Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398170.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1475.0, 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: 2161
ACGTcount: A:0.20, C:0.08, G:0.07, T:0.23
Warning! 915 characters in sequence are not A, C, G, or T
Found at i:417 original size:170 final size:170
Alignment explanation
Indices: 1--990 Score: 796
Period size: 170 Copynumber: 5.8 Consensus size: 170
* * * * *
1 TAAATGA-TTTTATAACCTCATAATT-GATTTTAATTTTAA-TTTTTTATATTTTTTTATTAACA
1 TAAATGAGTTTT-TAATCTCATAATTAG-TTTTAAGTTGAACTTTTTTACA-TTTTTTATTAAAA
* * * * * * ******
63 TAGATTATAATTTATTGTTTTCCTTGAGAAACATGAAGAAAAAGATATCCATTGGCAAGNNNNNN
63 CAGATTATAATTGAATGTCTACC-TCAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGT
**** * * * * * *
128 NNNNTTATAGTCACCCATGCCTTCAAAAGGCTTATTACTCGATT
127 CCATTTATAGTCATCCATACCTTCGAAAGCCTTATGACTCGCTT
* * ** * *********
172 TAAAT-AGTTTTTTAATATTATAATTAGTTTTAAGTTGAACTTTTTTGTA-ATTTTNNNNNNNNN
1 TAAATGAG-TTTTTAATCTCATAATTAGTTTTAAGTTGAACTTTTTTACATTTTTTATTAAAACA
* * * * *
235 NATTATAATTGAATGACTACCTCGAGAAACATGAAGAAAAAGATATTCAGTGGCATGAAAAGTCC
65 GATTATAATTGAATGTCTACCTC-AGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCC
* * * *
300 TTTTGTAGTCATCCATGCCTTCGAAAGCCTTATTACTCGCTT
129 ATTTATAGTCATCCATACCTTCGAAAGCCTTATGACTCGCTT
* * *****
342 TAAATGA-TATTTAATCTCATAACTAGTTTTAAGTTGAACTTTTTTACATTTTTTATTAANNNNN
1 TAAATGAGTTTTTAATCTCATAATTAGTTTTAAGTTGAACTTTTTTACATTTTTTATTAAAACAG
***** * * * * * **
406 NNNNNAATTGAATGTCTGCCTTAAGGAACGTGAAGAAAAATATATCCATTGGCAAGAATCGTCCA
66 ATTATAATTGAATGTCTACC-TCAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCA
*
471 TTTATACTCATCCATACCTTCGAAAGCCTTATGACTCGCTT
130 TTTATAGTCATCCATACCTTCGAAAGCCTTATGACTCGCTT
* *
512 TAAAT-AGTTTTCTAATCTCATAATTGGTTTTAAGTTGAACTTTTTTAAATTTTTTATTAAAACA
1 TAAATGAGTTTT-TAATCTCATAATTAGTTTTAAGTTGAACTTTTTTACATTTTTTATTAAAACA
* * * *
576 GATTATAATTGAATGTCTTCCTCAAAAAAATGAAGAAAATGATATCCATTGGCAAGAAAAGTCCA
65 GATTATAATTGAATGTCTACCTCAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCA
*
641 TTTATTGTCA-CTCATACCTTCGAAAGCCTTATGACTCGCTT
130 TTTATAGTCATC-CATACCTTCGAAAGCCTTATGACTCGCTT
*
682 TAAATGATTTTTTAATCTCATAATTTAG-TTTAAGTTGAACTTTTTTACATTTTTTATTAAAACA
1 TAAATGAGTTTTTAATCTCATAA-TTAGTTTTAAGTTGAACTTTTTTACATTTTTTATTAAAACA
* * * * * * *
746 GATTATAATTAAACGTCTGCCTCAAAAAATATAAAGAAAATGATATCCATTGGCAAGAAAAGTCC
65 GATTATAATTGAATGTCTACCTC-AGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCC
* ********** * *
811 ATTTATAGTCACCCATANNNNNNNNNNCCTTATTACTCGCCT
129 ATTTATAGTCATCCATACCTTCGAAAGCCTTATGACTCGCTT
* * * * * *
853 TAAAT-ATTTTTATAACCTCATAATT-GATTTTAAGTTCAATTTTTTTATAATTTTTATTAAAAC
1 TAAATGAGTTTT-TAATCTCATAATTAG-TTTTAAGTTGAACTTTTTTACATTTTTTATTAAAAC
* * * * *
916 AGATTACAATTAAATGTCTATCTTGAGAAACTTGAAGAAAAAGATATCCATTGGCAAGAAAAGTC
64 AGATTATAATTGAATGTCTA-CCTCAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTC
981 CATTTATAGT
128 CATTTATAGT
991 NNNNNNNNNN
Statistics
Matches: 664, Mismatches: 136, Indels: 38
0.79 0.16 0.05
Matches are distributed among these distances:
169 39 0.06
170 341 0.51
171 268 0.40
172 16 0.02
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.38
Consensus pattern (170 bp):
TAAATGAGTTTTTAATCTCATAATTAGTTTTAAGTTGAACTTTTTTACATTTTTTATTAAAACAG
ATTATAATTGAATGTCTACCTCAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCAT
TTATAGTCATCCATACCTTCGAAAGCCTTATGACTCGCTT
Found at i:801 original size:341 final size:340
Alignment explanation
Indices: 236--990 Score: 879
Period size: 341 Copynumber: 2.2 Consensus size: 340
226 NNNNNNNNNN
* * * * * *
236 ATTATAATTGAATGACTACCTCGAGAAACATGAAGAAAAAGATATTCAGTGGCATGAAAAGTCCT
1 ATTATAATTGAATGTCTTCCTC-AGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCA
* * *
301 TTTGTAGTCATCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGATATTTAATCTCATAACT
65 TTTATAGTCATCCATACCTTCGAAAGCCTTATGACTCGCTTTAAATGATATTTAATCTCATAACT
********** * * * *
366 AGTTTTAAGTTGAACTTTTTTACATTTTTTATTAANNNNNNNNNNAATTGAATGTCTGCCTTAAG
130 AGTTTTAAGTTGAACTTTTTTACATTTTTTATTAAAACAGATTATAATTAAACGTCTGCCTCAAA
* * * ** *
431 GAACGTGAAGAAAAATATATCCATTGGCAAGAATCGTCCATTTATACTCATCCATACCTTCGAAA
195 AAACATAAAGAAAAATATATCCATTGGCAAGAAAAGTCCATTTATACTCACCCATACCTTCGAAA
* * * * *
496 GCCTTATGACTCGCTTTAAATAGTTTTCTAATCTCATAATTGGTTTTAAGTTGAACTTTTTTA-A
260 GCCTTATGACTCGCCTTAAATAGTTTTATAACCTCATAATTGATTTTAAGTTCAACTTTTTTATA
560 ATTTTTTATTAAAACAG
325 A-TTTTTATTAAAACAG
* * *
577 ATTATAATTGAATGTCTTCCTCAAAAAAATGAAGAAAATGATATCCATTGGCAAGAAAAGTCCAT
1 ATTATAATTGAATGTCTTCCTCAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCAT
* *
642 TTATTGTCA-CTCATACCTTCGAAAGCCTTATGACTCGCTTTAAATGATTTTTTAATCTCATAAT
66 TTATAGTCATC-CATACCTTCGAAAGCCTTATGACTCGCTTTAAATGA-TATTTAATCTCATAA-
*
706 TTAG-TTTAAGTTGAACTTTTTTACATTTTTTATTAAAACAGATTATAATTAAACGTCTGCCTCA
128 CTAGTTTTAAGTTGAACTTTTTTACATTTTTTATTAAAACAGATTATAATTAAACGTCTGCCTCA
* * ******
770 AAAAATATAAAG-AAAATGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATANNNNNN
193 AAAAACATAAAGAAAAAT-ATATCCATTGGCAAGAAAAGTCCATTTATACTCACCCATACCTTCG
**** * * *
834 NNNNCCTTATTACTCGCCTTAAATATTTTTATAACCTCATAATTGATTTTAAGTTCAATTTTTTT
257 AAAGCCTTATGACTCGCCTTAAATAGTTTTATAACCTCATAATTGATTTTAAGTTCAACTTTTTT
899 ATAATTTTTATTAAAACAG
322 ATAATTTTTATTAAAACAG
* * * * *
918 ATTACAATTAAATGTCTATCTTGAGAAACTTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCA
1 ATTATAATTGAATGTCT-TCCTCAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCA
983 TTTATAGT
65 TTTATAGT
991 NNNNNNNNNN
Statistics
Matches: 344, Mismatches: 64, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
339 1 0.00
340 82 0.24
341 208 0.60
342 53 0.15
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.36
Consensus pattern (340 bp):
ATTATAATTGAATGTCTTCCTCAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCAT
TTATAGTCATCCATACCTTCGAAAGCCTTATGACTCGCTTTAAATGATATTTAATCTCATAACTA
GTTTTAAGTTGAACTTTTTTACATTTTTTATTAAAACAGATTATAATTAAACGTCTGCCTCAAAA
AACATAAAGAAAAATATATCCATTGGCAAGAAAAGTCCATTTATACTCACCCATACCTTCGAAAG
CCTTATGACTCGCCTTAAATAGTTTTATAACCTCATAATTGATTTTAAGTTCAACTTTTTTATAA
TTTTTATTAAAACAG
Done.