Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402145.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5236.0, 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: 3687
ACGTcount: A:0.26, C:0.09, G:0.10, T:0.26
Warning! 1067 characters in sequence are not A, C, G, or T
Found at i:441 original size:172 final size:170
Alignment explanation
Indices: 145--983 Score: 753
Period size: 172 Copynumber: 4.9 Consensus size: 170
135 ATAAAATAAA
* * *
145 TTAAATGATTTTATAATCTCATAATTGATTTTACGTTCAATTATGTTTAC-ATTATTGGTTAAAA
1 TTAAATGGTTTTATAATCTCAAAATTGATTTTACGTTCAATT-TTTTTACAATT-TTGGTTAAAA
* * * * * * * * *
209 CAGATTATAATTAAATATTTACCTCAAGAAACGTGAGGAAAAAGGCATTTATTAGCAAGAAAAGT
64 CAGAGTATAATTGAATGTCTACCTC-AGAAACATGAAGAAAAAGCCATTCATTGGCAAGAAAAGT
* * * *
274 CCACTTATAGCCATCCATTCCTTCAAAAGCATTATTACTCACT
128 CCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACT
* *
317 TTAAATGGTTTTGTAATCTCAAAATTGATTTTACGTTCAATTTTATTTACAATTTTGGTTAAAAG
1 TTAAATGGTTTTATAATCTCAAAATTGATTTTACGTTCAATTTT-TTTACAATTTTGGTTAAAAC
* *
382 AGAGTATAATTGAATGTCTACCTCATGAAACATGAACAAAAAGCCATTCATTGGCAAGAAAAGAC
65 AGAGTATAATTGAATGTCTACCTCA-GAAACATGAAGAAAAAGCCATTCATTGGCAAGAAAAGTC
* * *
447 CATTTATAATCACCCATTCCTTCAAAAACCTTGTTACTCACT
129 CATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACT
********** * * *
489 TTNNNNNNNNNNATAATCTCAAAATTGATTTTAAGTTAAATTTGTTTTACATTTTTGGTTAAAAC
1 TTAAATGGTTTTATAATCTCAAAATTGATTTTACGTTCAATTT-TTTTACAATTTTGGTTAAAAC
* * **
554 AG-GTTATAATTGAATGTTTACCTTGAGAAATGTGAAG-AAAAGCCATTCATTGAG-AAGAAAAG
65 AGAG-TATAATTGAATGTCTACC-TCAGAAACATGAAGAAAAAGCCATTCATTG-GCAAGAAAAG
* * * * *
616 TCCATTTATTGTAACCCATTCTTTTAAAAGCCTTATTAATCACT
127 TCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACT
* * * *
660 TTAAATGGGTTTATAATCT-AATAATTGATTTT-CAGTTGAATTTTTCT-CTATTTTTGGTTAAA
1 TTAAATGGTTTTATAATCTCAA-AATTGATTTTAC-GTTCAATTTTTTTAC-AATTTTGGTTAAA
* * *
722 ATAGACTATAATTGAATGTCTACCTCAAATAACATGAAGAGAAAAG-CATTCATTGGCAAGACAA
63 ACAGAGTATAATTGAATGTCTACCTCAGA-AACATGAAGA-AAAAGCCATTCATTGGCAAGA-AA
* * * * ****
786 A-TGCATTTATAGTCTCCCAGTCCTTTAAAAGCCTTATTACTNNNN
125 AGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACT
****** * * *
831 NNNNNNGGTTTTATAATCTCAAAATTGATTCTAGGTTCAATTTGTTTTAGC-ATTATTGGCTAAA
1 TTAAATGGTTTTATAATCTCAAAATTGATTTTACGTTCAATTT-TTTTA-CAATT-TTGGTTAAA
* * * * **
895 ACAGATTATAAGTGAATGTCTACATCAAGAAACAAGAAGAAAAAGGTATTCATTGGCAAGAAAAG
63 ACAGAGTATAATTGAATGTCTACCTC-AGAAACATGAAGAAAAAGCCATTCATTGGCAAGAAAAG
*
960 TCTATTTATAGTCACCCATTCCTT
127 TCCATTTATAGTCACCCATTCCTT
984 NNNNNNNNNN
Statistics
Matches: 535, Mismatches: 107, Indels: 49
0.77 0.15 0.07
Matches are distributed among these distances:
169 4 0.01
170 46 0.09
171 163 0.30
172 240 0.45
173 79 0.15
174 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (170 bp):
TTAAATGGTTTTATAATCTCAAAATTGATTTTACGTTCAATTTTTTTACAATTTTGGTTAAAACA
GAGTATAATTGAATGTCTACCTCAGAAACATGAAGAAAAAGCCATTCATTGGCAAGAAAAGTCCA
TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACT
Found at i:612 original size:20 final size:21
Alignment explanation
Indices: 587--626 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
577 TGAGAAATGT
587 GAAGAAAAG-CCATTCATTGA
1 GAAGAAAAGTCCATTCATTGA
*
607 GAAGAAAAGTCCATTTATTG
1 GAAGAAAAGTCCATTCATTG
627 TAACCCATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (21 bp):
GAAGAAAAGTCCATTCATTGA
Found at i:795 original size:342 final size:333
Alignment explanation
Indices: 154--983 Score: 775
Period size: 343 Copynumber: 2.4 Consensus size: 333
144 ATTAAATGAT
* * *
154 TTTATAATCTCATAATTGATTTTACGTTCAATTATGTTTACATTATTGGTTAAAACAGATTATAA
1 TTTATAATCTCAAAATTGATTTTAAGTTAAATTATGTTTACATTATTGGTTAAAACAGATTATAA
* * *
219 TTAAATATTTACCTCAAGAAACGTGAGGAAAAAGGCATTTATTAGCAAGAAAAGTCCACTTATAG
66 TTAAATATTTACCTCAAGAAACGTGAAGAAAAAGCCATTCATTAGCAAGAAAAGTCCACTTATAG
* * * * *
284 CCATCCATTCCTTCAAAAGCATTATTACTCACTTTAAATGGTTTTGTAATCTCAAAATTGATTTT
131 CAACCCATTCCTTCAAAAGCATTATTAATCACTTTAAATGGGTTTATAATCTCAAAATTGATTTT
* * *
349 ACGTTCAATTTTATTTACAATTTTGGTTAAAAGAGAGTATAATTGAATGTCTACCTCATGAAACA
196 ACGTTCAATTTTATCTACAATTTTGGTTAAAAGAGACTATAATTGAATGTCTACCTCATAAAACA
*
414 TGAACAAAAAGCCATTCATTGGCAAGAAAAGACCATTTATAATCACCCATTCCTTCAAAAACCTT
261 TGAACAAAAAGCCATTCATTGGCAAGAAAAGA-CATTTATAATCACCCAGTCCTTCAAAAACCTT
*
479 GTTACTCAC
325 ATTACTCAC
*
488 TTTNNNNNNNNNNATAATCTCAAAATTGATTTTAAGTTAAATT-TGTTTTACATTTTTGGTTAAA
1 TTT----------ATAATCTCAAAATTGATTTTAAGTTAAATTATG-TTTACATTATTGGTTAAA
* * * ** *
552 ACAGGTTATAATTGAATGTTTACCTTGAGAAATGTGAAG-AAAAGCCATTCATTGAG-AAGAAAA
55 ACAGATTATAATTAAATATTTACCTCAAGAAACGTGAAGAAAAAGCCATTCATT-AGCAAGAAAA
* * * * * *
615 GTCCATTTATTGTAACCCATTCTTTTAAAAGCCTTATTAATCACTTTAAATGGGTTTATAATCT-
119 GTCCACTTATAGCAACCCATTCCTTCAAAAGCATTATTAATCACTTTAAATGGGTTTATAATCTC
* * *
679 AATAATTGATTTT-CAGTTGAATTTT-TCT-CTATTTTTGGTTAAAATAGACTATAATTGAATGT
184 AA-AATTGATTTTAC-GTTCAATTTTATCTAC-AATTTTGGTTAAAAGAGACTATAATTGAATGT
* * *
741 CTACCTCA-AATAACATGAAGAGAAAAG-CATTCATTGGCAAGACAAATG-CATTTATAGTCTCC
246 CTACCTCATAA-AACATGAACA-AAAAGCCATTCATTGGCAAGA-AAA-GACATTTATAATCACC
* * ***
803 CAGTCCTTTAAAAGCCTTATTACTNNNNNNNNNNGGT
307 CAGTCCTTCAAAAACCTTATTACT----------CAC
* * * *
840 TTTATAATCTCAAAATTGATTCTAGGTTCAATT-TGTTTTAGCATTATTGGCTAAAACAGATTAT
1 TTTATAATCTCAAAATTGATTTTAAGTTAAATTATG-TTTA-CATTATTGGTTAAAACAGATTAT
* * * * * ** ** * * *
904 AAGTGAATGTCTACATCAAGAAACAAGAAGAAAAAGGTATTCATTGGCAAGAAAAGTCTATTTAT
64 AATTAAATATTTACCTCAAGAAACGTGAAGAAAAAGCCATTCATTAGCAAGAAAAGTCCACTTAT
969 AGTC-ACCCATTCCTT
129 AG-CAACCCATTCCTT
984 NNNNNNNNNN
Statistics
Matches: 402, Mismatches: 61, Indels: 56
0.77 0.12 0.11
Matches are distributed among these distances:
334 3 0.01
341 2 0.00
342 132 0.33
343 144 0.36
344 118 0.29
352 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.35
Consensus pattern (333 bp):
TTTATAATCTCAAAATTGATTTTAAGTTAAATTATGTTTACATTATTGGTTAAAACAGATTATAA
TTAAATATTTACCTCAAGAAACGTGAAGAAAAAGCCATTCATTAGCAAGAAAAGTCCACTTATAG
CAACCCATTCCTTCAAAAGCATTATTAATCACTTTAAATGGGTTTATAATCTCAAAATTGATTTT
ACGTTCAATTTTATCTACAATTTTGGTTAAAAGAGACTATAATTGAATGTCTACCTCATAAAACA
TGAACAAAAAGCCATTCATTGGCAAGAAAAGACATTTATAATCACCCAGTCCTTCAAAAACCTTA
TTACTCAC
Done.