Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401341.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4478.0, 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, 766
Length: 1277
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.33
Warning! 142 characters in sequence are not A, C, G, or T
Found at i:242 original size:28 final size:28
Alignment explanation
Indices: 184--371 Score: 150
Period size: 28 Copynumber: 6.4 Consensus size: 28
174 ATTAAGATAA
* * *
184 AAATATGTTATCCTGTCTAAATTGAGAC
1 AAATATGTTTTCTTGTCTAAATTAAGAC
* *
212 AAATATGTTTTCTTATCTAAATTAAGGCAA
1 AAATATGTTTTCTTGTCTAAATTAA-G-AC
242 AACATAT-TTTTCTTGTCTTAAATTAAGAC
1 AA-ATATGTTTTCTTGTC-TAAATTAAGAC
271 TAACATAT-TTTT-TTGTCTAAATTAAGACC
1 -AA-ATATGTTTTCTTGTCTAAATTAAGA-C
* *
300 AAACAAT-TTTTCTTCTCTAAATTAAGTCAAAGAC
1 AAA-TATGTTTTCTTGTCTAAA-T---T--AAGAC
*
334 AAACATGTTTTCTTGTCTAAATTAAGAC
1 AAATATGTTTTCTTGTCTAAATTAAGAC
362 AAATATGTTT
1 AAATATGTTT
372 AAGCTGTCAT
Statistics
Matches: 133, Mismatches: 12, Indels: 30
0.76 0.07 0.17
Matches are distributed among these distances:
27 1 0.01
28 53 0.40
29 16 0.12
30 26 0.20
31 12 0.09
33 4 0.03
34 17 0.13
35 4 0.03
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.40
Consensus pattern (28 bp):
AAATATGTTTTCTTGTCTAAATTAAGAC
Found at i:304 original size:29 final size:29
Alignment explanation
Indices: 197--361 Score: 129
Period size: 29 Copynumber: 5.5 Consensus size: 29
187 TATGTTATCC
* * * *
197 TGTCTAAATTGAGA-CAAATATGTTTTCT
1 TGTCTAAATTAAGACCAAACATATTTTTT
* * *
225 TATCTAAATTAAGGCAAAACATATTTTTCT
1 TGTCTAAATTAAGACCAAACATATTTTT-T
*
255 TGTCTTAAATTAAGA-CTAACATATTTTTT
1 TGTC-TAAATTAAGACCAAACATATTTTTT
284 TGTCTAAATTAAGACCAAACA-ATTTTTCT
1 TGTCTAAATTAAGACCAAACATATTTTT-T
* * * *
313 TCTCTAAATTAAGTCAAAGACAAACATGTTTTCT
1 TGTCTAAATTAAG----A-CCAAACATATTTTTT
347 TGTCTAAATTAAGAC
1 TGTCTAAATTAAGAC
362 AAATATGTTT
Statistics
Matches: 108, Mismatches: 18, Indels: 21
0.73 0.12 0.14
Matches are distributed among these distances:
28 27 0.25
29 32 0.30
30 16 0.15
31 9 0.08
33 1 0.01
34 19 0.18
35 4 0.04
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (29 bp):
TGTCTAAATTAAGACCAAACATATTTTTT
Found at i:338 original size:34 final size:35
Alignment explanation
Indices: 294--364 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 35
284 TGTCTAAATT
*
294 AAGACCAAACAAT-TTTTCTTCTCTAAATTAAGTCA
1 AAGACCAAAC-ATGTTTTCTTCTCTAAATTAAGACA
*
329 AAGA-CAAACATGTTTTCTTGTCTAAATTAAGACA
1 AAGACCAAACATGTTTTCTTCTCTAAATTAAGACA
363 AA
1 AA
365 TATGTTTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 2 0.06
34 27 0.82
35 4 0.12
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.32
Consensus pattern (35 bp):
AAGACCAAACATGTTTTCTTCTCTAAATTAAGACA
Found at i:351 original size:63 final size:59
Alignment explanation
Indices: 201--364 Score: 179
Period size: 59 Copynumber: 2.7 Consensus size: 59
191 TTATCCTGTC
* * * * *
201 TAAATTGAGACAAATATGTTTTCTTATCTAAATTAAGGCAAAACATATTTTTCTTGTCT
1 TAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACAAAACATATTTTTCTTCTCT
* * * *
260 TAAATTAAGACTAACATATTTTTTTGTCTAAATTAAGACCAAACA-ATTTTTCTTCTC-
1 TAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACAAAACATATTTTTCTTCTCT
317 TAAATTAAGTCAAAGACAAACATGTTTTCTTGTCTAAATTAAGACAAA
1 TAAA-T---T--AAGACAAACATGTTTTCTTGTCTAAATTAAGACAAA
365 TATGTTTAAG
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
57 4 0.05
58 12 0.14
59 37 0.43
61 1 0.01
63 32 0.37
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (59 bp):
TAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACAAAACATATTTTTCTTCTCT
Done.