Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398982.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2264.0, 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, 689
Length: 1149
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.34
Warning! 44 characters in sequence are not A, C, G, or T
Found at i:564 original size:170 final size:171
Alignment explanation
Indices: 1--1149 Score: 643
Period size: 171 Copynumber: 6.7 Consensus size: 171
* * * * *
1 TAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAAT-GAACTTTTTTTTCCAAATAA
1 TAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG-ACTTTTCTTACC-AATAA
** * * * ** ** * * *
65 ATGGGTTTTTATACATGTTTCTTAAGG-CAGTTATTCAATTATAGTCAGTTTTAACTAAAAATGT
64 ATGTATTTTTCTTCACGTTTCTCGAGGTC-GACATTCAATTATAATCTGTTTTAACCAAAAATGT
* * * **
129 GAAAAACATTGAACTTAAAATCAATTTTGAGATTATAAAATTATT
128 -AAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAACCATT
********** * * * *
174 TAAAACGAGTANNNNNNNNNNTGAAGAAATGAGTGACTATAAATGGACTTTTCTTACCAATGAAT
1 TAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATAAAT
*** * * ** * * *
239 ACCTTTTTCTTCACATTTCT-TATCATAGACATTCAATAATAAT-TTTTTTAACCAAAACA-GTA
66 GTATTTTTCTTCACGTTTCTCGA-GGTCGACATTCAATTATAATCTGTTTTAACCAAAA-ATGTA
* * * ******
301 AAAAACATTGAAGTTAAAATCAATTTTGAGATTATAAANNNNNN
129 AAAAA-ATTAAACTTAAAATCAATTATGAGATTATAAAACCATT
****** * * * * * *
345 NNNNGTGAGTAATAAGGCTTTTCAAGGAATTGGTGGCTATAAATAGACTTTTCTTGCTAATGAAT
1 TAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATAAAT
* * * * *
410 GTATTTTTCTTCATGTTTCTCGAGGTCGACATTCCATTATACTTTGTTTTAACCCAAAATGT-AA
66 GTATTTTTCTTCACGTTTCTCGAGGTCGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAA
* *
474 AAAACTAAACTTAAAATCCATTATGAGATTATAAAACCATT
131 AAAATTAAACTTAAAATCAATTATGAGATTATAAAACCATT
* * * *
515 TAAAACGAGTAATAAGGCTTTTGAACGAATGGGAGATTATAATTAGACTTTTCTT-CCAAATAAA
1 TAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACC-AATAAA
* * * * * * **
579 TG-AGTTTTTCTACACGTTTCTCGAAG-CAAGCAATCAATTATAGTCAGTTTTAATAAAAAATGT
65 TGTA-TTTTTCTTCACGTTTCTCGAGGTCGA-CATTCAATTATAATCTGTTTTAACCAAAAATGT
* * * *******
642 AAAAAAATTCAACTCAAAATCAATTATGAGTTTATAANNNNNNN
128 AAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAACCATT
******* *
686 NNNNNNNAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTGCTTACCAATAAAT
1 TAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATAAAT
** * * * * * * *
751 GCCTTTTTCTTCACATTTCACAAGGTAGACATTCAATTATAATCTATTATAACCAAAAATATAAA
66 GTATTTTTCTTCACGTTTCTCGAGGTCGACATTCAATTATAATCTGTTTTAACCAAAAATGT-AA
* * *
816 AAAAATTAAACTTAAAATAAATTTTGAGATTATAAAACTATT
130 AAAAATTAAACTTAAAATCAATTATGAGATTATAAAACCATT
* * * * * *
858 TAAAGCGACTAATAAGGCTTTTGAAAGAGTGGGTGACTATAAATAAACTTTTCTTACCAATGAAT
1 TAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATAAAT
* * * ** * * **
923 GT-TTTTTCTTCTCGTTTCTCAAAGAAGACATTCAATTATAGTCTATTTTAATAAAAAATGTAAA
66 GTATTTTTCTTCACGTTTCTCGAGGTCGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAA
********** *
987 AAAATTNNNNNNNNNNTCAATTATGAGATTATAAGACCATT
131 AAAATTAAACTTAAAATCAATTATGAGATTATAAAACCATT
** * * * * * *
1028 TAAAGTGAGTGATAAGGCTTTTG-AGAGAATGAGAGACTCTAAATGGACTTTTCTT-CCAAAGAA
1 TAAAACGAGTAATAAGGCTTTTGAAG-GAATGGGTGACTATAAATAGACTTTTCTTACC-AATAA
* * * * * * * *
1091 ATGAATTTTT-TCACACGTTTC-CTAAGGTGGGCTTTCAATTATAGTTTGTTTTAACCAAA
64 ATGTATTTTTCT-TCACGTTTCTC-GAGGTCGACATTCAATTATAATCTGTTTTAACCAAA
Statistics
Matches: 723, Mismatches: 232, Indels: 44
0.72 0.23 0.04
Matches are distributed among these distances:
169 7 0.01
170 206 0.28
171 333 0.46
172 135 0.19
173 41 0.06
174 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.34
Consensus pattern (171 bp):
TAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATAAAT
GTATTTTTCTTCACGTTTCTCGAGGTCGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAA
AAAATTAAACTTAAAATCAATTATGAGATTATAAAACCATT
Found at i:663 original size:341 final size:330
Alignment explanation
Indices: 349--992 Score: 729
Period size: 341 Copynumber: 1.9 Consensus size: 330
339 NNNNNNNNNN
* * * * * * *
349 GTGAGTAATAAGGCTTTTCAAGGAATTGGTGGCTATAAATAGACTTTTCTTGCTAATGAATGTAT
1 GTGAGTAATAAGGCTTTTCAAGGAATGGGTGACTATAAATAGACTTTGCTTACCAATAAATGCAT
** * * * * * * * * * *
414 TTTTCTTCATGTTTCTCGAGGTCGACATTCCATTATACTTTGTTTTAACCCAAAATGT-AAAAAA
66 TTTTCTTCACATTTCACAAGGTAGACATTCAATTATAATCTATTATAACCAAAAATATAAAAAAA
** * *
478 CTAAACTTAAAATCCATTATGAGATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAACGA
131 CTAAACTTAAAATAAATTATGAGATTATAAAACCATTTAAAACGACTAATAAGGCTTTTGAAAGA
* * * *
543 ATGGGAGATTATAATTAGACTTTTCTT-CCAAATAAATGAGTTTTTCTACACGTTTCTCGAAGCA
196 ATGGGAGACTATAAATAAACTTTTCTTACC-AATAAATG-GTTTTTCTACACGTTTCTCAAAG-A
607 AG-CAATCAATTATAGTC-AGTTTTAATAAAAAATGTAAAAAAATTCAACTCAAAATCAATTATG
258 AGACAATCAATTATAGTCTA-TTTTAATAAAAAATGTAAAAAAATTCAACTCAAAATCAATTATG
670 AGTTTATAA
322 AGTTTATAA
*** *
679 NNNNNNNNNNNNNNAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTGCTTACC
1 -----------GTGAGTAATAAGGCTTTTCAAGGAATGGGTGACTATAAATAGACTTTGCTTACC
*
744 AATAAATGCCTTTTTCTTCACATTTCACAAGGTAGACATTCAATTATAATCTATTATAACCAAAA
55 AATAAATGCATTTTTCTTCACATTTCACAAGGTAGACATTCAATTATAATCTATTATAACCAAAA
* * * *
809 ATATAAAAAAAATTAAACTTAAAATAAATTTTGAGATTATAAAACTATTTAAAGCGACTAATAAG
120 ATAT-AAAAAAACTAAACTTAAAATAAATTATGAGATTATAAAACCATTTAAAACGACTAATAAG
* * * * * *
874 GCTTTTGAAAGAGTGGGTGACTATAAATAAACTTTTCTTACCAATGAATGTTTTTTCTTCTCGTT
184 GCTTTTGAAAGAATGGGAGACTATAAATAAACTTTTCTTACCAATAAATGGTTTTTCTACACGTT
*
939 TCTCAAAGAAGACATTCAATTATAGTCTATTTTAATAAAAAATGTAAAAAAATT
249 TCTCAAAGAAGACAATCAATTATAGTCTATTTTAATAAAAAATGTAAAAAAATT
993 NNNNNNNNNN
Statistics
Matches: 255, Mismatches: 43, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
341 102 0.40
342 58 0.23
343 93 0.36
344 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (330 bp):
GTGAGTAATAAGGCTTTTCAAGGAATGGGTGACTATAAATAGACTTTGCTTACCAATAAATGCAT
TTTTCTTCACATTTCACAAGGTAGACATTCAATTATAATCTATTATAACCAAAAATATAAAAAAA
CTAAACTTAAAATAAATTATGAGATTATAAAACCATTTAAAACGACTAATAAGGCTTTTGAAAGA
ATGGGAGACTATAAATAAACTTTTCTTACCAATAAATGGTTTTTCTACACGTTTCTCAAAGAAGA
CAATCAATTATAGTCTATTTTAATAAAAAATGTAAAAAAATTCAACTCAAAATCAATTATGAGTT
TATAA
Done.