Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3469.0, 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, 922
Length: 1537
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.28
Warning! 358 characters in sequence are not A, C, G, or T
Found at i:1151 original size:171 final size:168
Alignment explanation
Indices: 613--1537 Score: 726
Period size: 171 Copynumber: 5.4 Consensus size: 168
603 NNNNNNNNNN
* * * *
613 AGCCTTCAAAAGCCTTATTACTC-CTTTTATATGGTTTTGTAATCTCATAATTGATTTTAAGCTG
1 AGCCTTCAAAAGCCTTATTACTCTC-TTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTA
* * * * * * **
677 AATGGTTTTCACAGTTTTAG-TTAAA-ATAGATTATAATGGAATGTTTACC-TCGAGAAATATGA
65 AAT--TTTTC-TATTTTTTGATTAAACA-A-ATTATAATTGAATGTTTTCCTTAG-GAAACCTGA
* *
739 AGAAAAAGCCATCCATTGGCAAGAAAGGCCCATTTATAGTTACCCA
124 AGAAAAAGCCATTCATTGGCAAGAAA-GCCCATTTATAGTCACCCA
* * * * * *
785 AGCCTTTAAAAGCCTAATTACCCTCTATAAATAGTTTTATAATCTCATAATTGATTTTAGGTTAA
1 AGCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAA
* * * *
850 ATTGTTTTCTA-TTTTTGATTAAACAGATTATAATTGAATGTTTTTCATAGGAAACCCGAAGAAA
66 A-T-TTTTCTATTTTTTGATTAAACAAATTATAATTGAATGTTTTCCTTAGGAAACCTGAAGAAA
* * *
914 AAGCTATTCATTGGTAAAAAAAGCCCATTTATAGTCACCCA
129 AAGCCATTCATTGG-CAAGAAAGCCCATTTATAGTCACCCA
********** *
955 AGCCTTCANNNNNNNNNNTACTCTCTTTAAATGGTTTTATAA-CTTCAAAATTGATTTTAAGTTA
1 AGCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTTATAATC-TCATAATTGATTTTAAGTTA
** *
1019 AATTTTTCTATTTTTTTG-TCTAGCCCAAATTATAATTGAATGTTTTCCTTAGGAAACCTAAAGA
65 AATTTTTCTA-TTTTTTGAT-TA-AACAAATTATAATTGAATGTTTTCCTTAGGAAACCTGAAGA
* **
1083 AAAAGTCATTCATTGGCAAGAAGAGCCCATTTATAGAAACCCA
127 AAAAGCCATTCATTGGCAAGAA-AGCCCATTTATAGTCACCCA
* * * *
1126 AGCCTTCAAATA-CCTTATCACTCTCTTTAAATGGTCTTATATTCTCAGAATTGATTTTAAGTT-
1 AGCCTTCAAA-AGCCTTATTACTCTCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTA
* * * * * *
1189 GAGTTTTCATATATTTTTGATTAAAACATATTACAATTGAGTGTTTTCCTT-GAGAAACATGAAG
65 AATTTTTC-TAT-TTTTTGATT-AAACAAATTATAATTGAATGTTTTCCTTAG-GAAACCTGAAG
* * * * *
1253 AAAAAGCCATTCATTGGTACAA-AAAGTCAAATTATAGTCTCCTA
126 AAAAAGCCATTCATTGG--CAAGAAAGCCCATTTATAGTCACCCA
* * *
1297 AGCCTTCAAAAGCCTTATTACTCTCTTTAAATCGTTATATAATCTCATAATTGATTTGAAGTTGA
1 AGCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTT-A
********* * * * * * *
1362 NNNNNNNNNNA-TTTTTGGTTAACACATATTATAATTGAAT-TCTTACC-TCGAGAAGCTTGAAG
65 -AATTTTTCTATTTTTTGATTAA-ACAAATTATAATTGAATGT-TTTCCTTAG-GAAACCTGAAG
* * * *
1424 AAAAACCCACTCATTGGCAAGAAAAGCTCATTTAAAGTCACCCA
126 AAAAAGCCATTCATTGGCAAG-AAAGCCCATTTATAGTCACCCA
* * * *
1468 AGCCTTCAAAAACCTAATTACTGTCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGA
1 AGCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAA
1533 ATTTT
66 ATTTT
Statistics
Matches: 595, Mismatches: 128, Indels: 63
0.76 0.16 0.08
Matches are distributed among these distances:
168 7 0.01
169 6 0.01
170 136 0.23
171 374 0.63
172 66 0.11
173 6 0.01
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.36
Consensus pattern (168 bp):
AGCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAA
ATTTTTCTATTTTTTGATTAAACAAATTATAATTGAATGTTTTCCTTAGGAAACCTGAAGAAAAA
GCCATTCATTGGCAAGAAAGCCCATTTATAGTCACCCA
Done.