Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400192.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3406.0, 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: 1873
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.30
Warning! 295 characters in sequence are not A, C, G, or T
Found at i:318 original size:171 final size:170
Alignment explanation
Indices: 6--772 Score: 630
Period size: 171 Copynumber: 4.5 Consensus size: 170
1 AAATC
* * *
6 CTTT-GAAGGCATGGGTGACTATAAATGGACTTTTCTTGTCAATGGATATGTTTTTCTTCATGTT
1 CTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTT
* * ** ** * **************
70 TTTCGAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAANNNNNNNNNNNNNN
66 TCTCAAGACAAACATTCAATTATAATC-AATTTAAAAAAAAATATAAAAAAATTCAAATTAAAAT
*
135 NAATTATGAGGTTAT-AAAATCATTTAAAGCGAGTAATAAAG
130 CAATTATGAGGTTATAAAAAT-ATTTAAAGCGAGTAATAAAG
** * *
176 CTTTTAAAGGCAAGGGTGACTATAAATGGACTTTGT-ATGCCAATGGATATCTTTTTCTTCACGT
1 CTTTCGAAGGCATGGGTGACTATAAATGGACTTT-TCTTGCCAATGGATATCTTTTTCTTCACGT
** * ***********
240 TTCTTGAGGCAAACATTCAATTATAATNNNNNNNNNNNNAAAATATAAAAAAATTCAAATTAAAA
65 TTCTCAAGACAAACATTCAATTATAAT-CAATTTAAAAAAAAATATAAAAAAATTCAAATTAAAA
* *
305 TCAATTGTGAGGTTATAAAAATATTTAATGCGAGTAATAAAG
129 TCAATTATGAGGTTATAAAAATATTTAAAGCGAGTAATAAAG
* **********
347 CTTTCGAAGGCATGTGTGACTATAAATGGACTTTTNNNNNNNNNNGATATCTTTTTCTTCACGTT
1 CTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTT
* * * * * * * * *
412 TCTCAAGATAGAGATTCATTTATAATCTATTTCAATAAAAATTATAAAAAATTTCAAATCAAAAT
66 TCTCAAGACAAACATTCAATTATAATCAATTT-AAAAAAAAATATAAAAAAATTCAAATTAAAAT
* * *
477 CAATTGTGAGGTTACAAAAATATTTAAAGCGAGTAATAAGG
130 CAATTATGAGGTTATAAAAATATTTAAAGCGAGTAATAAAG
* * * * *
518 CTTTGGAAGGCATGGGTCACCATAAATGGACTTTTCTTGCCAATGGATATCTTTTTGTTCAGGTT
1 CTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTT
* * * * *
583 TCACGAGACAGACATTTAATTATAAT-ATATTTTAATAAAAAATATAAAAAAATTCAAATTAAAA
66 TCTCAAGACAAACATTCAATTATAATCA-A-TTTAAAAAAAAATATAAAAAAATTCAAATTAAAA
* * *
647 TCAAATATGAGTTTGTAAAAATATTTAAAGCGAGTAAT-AAG
129 TCAATTATGAGGTTATAAAAATATTTAAAGCGAGTAATAAAG
* * * *
688 CCTTCCGAAGGCATGAGCT-ACTATAAATGGACTTTTCTTACCAATGGATATC-TTTTCTTCATG
1 -CTTTCGAAGGCATG-GGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACG
*
751 TTTCTCAAGGCAAACATTCAAT
64 TTTCTCAAGACAAACATTCAAT
773 NNNNNNNNNN
Statistics
Matches: 469, Mismatches: 118, Indels: 20
0.77 0.19 0.03
Matches are distributed among these distances:
170 33 0.07
171 425 0.91
172 11 0.02
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.34
Consensus pattern (170 bp):
CTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTT
TCTCAAGACAAACATTCAATTATAATCAATTTAAAAAAAAATATAAAAAAATTCAAATTAAAATC
AATTATGAGGTTATAAAAATATTTAAAGCGAGTAATAAAG
Found at i:740 original size:342 final size:341
Alignment explanation
Indices: 136--759 Score: 761
Period size: 342 Copynumber: 1.8 Consensus size: 341
126 NNNNNNNNNN
* * * *
136 AATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAAGCTTTTAAAGGCAAGGGTGACTATAA
1 AATTATGAGGTTAAAAAATCATTTAAAGCGAGTAATAAAGCTTTGAAAGGCAAGGGTCACCATAA
** *
201 ATGGACTTTGTATGCCAATGGATATCTTTTTCTTCACGTTTCTTGAGGCAAACATTCAATTATAA
66 ATGGACTTTGTATGCCAATGGATATCTTTTTCTTCACGTTTCACGAGACAAACATTCAATTATAA
************ * *
266 TNNNNNNNNNNNNAAAATATAAAAAAATTCAAATTAAAATCAATTGTGAGGTTATAAAAATATTT
131 TATATTTTAATAAAAAATATAAAAAAATTCAAATTAAAATCAAATATGAGGTTATAAAAATATTT
* * * **********
331 AATGCGAGTAATAAAGCTTTCGAAGGCATGTGTGACTATAAATGGACTTTTNNNNNNNNNNGATA
196 AAAGCGAGTAATAAAGCTTCCGAAGGCATGAGTGACTATAAATGGACTTTTCTTACCAATGGATA
396 TCTTTTTCTTCACGTTTCTCAAGATAGAGATTCATTTATAATCTATTTCAATAAAAATTATAAAA
261 TC-TTTTCTTCACGTTTCTCAAGATAGAGATTCATTTATAATCTATTTCAATAAAAATTATAAAA
461 AATTTCAAATCAAAATC
325 AATTTCAAATCAAAATC
* * * *
478 AATTGTGAGGTTACAAAAAT-ATTTAAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTCACCATA
1 AATTATGAGGTTA-AAAAATCATTTAAAGCGAGTAATAAAGCTTTGAAAGGCAAGGGTCACCATA
* * * * *
542 AATGGACTTT-TCTTGCCAATGGATATCTTTTTGTTCAGGTTTCACGAGACAGACATTTAATTAT
65 AATGGACTTTGT-ATGCCAATGGATATCTTTTTCTTCACGTTTCACGAGACAAACATTCAATTAT
* *
606 AATATATTTTAATAAAAAATATAAAAAAATTCAAATTAAAATCAAATATGAGTTTGTAAAAATAT
129 AATATATTTTAATAAAAAATATAAAAAAATTCAAATTAAAATCAAATATGAGGTTATAAAAATAT
671 TTAAAGCGAGTAAT-AAGCCTTCCGAAGGCATGAGCT-ACTATAAATGGACTTTTCTTACCAATG
194 TTAAAGCGAGTAATAAAG-CTTCCGAAGGCATGAG-TGACTATAAATGGACTTTTCTTACCAATG
*
734 GATATCTTTTCTTCATGTTTCTCAAG
257 GATATCTTTTCTTCACGTTTCTCAAG
760 GCAAACATTC
Statistics
Matches: 232, Mismatches: 46, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
341 23 0.10
342 203 0.88
343 6 0.03
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.33
Consensus pattern (341 bp):
AATTATGAGGTTAAAAAATCATTTAAAGCGAGTAATAAAGCTTTGAAAGGCAAGGGTCACCATAA
ATGGACTTTGTATGCCAATGGATATCTTTTTCTTCACGTTTCACGAGACAAACATTCAATTATAA
TATATTTTAATAAAAAATATAAAAAAATTCAAATTAAAATCAAATATGAGGTTATAAAAATATTT
AAAGCGAGTAATAAAGCTTCCGAAGGCATGAGTGACTATAAATGGACTTTTCTTACCAATGGATA
TCTTTTCTTCACGTTTCTCAAGATAGAGATTCATTTATAATCTATTTCAATAAAAATTATAAAAA
ATTTCAAATCAAAATC
Done.