Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402071.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5168.0, 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, 699
Length: 1165
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.31
Warning! 236 characters in sequence are not A, C, G, or T
Found at i:615 original size:171 final size:161
Alignment explanation
Indices: 308--1155 Score: 374
Period size: 171 Copynumber: 5.0 Consensus size: 161
298 NNNNNNNNAT
* * * * * * *
308 ATTTTTTATTAAAATAATTTATAATTGAATGTCTGCCTTGAGAAACGTGAAGTAAAAGATATTCA
1 ATTTTCTATTAAAACAAATTATAATTGAATGTCTACCTTAAGAAACGTGAAGAAAAAGATATCCA
* * * * * *
373 TTGGCATGAAATGTCTATTTAGAGTCACCCATGCTTTCGAAAGTCTTGTTACTCGCATTAAAAAA
66 TTGGCAAGAAAAGTCAATTTAGAGTCACCCATGCTTTCGAAAGCCTTATTACTCACATTAAAAAA
438 TTTTATAACCTCATAATTGATTTTAATTTGA
131 TTTTATAACCTCATAATTGATTTTAATTTGA
* * *
469 ANNNNNNNNNNTTTTCTATTAAAACAAATTATAATTTAATGTCTACTTTAAGAAACGTTAAGAAA
1 A----------TTTTCTATTAAAACAAATTATAATTGAATGTCTACCTTAAGAAACGTGAAGAAA
* *
534 AATATATCCATTGGCAAGAAAAGTCAATTTATAGTCACCCATGCTTTCGAAAGCCTTATTACTCA
56 AAGATATCCATTGGCAAGAAAAGTCAATTTAGAGTCACCCATGCTTTCGAAAGCCTTATTACTCA
*** ** *
599 CATTAAATGTTTTTATAACCNNNNNNNNNNTTTTAATTTGAATTT--TTT-A
121 CATTAAAAAATTTTATAACC----------TCATAA-TTGATTTTAATTTGA
* * * ** * * * * *
648 TATTTTTTATTAAAACAGATTTTAATTGAATAACTGCCTTGAGAAATGTAAAGAGAAAGATATCC
1 -ATTTTCTATTAAAACAAATTATAATTGAATGTCTACCTTAAGAAACGTGAAGAAAAAGATATCC
* * * ************** ** *
713 ATTGTCAAGAAAAGTCCATTTAGAGTCACCAATGCTNNNNNNNNNNNNNNTACTCGTATTAAATA
65 ATTGGCAAGAAAAGTCAATTTAGAGTCACCCATGCTTTCGAAAGCCTTATTACTCACATTAAAAA
*
778 ATTTTATAACCTCATAATTGATTTTGATTTGA
130 ATTTTATAACCTCATAATTGATTTTAATTTGA
* * * *
810 ATTTTTTATATTTTTTATCAAAACAGATTATAATTGAATGTCTACTTTGAGAAACGTGAAGAAAC
1 A--TTTTCTA-----T-T-AAAACAAATTATAATTGAATGTCTACCTTAAGAAACGTGAAGAAA-
********************* * * *
875 AAG-TATCCNNNNNNNNNNNNNNNNNNNNNATAGTCACCCATGCCTTCGAAAGCCTTATTACTCG
56 AAGATATCCATTGGCAAGAAAAGTCAATTTAGAGTCACCCATGCTTTCGAAAGCCTTATTACTCA
* * * *
939 CATTAAATATTTTTATAACTTCATAACTGATTTTAATTTGA
121 CATTAAAAAATTTTATAACCTCATAATTGATTTTAATTTGA
* * * * * *
980 ATTTTTTTATNNNNNNNNNNAAAACAGATTATAATTGAATGTCTGA-CTTAAAAAATGTGAAGGA
1 A-TTTTCTAT---------TAAAACAAATTATAATTGAATGTCT-ACCTTAAGAAACGTGAAGAA
* * * * *
1044 AAAGATATCTATTGTCAAGAAAAGTCCATTTAGAGTCACCCATACTTTCGAAAGCCTTGTTACTC
55 AAAGATATCCATTGGCAAGAAAAGTCAATTTAGAGTCACCCATGCTTTCGAAAGCCTTATTACTC
* *
1109 ACATTAAATAATTTTATAACCTCATAATTGATTTTAATTTTA
120 ACATTAAAAAATTTTATAACCTCATAATTGATTTTAATTTGA
1151 ATTTT
1 ATTTT
1156 TTATATTTTT
Statistics
Matches: 489, Mismatches: 153, Indels: 81
0.68 0.21 0.11
Matches are distributed among these distances:
159 7 0.01
160 4 0.01
161 5 0.01
162 1 0.00
163 6 0.01
164 1 0.00
168 1 0.00
169 8 0.02
170 208 0.43
171 231 0.47
172 1 0.00
179 1 0.00
180 4 0.01
181 4 0.01
182 7 0.01
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.36
Consensus pattern (161 bp):
ATTTTCTATTAAAACAAATTATAATTGAATGTCTACCTTAAGAAACGTGAAGAAAAAGATATCCA
TTGGCAAGAAAAGTCAATTTAGAGTCACCCATGCTTTCGAAAGCCTTATTACTCACATTAAAAAA
TTTTATAACCTCATAATTGATTTTAATTTGA
Done.