Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015118.1 Kokia drynarioides strain JFW-HI SEQ_130162, 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: 36355
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 126 characters in sequence are not A, C, G, or T
Found at i:3991 original size:22 final size:23
Alignment explanation
Indices: 3966--4021 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 23
3956 CGATATGAGG
3966 AAAAATAGAAG-AAACATAATT-
1 AAAAATAGAAGAAAACATAATTA
* *
3987 AAAAATAAAAGAAAATATAATTAA
1 AAAAATAGAAGAAAACATAATT-A
4011 AAGAAATAGAA
1 AA-AAATAGAA
4022 AATAAAGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 10 0.36
22 9 0.32
24 2 0.07
25 7 0.25
ACGTcount: A:0.71, C:0.02, G:0.09, T:0.18
Consensus pattern (23 bp):
AAAAATAGAAGAAAACATAATTA
Found at i:4022 original size:22 final size:22
Alignment explanation
Indices: 3966--4025 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
3956 CGATATGAGG
* *
3966 AAAAATAGAAG-AAACATAATT
1 AAAAATAAAAGAAAATATAATT
3987 AAAAATAAAAGAAAATATAATT
1 AAAAATAAAAGAAAATATAATT
*
4009 AAAAGA-AATAGAAAATA
1 AAAA-ATAAAAGAAAATA
4026 AAGAAGTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.29
22 23 0.68
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.08, T:0.18
Consensus pattern (22 bp):
AAAAATAAAAGAAAATATAATT
Found at i:4027 original size:16 final size:16
Alignment explanation
Indices: 3986--4027 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3976 GAAACATAAT
3986 TAAAAATAAAAGAAAA
1 TAAAAATAAAAGAAAA
* *
4002 TATAATTAAAAG-AAA
1 TAAAAATAAAAGAAAA
4017 TAGAAAATAAA
1 TA-AAAATAAA
4028 GAAGTCAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (16 bp):
TAAAAATAAAAGAAAA
Found at i:9507 original size:28 final size:28
Alignment explanation
Indices: 9447--9507 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
9437 GATAAATAAG
**
9447 AATTT-TAAAAATTTAATTTATCTTTTT
1 AATTTATAAAAATTTAATTTATCTACTT
** *
9474 TTTTTATAGAAATTTAATTTATCTACTT
1 AATTTATAAAAATTTAATTTATCTACTT
9502 AATTTA
1 AATTTA
9508 CATTAAATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (28 bp):
AATTTATAAAAATTTAATTTATCTACTT
Found at i:26188 original size:28 final size:28
Alignment explanation
Indices: 26152--26208 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
26142 GGAATATGGC
26152 GAATGTTAAGTCTGTTAATACGCCTATG
1 GAATGTTAAGTCTGTTAATACGCCTATG
26180 GAATGTTAAGTCTGTTAATACGCCTATG
1 GAATGTTAAGTCTGTTAATACGCCTATG
26208 G
1 G
26209 TTAGTTCCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (28 bp):
GAATGTTAAGTCTGTTAATACGCCTATG
Done.