Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398104.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1408.0, 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: 8704
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.20
Warning! 3933 characters in sequence are not A, C, G, or T
Found at i:1845 original size:171 final size:171
Alignment explanation
Indices: 1036--1872 Score: 603
Period size: 171 Copynumber: 4.9 Consensus size: 171
1026 NNNNNNNNNN
* * * * **
1036 AATCAATTAT-AAGATTATAAAAATCATATAAAGCGAGTAATAAGGCTTTCGAAGACATTG-GTG
1 AATCAATTATGACG-TTATAAAAAT-ATTTAAAGCAAGTAATAAGGCTTTTGAAGGTA-TGAGTG
* ** ** * * *
1099 GCTATAAATGGACTTTTCTTACCAATAGATATCTTTTTCTTCATGTTTCCCAAGGTAGACATTCA
63 ACTATAAATAAACTTTTCTTGTCAATGGATATCTTTTTCTTCATGTTTCCTATGGTAGACATTCA
********** * * * * * *
1164 ATTNNNNNNNNNNTTAATAAAACATGTAAAAAATTTTAATTTAA
128 ATTATAATATGTTTTAACAAAAAATATAAAAAAATTCAACTTAA
* * * ** * **
1208 AATCAATTATGAAGTTAT-CAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGACATGGGTGGT
1 AATCAATTATGACGTTATAAAAAT-ATTTAAAGCAAGTAATAAGGCTTTTGAAGGTATGAGTGAC
** * * * *
1272 TATAAATGGACTTTTCTTGCCAACGGATAGT-TTTTTCTTCACGTTTCTTGA-GGTAGACATTCA
65 TATAAATAAACTTTTCTTGTCAATGGATA-TCTTTTTCTTCATGTTTCCT-ATGGTAGACATTCA
*********** *
1335 ATTATAANNNNNNNNNNTAAAAAATATAAAAATATTCAACTTAA
128 ATTATAATATGTTTTAACAAAAAATATAAAAAAATTCAACTTAA
* * * * *
1379 AATCAATTATGACGTTATAAAAATATTTAAAGCAAGTAACAATGCTTTTGAAGCTATGGGTGGCT
1 AATCAATTATGACGTTATAAAAATATTTAAAGCAAGTAATAAGGCTTTTGAAGGTATGAGTGACT
* * * * *
1444 ATAAATGAACTTTTCATGTTAATGGATATCTTTTTCTTCACGTTT-CAAGTGGTAGACATTCAAT
66 ATAAATAAACTTTTCTTGTCAATGGATATCTTTTTCTTCATGTTTCCTA-TGGTAGACATTCAAT
* * * **********
1508 TATAATTTATTTTAATAAAAAATATAANNNNNNNNNNCTTAA
130 TATAATATGTTTTAACAAAAAATATAAAAAAATTCAACTTAA
** * *
1550 AATCAATTATG-CGATTAT-AAAATAATTTAAAGCGTGCAATAAGGCTTTCGAA-GTCATGAGTG
1 AATCAATTATGACG-TTATAAAAAT-ATTTAAAGCAAGTAATAAGGCTTTTGAAGGT-ATGAGTG
* * * * * * *
1612 ACTATAAATAGACTTTACTTGCCAATGGATATCTTTCTCTCCATGTTTCTTGTGGTAGACATTCA
63 ACTATAAATAAACTTTTCTTGTCAATGGATATCTTTTTCTTCATGTTTCCTATGGTAGACATTCA
*
1677 ATTATAATATGTTTTAACAAAAAATATAAAAAAATTTAACTTAA
128 ATTATAATATGTTTTAACAAAAAATATAAAAAAATTCAACTTAA
* * * **
1721 AATCAGTTATGACGTTATAAAAATTTTTCAAGCAAGTAATAAGGCTTTTGAAGGTATTTGTGACT
1 AATCAATTATGACGTTATAAAAATATTTAAAGCAAGTAATAAGGCTTTTGAAGGTATGAGTGACT
* * *
1786 ATAAATAAACTTTTCTTATCAATGGATATCTTTTTCTTCATGTTTCCTATGGCAGACATTCAAAT
66 ATAAATAAACTTTTCTTGTCAATGGATATCTTTTTCTTCATGTTTCCTATGGTAGACATTCAATT
* * *
1851 ATTATCTGTTTTAACAGAAAAT
131 ATAATATGTTTTAACAAAAAAT
1873 GTAGCAAAAC
Statistics
Matches: 535, Mismatches: 115, Indels: 31
0.79 0.17 0.05
Matches are distributed among these distances:
169 1 0.00
170 11 0.02
171 491 0.92
172 29 0.05
173 3 0.01
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.36
Consensus pattern (171 bp):
AATCAATTATGACGTTATAAAAATATTTAAAGCAAGTAATAAGGCTTTTGAAGGTATGAGTGACT
ATAAATAAACTTTTCTTGTCAATGGATATCTTTTTCTTCATGTTTCCTATGGTAGACATTCAATT
ATAATATGTTTTAACAAAAAATATAAAAAAATTCAACTTAA
Found at i:1894 original size:342 final size:342
Alignment explanation
Indices: 1201--1903 Score: 755
Period size: 342 Copynumber: 2.1 Consensus size: 342
1191 AAAAAATTTT
* * * *
1201 AATTTAAAATCAATTATGAAGTTATCAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGACATG
1 AATTTAAAATCAATTATGAAGTTATAAAATAATTTAAAGCGAGCAATAAGGCTTTCGAAGACATG
* ** * * * *
1266 GGTGGTTATAAATGGACTTTTCTTGCCAACGGATAGTTTTTTCTTCACGTTTCTTGAGGTAGACA
66 AGTGACTATAAATAGACTTTACTTGCCAACGGATAGTTTTCTCTCCACGTTTCTTGAGGTAGACA
*********** *
1331 TTCAATTATAANNNNNNNNNNTAAAAAATATAAAAATATTCAACTTAAAATCAATTATGACGTTA
131 TTCAATTATAATATGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGACGTTA
* * *
1396 TAAAAATATTTAAAGCAAGTAACAATGCTTTTGAAGCTATGGGTGGCTATAAATGAACTTTTCAT
196 TAAAAATATTTAAAGCAAGTAACAAGGCTTTTGAAGCTATGGGTGACTATAAATAAACTTTTCAT
* * * * * *
1461 GTTAATGGATATCTTTTTCTTCACGTTTCAAGTGGTAGACATTCAATTATAATTTATTTTAATAA
261 ATCAATGGATATCTTTTTCTTCACGTTTCAAGTGGCAGACATTCAAATATAATCTATTTTAACAA
********
1526 AAAATATAANNNNNNNN
326 AAAATATAACAAAACTC
*** * * *
1543 NNCTTAAAATCAATTATG-CGATTATAAAATAATTTAAAGCGTGCAATAAGGCTTTCGAAGTCAT
1 AATTTAAAATCAATTATGAAG-TTATAAAATAATTTAAAGCGAGCAATAAGGCTTTCGAAGACAT
* * *
1607 GAGTGACTATAAATAGACTTTACTTGCCAATGGATA-TCTTTCTCTCCATGTTTCTTGTGGTAGA
65 GAGTGACTATAAATAGACTTTACTTGCCAACGGATAGT-TTTCTCTCCACGTTTCTTGAGGTAGA
* *
1671 CATTCAATTATAATATGTTTTAACAAAAAATATAAAAAAATTTAACTTAAAATCAGTTATGACGT
129 CATTCAATTATAATATGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGACGT
* * * * **
1736 TATAAAAATTTTTCAAGCAAGTAATAAGGCTTTTGAAGGTATTTGTGACTATAAATAAACTTTTC
194 TATAAAAATATTTAAAGCAAGTAACAAGGCTTTTGAAGCTATGGGTGACTATAAATAAACTTTTC
* * * * *
1801 TTATCAATGGATATCTTTTTCTTCATGTTTCCTA-TGGCAGACATTCAAATATTATCTGTTTTAA
259 ATATCAATGGATATCTTTTTCTTCACGTTT-CAAGTGGCAGACATTCAAATATAATCTATTTTAA
* * *
1865 CAGAAAATGTAGCAAAACTC
323 CAAAAAATATAACAAAACTC
* *
1885 AATTTAAAATTAAATATGA
1 AATTTAAAATCAATTATGA
1904 TATTAAAAAA
Statistics
Matches: 287, Mismatches: 70, Indels: 7
0.79 0.19 0.02
Matches are distributed among these distances:
341 2 0.01
342 283 0.99
343 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.36
Consensus pattern (342 bp):
AATTTAAAATCAATTATGAAGTTATAAAATAATTTAAAGCGAGCAATAAGGCTTTCGAAGACATG
AGTGACTATAAATAGACTTTACTTGCCAACGGATAGTTTTCTCTCCACGTTTCTTGAGGTAGACA
TTCAATTATAATATGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGACGTTA
TAAAAATATTTAAAGCAAGTAACAAGGCTTTTGAAGCTATGGGTGACTATAAATAAACTTTTCAT
ATCAATGGATATCTTTTTCTTCACGTTTCAAGTGGCAGACATTCAAATATAATCTATTTTAACAA
AAAATATAACAAAACTC
Done.