Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014584.1 Kokia drynarioides strain JFW-HI SEQ_129623, 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: 28808
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:10858 original size:30 final size:31
Alignment explanation
Indices: 10818--10891 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
10808 ACTTTTTTCC
* * *
10818 TATTTCTAATTTAACCACTCAACTTTTGA-A
1 TATTTATAATTTAACCACACAACTTTTCACA
* * *
10848 TATTTATAATTTGACCCCACTACTTTTCACA
1 TATTTATAATTTAACCACACAACTTTTCACA
*
10879 TATTTACAATTTA
1 TATTTATAATTTA
10892 GTCTATATCA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
30 23 0.66
31 12 0.34
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.45
Consensus pattern (31 bp):
TATTTATAATTTAACCACACAACTTTTCACA
Found at i:13010 original size:43 final size:43
Alignment explanation
Indices: 12962--13086 Score: 169
Period size: 43 Copynumber: 2.9 Consensus size: 43
12952 GACATTGAGA
* **
12962 GGAACACTGTTTCCTAAAATTGAAAGTATGTGATTGATTGTGT
1 GGAACACTGTTTCCTAATATTGAAAGTATGTGATTGATTGAAT
* ** *
13005 GGAACACTATTTCCTAATATTGAAAGTATGTGAACGAATGAAT
1 GGAACACTGTTTCCTAATATTGAAAGTATGTGATTGATTGAAT
* *
13048 GGAACACTGTTTCCTAATATTTATAGTATGTGATTGATT
1 GGAACACTGTTTCCTAATATTGAAAGTATGTGATTGATT
13087 AAGAGCATGA
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (43 bp):
GGAACACTGTTTCCTAATATTGAAAGTATGTGATTGATTGAAT
Found at i:13797 original size:16 final size:17
Alignment explanation
Indices: 13773--13811 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
13763 AAGATTGTGG
*
13773 TTTGAGATTG-TTTTGC
1 TTTGGGATTGATTTTGC
*
13789 TTTGGGATTGATTTTGT
1 TTTGGGATTGATTTTGC
13806 TTTGGG
1 TTTGGG
13812 CTTACATGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.10, C:0.03, G:0.31, T:0.56
Consensus pattern (17 bp):
TTTGGGATTGATTTTGC
Found at i:16540 original size:48 final size:48
Alignment explanation
Indices: 16440--16529 Score: 112
Period size: 48 Copynumber: 1.9 Consensus size: 48
16430 TTTCTGGAAA
* * ***
16440 AAAAAAATGAACGATTCACCTTTCAAAGTGAGAGGGAGAGTTTGAATT
1 AAAAAAATAAACGATTCACCTTTCAAAGTGAGAAGGAGAGAAAGAATT
*
16488 AAAAAAATAAACGATTCATCTTTCAAAGTGA-AAGGA-AGAAAG
1 AAAAAAATAAACGATTCACCTTTCAAAGTGAGAAGGAGAGAAAG
16530 CATTCGAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
46 3 0.08
47 4 0.11
48 29 0.81
ACGTcount: A:0.48, C:0.10, G:0.20, T:0.22
Consensus pattern (48 bp):
AAAAAAATAAACGATTCACCTTTCAAAGTGAGAAGGAGAGAAAGAATT
Found at i:24376 original size:14 final size:14
Alignment explanation
Indices: 24354--24387 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
24344 TTTTACATGT
* *
24354 ATTGCTTCTTTGTA
1 ATTGATTCTGTGTA
24368 ATTGATTCTGTGTA
1 ATTGATTCTGTGTA
24382 ATTGAT
1 ATTGAT
24388 CATATAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.09, G:0.18, T:0.53
Consensus pattern (14 bp):
ATTGATTCTGTGTA
Found at i:25766 original size:12 final size:12
Alignment explanation
Indices: 25733--25766 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
25723 TATCATTATA
25733 AATAAACGAGTC
1 AATAAACGAGTC
*
25745 -ATAAATGAGTC
1 AATAAACGAGTC
25756 AATAAACGAGT
1 AATAAACGAGT
25767 TTATAGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.21
Consensus pattern (12 bp):
AATAAACGAGTC
Done.