Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005864.1 Kokia drynarioides strain JFW-HI SEQ_120185, 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: 31409
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:544 original size:19 final size:19
Alignment explanation
Indices: 522--566 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
512 TTGAAGCAGC
522 TGGTGGCAGTGCAAGTTGT
1 TGGTGGCAGTGCAAGTTGT
541 TGGTGGCAGTGCAAGTTGT
1 TGGTGGCAGTGCAAGTTGT
560 TGGTGGC
1 TGGTGGC
567 GCAACTTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.13, C:0.11, G:0.44, T:0.31
Consensus pattern (19 bp):
TGGTGGCAGTGCAAGTTGT
Found at i:737 original size:13 final size:13
Alignment explanation
Indices: 719--744 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
709 TTGGACTTGA
719 TTTGTAATTAGAC
1 TTTGTAATTAGAC
732 TTTGTAATTAGAC
1 TTTGTAATTAGAC
745 ATTATTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
TTTGTAATTAGAC
Found at i:766 original size:6 final size:6
Alignment explanation
Indices: 755--795 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
745 ATTATTTAAA
755 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATT TCAAAT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAAT
796 AAACTTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
4 2 0.06
5 2 0.06
6 21 0.68
7 6 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (6 bp):
TAAATT
Found at i:783 original size:17 final size:16
Alignment explanation
Indices: 761--823 Score: 72
Period size: 17 Copynumber: 3.8 Consensus size: 16
751 TAAATAAATT
761 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
778 TAAATTTAAATTTCAAA
1 TAAATTTAAATTT-AAA
* *
795 TAAACTTAATTTTAAAA
1 TAAATTTAAATTT-AAA
*
812 TAAATTCAAATT
1 TAAATTTAAATT
824 CTGTTGGGTC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 38 0.97
18 1 0.03
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:783 original size:23 final size:23
Alignment explanation
Indices: 748--795 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
738 ATTAGACATT
748 ATTTAAATAAATTTAAATTT-AA
1 ATTTAAATAAATTTAAATTTCAA
770 ATTTATAATAAATTTAAATTTCAA
1 ATTTA-AATAAATTTAAATTTCAA
794 AT
1 AT
796 AAACTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.21
23 15 0.62
24 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAAATAAATTTAAATTTCAA
Found at i:7622 original size:15 final size:15
Alignment explanation
Indices: 7602--7653 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
7592 ACTACAAAAC
7602 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
7617 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
7636 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
7651 ATT
1 ATT
7654 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:8460 original size:2 final size:2
Alignment explanation
Indices: 8453--8477 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8443 ATCATTGAGA
8453 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
8478 ATTTTTAGTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.