Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398697.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1983.0, 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: 2028
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.26
Warning! 678 characters in sequence are not A, C, G, or T
Found at i:538 original size:171 final size:170
Alignment explanation
Indices: 126--544 Score: 425
Period size: 170 Copynumber: 2.5 Consensus size: 170
116 NNNNNNNNNN
* *
126 TTTACATTTTTCATTAAAACAGGC-TATAATTGAATGT-TGACCCTGAGAAATGCGAAGAAAAAA
1 TTTACATTTTTCATTAAAACA-GCATATAATTGAATGTCTG-CCTTGAGAAATGTGAAGAAAAAA
* * * * * *
189 GCATTTATTGGCAAGAAAAGTCTATTTATAGCCTCGCATTCCTTCAAAAGCCTTTTGACTCGCTT
64 GCATTCATTAGCAAGAAAAGTCCATCTATAGCCGCCCATTCCTTCAAAAGCCTTTTGACTCGCTT
** ****
254 TAAATGGTTTATAATCTAATATTTGATTTTAAGTTGAANNNN
129 TAAATGGTTTATAATCTAATAACTGATTTTAAGTTGAATTGT
****** * * ** ** ** * *
296 NNNNNNTTTTTGATTAAAACAGACA-ATAAATGAATGTCTATCTCAAGAAACATAAAGGAAAAAG
1 TTTACATTTTTCATTAAAACAG-CATATAATTGAATGTCTGCCTTGAGAAATGTGAAGAAAAAAG
* * *
360 TATTCATTATCAAGAAAAGTCCATCTATAGTCGCCCATTCCTTCAAAAGCCTTATT-ACTCAG-T
65 CATTCATTAGCAAGAAAAGTCCATCTATAGCCGCCCATTCCTTCAAAAGCCTT-TTGACTC-GCT
*
423 TTAAATGGTTTTATAATGTAATAACTGATTTTAAGTTGAATTGT
128 TTAAATGG-TTTATAATCTAATAACTGATTTTAAGTTGAATTGT
*
467 TTTACATTTTTTATTAAAACAGCATATAATTGAATGTCTGCCTTGAGAAATGTGAAGAAAAAAGC
1 TTTACATTTTTCATTAAAACAGCATATAATTGAATGTCTGCCTTGAGAAATGTGAAGAAAAAAGC
*
532 ATTCATTGGCAAG
66 ATTCATTAGCAAG
545 NNNNNNNNNN
Statistics
Matches: 189, Mismatches: 53, Indels: 13
0.74 0.21 0.05
Matches are distributed among these distances:
169 1 0.01
170 100 0.53
171 88 0.47
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.34
Consensus pattern (170 bp):
TTTACATTTTTCATTAAAACAGCATATAATTGAATGTCTGCCTTGAGAAATGTGAAGAAAAAAGC
ATTCATTAGCAAGAAAAGTCCATCTATAGCCGCCCATTCCTTCAAAAGCCTTTTGACTCGCTTTA
AATGGTTTATAATCTAATAACTGATTTTAAGTTGAATTGT
Done.