Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004279.1 Kokia drynarioides strain JFW-HI SEQ_117570, 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: 50717
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:31196 original size:3 final size:3
Alignment explanation
Indices: 31188--31214 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
31178 GGGTATATCG
31188 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
31215 GGAGGAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:34894 original size:51 final size:51
Alignment explanation
Indices: 34829--35064 Score: 382
Period size: 51 Copynumber: 4.6 Consensus size: 51
34819 TGGTGACTCT
* *
34829 GTATATGTTCGGGATTCAATGTTTCCACCTTGCTGCTGTTGTTGTAGCTGA
1 GTATATGTTTGGGATTCAATGTTTCCACCTTGCTGCTGTTGTGGTAGCTGA
* * *
34880 GTATATGTTTGGGATTCAATGTTTCCACCTTGATGTTGTTGTGGCAGCTGA
1 GTATATGTTTGGGATTCAATGTTTCCACCTTGCTGCTGTTGTGGTAGCTGA
* *
34931 GTATATGTTTGGTATTCAACGTTTCCACCTTGCTGCTGTTGTGGTAGCTGA
1 GTATATGTTTGGGATTCAATGTTTCCACCTTGCTGCTGTTGTGGTAGCTGA
* *
34982 GTATATGTTTGGGATTCGATGTTACCACCTTGCTGCTGTTGTGGTAGCTGA
1 GTATATGTTTGGGATTCAATGTTTCCACCTTGCTGCTGTTGTGGTAGCTGA
*
35033 GTGTATGTTTGGGATTCAATGTTTCCACCTTG
1 GTATATGTTTGGGATTCAATGTTTCCACCTTG
35065 TTGGTTCGGC
Statistics
Matches: 168, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 168 1.00
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.41
Consensus pattern (51 bp):
GTATATGTTTGGGATTCAATGTTTCCACCTTGCTGCTGTTGTGGTAGCTGA
Found at i:35953 original size:2 final size:2
Alignment explanation
Indices: 35948--35986 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
35938 GCAGAACTGA
35948 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
35987 CTGCTATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40965 original size:3 final size:3
Alignment explanation
Indices: 40957--40981 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40947 AGACTACAAC
40957 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
40982 GTGGTGCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:41427 original size:23 final size:23
Alignment explanation
Indices: 41407--41450 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
41397 TCTAAAAAGT
41407 ATAAAAATTAAATTCTTAAAAAAA
1 ATAAAAATTAAATTCTT-AAAAAA
41431 ATAAAAATTAAATT-TTAAAA
1 ATAAAAATTAAATTCTTAAAA
41451 TTTTAAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 2 0.10
24 14 0.70
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
ATAAAAATTAAATTCTTAAAAAA
Found at i:44217 original size:18 final size:18
Alignment explanation
Indices: 44181--44215 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
44171 TTCATATCAT
*
44181 TATTTAAAAATAATAAAA
1 TATTTAAAAATAAAAAAA
44199 TATTT-AAAATAAAAAAA
1 TATTTAAAAATAAAAAAA
44216 ATTACTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TATTTAAAAATAAAAAAA
Found at i:44597 original size:19 final size:19
Alignment explanation
Indices: 44573--44610 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
44563 GAAATTATAT
* *
44573 TATTTTATATTTATATTTA
1 TATTTTATAATTAAATTTA
44592 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
44611 AAATAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTTTATAATTAAATTTA
Found at i:45823 original size:19 final size:19
Alignment explanation
Indices: 45775--45812 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
45765 ATGAGGAATA
45775 GATCTCACAAGTGGTTAGC
1 GATCTCACAAGTGGTTAGC
45794 GATCTCACAAGTGGTTAGC
1 GATCTCACAAGTGGTTAGC
45813 TTTTCCACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (19 bp):
GATCTCACAAGTGGTTAGC
Done.