Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000846.1 Kokia drynarioides strain JFW-HI SEQ_111947, 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: 20805
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:377 original size:13 final size:13
Alignment explanation
Indices: 359--385 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
349 TTTTAAATAT
359 ATAAAAATAAAAA
1 ATAAAAATAAAAA
372 ATAAAAATAAAAA
1 ATAAAAATAAAAA
385 A
1 A
386 ACACGTGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
ATAAAAATAAAAA
Found at i:12968 original size:3 final size:3
Alignment explanation
Indices: 12960--12987 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12950 CATAATATAT
12960 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12988 AAGCATATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:18436 original size:10 final size:10
Alignment explanation
Indices: 18423--18453 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
18413 ATTAGTTAAT
18423 ATAAAATATA
1 ATAAAATATA
18433 ATAAAATATA
1 ATAAAATATA
*
18443 ATAAAAAATA
1 ATAAAATATA
18453 A
1 A
18454 CATGAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
ATAAAATATA
Found at i:20012 original size:17 final size:17
Alignment explanation
Indices: 19989--20117 Score: 150
Period size: 17 Copynumber: 7.4 Consensus size: 17
19979 CCAAATTCCC
19989 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
20006 ATTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
20024 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
*
20042 TTTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAA
* *
20059 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
20076 TTTAAATTTTTTTTTAAA
1 TTTAAA-TTTATTTTAAA
* *
20094 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
20111 TTTAAAT
1 TTTAAAT
20118 GAAGCGGAAA
Statistics
Matches: 92, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
17 51 0.55
18 38 0.41
19 3 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:20028 original size:35 final size:34
Alignment explanation
Indices: 19989--20117 Score: 150
Period size: 35 Copynumber: 3.7 Consensus size: 34
19979 CCAAATTCCC
* * *
19989 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAATTTAAATTTATTT-TAAA
*
20024 TTTAAATTTATTTTTAAATTTAAATTTATTTTGAA
1 TTTAAATTTA-TTTTAAATTTAAATTTATTTTAAA
* * *
20059 TTTAAATTTAATTTAAGTTTAAATTTTTTTTTAAA
1 TTTAAATTTATTTTAAATTTAAA-TTTATTTTAAA
* *
20094 TTTAAAATTATTATAAATTTAAAT
1 TTTAAATTTATTTTAAATTTAAAT
20118 GAAGCGGAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
34 12 0.15
35 50 0.62
36 18 0.22
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTTAAA
Found at i:20030 original size:6 final size:6
Alignment explanation
Indices: 20021--20117 Score: 76
Period size: 6 Copynumber: 16.7 Consensus size: 6
20011 ATTTGTTTAA
** * *
20021 AAATTT AAATTT ATTTTT AAATTT AAATTT -ATTTT GAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *** *
20068 -AATTT AAGTTT AAATTT TTTTTT AAATTT AAAATT --ATTAT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATT-T AAATTT
20114 AAAT
1 AAAT
20118 GAAGCGGAAA
Statistics
Matches: 69, Mismatches: 17, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
4 2 0.03
5 10 0.14
6 54 0.78
7 3 0.04
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (6 bp):
AAATTT
Found at i:20154 original size:12 final size:12
Alignment explanation
Indices: 20139--20165 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20129 ACAAAATTTT
20139 AAAAAAAAGTCC
1 AAAAAAAAGTCC
20151 AAAAAAAAGTCC
1 AAAAAAAAGTCC
20163 AAA
1 AAA
20166 TTACATTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.15, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAAAAAGTCC
Done.