Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006365.1 Kokia drynarioides strain JFW-HI SEQ_120941, 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: 5021
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:957 original size:91 final size:91
Alignment explanation
Indices: 840--1023 Score: 352
Period size: 92 Copynumber: 2.0 Consensus size: 91
830 AAAATAATAT
840 AAGGAAATGGAGTTTCTGAAAAAAAAAAGAGCTAATGATATG-TTTTTTTTTTTCATATTACCGC
1 AAGGAAATGGAGTTTCTGAAAAAAAAAAGAGCTAATGATATGTTTTTTTTTTTTCATATTACCGC
904 ATTAATACAGAACAAACGTTTTGAAG
66 ATTAATACAGAACAAACGTTTTGAAG
930 NAAGGAAATGGAGTTTCTGAAAAAAAAAAGAGCTAATGATATGTTTTTTTTTTTTCATATTACCG
1 -AAGGAAATGGAGTTTCTGAAAAAAAAAAGAGCTAATGATATGTTTTTTTTTTTTCATATTACCG
995 CATTAATACAGAACAAACGTTTTGAAG
65 CATTAATACAGAACAAACGTTTTGAAG
1022 AA
1 AA
1024 ACCCCTTAAA
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
91 44 0.48
92 48 0.52
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.33
Consensus pattern (91 bp):
AAGGAAATGGAGTTTCTGAAAAAAAAAAGAGCTAATGATATGTTTTTTTTTTTTCATATTACCGC
ATTAATACAGAACAAACGTTTTGAAG
Found at i:1235 original size:12 final size:12
Alignment explanation
Indices: 1184--1238 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
1174 GTAAAAAAAT
*
1184 ACCAAAACAGCA
1 ACCAAAACAACA
*
1196 ACCAAAACAATA
1 ACCAAAACAACA
* *
1208 A-AAAAATAAC-
1 ACCAAAACAACA
*
1218 AGCAAAACAACA
1 ACCAAAACAACA
1230 ACCAAAACA
1 ACCAAAACA
1239 GTAAAAAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
10 1 0.03
11 13 0.39
12 19 0.58
ACGTcount: A:0.67, C:0.25, G:0.04, T:0.04
Consensus pattern (12 bp):
ACCAAAACAACA
Done.