Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403094.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_76.0, 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: 4307
ACGTcount: A:0.25, C:0.08, G:0.09, T:0.25
Warning! 1419 characters in sequence are not A, C, G, or T
Found at i:898 original size:172 final size:172
Alignment explanation
Indices: 592--974 Score: 529
Period size: 172 Copynumber: 2.2 Consensus size: 172
582 NNNNNNNNNN
*
592 GCGAGTAACAAGGCTTTTAAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCTATGAATGCCT
1 GCGAGTAATAAGGCTTTTAAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCTATGAATGCCT
* * * *
657 TTTTCATCACGTTTCTGGTGGTAGACAGTCAATTATAATCTGTTTCAACAAAAACTATACAAAGA
66 TTTTCATCACGTTTCTCGAGATAGACAATCAATTATAATCTGTTTCAACAAAAACTATACAAAGA
* *
722 ATTCAAATTAAAACT-AATTTTGAGATTATAAAATC-ATTTAAA
131 ATTCAAAATAAAA-TAAAATTTGAGATTATAAAA-CAATTTAAA
* *
764 GTGAGTAATAAGGCTTTTAAAGGAATATGTGACTATAAATGGACTTTTCTTGCCTATGAATGCCT
1 GCGAGTAATAAGGCTTTTAAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCTATGAATGCCT
* * * * * *
829 TTTTCATCATGTTTTTCGAGATAGACAATCAATTATAATCTGTTTTAACCCAAAA-TATGCAAGG
66 TTTTCATCACGTTTCTCGAGATAGACAATCAATTATAATCTGTTTCAA-CAAAAACTATACAAAG
* *
893 AATTCAAAATAAAATAAAATTTGAGATTATAACACAATTTGAA
130 AATTCAAAATAAAATAAAATTTGAGATTATAAAACAATTTAAA
* ** *
936 GCGAGTAATATGATTTTTAAAGGAATGGGTGACTATAAA
1 GCGAGTAATAAGGCTTTTAAAGGAATAGGTGACTATAAA
975 NNNNNNNNNN
Statistics
Matches: 185, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
171 2 0.01
172 178 0.96
173 5 0.03
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (172 bp):
GCGAGTAATAAGGCTTTTAAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCTATGAATGCCT
TTTTCATCACGTTTCTCGAGATAGACAATCAATTATAATCTGTTTCAACAAAAACTATACAAAGA
ATTCAAAATAAAATAAAATTTGAGATTATAAAACAATTTAAA
Found at i:1687 original size:172 final size:168
Alignment explanation
Indices: 1504--2095 Score: 453
Period size: 172 Copynumber: 3.5 Consensus size: 168
1494 NNNNNNNNNN
* * *
1504 AAATGAATTTTGAGTTTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTAATGGAATAGGTGAC
1 AAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTAA-GGAATAGGTGAC
* * * * *
1569 TATAAATGGTCTTTTCTTGCCAATATTTACCTTTTTCTTTACATTTCTCAAGGTAGACAGTCAAT
65 TATAAATGGACTTTTCTTGCCAATA-ATACCTTTTTCTTCACATTTCTCAAGGAAGACATTCAAT
* *
1634 TATATTTTATTTTACATGAAAATGTAAAACAAATTGAACTTA
129 TATAATTTATTTTACATAAAAATGTAAAA-AAATT-AACTTA
* * * ********* *
1676 AAATCAATTTTGAGAATATAAAA-CTTTTTAAAGCGAGTNNNNNNNNNNTTGAAGGAATAGGTGA
1 AAATCAATTATGAGATTATAAAATC-ATTTAAAGCGAGT-AATAAGGCTTTTAAGGAATAGGTGA
* * *
1740 CTATAAATGGACTTTTCATT-CCAATAAATGCCTATCTCTTCACATTT-TCCAAGGAAGACATTC
64 CTATAAATGGACTTTTC-TTGCCAAT-AATACCTTTTTCTTCACATTTCT-CAAGGAAGACATTC
*** * **
1803 AATTATGGCCTT-CTTTATC-TAAAAATGTAAAAAAAAAAAACTTA
126 AATTAT-AATTTATTTTA-CATAAAAATGT-AAAAAAATTAACTTA
* * * * * *
1847 AAATCAATTATGAGAGTATGAAACCTTTTAAAGCGAGTAATAAGGCTTTTGACGGAATGGGTGAC
1 AAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTT-AAGGAATAGGTGAC
********** * * * * *
1912 TNNNNNNNNNNTTTTCTTGTCAATGAATACTTTTTTCTTCACATTTCT--TGTGCAGACATTAAA
65 TATAAATGGACTTTTCTTGCCAAT-AATACCTTTTTCTTCACATTTCTCAAG-GAAGACATTCAA
*
1975 TTATAATCTATTTTA-ATAAAAAATGTAAAAAAATATAACTTA
128 TTATAATTTATTTTACAT-AAAAATGTAAAAAAAT-TAACTTA
* * *
2017 AAATTAATTATGAAATTATAAAATCAATTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGAC
1 AAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTT-AAGGAATAGGTGAC
2082 TATAAATGGACTTT
65 TATAAATGGACTTT
2096 NNNNNNNNNN
Statistics
Matches: 314, Mismatches: 89, Indels: 36
0.72 0.20 0.08
Matches are distributed among these distances:
169 10 0.03
170 96 0.31
171 80 0.25
172 114 0.36
173 14 0.04
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (168 bp):
AAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTAAGGAATAGGTGACT
ATAAATGGACTTTTCTTGCCAATAATACCTTTTTCTTCACATTTCTCAAGGAAGACATTCAATTA
TAATTTATTTTACATAAAAATGTAAAAAAATTAACTTA
Found at i:3886 original size:172 final size:171
Alignment explanation
Indices: 3504--3916 Score: 542
Period size: 172 Copynumber: 2.4 Consensus size: 171
3494 NNNNNNNNNN
*
3504 ACAAGAAAAGTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTATTACTCACTGTAAAAGGTTT
1 ACAAGAAAAGTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTATTACTCACTTTAAAAGGTTT
* * ** * * * **
3569 TATAATCTCATGATTGATTTTAAGTTGAATTTTTTTATATTTGTTATTAAAACAGATTATAATTA
66 TATATTATCAAAATTAATTTTAAGTTCAATTTTTTTACATTTGCCATTAAAACAGATTATAATTA
** * *
3634 AATGTCTAGCTCAAGAAACATGAAAAAAAAGATATTGATTG
131 AACATCTACCTCAAGAAACATGAAAAAAAAGATATTCATTG
* *
3675 ACAAGAAAAGTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTACTATTCACTTTAAAAGGTTT
1 ACAAGAAAAGTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTATTACTCACTTTAAAAGGTTT
3740 TATATTATCAAAATTAATTTTAAGTTCAATTTTTTTTACATTT-CCATGTAAAACAGATTATAAT
66 TATATTATCAAAATTAATTTTAAGTTCAA-TTTTTTTACATTTGCCAT-TAAAACAGATTATAAT
* * * *
3804 TGACCATCTACCTTAAGAAACAT-AAAGAAAAAGGTATTCATTG
129 TAAACATCTACCTCAAGAAACATGAAA-AAAAAGATATTCATTG
** * ** * *
3847 GTAAGAAAAGTCCATTTATAGTAACTCATTCCCTCAAAAGCTTTATTACTCGCTTTAAAAGGTTT
1 ACAAGAAAAGTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTATTACTCACTTTAAAAGGTTT
3912 TATAT
66 TATAT
3917 NNNNNNNNNN
Statistics
Matches: 210, Mismatches: 29, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
171 90 0.43
172 120 0.57
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (171 bp):
ACAAGAAAAGTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTATTACTCACTTTAAAAGGTTT
TATATTATCAAAATTAATTTTAAGTTCAATTTTTTTACATTTGCCATTAAAACAGATTATAATTA
AACATCTACCTCAAGAAACATGAAAAAAAAGATATTCATTG
Done.