Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398603.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1893.0, 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, 1000
Length: 5707
ACGTcount: A:0.26, C:0.08, G:0.09, T:0.25
Warning! 1808 characters in sequence are not A, C, G, or T
Found at i:2078 original size:164 final size:168
Alignment explanation
Indices: 1772--2089 Score: 392
Period size: 164 Copynumber: 1.9 Consensus size: 168
1762 NNNNNNNNNN
* *
1772 TTTTCTTTATCTTTTTTGAGGCAAACATTCAATTATAATATATTTTAATAAAAAATATATAAAAA
1 TTTTCTTCATCTTTCTTGAGGCAAACATTCAATTATAATATATTTTAAT-AAAAATATATAAAAA
* * * ****
1837 TTTAAATTAAAATCAATTATGAGGTTGTAACATCATTTAAAGCGAGTAATAAAGCTTTTGANNNN
65 --TAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAACGAGTAATAAAGCTTTTGAAGGC
******
1902 NNNNNNGACTATAAATGGACTTTTCCTGCAAACGGATATGT
128 ATTGGTGACTATAAATGGACTTTTCCTGCAAACGGATATGT
* * * * *
1943 TTTTCTTCATGTTTCTTGAGTCAAACATTCGATTATACTCTATTTTAAT-AAAA-A-ATAAAAA-
1 TTTTCTTCATCTTTCTTGAGGCAAACATTCAATTATAATATATTTTAATAAAAATATATAAAAAT
*
2004 AAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAACGAGTACTAAAGCTTTTGAAGGCATT
66 AAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAACGAGTAATAAAGCTTTTGAAGGCATT
2069 GGTGACTATAAATGGACTTTT
131 GGTGACTATAAATGGACTTTT
2090 TTTGCTAATG
Statistics
Matches: 126, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
164 72 0.57
167 7 0.06
168 1 0.01
169 4 0.03
171 42 0.33
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.37
Consensus pattern (168 bp):
TTTTCTTCATCTTTCTTGAGGCAAACATTCAATTATAATATATTTTAATAAAAATATATAAAAAT
AAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAACGAGTAATAAAGCTTTTGAAGGCATT
GGTGACTATAAATGGACTTTTCCTGCAAACGGATATGT
Found at i:4289 original size:171 final size:170
Alignment explanation
Indices: 4098--4491 Score: 396
Period size: 171 Copynumber: 2.3 Consensus size: 170
4088 NNNNNNNNNN
*
4098 AAAATATAAAAAAATTTAACTTAAAATTAATTATGAGGTTATAAAAACATTTAAAGCAAGTCATA
1 AAAATAT-AAAAAATTTAACTTAAAATTAATTATGAGGTTATAAAAACATTTAAAGCAAGTAATA
* ** ** * *
4163 AGGCTTTCGAAGGCATGGGTGACTACAAAAAGACTTCTGCCACCGATGGATATCATTTTCTTTAC
65 ACGCTTTCGAAAACATAAGTGACTACAAAAAGACTTCTGCCACCAATGGATATCATTTTCTTCAC
* * * * *
4228 GTTTTTTAAGGTAAACATTCAATTATAATCTGTTTTAAGAA
130 GTTTCTCAAGGAAAACATTAAATTATAATATGTTTTAAGAA
* ********** *
4269 AAAATATAAAAAAGTTTAACTTAAAACTAATT-NNNNNNNNNNAAAACTATTTAAAGCGAGTAAT
1 AAAATATAAAAAA-TTTAACTTAAAATTAATTATGAGGTTATAAAAAC-ATTTAAAGCAAGTAAT
** * **** *
4333 AACGCTTTCGAAAACATAAGTGACTACAAATGGACTTGTTTGGCCAATGGATATCTTTTTCTTCA
64 AACGCTTTCGAAAACATAAGTGACTACAAAAAGACTTCTGCCACCAATGGATATCATTTTCTTCA
* *
4398 CGTTTCTCGAGGAAAACATTAAATTATAATATGTTTTAATAA
129 CGTTTCTCAAGGAAAACATTAAATTATAATATGTTTTAAGAA
* * *
4440 AAATATATAAAAAA-TTAAATTAAAATCAATTATGAGGTTATAAAATCATTTA
1 AAA-ATATAAAAAATTTAACTTAAAATTAATTATGAGGTTATAAAAACATTTA
4492 NNNNNNNNNN
Statistics
Matches: 170, Mismatches: 49, Indels: 9
0.75 0.21 0.04
Matches are distributed among these distances:
170 30 0.18
171 130 0.76
172 10 0.06
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.33
Consensus pattern (170 bp):
AAAATATAAAAAATTTAACTTAAAATTAATTATGAGGTTATAAAAACATTTAAAGCAAGTAATAA
CGCTTTCGAAAACATAAGTGACTACAAAAAGACTTCTGCCACCAATGGATATCATTTTCTTCACG
TTTCTCAAGGAAAACATTAAATTATAATATGTTTTAAGAA
Done.