Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010945.1 Kokia drynarioides strain JFW-HI SEQ_125913, 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: 14944
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:795 original size:36 final size:35
Alignment explanation
Indices: 734--810 Score: 118
Period size: 36 Copynumber: 2.2 Consensus size: 35
724 TTGTGTGATC
* * *
734 CAAATTCTAAGAGATTGCTTGCAAGTTAAGTTAAA
1 CAAAATCTAAGAGATTACTTGCAAGTCAAGTTAAA
769 CAAAATCTAAGAGAATTACTTGCAAGTCAAGTTAAA
1 CAAAATCTAAGAG-ATTACTTGCAAGTCAAGTTAAA
805 CAAAAT
1 CAAAAT
811 ATATTATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 12 0.32
36 26 0.68
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.27
Consensus pattern (35 bp):
CAAAATCTAAGAGATTACTTGCAAGTCAAGTTAAA
Found at i:856 original size:24 final size:24
Alignment explanation
Indices: 829--879 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
819 TTTCTAGAAG
* *
829 ATTTAGTAGTATAATATATTTAGC
1 ATTTAGTAGCATAAAATATTTAGC
* *
853 ATTTATTAGCATAAAATATTTTGC
1 ATTTAGTAGCATAAAATATTTAGC
877 ATT
1 ATT
880 GATTAGAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (24 bp):
ATTTAGTAGCATAAAATATTTAGC
Found at i:884 original size:24 final size:24
Alignment explanation
Indices: 839--885 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
829 ATTTAGTAGT
* *
839 ATAATATATTTAGCATTTATTAGC
1 ATAAAATATTTAGCATTGATTAGC
*
863 ATAAAATATTTTGCATTGATTAG
1 ATAAAATATTTAGCATTGATTAG
886 AATTAGGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (24 bp):
ATAAAATATTTAGCATTGATTAGC
Found at i:7530 original size:15 final size:16
Alignment explanation
Indices: 7504--7533 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
7494 TGAGGAAAAA
7504 TAAAACAAAATAGAAT
1 TAAAACAAAATAGAAT
7520 TAAAA-AAAATAGAA
1 TAAAACAAAATAGAA
7534 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (16 bp):
TAAAACAAAATAGAAT
Found at i:8323 original size:14 final size:14
Alignment explanation
Indices: 8306--8346 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
8296 TTTAAACTCT
8306 AAAAGATAAATACA
1 AAAAGATAAATACA
8320 AAAAGAT-AA-ACA
1 AAAAGATAAATACA
*
8332 TAAA-ATAAATACA
1 AAAAGATAAATACA
8345 AA
1 AA
8347 TTTAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 2 0.09
12 8 0.35
13 6 0.26
14 7 0.30
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.15
Consensus pattern (14 bp):
AAAAGATAAATACA
Found at i:8359 original size:19 final size:19
Alignment explanation
Indices: 8335--8379 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
8325 ATAAACATAA
8335 AATAAATACAAAT-TTAAAT
1 AATAAATA-AAATCTTAAAT
*
8354 AATAAATAATATCTTAAAT
1 AATAAATAAAATCTTAAAT
*
8373 ATTAAAT
1 AATAAAT
8380 CCTAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AATAAATAAAATCTTAAAT
Found at i:10433 original size:21 final size:21
Alignment explanation
Indices: 10409--10459 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
10399 AAGATAGTTT
*
10409 TACCGATACAAGTGA-GACTTC
1 TACCGATACAAGTCATG-CTTC
* *
10430 TACCAAAACAAGTCATGCTTC
1 TACCGATACAAGTCATGCTTC
*
10451 TACTGATAC
1 TACCGATAC
10460 TAAAAACTCC
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.25
Consensus pattern (21 bp):
TACCGATACAAGTCATGCTTC
Found at i:12237 original size:12 final size:13
Alignment explanation
Indices: 12198--12239 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
12188 TTTCTTGGAC
12198 ATAAAATA-AATAA
1 ATAAAATAGAA-AA
12211 ATAAAATAGAAAA
1 ATAAAATAGAAAA
*
12224 ATAAAA-ATAAAA
1 ATAAAATAGAAAA
12236 ATAA
1 ATAA
12240 TTGGGTTGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 9 0.33
13 16 0.59
14 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (13 bp):
ATAAAATAGAAAA
Done.