Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013492.1 Kokia drynarioides strain JFW-HI SEQ_128518, 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: 12626
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2366 original size:17 final size:17
Alignment explanation
Indices: 2346--2378 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2336 TTAAAAATGG
2346 TAAA-GATATAAATTATT
1 TAAATGATA-AAATTATT
2363 TAAATGATAAAATTAT
1 TAAATGATAAAATTAT
2379 ATTTTTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
TAAATGATAAAATTATT
Found at i:3577 original size:23 final size:23
Alignment explanation
Indices: 3551--3620 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
3541 TTTATTTAAC
* *
3551 TTAATCGAACATGTTTACGAATA
1 TTAATCGAACATGTTCACGAACA
* *
3574 TTAAACGAACATGTTCATGAACA
1 TTAATCGAACATGTTCACGAACA
*
3597 TATAATTGAACATGTTCACGAACA
1 T-TAATCGAACATGTTCACGAACA
3621 ATGTTAATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:3650 original size:4 final size:4
Alignment explanation
Indices: 3641--3665 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3631 ATAATAAACA
3641 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
3666 CGCACATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:5938 original size:7 final size:7
Alignment explanation
Indices: 5926--5986 Score: 56
Period size: 7 Copynumber: 8.7 Consensus size: 7
5916 AAATAAACCC
5926 AATTTTA
1 AATTTTA
5933 AATTTTAA
1 AATTTT-A
5941 AATTTTA
1 AATTTTA
*
5948 AATTATTTT
1 AA-T-TTTA
*
5957 AAGTTTA
1 AATTTTA
5964 AA-TTT-
1 AATTTTA
5969 -ATTTTA
1 AATTTTA
5975 AATTTTA
1 AATTTTA
5982 AATTT
1 AATTT
5987 AAGATTTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 3 0.07
7 25 0.56
8 8 0.18
9 5 0.11
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (7 bp):
AATTTTA
Found at i:5957 original size:18 final size:17
Alignment explanation
Indices: 5926--5985 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
5916 AAATAAACCC
*
5926 AATTTTAAA-T-TTTAA
1 AATTTTAAATTATTTTA
5941 AATTTTAAATTATTTT-
1 AATTTTAAATTATTTTA
*
5957 AAGTTTAAATTTATTTTA
1 AATTTTAAA-TTATTTTA
5975 AATTTTAAATT
1 AATTTTAAATT
5986 TAAGATTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
15 9 0.24
16 9 0.24
17 12 0.32
18 8 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
AATTTTAAATTATTTTA
Found at i:5986 original size:18 final size:18
Alignment explanation
Indices: 5934--5987 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
5924 CCAATTTTAA
5934 ATTTTAAAATTTTAAA-TT
1 ATTTT-AAATTTTAAATTT
*
5952 ATTTT-AAGTTTAAATTT
1 ATTTTAAATTTTAAATTT
5969 ATTTTAAATTTTAAATTT
1 ATTTTAAATTTTAAATTT
5987 A
1 A
5988 AGATTTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 8 0.25
17 7 0.22
18 17 0.53
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATTTTAAATTTTAAATTT
Found at i:5999 original size:24 final size:23
Alignment explanation
Indices: 5926--6000 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 23
5916 AAATAAACCC
5926 AATTTTAAATTTTAAAATTTTAAATT-
1 AATTTTAAA-TTT-AAA-TTT-AATTA
* *
5952 -ATTTTAAGTTTAAATTTATTTTA
1 AATTTTAAATTTAAATTTA-ATTA
5975 AATTTTAAATTTAAGATTTAATTA
1 AATTTTAAATTTAA-ATTTAATTA
5999 AA
1 AA
6001 AGTCCAAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
21 1 0.02
22 5 0.12
23 3 0.07
24 20 0.49
25 12 0.29
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (23 bp):
AATTTTAAATTTAAATTTAATTA
Done.