Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005790.1 Kokia drynarioides strain JFW-HI SEQ_120062, 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: 24783
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:7965 original size:26 final size:25
Alignment explanation
Indices: 7926--7985 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
7916 TTTTTTTACC
*
7926 CAAATAATATAAAAATA-ATTAATTA
1 CAAA-AATATAAAAACATATTAATTA
7951 TCAAAAATATGAAAAACATATTAATTA
1 -CAAAAATAT-AAAAACATATTAATTA
*
7978 CGAAAATA
1 CAAAAATA
7986 AACATTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 5 0.17
26 17 0.57
27 8 0.27
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (25 bp):
CAAAAATATAAAAACATATTAATTA
Found at i:9350 original size:25 final size:26
Alignment explanation
Indices: 9304--9369 Score: 116
Period size: 26 Copynumber: 2.5 Consensus size: 26
9294 ATTTAAACAA
9304 AAAAATTTTATTTTTCGAAAAATAAAT
1 AAAAA-TTTATTTTTCGAAAAATAAAT
9331 AAAAATTTATTTTTCGAAAAATAAAT
1 AAAAATTTATTTTTCGAAAAATAAAT
9357 -AAAATTTATTTTT
1 AAAAATTTATTTTT
9370 AGTTAGAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 13 0.33
26 21 0.54
27 5 0.13
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (26 bp):
AAAAATTTATTTTTCGAAAAATAAAT
Found at i:10313 original size:3 final size:3
Alignment explanation
Indices: 10305--10330 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10295 TATACAAGTT
10305 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
10331 CCTCAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:10457 original size:28 final size:29
Alignment explanation
Indices: 10397--10458 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
10387 AAAGAGTTTT
* *
10397 TTTTTTTTCATAATTTTTGGAATTATAAG
1 TTTTATTTCATAATTTTTGAAATTATAAG
*
10426 TTTTATTT-ATAATTTTTTGAAATTTTAA-
1 TTTTATTTCATAA-TTTTTGAAATTATAAG
10454 TTTTA
1 TTTTA
10459 ACATTTGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 9 0.31
29 20 0.69
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (29 bp):
TTTTATTTCATAATTTTTGAAATTATAAG
Found at i:19236 original size:33 final size:34
Alignment explanation
Indices: 19195--19275 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 34
19185 TGTTTTTATG
**
19195 TTTAAATCGATTGTCATGTT-GAAATACTGTTTCT
1 TTTAAATCGATTGTCATGTTAG-AATACTCCTTCT
* *
19229 TTT-AATCGATTATTATGTTAGAATACTCCTTCT
1 TTTAAATCGATTGTCATGTTAGAATACTCCTTCT
*
19262 TTTAAATCAATTGT
1 TTTAAATCGATTGT
19276 TTATATCCCT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
33 27 0.69
34 12 0.31
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.48
Consensus pattern (34 bp):
TTTAAATCGATTGTCATGTTAGAATACTCCTTCT
Found at i:20191 original size:2 final size:2
Alignment explanation
Indices: 20184--20209 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20174 CTATGTCTCA
20184 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
20210 TAAAGCATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.