Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402409.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5489.0, 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: 2049
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.35
Warning! 208 characters in sequence are not A, C, G, or T
Found at i:962 original size:171 final size:171
Alignment explanation
Indices: 445--1221 Score: 451
Period size: 171 Copynumber: 4.6 Consensus size: 171
435 NNNNNNNNNN
** * ** * * *
445 AATTGATTTTAAGTTGAATGGTTTTACATTTTTTGTTAAAACAGACTATTCTTGATTGCCTACTT
1 AATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTCAAAACAGACTATAATTGAATGTCTACCT
* * * ********
510 GGAGAAACGTC-A-AG-AAAAGATATTCATTTG-CAAGAAAAATCCATTTATAGTCANNNNNNNN
66 CGAGAAAC--CAATAGAAAAAGACATTCA-TTGACAAGAAAAATCCATTTATAGCCACCATTTCC
** * * * *
571 NNCAAAAGCCTTATTACTCA-TTTTAAATACTTTTATAATCTC--
128 TTCAAAAGGCTTATTACT-AGCTGTAAATAGTTTTATAATCTCAT
** * * * * * * *
613 AATTGATTTTAAGTCAAATTTGTTTATATTTTTCGTTAAAA-TGTACTATAACTAAATGTCTACC
1 AATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTCAAAACAG-ACTATAATTGAATGTCTACC
* * * * ** **
677 TC-AAAAAACAAGAAGAAAAA-AGCATTCATTGGCAAGAAAGCTCCATTTATAGTTACTCA-TTC
65 TCGAGAAACCAA-TAGAAAAAGA-CATTCATTGACAAGAAAAATCCATTTATAGCCAC-CATTTC
* * * * *********
739 TTTCAAAAGCCTTATTACTCGCTGTAAATGGTTTTANNNNNNNNN
127 CTTCAAAAGGCTTATTACTAGCTGTAAATAGTTTTATAATCTCAT
* * * *
784 NATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTCAAAACAGACTGTAATTGAATGTCTACTT
1 AATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTCAAAACAGACTATAATTGAATGTCTACCT
** * * *
849 CGAGAAACCAATAGAAAAAGACATTCATTGGTAAGAAAAGTTCATTTATAGCCACTCATTT-TTT
66 CGAGAAACCAATAGAAAAAGACATTCATTGACAAGAAAAATCCATTTATAGCCAC-CATTTCCTT
* *
913 CAAAA-GCTTTATTGCTTGCTGTAAAT-GATTTTATAATCTCAT
130 CAAAAGGC-TTATTACTAGCTGTAAATAG-TTTTATAATCTCAT
* * * * * * ** ***
955 AATTGATTTTAAATTGTATTTTTTTATATTTTTTTATTAAAATAGACTATTGTTGAATG-CNNNN
1 AATTGATTTTAAGTTGAATTTTTTTACA-TTTTTTGTCAAAACAGACTATAATTGAATGTC-TAC
****** * * *
1019 NNNNNNAAA-C-AT-GAAGAAAAGGCATTCATTGACAAGAAAAATCCATTTATAGTCACCCTTTC
64 CTCGAGAAACCAATAG-A-AAAAGACATTCATTGACAAGAAAAATCCATTTATAGCCACCATTTC
1081 CTTCAAAAGGCTTATTACTAGCTGTAAATAGTTTTATAATCTCAT
127 CTTCAAAAGGCTTATTACTAGCTGTAAATAGTTTTATAATCTCAT
*
1126 AATTGATTTTAAGTT-ATATTTTTTTACATTTTTTGTCAAAACAGACTAAAATTGAATGTCTACC
1 AATTGATTTTAAGTTGA-ATTTTTTTACATTTTTTGTCAAAACAGACTATAATTGAATGTCTACC
* * *
1190 TCGGGAAACTAGA-AGACAAAGACATTCATTGA
65 TCGAGAAACCA-ATAGAAAAAGACATTCATTGA
1222 TTTAAATGGC
Statistics
Matches: 452, Mismatches: 127, Indels: 57
0.71 0.20 0.09
Matches are distributed among these distances:
165 1 0.00
166 1 0.00
167 5 0.01
168 54 0.12
169 57 0.13
170 36 0.08
171 255 0.56
172 41 0.09
173 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.37
Consensus pattern (171 bp):
AATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTCAAAACAGACTATAATTGAATGTCTACCT
CGAGAAACCAATAGAAAAAGACATTCATTGACAAGAAAAATCCATTTATAGCCACCATTTCCTTC
AAAAGGCTTATTACTAGCTGTAAATAGTTTTATAATCTCAT
Done.