Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400682.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3866.0, 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: 4098
ACGTcount: A:0.25, C:0.06, G:0.07, T:0.22
Warning! 1643 characters in sequence are not A, C, G, or T
Found at i:2412 original size:171 final size:169
Alignment explanation
Indices: 2062--3210 Score: 680
Period size: 171 Copynumber: 6.7 Consensus size: 169
2052 AAGGTATAAG
* * * *
2062 TGACTATAAATAGAC-ATTCTTTACCAATGGATA-CGTTTTTCTTCACGTTTCTGGATA--TAGA
1 TGACTATAAATGGACTTTTC-TTACCAATAGATATC-TTTTTCTTCACGTTTC-GCA-AGGTAGA
* * * * * * * *
2123 TATTCAATTATAATATATTTTTATAAAAGATATAGAAAAATTAAACTTAAATTTAATTATGACAT
62 TATTCAATTATAATCTATTTTAAAAAAATATATAAAAAAATTAAACTTAAAATCAATTATGAGAT
* ********** * *
2188 TATAAAATCATTTAAAGCGAGTAATANNNNNNNNNNAGGCATGGG
127 TATAAAA-CCTTTAAAGCGAGTAATAAGGCTTTCGAAGG-ATTGA
** * *
2233 TGACTATAAATAAACTTTTCTTGCCAATAGATATCTTTTTCTTCACGTTTCGCAAGGTAAATATT
1 TGACTATAAATGGACTTTTCTTACCAATAGATATCTTTTTCTTCACGTTTCGCAAGGTAGATATT
* ********
2298 CAATTATAATCTATTTTAAGAAAAAAATATAAAAAAATT-AACTTAAAATCAATTATNNNNNNNN
66 CAATTATAATCTATTTTAA-AAAAATATATAAAAAAATTAAACTTAAAATCAATTATGAGATTAT
** * *
2362 NNAACCGTTTAAAGCGAGTAATAAGGCTTTCGAATGCTTAGA
130 AAAACC-TTTAAAGCGAGTAATAAGGCTTTCGAAGGATT-GA
** * * * * ********** *
2404 AAACTATAAATGGACTTTTTTTACCAATGGATATCTTTTTTTTCACATTNNNNNNNNNNGACATT
1 TGACTATAAATGGACTTTTCTTACCAATAGATATCTTTTTCTTCACGTTTCGCAAGGTAGATATT
* * * * * *
2469 TAATTATAATATGTTTTAAAAATATATATAAAAAAATTGAACTTAAATTCAATTATGAGATTATA
66 CAATTATAATCTATTTTAAAAAAATATATAAAAAAATTAAACTTAAAATCAATTATGAGATTATA
* * * * * *
2534 AAATCCTTGAAAGCGAGTTATAAGGTTTTGGAAGGAATGGG
131 AAA-CCTTTAAAGCGAGTAATAAGGCTTTCGAAGG-ATTGA
* * * * *
2575 TGATTATAAATGGACTTTTCTTACGAATAGATATCTTTTTCTTGATGTTTCTCAAGGTAGATATT
1 TGACTATAAATGGACTTTTCTTACCAATAGATATCTTTTTCTTCACGTTTCGCAAGGTAGATATT
* * *********
2640 CAATTATAATCTA-TTTAATAAAAATGTA-AAAAAAATT-AACTTAAAATTAATTANNNNNNNNN
66 CAATTATAATCTATTTTAA-AAAAATATATAAAAAAATTAAACTTAAAATCAATTATGAGATTAT
*
2702 NAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGGATTGA
130 AAAACC-TTTAAAGCGAGTAATAAGGCTTTCGAA-GGATTGA
* * **
2744 TGACTATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTTCACGTTT-GTCGATATAGATAT
1 TGACTATAAATGGACTTTTCTTACCAATAGATATCTTTTTCTTCACGTTTCG-CAAGGTAGATAT
* * * * * *
2808 TCAATTATAATCTGTTTTAATAAAAGATATTAAAAAATTAAACTTAAATTCAATTATGGGATTAT
65 TCAATTATAATCTATTTTAAAAAAATATATAAAAAAATTAAACTTAAAATCAATTATGAGATTAT
* ********* *
2873 AAAAACATTTAAAGCGAGTAATAAGGCTTTNNNNNNNNNNGG
130 -AAAACCTTTAAAGCGAGTAATAAGGCTTT-CGAAGGATTGA
**
2915 TGACTATAAATGGACTTTTCTTGGCAAT-GAATATCTTTTTCTTCATAC-TTTCTG--AGGTAGA
1 TGACTATAAATGGACTTTTCTTACCAATAG-ATATCTTTTTCTTC--ACGTTTC-GCAAGGTAGA
* * * * **
2976 CATTCAATTATAATTTCTTTTAACAAAAA-ATATAAAAAGATTCTACTTAAAA-CTAATTATGAG
62 TATTCAATTATAATCTATTTTAA-AAAAATATATAAAAAAATTAAACTTAAAATC-AATTATGAG
* * * ********
3039 ATTATAAAACTATTTAAAACGAGTAATAAGGCTTCCNNNNNNNNNNG-
125 ATTATAAAAC-CTTTAAAGCGAGTAATAAGGCTTTC--GAAGGATTGA
* * **
3086 TGACTATAAATGGAC-TTTCTTTGCCAATAGATA-CGTTTTTCTTCACGTTTC-TAGATATAGAT
1 TGACTATAAATGGACTTTTC-TTACCAATAGATATC-TTTTTCTTCACGTTTCGCA-AGGTAGAT
* * * *
3148 ATTCAATTGTAATCTATTTTAATAAAAGATATAAAAAAATTAAACTTAAATTCAATTATGAGA
63 ATTCAATTATAATCTATTTTAAAAAAATATATAAAAAAATTAAACTTAAAATCAATTATGAGA
3211 NNNNNNNNNN
Statistics
Matches: 748, Mismatches: 192, Indels: 76
0.74 0.19 0.07
Matches are distributed among these distances:
168 2 0.00
169 119 0.16
170 70 0.09
171 509 0.68
172 45 0.06
173 2 0.00
174 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.36
Consensus pattern (169 bp):
TGACTATAAATGGACTTTTCTTACCAATAGATATCTTTTTCTTCACGTTTCGCAAGGTAGATATT
CAATTATAATCTATTTTAAAAAAATATATAAAAAAATTAAACTTAAAATCAATTATGAGATTATA
AAACCTTTAAAGCGAGTAATAAGGCTTTCGAAGGATTGA
Done.