Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399733.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2977.0, 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: 2152
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.26
Warning! 639 characters in sequence are not A, C, G, or T
Found at i:904 original size:170 final size:171
Alignment explanation
Indices: 587--994 Score: 459
Period size: 170 Copynumber: 2.4 Consensus size: 171
577 GGAAATGTGT
* * * * **
587 AGAAAAAGCTTATTCGTTGAGAACAAAAGTCCATTTATAGCCACCCATTCTTTCAAAATCCTTAT
1 AGAAAAAGC-TATTCATTGAGAAAAAAAGTCCATTTATAGTCAACCATTCTTTCAAAAAGCTTAT
* *** * * * *
652 TACTCGTCTTAGGTGGTTTAATAATCTCATAATTGATTTTAAGTTTAATGTTTTTATATTTTTAG
65 TACTCCTCTTAAACGGTTTAATAATCTCATAATTGACTTTAAGGTGAATGTTTTTACATTTTTAG
* * * * *
717 TTAAAACAGTCTATAATTAAATGCTTGCCTCGAGAAACATGA
130 TTAAAACAATCTATAATTAAATACATACCTCAAGAAACATGA
759 A-AAAAAGCTATTCATTGAGAAAAAAAGTCCATTTATAGTCAACCATTCTTTCAAAAAGCTTATT
1 AGAAAAAGCTATTCATTGAGAAAAAAAGTCCATTTATAGTCAACCATTCTTTCAAAAAGCTTATT
* * * *
823 ACTCACT-TTAAACGGTTTTATAATCTGATAATTGACTTTAAGGTGAATTTTTTTACATTTTTTG
66 ACTC-CTCTTAAACGGTTTAATAATCTCATAATTGACTTTAAGGTGAATGTTTTTACATTTTTAG
* *
887 TTTAAACAAAT-TATAATTGAATACATACCTCAAGAAACATGA
130 TTAAAAC-AATCTATAATTAAATACATACCTCAAGAAACATGA
** * *
929 AGAAATAAGC-ATTCATT-AGGAAGCAAAGTCCATTTATAGTC-ACTCATTCCTTCAAAAGGCTT
1 AGAAA-AAGCTATTCATTGA-GAAAAAAAGTCCATTTATAGTCAAC-CATTCTTTCAAAAAGCTT
991 ATTA
63 ATTA
995 ATNNNNNNNN
Statistics
Matches: 201, Mismatches: 29, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
170 136 0.68
171 60 0.30
172 5 0.02
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (171 bp):
AGAAAAAGCTATTCATTGAGAAAAAAAGTCCATTTATAGTCAACCATTCTTTCAAAAAGCTTATT
ACTCCTCTTAAACGGTTTAATAATCTCATAATTGACTTTAAGGTGAATGTTTTTACATTTTTAGT
TAAAACAATCTATAATTAAATACATACCTCAAGAAACATGA
Done.