Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398831.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2114.0, 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: 2030
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.31
Warning! 401 characters in sequence are not A, C, G, or T
Found at i:1341 original size:170 final size:169
Alignment explanation
Indices: 952--1665 Score: 589
Period size: 170 Copynumber: 4.2 Consensus size: 169
942 NNNNNNNNNN
* *
952 CTCGCTTTAAATAGTTTTATAATCTTATAATTGATTTTAAGCTGAATTTTTTACAATTTTA-GTT
1 CTCGCTTTAAATTGTTTTATAATCTTATAATTGATTTTAAGCTGAATTTTTTAC-ATTTTATCTT
* * * *
1016 AAAACAGACTATAAATGAATGTCTACCTTGAGAAATGTGAAGAAAAATACATTTATTGGTAA-AT
65 AAAACAGACTATAATTGAATGTCTACCTTGAGAAATGTGAAGAAAAAAACATTCATTGGCAAGA-
** *
1080 AAAGTCCGTTATAGTCACCCATTCCTTGAAAAACCTTATTA
129 AAAGTCATTTATAGTCACCCATTCCTTCAAAAACCTTATTA
* *
1121 CTCGCTTTAAA-TGATTTTATAATCTTGTAACTGATTTTAAGCTGAATTTTTTACATTTTATCTT
1 CTCGCTTTAAATTG-TTTTATAATCTTATAATTGATTTTAAGCTGAATTTTTTACATTTTATCTT
* * * * *
1185 AAAACAGACTATAATTGAATGTCCACCTTGGGAAACGTGATGAAAAAAACATTCATGGGCAAGAA
65 AAAACAGACTATAATTGAATGTCTACCTTGAGAAATGTGAAGAAAAAAACATTCATTGGCAAGAA
*** * *****
1250 AAGTTCATTTATAGTCATTTATTCCTTCAAAAGCCTNNNNN
130 AAG-TCATTTATAGTCACCCATTCCTTCAAAAACCTTATTA
***** * ** * *
1291 NNNNNTTTAAATTGTTTTATAATCTCATAATTGATTTTAATTTAAATTTTTTTTATATTTT-TCA
1 CTCGCTTTAAATTGTTTTATAATCTTATAATTGATTTTAAGCTGAA--TTTTTTACATTTTATC-
* * * * **
1355 TTAAATAAAAAATATAATTGAATGTCTA-CTAAGAGAAATGTGAAGAAAAAGGCATTCATTGGCA
63 TTAAA-ACAGACTATAATTGAATGTCTACCT-TGAGAAATGTGAAGAAAAAAACATTCATTGGCA
**********
1419 AGAAAAGCTCATTTATAGTCACCCATTCCTTCAANNNNNNNNNNA
126 AGAAAAG-TCATTTATAGTCACCCATTCCTTCAAAAACCTTATTA
* * * * * * *
1464 CTCGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGCTGATTTTTTTAAAATTTTTTATT
1 CTCGCTTTAAATTGTTTTATAATCTTATAATTGATTTTAAGCTGAATTTTTT-ACATTTTATCTT
* * * * * * *
1529 AAAATAGACTAAAATTGAATGTTTGCCTTG-GAAAATGTG--TAAAAAAGCTATTCATTGGGAAG
65 AAAACAGACTATAATTGAATGTCTACCTTGAG-AAATGTGAAGAAAAAAAC-ATTCATTGGCAAG
* *** * *
1591 AAAAGTCCACTTATAGTCATGTATTTCTTCAAAAGCCTTATTA
128 AAAAGT-CATTTATAGTCACCCATTCCTTCAAAAACCTTATTA
* *
1634 CTCGCTTTAAATGGTTTTATAATCTCATAATT
1 CTCGCTTTAAATTGTTTTATAATCTTATAATT
1666 NNNNNNNNNN
Statistics
Matches: 432, Mismatches: 97, Indels: 31
0.77 0.17 0.06
Matches are distributed among these distances:
168 7 0.02
169 116 0.27
170 129 0.30
171 34 0.08
172 32 0.07
173 114 0.26
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.38
Consensus pattern (169 bp):
CTCGCTTTAAATTGTTTTATAATCTTATAATTGATTTTAAGCTGAATTTTTTACATTTTATCTTA
AAACAGACTATAATTGAATGTCTACCTTGAGAAATGTGAAGAAAAAAACATTCATTGGCAAGAAA
AGTCATTTATAGTCACCCATTCCTTCAAAAACCTTATTA
Done.