAACTT
1 CCTAAAAATTCCATTTTTGA-CCCTGAAACTT-CCAAAATTCCATTTTTAACTCCGAAACTT
319 CCT-AAAATTACCATTTT
1 CCTAAAAATT-CCATTTT
336 ACCCCTGGAT
Statistics
Matches: 67, Mismatches: 3, Indels: 12
0.82 0.04 0.15
Matches are distributed among these distances:
58 6 0.09
59 48 0.72
60 13 0.19
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (60 bp):
CCTAAAAATTCCATTTTTGACCCTGAAACTTCCAAAATTCCATTTTTAACTCCGAAACTT
Done.