Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401338.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4475.0, 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, 752
Length: 1254
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.36
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:323 original size:170 final size:171
Alignment explanation
Indices: 1--364 Score: 389
Period size: 170 Copynumber: 2.1 Consensus size: 171
* * * **
1 AACATGAAGAAAAAGATATCTATTAGCAAGAAAAGTCCATTTATAGTCACCCATAGCTTCGAAAG
1 AACATGAAGAAAAAGATATCCATTAGCAAAAAAAGTCCATTTACAGTCACCCATAGCTTAAAAAG
* * * * * * *
66 CTTTATTACTCACTTTAAATGTTCTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACAT
66 CCTTATTACTCACTTTAAATATTCTTATAATCTCATAATTAATTTAAAATTGAATTTTGTCACAT
* * *
131 TTTGGGCTAAAAAAAAAATAATTTAATAT-T-TACCTTAGGA
131 TTTGGACTAAAAAAAAAATAATTTAA-ATGTCTACCTCAAGA
* *
171 AACGTGAAGAAAAAGATATCCATT-G-ATATAAAAAGTCCATTTACAGTCACCTAT-GCCTTAAA
1 AACATGAAGAAAAAGATATCCATTAGCA-A-AAAAAGTCCATTTACAGTCACCCATAG-CTTAAA
* * *
233 AAGCCTTATTACTCGC-TTAAATATTTTTATAATCTCATAATTAATTTAAAATTGAGTTTTGTCA
63 AAGCCTTATTACTCACTTTAAATATTCTTATAATCTCATAATTAATTTAAAATTGAATTTTGTCA
** ** * * * *
297 TGTTTTTTATTAAAACAGATAATAATTTAAATGTCTGCCTCAAGA
128 CATTTTGGACTAAAA-AAAAAATAATTTAAATGTCTACCTCAAGA
342 AACATGAAGAAAAAGATATCCAT
1 AACATGAAGAAAAAGATATCCAT
365 NNNNNNNNNN
Statistics
Matches: 159, Mismatches: 29, Indels: 11
0.80 0.15 0.06
Matches are distributed among these distances:
168 1 0.01
169 54 0.34
170 75 0.47
171 29 0.18
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (171 bp):
AACATGAAGAAAAAGATATCCATTAGCAAAAAAAGTCCATTTACAGTCACCCATAGCTTAAAAAG
CCTTATTACTCACTTTAAATATTCTTATAATCTCATAATTAATTTAAAATTGAATTTTGTCACAT
TTTGGACTAAAAAAAAAATAATTTAAATGTCTACCTCAAGA
Found at i:776 original size:170 final size:172
Alignment explanation
Indices: 444--782 Score: 377
Period size: 170 Copynumber: 2.0 Consensus size: 172
434 NNNNNNNNTA
* *
444 ATTGATTTTAAGTTGAATTTTTGTTTACATTTTTTATTAAAACATATAATAATTGAATGTCTACC
1 ATTGATTTTAAGTTGAATTTTTGTTTACATTTTTGATTAAAACATATAATAATGGAATGTCTACC
* * * * *
509 TCAAAAAAATGAAGAAAAAGATATCCACCAGTAAGAAAAACCCATTTATAGTCATTGATGTCTTC
66 TCAAAAAAATGAAGAAAAAGATATCCACCAGTAAGAAAAACCAATTTAAAGTCACTGATGCCTTA
574 GAATGCCTTATTACTCATTTCAAATATTTTTATAATCTCGTC
131 GAATGCCTTATTACTCATTTCAAATATTTTTATAATCTCGTC
* * * *
616 ATTGATTTTAAGTTGAA-TTTT-TTT-CATTTTTGGTTAAAACATATTATAATGGAATTTTTACC
1 ATTGATTTTAAGTTGAATTTTTGTTTACATTTTTGATTAAAACATATAATAATGGAATGTCTACC
* * ** * *** *
678 TTGAGAAACGTGAAGAAAAATATATCCATTGGTAAGAAAAGCCAATTTAAAGTCACCT-ATGCCT
66 -TCAAAAAAATGAAGAAAAAGATATCCACCAGTAAGAAAAACCAATTTAAAGTCA-CTGATGCCT
* * *
742 GTATAA-GCCTT-TTCACTCGCTTT-AAATGTTTTTATAATCTC
129 -TAGAATGCCTTATT-ACTC-ATTTCAAATATTTTTATAATCTC
783 ANNNNNNNNN
Statistics
Matches: 139, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
169 34 0.24
170 77 0.55
171 11 0.08
172 17 0.12
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (172 bp):
ATTGATTTTAAGTTGAATTTTTGTTTACATTTTTGATTAAAACATATAATAATGGAATGTCTACC
TCAAAAAAATGAAGAAAAAGATATCCACCAGTAAGAAAAACCAATTTAAAGTCACTGATGCCTTA
GAATGCCTTATTACTCATTTCAAATATTTTTATAATCTCGTC
Done.