Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401510.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4637.0, 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: 2471
ACGTcount: A:0.24, C:0.09, G:0.08, T:0.24
Warning! 848 characters in sequence are not A, C, G, or T
Found at i:1974 original size:171 final size:170
Alignment explanation
Indices: 1726--2471 Score: 557
Period size: 171 Copynumber: 4.4 Consensus size: 170
1716 CGAAATATAT
* * * * * * * * * *
1726 AGAAAAAACCATTCATTGAGAAGAAAAATCTATTTTTCGTAACCCATTCTTTCGAAAGCCTTATT
1 AGAAACAAGCATT-ATTGAGAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATT
** * **
1791 ACTCGGTTTAAATAATTTTATAGCCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCT-
65 ACTCACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTT-TA
* * * * * *
1855 TTTAAACAGACAATAATAGAATGTTTATCTCGAGAAACATGT
129 TTAAAACAGACAATAATAGAATGTCTACCTCAAGAAACGTGA
*
1897 AGAAA-AAGCATTTAATTGAGAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGGTTAT
1 AGAAACAAGCA-TT-ATTGAGAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTAT
********** *
1961 TACTCACTTTAAATAGTTTTATAATCTCATAATTNNNNNNNNNNTGAATGTTTTTACATTTTTTA
64 TACTCACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTA
* * * * * * *
2026 TTAAAACATACTATAATTGAATGTTTGCCTCTAGAAATGTGA
129 TTAAAACAGACAATAATAGAATGTCTACCTCAAGAAACGTGA
* * * * * * * * *
2068 AGAAACAAGAATTCTTTGATAAGAGAAGTCTATTTAGAGTCACCTATTCCTTCAAAAAGCTTGTT
1 AGAAACAAGCATT-ATTGAGAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATT
* * ** * ********* *
2133 ATTCGCTTTAAACGGTTTTATAATCTCGTAATTGATTTTAAGTTGAATNNNNNNNNNNTTTTCT-
65 ACTCACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAAT-TTTTTTACATTTTTTA
* * * *
2197 TTAAAACAGATAATAATTGAATGTCTAACTCAAGAAACGTGC
129 TTAAAACAGACAATAATAGAATGTCTACCTCAAGAAACGTGA
* * * *
2239 AGAAA-AAGCCATTGATTTAGAAGAAAAAGTTCATTTATAGACACCCATTCCTTCCAAAGGCTTA
1 AGAAACAAG-CATT-ATTGAGAAG-AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTA
**********
2303 TTACTCACTTTAAATAGTTTTATANNNNNNNNNNTGATTTTAAGTTG-ATTTTTTTACATTTTTT
63 TTACTCACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTT
* *
2367 ATTAAAACAGACTATAATAGAATGTCTACCTCAAGAAGCGTGA
128 ATTAAAACAGACAATAATAGAATGTCTACCTCAAGAAACGTGA
* * * * * *
2410 AGAAACATGCATTCATTGACAAGAAAAGTCCATTTAGAGTCACCTATTCCTTTAAAAAGCTT
1 AGAAACAAGCATT-ATTGAGAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTT
Statistics
Matches: 430, Mismatches: 137, Indels: 17
0.74 0.23 0.03
Matches are distributed among these distances:
170 45 0.10
171 310 0.72
172 75 0.17
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.36
Consensus pattern (170 bp):
AGAAACAAGCATTATTGAGAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTA
CTCACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTATT
AAAACAGACAATAATAGAATGTCTACCTCAAGAAACGTGA
Done.