Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001983.1 Kokia drynarioides strain JFW-HI SEQ_113835, 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: 8437
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:54 original size:6 final size:6
Alignment explanation
Indices: 43--81 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
33 TGATCAAAAT
* * *
43 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
82 TATAAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:276 original size:37 final size:38
Alignment explanation
Indices: 209--287 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 38
199 ATGTCATTAT
* *
209 TTTACTTCGGATAGATTCGATGAGGTACTAGGTACCAC
1 TTTACTTCGGATAGATCCGATGAGGCACTAGGTACCAC
* **
247 TTTACTTCGGCTAGA-CCGATGAGGCACTAGGTGTCAC
1 TTTACTTCGGATAGATCCGATGAGGCACTAGGTACCAC
284 TTTA
1 TTTA
288 TTGCTTCGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 22 0.61
38 14 0.39
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (38 bp):
TTTACTTCGGATAGATCCGATGAGGCACTAGGTACCAC
Found at i:3183 original size:20 final size:20
Alignment explanation
Indices: 3157--3206 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3147 AAAAGAGAAT
*
3157 AAAAATTAAAGGAA-AAAAA
1 AAAAATTAAAAGAATAAAAA
*
3176 AGAAAATTAAAAGAATATAAA
1 A-AAAATTAAAAGAATAAAAA
3197 AAAAATTAAA
1 AAAAATTAAA
3207 TTGATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 1 0.04
20 21 0.78
21 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (20 bp):
AAAAATTAAAAGAATAAAAA
Found at i:3196 original size:10 final size:11
Alignment explanation
Indices: 3158--3206 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
3148 AAAGAGAATA
*
3158 AAAATTAAAGG
1 AAAATTAAAAG
3169 AAAA--AAAAG
1 AAAATTAAAAG
3178 AAAATTAAAAG
1 AAAATTAAAAG
*
3189 AATA-TAAAA-
1 AAAATTAAAAG
3198 AAAATTAAA
1 AAAATTAAA
3207 TTGATTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
9 11 0.34
10 9 0.28
11 12 0.38
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAATTAAAAG
Found at i:3579 original size:22 final size:22
Alignment explanation
Indices: 3553--3598 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
3543 TTATTGTTAC
3553 ATAAAATTTTAATTTTGAATTA
1 ATAAAATTTTAATTTTGAATTA
3575 ATAAAATTTTAATTTTGAATTA
1 ATAAAATTTTAATTTTGAATTA
3597 AT
1 AT
3599 TATGTAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
ATAAAATTTTAATTTTGAATTA
Done.