Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398783.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2067.0, 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: 3950
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.28
Warning! 1077 characters in sequence are not A, C, G, or T
Found at i:1460 original size:172 final size:169
Alignment explanation
Indices: 978--1464 Score: 442
Period size: 171 Copynumber: 2.8 Consensus size: 169
968 NNNNNNNNTG
* * *
978 TATAACCTCATAATTAGTTTTAAGTTAAATTTTTTTACA-ATTTTTATAAAAAAAAATTATAATT
1 TATAACCTCATAATTA-TTTTAAGTTAAATTTTTTTATATATTTTT-T-AAAATAGATTATAATT
* * * * * * *
1042 GAATGTCTGCCTCTAGAAACCTTAACAAAAAGATATCCATTGGTAAGAAAAGTCCATTTATAGTC
63 GAATGTTTGCCTCGAGAAACGTAAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTCATAGTC
* * * *
1107 ACCCACGCTTTCAAAAGCTTTATTACTCGCTTTAAATGATTT
128 ACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGATTT
********** *
1149 TATAACCTCATAATTAATTNNNNNNNNNNTTTTTTTATATTTTTTATTAAAATAGATTATAATTG
1 TATAACCTCATAATT-ATTTTAAGTTAAATTTTTTTATATATTTT-TTAAAATAGATTATAATTG
** * **********
1214 AATGTTTGCCTCGAGAAACGGGAAGAAATAGATATCCATTGGCAAGAAAAGTNNNNNNNNNNTCA
64 AATGTTTGCCTCGAGAAACGTAAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTCATAGTCA
* *
1279 CCTATGCCTTCGAAAGCCTTATTACTCGAC-TTAAATGTTTT
129 CCCATGCCTTCGAAAGCCTTATTACTCG-CTTTAAATGATTT
* *
1320 TA-AAGCCTCATAATTGATTTTGAGTTTAATTTTTTTTATATATTTTCTTAAAATAGATTATAAT
1 TATAA-CCTCATAATT-ATTTTAAG-TTAAATTTTTTTATATATTTT-TTAAAATAGATTATAAT
* * *
1384 TAAATGTTTAG-CTCGAGAAACGTAAAGAAAAAGATATTCATTGACAAGAAAAGTCCATTCATAG
62 TGAATGTTT-GCCTCGAGAAACGTAAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTCATAG
1448 TCACCCATGCCTTCGAA
126 TCACCCATGCCTTCGAA
1465 NNNNNNNNNN
Statistics
Matches: 241, Mismatches: 68, Indels: 13
0.75 0.21 0.04
Matches are distributed among these distances:
170 2 0.01
171 136 0.56
172 101 0.42
173 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.36
Consensus pattern (169 bp):
TATAACCTCATAATTATTTTAAGTTAAATTTTTTTATATATTTTTTAAAATAGATTATAATTGAA
TGTTTGCCTCGAGAAACGTAAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTCATAGTCACC
CATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGATTT
Found at i:3156 original size:172 final size:171
Alignment explanation
Indices: 2846--3327 Score: 364
Period size: 172 Copynumber: 2.8 Consensus size: 171
2836 NNNNNNATTG
* * * *
2846 ATTTTAATTTGAATTTTTTTATAATTTTCTTTAAAACAGATTATAATTGACTCTTTGCCTAGAGA
1 ATTTTAATTTAAAATTTTTTATAATTTTCTTTAAAACAGATTATAATTGAATCTTTACCTAGAGA
********** *
2911 AACGTGAAGAAAAAGATATACATTGGCAAGAAAAGTCCATNNNNNNNNNNCCATGCCTTCAAAAG
66 AACGTGAAGAAAAAGATATACATTGGCAAGAAAAGTCCATATTATGGTAACCATACCTTCAAAAG
*
2976 CGTTATTACTCGCTTTAAATGATTTTATAACCTCATAATAT
131 CCTTATTACTCGCTTTAAATGATTTTATAACCTCATAATAT
* * *
3017 ATTTTAATTTAAAATTTTTTAT-ATTTTTTATTAAAAACAGATTATAATTGAATGTTTACCTCGA
1 ATTTTAATTTAAAATTTTTTATAATTTTCT-TT-AAAACAGATTATAATTGAATCTTTACCTAGA
* * * ** *
3081 GAAACGTTAAGAAAAATATATCCATTGGTGAGAAAAGTCCAT-TTATGGTAACACATACCTTCGA
64 GAAACGTGAAGAAAAAGATATACATTGGCAAGAAAAGTCCATATTATGGTAAC-CATACCTTCAA
********** * *
3145 AAGCCTTATTACNNNNNNNNNNTGATTGTATAACCTCATAATTT
128 AAGCCTTATTACTCGCTTTAAATGATTTTATAACCTCATAATAT
* ** * * * * * * *
3189 GTTTTAGGTTGAATTTTTTTATAACTTTT-ATAAAAACAGATCATAATTGAA-CGTCTGCCTTA-
1 ATTTTAATTTAAAATTTTTTATAA-TTTTCTTTAAAACAGATTATAATTGAATC-TTTACC-TAG
** * * * * *
3251 AGAAACCAGAACAAAAAGATATACATTGGCAAGAAAAGTCTAT-TTATAGTCACCTATTCCTTCA
63 AGAAACGTGAAGAAAAAGATATACATTGGCAAGAAAAGTCCATATTATGGTAACC-ATACCTTCA
*
3315 AAAGACTTATTAC
127 AAAGCCTTATTAC
3328 NNNNNNNNNN
Statistics
Matches: 241, Mismatches: 62, Indels: 16
0.76 0.19 0.05
Matches are distributed among these distances:
170 7 0.03
171 106 0.44
172 123 0.51
173 1 0.00
174 4 0.02
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.35
Consensus pattern (171 bp):
ATTTTAATTTAAAATTTTTTATAATTTTCTTTAAAACAGATTATAATTGAATCTTTACCTAGAGA
AACGTGAAGAAAAAGATATACATTGGCAAGAAAAGTCCATATTATGGTAACCATACCTTCAAAAG
CCTTATTACTCGCTTTAAATGATTTTATAACCTCATAATAT
Done.