Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398483.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1779.0, 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: 3827
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.19
Warning! 1999 characters in sequence are not A, C, G, or T
Found at i:2007 original size:171 final size:164
Alignment explanation
Indices: 1793--2162 Score: 357
Period size: 171 Copynumber: 2.2 Consensus size: 164
1783 NNNNNNACAG
* * * * **
1793 ATTATAATTAAATGTCTGCCTTAAAAACGTAAAGAAAATGATATCCATTGGGAAGAGTAGTCCAT
1 ATTATAATTGAATGTCTACCTAAAAAACGTAAAGAAAATGATATCCATTGGCAAGAAAAGTCCAT
* * **** *
1858 TTATAATCACCCATGCTTTCA-AAAGCCTTANNNNNNNNNNTAAATGATTTTATAACCTCGTAAT
66 TCATAATCACCCATGCCTT-AGAAAGCCTTA------TTACTAAATGATTTTATAACCTCATAAT
*
1922 TGATTTTAATTT-AATTTTTTTTATAATTTTTATTAAAATAA
124 TGATTTTAATTTAAATTTTTTTTAT-ATTTTTATTAAAACAA
* * * *
1963 ATTATAATTGAATGTTTTCCTAAAAAAACTTGAAGAAAATGATATCCATTGGCAAGAAAAGTCCA
1 ATTATAATTGAATGTCTACCT-AAAAAACGTAAAGAAAATGATATCCATTGGCAAGAAAAGTCCA
* ****
2028 TTCATAGTCACCCATGCCTTAGAAAGCCTTATTACNNNNNNNNNNTGATTTTATAACCTCATAAT
65 TTCATAATCACCCATGCCTTAGAAAGCCTTATTAC------TAAATGATTTTATAACCTCATAAT
*
2093 TGATTTTAATTTAAATTTTTTTTATTTTTTTATTAAAACAA
124 TGATTTTAATTTAAATTTTTTTTATATTTTTATTAAAACAA
*
2134 AATATAATTGAATGTCTACCTCAAAAAAC
1 ATTATAATTGAATGTCTACCT-AAAAAAC
2163 ATNNNNNNNN
Statistics
Matches: 164, Mismatches: 27, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
170 19 0.12
171 133 0.81
172 12 0.07
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.37
Consensus pattern (164 bp):
ATTATAATTGAATGTCTACCTAAAAAACGTAAAGAAAATGATATCCATTGGCAAGAAAAGTCCAT
TCATAATCACCCATGCCTTAGAAAGCCTTATTACTAAATGATTTTATAACCTCATAATTGATTTT
AATTTAAATTTTTTTTATATTTTTATTAAAACAA
Found at i:2250 original size:171 final size:171
Alignment explanation
Indices: 1898--2272 Score: 367
Period size: 171 Copynumber: 2.2 Consensus size: 171
1888 NNNNNNNNNN
* *
1898 TAAATGATTTTATAACCTCGTAATTGATTTTAATTTAATTTTTTTTATAATTTTTATTAAAATAA
1 TAAATGATTTTATAACCTCATAATTGATTTTAATTTAATTTTTTTTATAATTTTTATTAAAACAA
* * * *
1963 ATTATAATTGAATGTTTTCCTAAAAAAACTTGAAGAAAATGATATCCATTGGCAAGAAAAGTCCA
66 AATATAATTGAATGTCTACCTAAAAAAACATGAAGAAAATGATATCCATTGGCAAGAAAAGTCCA
* * * ******
2028 TTCATAGTCACCCATGCCTTAGAAAGCCTTATTACNNNNNN
131 TTCATAGTCACCCATACCTTAGAAAACCTTATGACTCGCTT
**** *
2069 NNNNTGATTTTATAACCTCATAATTGATTTTAATTTAAATTTTTTTTAT-TTTTTTATTAAAACA
1 TAAATGATTTTATAACCTCATAATTGATTTTAATTT-AATTTTTTTTATAATTTTTATTAAAACA
* ********** *
2133 AAATATAATTGAATGTCTACCTCAAAAAACATNNNNNNNNNNATATCCATTGGCAAGAGAAGTCC
65 AAATATAATTGAATGTCTACCTAAAAAAACATGAAGAAAATGATATCCATTGGCAAGAAAAGTCC
* * *
2198 ATTTATTA-TTACCCATACCTTTGAAAACCTTATGACTCGCTT
130 ATTCA-TAGTCACCCATACCTTAGAAAACCTTATGACTCGCTT
* * * *
2240 TAAATGATTTTTTAATCTCATAATCGGTTTTAA
1 TAAATGATTTTATAACCTCATAATTGATTTTAA
2273 GTTGAANNNN
Statistics
Matches: 159, Mismatches: 43, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
171 145 0.91
172 14 0.09
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.39
Consensus pattern (171 bp):
TAAATGATTTTATAACCTCATAATTGATTTTAATTTAATTTTTTTTATAATTTTTATTAAAACAA
AATATAATTGAATGTCTACCTAAAAAAACATGAAGAAAATGATATCCATTGGCAAGAAAAGTCCA
TTCATAGTCACCCATACCTTAGAAAACCTTATGACTCGCTT
Done.