Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399171.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2444.0, 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: 3591
ACGTcount: A:0.24, C:0.09, G:0.08, T:0.24
Warning! 1270 characters in sequence are not A, C, G, or T
Found at i:1183 original size:173 final size:169
Alignment explanation
Indices: 869--1250 Score: 464
Period size: 173 Copynumber: 2.2 Consensus size: 169
859 ACATTTATTG
* * *
869 GCAAAAAAAGTCCATTTATAGTTACCAATTCCTTCAAATGCCTTATTACTCATTTAAATGGCTTT
1 GCAAGAAAAGTCCATTTATAGTCACC-ATT-CTTCAAATGCCCTATTACTCATTTAAATGGCTTT
* * *
934 ATATTCTCAAAATTAATTTTAAGTTCAAATTTCTTCACATTTTTCGTTAAAATAGATTATAATTG
64 ATAATCTCAAAATTAATTTGAAGTTCAAATTTCTTCACATTTTTCGTTAAAACAGATTATAATTG
* *
999 AATACCTAGCTTGAGAAAGA-AGAAGAAAAAGGTATTCACTC
129 AATACCTAGCTTAAGAAACATA-AAGAAAAAGGTATTCACTC
*
1040 GCAAGAAAAGTCCATTTATAGTCACTCATTCTTCTAGAA-GCCCTATTACTCACTTTAAATGGTT
1 GCAAGAAAAGTCCATTTATAGTCAC-CATTCTTC-A-AATGCCCTATTACTCA-TTTAAATGGCT
* * * *
1104 TTATAATCTCAAAATTGATTTGAAGTTCAAATGTTTTTTACA-TTTTCGGTTAAAACGGATTATA
62 TTATAATCTCAAAATTAATTTGAAGTTCAAAT-TTCTTCACATTTTTC-GTTAAAACAGATTATA
** * *
1168 ATTGAATTTCTAGCTTAAGAAACATAAAGAAAAAGGTATTCATTG
125 ATTGAATACCTAGCTTAAGAAACATAAAGAAAAAGGTATTCACTC
* **
1213 GTAAGAAAAGTTTATTTATAGTCACCCATTCCTTCAAA
1 GCAAGAAAAGTCCATTTATAGTCA-CCATT-CTTCAAA
1251 NNNNNNNNNN
Statistics
Matches: 182, Mismatches: 20, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
170 4 0.02
171 39 0.21
172 49 0.27
173 84 0.46
174 6 0.03
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (169 bp):
GCAAGAAAAGTCCATTTATAGTCACCATTCTTCAAATGCCCTATTACTCATTTAAATGGCTTTAT
AATCTCAAAATTAATTTGAAGTTCAAATTTCTTCACATTTTTCGTTAAAACAGATTATAATTGAA
TACCTAGCTTAAGAAACATAAAGAAAAAGGTATTCACTC
Found at i:1925 original size:172 final size:161
Alignment explanation
Indices: 1750--2084 Score: 329
Period size: 172 Copynumber: 2.0 Consensus size: 161
1740 AACATGAAGA
* * * *
1750 AAAAAG-CATTAATTGGTAAGAAAAGTCCATTTATAGTCACCCGTACCTTT-AAAAGCCTTATTA
1 AAAAAGACATTAATTGGCAAGAAAAGTCAATTTATAGTCACCCAT-CCTTTCAAAAGCCTTACTA
* * *
1813 CTAACTTTAAATGGCTTTATAATCTCAA-AATTGATTTAAATTTGAATTCT-TTATATATTTTTG
65 CTAACTTTAAATGGCTTTATAACCT-AATAATTGATTTAAAGTTAAATTCTCTTATAT-TTTTTG
1876 TCTAAAACAGATTATAATTGAATGTCTACCTTGNNNNNNNNNNAG
128 T-TAAAACAGATTATAATTGAATGTCTACCTTG----------AG
* * *
1921 AAAAAGACATTCATTGGCAAGAAAAGTCAATTTATAGTTACCCATTCTTTCAAAAGCCTTACTAC
1 AAAAAGACATTAATTGGCAAGAAAAGTCAATTTATAGTCACCCATCCTTTCAAAAGCCTTACTAC
* * * * * * * *
1986 TCATTTTAAATGGTTTTCTAACCTAATAATTGATTTTAGGTTAAATTTTCTTATGTTTTTTGTTA
66 TAACTTTAAATGGCTTTATAACCTAATAATTGATTTAAAGTTAAATTCTCTTATATTTTTTGTTA
* *
2051 GAACAGATTATAATTGAATGTTTACCTTG-G
131 AAACAGATTATAATTGAATGTCTACCTTGAG
2081 AAAA
1 AAAA
2085 CTGAAGAAAA
Statistics
Matches: 140, Mismatches: 20, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
160 5 0.04
171 41 0.29
172 89 0.64
173 5 0.04
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.38
Consensus pattern (161 bp):
AAAAAGACATTAATTGGCAAGAAAAGTCAATTTATAGTCACCCATCCTTTCAAAAGCCTTACTAC
TAACTTTAAATGGCTTTATAACCTAATAATTGATTTAAAGTTAAATTCTCTTATATTTTTTGTTA
AAACAGATTATAATTGAATGTCTACCTTGAG
Done.