Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012353.1 Kokia drynarioides strain JFW-HI SEQ_127355, 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: 6942
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:3519 original size:26 final size:25
Alignment explanation
Indices: 3490--3540 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
3480 ATTTTATATC
3490 CATT-TTTTCCTTATGTTCTTTTGAAG
1 CATTCTTTT-CTTAT-TTCTTTTGAAG
*
3516 CATTCTTTTTTTATTTCTTTTGAAG
1 CATTCTTTTCTTATTTCTTTTGAAG
3541 TCTTTACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 8 0.35
27 4 0.17
ACGTcount: A:0.16, C:0.14, G:0.10, T:0.61
Consensus pattern (25 bp):
CATTCTTTTCTTATTTCTTTTGAAG
Found at i:3537 original size:25 final size:28
Alignment explanation
Indices: 3500--3554 Score: 80
Period size: 25 Copynumber: 2.1 Consensus size: 28
3490 CATTTTTTCC
3500 TTATGTTCTTTTGAAG-CATT-CTTTTT
1 TTATGTTCTTTTGAAGTCATTACTTTTT
*
3526 TTAT-TTCTTTTGAAGTCTTTACTTTTT
1 TTATGTTCTTTTGAAGTCATTACTTTTT
3553 TT
1 TT
3555 TAACATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 11 0.42
26 7 0.27
27 8 0.31
ACGTcount: A:0.15, C:0.11, G:0.09, T:0.65
Consensus pattern (28 bp):
TTATGTTCTTTTGAAGTCATTACTTTTT
Found at i:5180 original size:26 final size:25
Alignment explanation
Indices: 5151--5201 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
5141 ATTTTATATC
5151 CATT-TTTTCCTTATGTTCTTTTGAAG
1 CATTCTTTT-CTTAT-TTCTTTTGAAG
*
5177 CATTCTTTTTTTATTTCTTTTGAAG
1 CATTCTTTTCTTATTTCTTTTGAAG
5202 TCTTTACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 8 0.35
27 4 0.17
ACGTcount: A:0.16, C:0.14, G:0.10, T:0.61
Consensus pattern (25 bp):
CATTCTTTTCTTATTTCTTTTGAAG
Found at i:5198 original size:25 final size:28
Alignment explanation
Indices: 5161--5215 Score: 80
Period size: 25 Copynumber: 2.1 Consensus size: 28
5151 CATTTTTTCC
5161 TTATGTTCTTTTGAAG-CATT-CTTTTT
1 TTATGTTCTTTTGAAGTCATTACTTTTT
*
5187 TTAT-TTCTTTTGAAGTCTTTACTTTTT
1 TTATGTTCTTTTGAAGTCATTACTTTTT
5214 TT
1 TT
5216 TAACATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 11 0.42
26 7 0.27
27 8 0.31
ACGTcount: A:0.15, C:0.11, G:0.09, T:0.65
Consensus pattern (28 bp):
TTATGTTCTTTTGAAGTCATTACTTTTT
Done.