Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005550.1 Kokia drynarioides strain JFW-HI SEQ_119652, 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: 22640
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:5054 original size:14 final size:14
Alignment explanation
Indices: 5012--5055 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
5002 GTACTTCTAC
5012 TTTTATAACCTTTA
1 TTTTATAACCTTTA
* *
5026 TTTTAGAACAACTTTT
1 TTTTATAAC--CTTTA
5042 TTTTATAACCTTTA
1 TTTTATAACCTTTA
5056 AATATTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 12 0.50
16 12 0.50
ACGTcount: A:0.30, C:0.14, G:0.02, T:0.55
Consensus pattern (14 bp):
TTTTATAACCTTTA
Found at i:10205 original size:3 final size:3
Alignment explanation
Indices: 10197--10233 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
10187 AAGTGGTTGT
10197 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
10234 CAGAAGAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:10559 original size:11 final size:12
Alignment explanation
Indices: 10534--10572 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
10524 CCAAATACAC
10534 AATAAATATTAA
1 AATAAATATTAA
*
10546 AATAAATGTT-A
1 AATAAATATTAA
10557 AAT-AATATTAA
1 AATAAATATTAA
10568 AATAA
1 AATAA
10573 TTGTAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 5 0.22
11 8 0.35
12 10 0.43
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (12 bp):
AATAAATATTAA
Found at i:10566 original size:22 final size:21
Alignment explanation
Indices: 10538--10580 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
10528 ATACACAATA
10538 AATATTAAAATAAATGTTAAAT
1 AATATTAAAATAAATG-TAAAT
*
10560 AATATTAAAATAATTGTAAAT
1 AATATTAAAATAAATGTAAAT
10581 TAACAAGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (21 bp):
AATATTAAAATAAATGTAAAT
Found at i:10728 original size:11 final size:11
Alignment explanation
Indices: 10651--10728 Score: 59
Period size: 11 Copynumber: 7.0 Consensus size: 11
10641 ATTCAAACAT
10651 TAATAACAAAA
1 TAATAACAAAA
* * *
10662 TAGTGACAACA
1 TAATAACAAAA
**
10673 TAATAATGAAA
1 TAATAACAAAA
*
10684 TAATAATAAAA
1 TAATAACAAAA
*
10695 CAATAACAAAA
1 TAATAACAAAA
*
10706 -AATATGAAAAAA
1 TAATA--ACAAAA
10718 TAATAACAAAA
1 TAATAACAAAA
10729 CAACATATTT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
10 4 0.08
11 38 0.75
12 5 0.10
13 4 0.08
ACGTcount: A:0.68, C:0.08, G:0.05, T:0.19
Consensus pattern (11 bp):
TAATAACAAAA
Found at i:16224 original size:24 final size:24
Alignment explanation
Indices: 16144--16209 Score: 132
Period size: 24 Copynumber: 2.8 Consensus size: 24
16134 AATCTTTCGG
16144 TTAAACTCTGTTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
16168 TTAAACTCTGTTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
16192 TTAAACTCTGTTTATTTG
1 TTAAACTCTGTTTATTTG
16210 ATTGAGTCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAAACTCTGTTTATTTGTTTCAA
Found at i:18134 original size:24 final size:24
Alignment explanation
Indices: 18083--18137 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
18073 TCTTTTAGTT
* * *
18083 AAACTTTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTATTTCAATC
18107 AAACTCTGTTTATTTATTT-AAGTC
1 AAACTCTGTTTATTTATTTCAA-TC
18131 AAACTCT
1 AAACTCT
18138 TATTAGTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.29, C:0.13, G:0.07, T:0.51
Consensus pattern (24 bp):
AAACTCTGTTTATTTATTTCAATC
Done.