Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403167.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_834.0, 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: 1962
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.31
Warning! 265 characters in sequence are not A, C, G, or T
Found at i:840 original size:170 final size:171
Alignment explanation
Indices: 413--1337 Score: 517
Period size: 170 Copynumber: 5.4 Consensus size: 171
403 TTCAAGGCAG
* * * * * * *
413 ACATTCAATTATAGCTTGTTTTAGCTAAAAATGTAAAAAGATTTAACTTAAAATCAATTA-TGAG
1 ACATTCAATTATAACCTGTTTTAACCAAAAATTTAAAAA-ATTCAACTTAAAATCAATTACAGAG
* ** ** *
477 ATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGAGATG-CTATAAATAG-ACT
65 ATTACAAAACCATTTAAAGTGAGTAATAAGAATTTTGAAGGAATGAG-TGACTATAAATGGAAC-
* * ** * * ** ** *
540 TTTTTTTGTCAACAAATAGCTTTTTCTTTACGTTTTTCGAGGCAG
128 TTTCTTAGTCAATGAAT-GCTTTTTCTTCATGTTTTTTAAGATAA
* * * ** * * * *
585 TCAGTCAATTCTAATTTGTTTTCACTAAAAATATAAAAAATTCAACTTAAAATCAATTA-TGAGA
1 ACATTCAATTATAACCTGTTTTAACCAAAAATTTAAAAAATTCAACTTAAAATCAATTACAGAGA
* ********** * *
649 TTATANNNNNNNNNNAAGTGAGTAATAAGAATTTTAAAGGAATGAGTGACTATAAATGGAAATTT
66 TTACAAAACCATTTAAAGTGAGTAATAAGAATTTTGAAGGAATGAGTGACTATAAATGGAACTTT
*
714 CTTA-CCAATGAATGCTTTTTTCTTCATGTTTTTTAAGATAA
131 CTTAGTCAATGAATGC-TTTTTCTTCATGTTTTTTAAGATAA
* ** * *
755 ACATTTAATTAT-ATTTGTTTTAACCAAAAATTTAAAAACATTTAGCTTAAAATCAATTA-AGAG
1 ACATTCAATTATAACCTGTTTTAACCAAAAATTTAAAAA-ATTCAACTTAAAATCAATTACAGAG
* * **
818 ATTACAAAACCATTTAAAGTGAGTAATAAGACTTTCGAAGGTGTG-GATGACTATAAATGG-ACT
65 ATTACAAAACCATTTAAAGTGAGTAATAAGAATTTTGAAGGAATGAG-TGACTATAAATGGAACT
* ************* *
881 TT-TCTAGTCAATGAATGGTTTTTTCTTCNNNNNNNNNNNNNTAG
129 TTCT-TAGTCAATGAAT-GCTTTTTCTTCATGTTTTTTAAGATAA
** * * * * * * * *
925 ACATTCAATTATAATTTGTTCTAACAAAAAATGTGAAATAATTCAGCCTAAAATTAATTACA-AA
1 ACATTCAATTATAACCTGTTTTAACCAAAAAT-TTAAAAAATTCAACTTAAAATCAATTACAGAG
* * * * *
989 ATTATAAAACTATTTAAAGCGAGTAATAA-AGATTTTGAAGGCATGAGTAACTATAAAT--AAGC
65 ATTACAAAACCATTTAAAGTGAGTAATAAGA-ATTTTGAAGGAATGAGTGACTATAAATGGAA-C
* * * * *
1051 TTT-TCTAGTCAATGAATGACTTTTTCTTCACGTTTCTCAAGGTCA
128 TTTCT-TAGTCAATGAATG-CTTTTTCTTCATGTTTTTTAAGATAA
* * * **
1096 ATATTCAATTATAACCTGTTTTAACCAAAAATGTAAGAAAATTCAACTTAAAAT-AAATATTG-G
1 ACATTCAATTATAACCTGTTTTAACCAAAAATTTAA-AAAATTCAACTTAAAATCAATTACAGAG
* * * * * * *
1159 ATTATAAAATCATTTAAAGAGAGTGATAAG-GTTTCTGAAGGAATGAAT-AGCTATAAATAG-AC
65 ATTACAAAACCATTTAAAGTGAGTAATAAGAATTT-TGAAGGAATGAGTGA-CTATAAATGGAAC
* *
1221 TTTCCTTA-TCAATGAATAGCTTTTTCTTCATGGTTTTTAAGACAA
128 TTT-CTTAGTCAATGAAT-GCTTTTTCTTCATGTTTTTTAAGATAA
* * * * * *
1266 GCATTCAATTATAGCCTATTTTAACTAAAAATATAAAAATATTCAACTTAAAATCAATTA-TGAG
1 ACATTCAATTATAACCTGTTTTAACCAAAAATTTAAAAA-ATTCAACTTAAAATCAATTACAGAG
1330 ATTACAAA
65 ATTACAAA
1338 NNNNNNNNNN
Statistics
Matches: 574, Mismatches: 150, Indels: 59
0.73 0.19 0.08
Matches are distributed among these distances:
168 1 0.00
169 39 0.07
170 258 0.45
171 236 0.41
172 40 0.07
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.35
Consensus pattern (171 bp):
ACATTCAATTATAACCTGTTTTAACCAAAAATTTAAAAAATTCAACTTAAAATCAATTACAGAGA
TTACAAAACCATTTAAAGTGAGTAATAAGAATTTTGAAGGAATGAGTGACTATAAATGGAACTTT
CTTAGTCAATGAATGCTTTTTCTTCATGTTTTTTAAGATAA
Done.