Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402204.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5292.0, 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, 885
Length: 1476
ACGTcount: A:0.29, C:0.09, G:0.10, T:0.27
Warning! 363 characters in sequence are not A, C, G, or T
Found at i:462 original size:171 final size:171
Alignment explanation
Indices: 13--832 Score: 691
Period size: 171 Copynumber: 4.8 Consensus size: 171
3 TTACAAAACT
* * * *
13 ATTTAAAGCGAGTAATAAGGCTTTCAAAGGCATGGGTGACTAGAAATAGACTTTTCTTACCAATT
1 ATTTAAAGCGAGTAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATG
* **********
78 GATATCTTTTTCTTCAGGTTTCTCAAGGCAAACATTCAATTATAATCTGTTTTNNNNNNNNNNAT
66 GATATCTTTTTCTTCACGTTTCTCAAGGCAAACATTCAATTATAATCTGTTTTAATACAAAATAT
* *
143 AAAAAAGT-TCAACTTAAAACTAATTATGAGATTATAAAATC
131 AAAAAAATCT-AAATTAAAACTAATTATGAGATTATAAAATC
* *
184 ATTTAAAGCGAGTAATAATGGCTTT-AAAGGTATGGGTGACTGTAAATGGACTTTTCTTGCCAAT
1 ATTTAAAGCGAGTAATAA-GGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAAT
* **********
248 GGATATCTTTTTCTTCACCTTTCTCAANNNNNNNNNNCAATTATAATCTGTTTTAATACAAAATA
65 GGATATCTTTTTCTTCACGTTTCTCAAGGCAAACATTCAATTATAATCTGTTTTAATACAAAATA
*
313 TAAAAAAATCTAAATTAAAA-TAAATTATGAGGTTATAAAATC
130 TAAAAAAATCTAAATTAAAACT-AATTATGAGATTATAAAATC
* * * *
355 TTTTAAAGCAAGTAATAAAGCTTTCAAAGGCATGGGTAACTATAAATGGACTTTTCTTGCCAATG
1 ATTTAAAGCGAGTAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATG
* * * * ********
420 GATATTTTTTTCTCCATGTTTCTCAAGGCAAACACTCAATTATAATCTGTTTTAATANNNNNNNN
66 GATATCTTTTTCTTCACGTTTCTCAAGGCAAACATTCAATTATAATCTGTTTTAATACAAAATAT
** * * * *
485 NNAAAAATCTAAATTCAAA-TCAATTATAAGGTTATAAAACC
131 AAAAAAATCTAAATTAAAACT-AATTATGAGATTATAAAATC
** ** ** * * *
526 ATTTAAAGCGTTTAATAAGGCTTTTGAAGATATCGGTGACTATAAATGTACTTTTCTTGCTAATG
1 ATTTAAAGCGAGTAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATG
* * * * * *** *
591 GGTATCTTTTTCTACACATTTCTCGAGGTAAACAAAAAATTATAATCTGTTTTAAT-CGTAAATA
66 GATATCTTTTTCTTCACGTTTCTCAAGGCAAACATTCAATTATAATCTGTTTTAATAC-AAAATA
* * * **
655 -AAAAAAAGTTTAACTTAAAACTAATTATGAGATTAAAAAANN
130 TAAAAAAA-TCTAAATTAAAACTAATTATGAGATTATAAAATC
********* * * * * *
697 NNNNNNNNAGAGTAATAAGGCTTTCGAAGGCATGGGTAACTAGAAATGGACCTTTCTTACCAATG
1 ATTTAAAGCGAGTAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATG
* * *
762 GATATCTTTTTCTTCACGTTTCTTAAGGAAAATATTCAATTATAATCTGTTTTAATA-ATAAATA
66 GATATCTTTTTCTTCACGTTTCTCAAGGCAAACATTCAATTATAATCTGTTTTAATACA-AAATA
826 TAAAAAA
130 TAAAAAA
833 GTTCAACTTA
Statistics
Matches: 502, Mismatches: 137, Indels: 19
0.76 0.21 0.03
Matches are distributed among these distances:
170 11 0.02
171 477 0.95
172 14 0.03
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.34
Consensus pattern (171 bp):
ATTTAAAGCGAGTAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATG
GATATCTTTTTCTTCACGTTTCTCAAGGCAAACATTCAATTATAATCTGTTTTAATACAAAATAT
AAAAAAATCTAAATTAAAACTAATTATGAGATTATAAAATC
Found at i:639 original size:342 final size:336
Alignment explanation
Indices: 14--823 Score: 774
Period size: 342 Copynumber: 2.4 Consensus size: 336
4 TACAAAACTA
* * *
14 TTTAAAGCGAGTAATAAGGCTTTCAAAGGCATGGGTGACTAGAAATAGACTTTTCTTACCAATTG
1 TTTAAAGC-AGTAATAAGGCTTTCAAAGGCATGGGTAACTAGAAATGGACTTTTCTTACCAATGG
* ****
79 ATATCTTTTTCTTCAGGTTTCTCAAGGCAAACATTCAATTATAATCTGTTTTNNNNNNNNNNATA
65 ATATCTTTTTCTTCACGTTTCTCAAGGCAAACATTCAATTATAATCTGTTTT------AATAATA
* * *
144 AAAAAGTTCAACTTAAAACTAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAATGGCTTT
124 AAAAAGTTCAAATTAAAACTAATTATAAGATTATAAAACCATTTAAAGCGAGTAATAATGGCTTT
* * * * *
209 AAAGGTATGGGTGACTGTAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACCTTTCTCA
189 AAAGATATCGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTACACATTTCTCA
***********
274 ANNNNNNNNNNCAATTATAATCTGTTTTAATAC-AAAATATAAAAAAA-TCTAAATTAAAA-TAA
254 AGGTAAACAAAAAATTATAATCTGTTTTAAT-CGAAAATA-AAAAAAAGTCTAAATTAAAACT-A
* *
336 ATTATGAGGTT-ATAAAATCT
316 ATTATGAGATTAAAAAAATCT
* * *
356 TTTAAAGCAAGTAATAAAGCTTTCAAAGGCATGGGTAACTATAAATGGACTTTTCTTGCCAATGG
1 TTTAAAGC-AGTAATAAGGCTTTCAAAGGCATGGGTAACTAGAAATGGACTTTTCTTACCAATGG
* * * * **
421 ATATTTTTTTCTCCATGTTTCTCAAGGCAAACACTCAATTATAATCTGTTTTAATANNNNNNNNN
65 ATATCTTTTTCTTCACGTTTCTCAAGGCAAACATTCAATTATAATCTGTTTTAATA-------AT
* * * **
486 NAAAAA--TCTAAATTCAAA-TCAATTATAAGGTTATAAAACCATTTAAAGCGTTTAATAA-GGC
123 AAAAAAGTTC-AAATTAAAACT-AATTATAAGATTATAAAACCATTTAAAGCGAGTAATAATGGC
* * * *
547 TTTTGAAGATATCGGTGACTATAAATGTACTTTTCTTGCTAATGGGTATCTTTTTCTACACATTT
186 -TTTAAAGATATCGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTACACATTT
* * * *
612 CTCGAGGTAAACAAAAAATTATAATCTGTTTTAATCGTAAATAAAAAAAAGTTTAACTTAAAACT
250 CTCAAGGTAAACAAAAAATTATAATCTGTTTTAATCGAAAATAAAAAAAAGTCTAAATTAAAACT
****
677 AATTATGAGATTAAAAAANNNNN
315 AATTATGAGATTAAAAAA-ATCT
***** * *
700 NNNNNAG-AGTAATAAGGCTTTCGAAGGCATGGGTAACTAGAAATGGACCTTTCTTACCAATGGA
1 TTTAAAGCAGTAATAAGGCTTTCAAAGGCATGGGTAACTAGAAATGGACTTTTCTTACCAATGGA
* * *
764 TATCTTTTTCTTCACGTTTCTTAAGGAAAATATTCAATTATAATCTGTTTTAATAATAAA
66 TATCTTTTTCTTCACGTTTCTCAAGGCAAACATTCAATTATAATCTGTTTTAATAATAAA
824 TATAAAAAAG
Statistics
Matches: 378, Mismatches: 75, Indels: 37
0.77 0.15 0.08
Matches are distributed among these distances:
335 2 0.01
341 14 0.04
342 350 0.93
343 10 0.03
344 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.34
Consensus pattern (336 bp):
TTTAAAGCAGTAATAAGGCTTTCAAAGGCATGGGTAACTAGAAATGGACTTTTCTTACCAATGGA
TATCTTTTTCTTCACGTTTCTCAAGGCAAACATTCAATTATAATCTGTTTTAATAATAAAAAAGT
TCAAATTAAAACTAATTATAAGATTATAAAACCATTTAAAGCGAGTAATAATGGCTTTAAAGATA
TCGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTACACATTTCTCAAGGTAAA
CAAAAAATTATAATCTGTTTTAATCGAAAATAAAAAAAAGTCTAAATTAAAACTAATTATGAGAT
TAAAAAAATCT
Done.