Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006607.1 Kokia drynarioides strain JFW-HI SEQ_121196, 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: 9697
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Warning! 42 characters in sequence are not A, C, G, or T
Found at i:3594 original size:16 final size:17
Alignment explanation
Indices: 3562--3598 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
3552 GTTTAAAAGT
3562 TTTAATTAATTAAATTTA
1 TTTAATTAA-TAAATTTA
3580 TTTAATTAA-AAATTTA
1 TTTAATTAATAAATTTA
3596 TTT
1 TTT
3599 TCATCCTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATTAATAAATTTA
Found at i:4036 original size:16 final size:16
Alignment explanation
Indices: 4015--4057 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 16
4005 ATATAAAATT
4015 ATTAAATTATTTTAAA
1 ATTAAATTATTTTAAA
4031 ATTAAA-T-TTTTAAA
1 ATTAAATTATTTTAAA
4045 ATATAAAATTATT
1 AT-T-AAATTATT
4058 AAAATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 9 0.39
15 2 0.09
16 9 0.39
17 1 0.04
18 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAAATTATTTTAAA
Found at i:4046 original size:25 final size:25
Alignment explanation
Indices: 3983--4044 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
3973 CAAATGATTT
* *
3983 TAAAATTATTAATTTTTTTTAAATA
1 TAAAATTATTAAATTATTTTAAATA
4008 TAAAATTATTAAATTATTTTAAA-A
1 TAAAATTATTAAATTATTTTAAATA
* *
4032 TTAAATTTTTAAA
1 TAAAATTATTAAA
4045 ATATAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 12 0.36
25 21 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TAAAATTATTAAATTATTTTAAATA
Found at i:4049 original size:40 final size:43
Alignment explanation
Indices: 3974--4068 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 43
3964 CCACATTAGC
* *
3974 AAATGATTTTAAAATTATTAATTTTTTTTAAATATAAAATTATT-
1 AAATTATTTTAAAATTA-TAA-TTTTTTAAAATATAAAATTATTA
4018 AAATTATTTTAAAATTA-AA-TTTTTAAAATATAAAATTATTA
1 AAATTATTTTAAAATTATAATTTTTTAAAATATAAAATTATTA
4059 AAATTATTTT
1 AAATTATTTT
4069 TATATTTTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
40 20 0.42
41 10 0.21
42 2 0.04
44 16 0.33
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (43 bp):
AAATTATTTTAAAATTATAATTTTTTAAAATATAAAATTATTA
Found at i:4059 original size:16 final size:14
Alignment explanation
Indices: 4015--4064 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 14
4005 ATATAAAATT
4015 ATTAAATTATTTTAAA
1 ATTAAATTA--TTAAA
*
4031 ATTAAATTTTTAAA
1 ATTAAATTATTAAA
4045 ATATAAAATTATTAAA
1 AT-T-AAATTATTAAA
4061 ATTA
1 ATTA
4065 TTTTTATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 8 0.27
15 2 0.07
16 20 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTAAATTATTAAA
Found at i:4998 original size:9 final size:9
Alignment explanation
Indices: 4984--5021 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
4974 AAATTAATAA
4984 TTAATAATT
1 TTAATAATT
4993 TTAATAATT
1 TTAATAATT
5002 TTAATAATT
1 TTAATAATT
5011 TT-AT-ATT
1 TTAATAATT
5018 TTAA
1 TTAA
5022 AAAAATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 5 0.18
8 3 0.11
9 20 0.71
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTAATAATT
Found at i:9506 original size:6 final size:6
Alignment explanation
Indices: 9481--9519 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
9471 ACAATTCATA
* * *
9481 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
9520 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Done.