Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401569.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4693.0, 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, 820
Length: 1368
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.33
Warning! 212 characters in sequence are not A, C, G, or T
Found at i:857 original size:172 final size:170
Alignment explanation
Indices: 1--1040 Score: 633
Period size: 171 Copynumber: 6.1 Consensus size: 170
* * * * *
1 ATAATCTCATAATTAATTTTAAGTTCAA-TTTTTTACATTTTTCATTAAAACAGACTATAATTAA
1 ATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATATTTTTCATTTAAACAGACTATAATTGA
* * *
65 ATGTCTACTTTGAGAAAT-ATGAA-AAACAAAGAATTCATTAGA-AAGAAAAGTATATTTATAGC
66 ATGTCTACCTTGAGAAATGA-GAAGAAA-AAAGCATTCATT-GACAAGAAAAGTCTATTTATAGC
* ** * * *
127 CT-ATCATTCCTTCAACAGGGTTTTTACTCGTTCTAAATGGTTTT
128 CTCA-CATTCCTTCAAAAGCCTTATTACTCATT-TAAATAGTTTT
* * * * *
171 ATGATCTCATAATTGATTTTAAGTTTAATTTTTTTTATATTTTTCATTAAAAAAAACTATAATTG
1 ATAATCTCATAATTGATTTTAAG-TTAAATTTTTTTATATTTTTCATTTAAACAGACTATAATTG
* *********** *
236 AATAG-CTGCCTTGAGAAACAT-A-AAGAAAAAAGNNNNNNNNNNTAAGAAAAGTCTATTTACAG
65 AAT-GTCTACCTTGAG-AA-ATGAGAAGAAAAAAGCATTCATTGACAAGAAAAGTCTATTTATAG
* * * *
298 CCTC-CAATTCTTTCAAAAGCCTGATTACTCGCTTTATAT-GATTTT
127 CCTCAC-ATTCCTTCAAAAGCCTTATTACTC-ATTTAAATAG-TTTT
********** * * * *
343 ATAATCTNNNNNNNNNNTTTAAGTTAAATTTTTTTATATTTTTGATTTAAATAGCCAATAATTGA
1 ATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATATTTTTCATTTAAACAGACTATAATTGA
* ** * * * * *
408 ATGTCTATCTCCAGAAACTTGA-AA-AAAAATA-CATTTATTGGCAAGAAAAGTCCATTTAAAGT
66 ATGTCTACCTTGAGAAA--TGAGAAGAAAAA-AGCATTCATTGACAAGAAAAGTCTATTTATAGC
* * ********
470 CACCCATTCCTTCAAAAG-CTTNNNNNNNNNNTTTAAATAGTTTT
128 CTCACATTCCTTCAAAAGCCTT--ATTACTCATTTAAATAGTTTT
* * *
514 CTAATCTCATAATTGATTTTAAGTTAAA-TTTTTTATATTTTTTA-TTAGAGCAGACTATAATTG
1 ATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATATTTTTCATTTA-AACAGACTATAATTG
** * * * ** * * * *
577 AATGTCTACCTCAAGAAACGTGAAG-AAAAAGTATTCGCTGGCAAGAAAATTCTATTTATAGTCA
65 AATGTCTACCTTGAGAAATGAGAAGAAAAAAGCATTCATTGACAAGAAAAGTCTATTTATAGCCT
* ** * *
641 CCCATTCCTTCTCAAGTCTTATTAATCGATTTAAATAGTTTT
130 CACATTCCTTCAAAAGCCTTATTACTC-ATTTAAATAGTTTT
* * *
683 ATAATCTCATAGTTGCTTTTAAGTTAAATTTTTTTACATTTTTCATTTTAAACAGACTATAATTG
1 ATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATATTTTTCA-TTTAAACAGACTATAATTG
* ** *
748 AATGTTTGTCTTGAGAAATGAGAAGAAAAAAGCATTCATTGATAAGAAAAGTCTATTTATAGCCT
65 AATGTCTACCTTGAGAAATGAGAAGAAAAAAGCATTCATTGACAAGAAAAGTCTATTTATAGCCT
* * *
813 CACATTCCTTCAATAGCCTTTTTACTCATTCTAAATAATTTT
130 CACATTCCTTCAAAAGCCTTATTACTCATT-TAAATAGTTTT
* * ********** * *
855 ATAATGTCATAATTGATTTTAAGTTCAANNNNNNNNNNTTTTTCATTAAAACAAACTATAATTGA
1 ATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATATTTTTCATTTAAACAGACTATAATTGA
* * * * * * * *
920 ATGTCTTCCTTAAGAAACGTGAAGAAAAAGGCATTGATTGGCAAAAAAAGTCTATTTATAGCCTT
66 ATGTCTACCTTGAGAAATGAGAAGAAAAAAGCATTCATTGACAAGAAAAGTCTATTTATAGCC-T
* *
985 C-TATTCCTTCAAAAGCCTTATTACTTACTTTAAA-AGGTTTT
130 CACATTCCTTCAAAAGCCTTATTACTCA-TTTAAATA-GTTTT
*
1026 ATAATCTAATAATTG
1 ATAATCTCATAATTG
1041 NNNNNNNNNN
Statistics
Matches: 658, Mismatches: 178, Indels: 67
0.73 0.20 0.07
Matches are distributed among these distances:
168 2 0.00
169 88 0.13
170 86 0.13
171 260 0.40
172 211 0.32
173 8 0.01
174 3 0.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.38
Consensus pattern (170 bp):
ATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATATTTTTCATTTAAACAGACTATAATTGA
ATGTCTACCTTGAGAAATGAGAAGAAAAAAGCATTCATTGACAAGAAAAGTCTATTTATAGCCTC
ACATTCCTTCAAAAGCCTTATTACTCATTTAAATAGTTTT
Done.