Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402252.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5336.0, 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, 657
Length: 1095
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.29
Warning! 219 characters in sequence are not A, C, G, or T
Found at i:861 original size:171 final size:170
Alignment explanation
Indices: 492--1094 Score: 466
Period size: 171 Copynumber: 3.5 Consensus size: 170
482 NNNNNNNNNN
* * * * * *
492 GATTTTAAGTTGAATTGTTTTATATTTTTTA-TTAAAACAGATTATAATTGAATGCCTACCCCA-
1 GATTTTAAGTTGAATTTTTTTACA-TTTTTAGTTAAAACAGACTATAATTGAATGTCTA-TCTAG
* ** * * * * *
555 AGAAACTTGTAGAAAAAGTCATTCATTGAGAAGCAAAGTCCATTTATAGTCACCCATTTCTTCAA
64 AGAAACATAAAGAAAAAG-CATTCATTTACAAGAAAAGTCCAGTTATAGTCACCCATTCCTTCAA
** * * ********** *
620 AAGCCTTATTTCTCGCTTNNNNNNNNNNTATAATCTCATAATT
128 AAAACTTATTACTCACTTAAAATGGTTTTATAATCTCAAAATT
* * *
663 GATTTTAAGCTGAATTTTTTAACATTTTTACTTAAAACAGACTATAATTGAATGTCTATCTAGAG
1 GATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGTCTATCTAGAG
* *
728 AAACATAAAGAAAAATGCATTCATTTGCAAGAAAAGT-CA-TTATGGTCACCCATTCCTTCAAAA
66 AAACATAAAGAAAAA-GCATTCATTTACAAGAAAAGTCCAGTTATAGTCACCCATTCCTTCAAAA
791 AGACTTATTACTCAC-TATAAATGGTTTTATAATCTCAAAATT
130 A-ACTTATTACTCACTTA-AAATGGTTTTATAATCTCAAAATT
* *
833 GATTTCAAGTTGAATTTTTTTTACATTTTTAGTTAAAACAGACTGTAATTGAAT-TCCTGCATC-
1 GATTTTAAGTTGAA-TTTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGT-CT--ATCT
** ********* *
896 A-AGAAACATGTAGAAAAAGNNNNNNNNNNATAAGAAAAGTCCAGTTATAGTCACCCATTCCTTC
62 AGAGAAACATAAAGAAAAAG-CATTCATTTACAAGAAAAGTCCAGTTATAGTCACCCATTCCTTC
* * * * *
960 AGAAACCTTATTACTCGCTTAAAATTGTTTTATAATCTCAGAATT
126 AAAAAACTTATTACTCACTTAAAATGGTTTTATAATCTCAAAATT
* ** * * * * * * *
1005 GATTTTATGTCCAATTATTTTATATTTTTGGTTAAATCAGACTATAATTGAATGTTTACCTCGAG
1 GATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGTCTATCTAGAG
*
1070 AAATATAAAGAAAAAGGCATTCATT
66 AAACATAAAGAAAAA-GCATTCATT
1095 G
Statistics
Matches: 336, Mismatches: 79, Indels: 34
0.75 0.18 0.08
Matches are distributed among these distances:
169 25 0.07
170 48 0.14
171 186 0.55
172 49 0.15
173 28 0.08
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.36
Consensus pattern (170 bp):
GATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGTCTATCTAGAG
AAACATAAAGAAAAAGCATTCATTTACAAGAAAAGTCCAGTTATAGTCACCCATTCCTTCAAAAA
ACTTATTACTCACTTAAAATGGTTTTATAATCTCAAAATT
Done.