Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397952.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1256.0, 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: 7416
ACGTcount: A:0.19, C:0.07, G:0.06, T:0.20
Warning! 3573 characters in sequence are not A, C, G, or T
Found at i:5866 original size:171 final size:170
Alignment explanation
Indices: 5400--5874 Score: 426
Period size: 171 Copynumber: 2.8 Consensus size: 170
5390 AAATCATATC
* * ** * * *
5400 ATAATTGAATGTTTACCTCAACAAACATGAAGAAAAGGGAATTCACTAGCAACAAAAGTCCATTC
1 ATAATTCAATGTTTACCTCAAGAAACATGAAGAAAAAAGAATTCATTGGCAAGAAAAGTCCATT-
* **********
5465 ATAGTCACCTATTCTTTCAAAAGCCTTATTA-TCGCTTTAAATGGTTTNNNNNNNNNNTAATTGA
65 ATAGTCACCTATTTTTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTAAAATCTCATAATTGA
*
5529 TTTTAAATTGAATGTTTTTACATTTTTGCTTAAAAAAGATT
130 TTTTAAATTGAATGTTTTTACATTTTTGCTTAAAAAAGACT
* * * * * *
5570 ATAATTGAATGTTTACCTC-TGAAAACATAAAGAAAAAGATAATT-ATTGACAAGAAAAGTCTAT
1 ATAATTCAATGTTTACCTCAAG-AAACATGAAGAAAAA-AGAATTCATTGGCAAGAAAAGTCCA-
* **********
5633 TTATAGTCACCCATTATTTT-AAAAGCCTTATTACTCGCTTTAAATGNNNNNNNNNNCTCATAAT
63 TTATAGTCACCTATT-TTTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTAAAATCTCATAAT
* *
5697 TGATTTTAAGTT-AATTTTTTTTACATTTTTGGC-TAAAACAA-ACT
127 TGATTTTAAATTGAA-TGTTTTTACATTTTT-GCTTAAAA-AAGACT
* * *
5741 A-AAGTTCAATGTTTACCTCAAGAAACGTGAAGAAAAAAGCATTCTTTGGCAAGAAAAGTCCATC
1 ATAA-TTCAATGTTTACCTCAAGAAACATGAAGAAAAAAGAATTCATTGGCAAGAAAAGTCCAT-
*
5805 TATAGTCACCTATTTTTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAAAATCTCATAATTG
64 TATAGTCACCTATTTTTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTAAAATCTCATAATTG
5870 ATTTT
129 ATTTT
5875 NNNNNNNNNN
Statistics
Matches: 247, Mismatches: 45, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
170 83 0.34
171 159 0.64
172 5 0.02
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.35
Consensus pattern (170 bp):
ATAATTCAATGTTTACCTCAAGAAACATGAAGAAAAAAGAATTCATTGGCAAGAAAAGTCCATTA
TAGTCACCTATTTTTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTAAAATCTCATAATTGAT
TTTAAATTGAATGTTTTTACATTTTTGCTTAAAAAAGACT
Done.