Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001017.1 Kokia drynarioides strain JFW-HI SEQ_112229, 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: 21274
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Found at i:10645 original size:17 final size:19
Alignment explanation
Indices: 10596--10646 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
10586 CCGCAGCCAC
* *
10596 CCTACCTATATATATATAA
1 CCTACATATATGTATATAA
10615 CCTACATATATGTATATAA
1 CCTACATATATGTATATAA
*
10634 GCTA-ATAT-TGTAT
1 CCTACATATATGTAT
10647 GACTTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 20 0.69
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (19 bp):
CCTACATATATGTATATAA
Found at i:12322 original size:20 final size:20
Alignment explanation
Indices: 12299--12360 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
12289 GGTATAAATC
12299 ATAATTTTCTTCTCCTAATT
1 ATAATTTTCTTCTCCTAATT
* *
12319 ATAATTTAT-TT-T-ATAAATC
1 ATAATTT-TCTTCTCCT-AATT
12338 ATAATTTTCTTCTCCTAATT
1 ATAATTTTCTTCTCCTAATT
12358 ATA
1 ATA
12361 CTTTATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
18 2 0.06
19 13 0.39
20 16 0.48
21 2 0.06
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (20 bp):
ATAATTTTCTTCTCCTAATT
Found at i:12336 original size:39 final size:39
Alignment explanation
Indices: 12291--12374 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
12281 AATTCAAGGG
12291 TATAAATCATAATTTTCTTCTCCTAATTATAATTTATTT
1 TATAAATCATAATTTTCTTCTCCTAATTATAATTTATTT
*
12330 TATAAATCATAATTTTCTTCTCCTAATTATACTTTATTT
1 TATAAATCATAATTTTCTTCTCCTAATTATAATTTATTT
12369 T-TAAAT
1 TATAAAT
12375 TATCATTAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 5 0.11
39 39 0.89
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (39 bp):
TATAAATCATAATTTTCTTCTCCTAATTATAATTTATTT
Found at i:14049 original size:16 final size:15
Alignment explanation
Indices: 14028--14057 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
14018 ATTCAAACTT
14028 AAAATTTTCTGAATCC
1 AAAATTTTCT-AATCC
14044 AAAATTTTCTAATC
1 AAAATTTTCTAATC
14058 TTAATTCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (15 bp):
AAAATTTTCTAATCC
Found at i:14707 original size:11 final size:11
Alignment explanation
Indices: 14691--14715 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
14681 GGATTTTATG
14691 AAAAAAAAGAA
1 AAAAAAAAGAA
14702 AAAAAAAAGAA
1 AAAAAAAAGAA
14713 AAA
1 AAA
14716 TGAAGTAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:20647 original size:6 final size:6
Alignment explanation
Indices: 20631--20661 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
20621 ATTCTCTCCT
20631 CCCCT- CCCCTC CCCCTC CCCCTC CCCCTC CC
1 CCCCTC CCCCTC CCCCTC CCCCTC CCCCTC CC
20662 ATTTCTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.84, G:0.00, T:0.16
Consensus pattern (6 bp):
CCCCTC
Found at i:20894 original size:12 final size:12
Alignment explanation
Indices: 20877--20906 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20867 CTGTATTATT
*
20877 AAAATGTGAGTA
1 AAAATGTAAGTA
20889 AAAATGTAAGTA
1 AAAATGTAAGTA
20901 AAAATG
1 AAAATG
20907 AATAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (12 bp):
AAAATGTAAGTA
Done.