Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400889.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4055.0, 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: 1690
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.26
Warning! 471 characters in sequence are not A, C, G, or T
Found at i:642 original size:172 final size:169
Alignment explanation
Indices: 1--1149 Score: 767
Period size: 171 Copynumber: 6.7 Consensus size: 169
* * * * * * * *
1 TTCATGTTTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAAAATGT-ATAAATAATTC
1 TTCACGTTTC-CAAGGCAAACATTCAATTATAATCTGTTCTAACTAAAAACGTCA-AAA-AGTTC
** * * * * *
65 AAATTTAAATCAATTTTGAGATTATAAAATCATTTGAAA-TGAGTAATAAGGCTTTTAAAAGAAT
63 AACCTAAAATCAATTATGAGATTATAAAACCATTT-AAAGTGAGTAATAAGGCTTTTGAAGGAAT
** * * * *
129 AAGTGACTGTAAATGGA-TTTTTCTTAGCAATGAATACCTTTTAC
127 GGGTGACTATAAATAGACTTTTT-TT-CCAATGAATACCTTTTTC
*** * * * * * * * *
173 TTTGTGTTTCTCGA-GCTAGACATTCATTTATAATCTGTTTTAACCAAAAATGT-AAAAACTTTG
1 TTCACGTTTC-CAAGGC-AAACATTCAATTATAATCTGTTCTAACTAAAAACGTCAAAAA-GTTC
* * * * * * ***
236 AACTTAACAT-ATATTTTTAGATTATAAAACCATTTTAAGTGAGTAATAAGGCTTTTAAAGGNNN
63 AACCTAAAATCA-ATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT
******* * * * * *
300 NNNNNNNTATAAATGGACTTTTCTTGCTAATAAATGCCTTTTTC
127 GGGTGACTATAAATAGACTTTT-TTTCCAATGAATACCTTTTTC
* * * * * *
344 TTAAGGTTTCCTAATGCAGATATTCAATTATATTCTGTTCTAACTAAAAACGTCAAAAAGTTCAA
1 TTCACGTTTCC-AAGGCAAACATTCAATTATAATCTGTTCTAACTAAAAACGTCAAAAAGTTCAA
********** *
409 CCTAAAATCAATTATGNNNNNNNNNNACCATTTAAAGTGAGTAATAAGGCTTTTCAAGGAATGGG
65 CCTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGG
*
474 TGACTATCAATAGACTTTTTTTACCAATGAATACCTTTTTC
130 TGACTATAAATAGACTTTTTTT-CCAATGAATACCTTTTTC
* * *
515 TTCATGTTTACCAAGGCAAACATTCAATTATAATCTGTTCTAACTAAAAAATGTGAAAAAGTTCA
1 TTCACGTTT-CCAAGGCAAACATTCAATTATAATCTGTTCTAACT-AAAAACGTCAAAAAGTTCA
* * *
580 AGCTAAAATCAATTATGAGATTATAAAACTATTTAAAATGAGTAATAAGG-TCTTTGAAGGAATG
64 ACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCT-TTTGAAGGAATG
** * * *
644 GGTGACTATAAGGAGACTTTTTTTTTCCAAAGAATGCCTTTCTC
128 GGTGACTATAAATAGAC--TTTTTTTCCAATGAATACCTTTTTC
* ** * * * * *
688 TTCACATTTCTTGAGGTAGACATTCAATTATAATCTGTTCTAACCAAAAACGTAAAAAAATT-AA
1 TTCACGTTTC-CAAGGCAAACATTCAATTATAATCTGTTCTAACTAAAAACGTCAAAAAGTTCAA
**********
752 CCTAAAATCAATTATGAGATTATAAAACCATNNNNNNNNNNTAATAAGGCTTTTGAAGGAATGGG
65 CCTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGG
* * * * * *
817 TAACTATAAATGGACTTTCTTGT-GAGTGAATGCCTTTTTC
130 TGACTATAAATAGACTTT-TTTTCCAATGAATACCTTTTTC
* * * * * * * ********
857 TTCACCTTTTTCAAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGT-ANNNNNNNNNN
1 TTCA-CGTTTCCAAGGCAAACATTCAATTATAATCTGTTCTAACTAAAAACGTCA--AAAAGTTC
* ** * *
921 AA-ATATAAATCAATTAAAAGATTATGAAACCATTTCAAGTGAGTAATAAGGCTTTTGAAGGAAT
63 AACCTA-AAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT
* *
985 GGGT-ACCTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTC
127 GGGTGA-CTATAAATAGACTTTT-TTTCCAATGAATACCTTTTTC
* *
1029 TTCAGGTTTCCTAAGGCAAACATTCAATTATAATCTGTTCTAAC-AAAAACGTCAAAAAGTTAAA
1 TTCACGTTTCC-AAGGCAAACATTCAATTATAATCTGTTCTAACTAAAAACGTCAAAAAGTTCAA
* * *
1093 CCAAAAATTAACTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAA
65 CCTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAA
1150 NNNNNNNNNN
Statistics
Matches: 754, Mismatches: 193, Indels: 62
0.75 0.19 0.06
Matches are distributed among these distances:
168 1 0.00
169 56 0.07
170 67 0.09
171 368 0.49
172 203 0.27
173 52 0.07
174 7 0.01
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.34
Consensus pattern (169 bp):
TTCACGTTTCCAAGGCAAACATTCAATTATAATCTGTTCTAACTAAAAACGTCAAAAAGTTCAAC
CTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGT
GACTATAAATAGACTTTTTTTCCAATGAATACCTTTTTC
Done.