Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399396.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2662.0, 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: 2141
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.34
Warning! 265 characters in sequence are not A, C, G, or T
Found at i:531 original size:170 final size:170
Alignment explanation
Indices: 1--628 Score: 547
Period size: 170 Copynumber: 3.7 Consensus size: 170
* * * * * ** *
1 AAGTCCATTTATAGTCACTCA-AGCTTTCAAAAGCTTTATTACTTGCTTTAAATATTTTTATAAT
1 AAGTTCATTTATAGTCACTCATA-CCTTC-GAAGCCTTATTGCTCACTTTAAATAGTTTTATAAT
* * * * *
65 CTCATAATTGATTTTTAAGTT-AAGTTTTTTAATATTTTTAGTTAAAACAGATTATATTTGAATG
64 CTCATAATTGA-TTCTAAGTTGAAGTTTTTTAATATTTTT-TTTAAAATAGATTATAATTAAATG
** * *
129 TCTG-CTTGGGAAATGTGAAG-AAATAGTCATTCATTGGCAAGAA
127 TCTGCCTTGGGAAACATGAAGCAAA-AGCCATTCATTGGGAAGAA
* * * * * * ** * * *
172 AAGATAATTTATAGTCTCCCATGCCTTCAAAAGCCTTATTAG-TCTGTTCAAATGGTGTTATAAT
1 AAGTTCATTTATAGTCACTCATACCTTC-GAAGCCTTATT-GCTCACTTTAAATAGTTTTATAAT
* * ** * * * *
236 CTCATAATTGATTCTAAGTTGAATTTTTTTTATATTATTGATTCAACTAGATTGTAATTACATGT
64 CTCATAATTGATTCTAAGTTGAAGTTTTTTAATATT-TTTTTTAAAATAGATTATAATTAAATGT
* * * * * *
301 ATGCCTTAGGAAACTTGAAGCAAAAGCTATCCATT-AGAAGGAA
128 CTGCCTTGGGAAACATGAAGCAAAAGCCATTCATTGGGAA-GAA
* **
344 AAGTCCATTTATAGTCACTCATACCTTCGTAAGTATTATTGCTCACTTTAAATAGTTTTATAATC
1 AAGTTCATTTATAGTCACTCATACCTTCG-AAGCCTTATTGCTCACTTTAAATAGTTTTATAATC
* * *
409 TCATAATTGATTCTAAGTTGAA-TTTTTTAATATTTTTTTTAAAATATATTATAACTAAATATCT
65 TCATAATTGATTCTAAGTTGAAGTTTTTTAATATTTTTTTTAAAATAGATTATAATTAAATGTCT
*
473 GCCTTGGGAAACATGAAGCAAAACCCATTCATTGGGAAGAA
130 GCCTTGGGAAACATGAAGCAAAAGCCATTCATTGGGAAGAA
* * * *
514 AAGTTCATTTATAGTCACTCA-AGCCTTTGAGAGCCTTATTACTCGCTTTAAAT-GTTTTTAGAA
1 AAGTTCATTTATAGTCACTCATA-CCTTCGA-AGCCTTATTGCTCACTTTAAATAG-TTTTATAA
* * * *
577 TATCATAATTGATTTTAAGTTGAA-TTTTTTTATATTTTTTATTAAAACAGAT
63 TCTCATAATTGATTCTAAGTTGAAGTTTTTTAATATTTTTT-TTAAAATAGAT
629 AATANNNNNN
Statistics
Matches: 363, Mismatches: 80, Indels: 28
0.77 0.17 0.06
Matches are distributed among these distances:
169 3 0.01
170 146 0.40
171 115 0.32
172 96 0.26
173 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (170 bp):
AAGTTCATTTATAGTCACTCATACCTTCGAAGCCTTATTGCTCACTTTAAATAGTTTTATAATCT
CATAATTGATTCTAAGTTGAAGTTTTTTAATATTTTTTTTAAAATAGATTATAATTAAATGTCTG
CCTTGGGAAACATGAAGCAAAAGCCATTCATTGGGAAGAA
Found at i:1551 original size:172 final size:168
Alignment explanation
Indices: 858--1912 Score: 636
Period size: 171 Copynumber: 6.2 Consensus size: 168
848 NNNNNNNNNN
* * * *
858 GTTTTCATAATCTCATAATTGATTTTAACTTGAATTTTTTTACATATTTGATTAAAAT-GTATTA
1 GTTTT-ATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATAT-TTTGGTTAAAATAG-AATA
* * *** * * * * *
922 AAATTGAATGTCTGGTTTGGGAAACATGAAGCAAAAGCTATCCATTGGCAAGAGAAGTCCATTTA
63 TATTTGAATGTCTACCTTGAGAAACATGAAGAAAAAGCCATCCATTAGCAAGAAAAGTCCA-TTA
* * * * * * * *
987 TAGTCACTCAAGTCTTTGAAATCCTTATTGCTCGCTTTAAATG
127 TAGTCACTCATGCCTTCGAAAGCTTTATTACT-GCCTTAAATA
* * * * *** * * *
1030 GTTTTATAATCTCATAATTAATTTTGAGTTAAATTTTTTTACATTTTCAACTAAACTA-ATTAAA
1 GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTT-GGTTAAAATAGAATATA
* ** * * * *
1094 ATTGAATGTCTGA-CTAAAGAGACATGAAGAAAAGGCCATTCACTAGCAAGAAAAGTCCATTTAT
65 TTTGAATGTCT-ACCTTGAGAAACATGAAGAAAAAGCCATCCATTAGCAAGAAAAGTCCA-TTAT
********** * *
1158 ANNNNNNNNNNCCTTCGAAAGCCTTATTACTTGCTTTAAATA
128 AGTCACTCATGCCTTCGAAAGCTTTATTAC-TGCCTTAAATA
* * * * ** *
1200 GTTTTATAA-CTTCATAATTGATTTTAAATTGGATTGTTTTACATTTTTTATTAAAATATG-TTA
1 GTTTTATAATC-TCATAATTGATTTTAAGTTGAATTTTTTTATA-TTTTGGTTAAAATA-GAATA
* * * * * *** * * *
1263 TAATTCACTATCTA-CTTCAGGAATTGTGAAGCAAAAGCCATCCATTTGCAGGAAAAGTCCATTT
63 TATTTGAATGTCTACCTTGA-GAAACATGAAGAAAAAGCCATCCATTAGCAAGAAAAGTCCA-TT
* * * *
1327 ATAGTCACTCAAGCCTTCGAAAG-TCATATTACTTGCTTTAAATG
126 ATAGTCACTCATGCCTTCGAAAGCT-TTATTAC-TGCCTTAAATA
* * * *
1371 GCTTTATAATATCAGAATTGATTTTAAGTTGATTTTTTTTTATATTTTGGGTTAAAATAGAATAT
1 GTTTTATAATCTCATAATTGATTTTAAGTTGA-ATTTTTTTATATTTT-GGTTAAAATAGAATAT
* * *
1436 ATTTGAATGTCTACCTTGAGAAACTTGAAGAAAAAGCCATTCATTAGCAAGAAAAGTTCACTTAT
64 ATTTGAATGTCTACCTTGAGAAACATGAAGAAAAAGCCATCCATTAGCAAGAAAAGTCCA-TTAT
* *
1501 AGTCACCCATGCCTTCAAAAGCTTTATTACCTGCCTTAAATA
128 AGTCACTCATGCCTTCGAAAGCTTTATTA-CTGCCTTAAATA
********** *
1543 GTTTTATAATCTCATAATT-ANNNNNNNNNNAAATTTTTTTATATTATTGGTTAAAATAGATTAT
1 GTTTTATAATCTCATAATTGA-TTTTAAGTTGAATTTTTTTATATT-TTGGTTAAAATAGAATAT
* * * * * * *
1607 AATTGAAAGTTTGCCTT-AGAAAACGTGAAGCAAAAGCCATCCATTAGAAAGAAAAGTCCATTCA
64 ATTTGAATGTCTACCTTGAG-AAACATGAAGAAAAAGCCATCCATTAGCAAGAAAAGTCCATT-A
* * * * * *
1671 TAATCACTTATGCCTTTGAAAGCATTATTACTCGCTTTAAATG
127 TAGTCACTCATGCCTTCGAAAGCTTTATTACT-GCCTTAAATA
********** * * *
1714 GTTTTATNNNNNNNNNNTTGATTTGAAGTTGAATTTTTTTACATTTTTTGTTAAAATAG-ATAGT
1 GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATA-TTTTGGTTAAAATAGAATA-T
* * * * *
1778 ATTTGAATGTCTACCTTGGGAAACATGAAGAAAAATCCATTCATTGGCAAGAAAAGTGCATCTAT
64 ATTTGAATGTCTACCTTGAGAAACATGAAGAAAAAGCCATCCATTAGCAAGAAAAGTCCAT-TAT
** *
1843 AGTCACTTGTGCCTTCGAAAGCTTTATTACTTCCTTTAAATA
128 AGTCACTCATGCCTTCGAAAGCTTTATTACTGCC-TTAAATA
1885 GTTTTATAATCTCATAATTGATTTTAAG
1 GTTTTATAATCTCATAATTGATTTTAAG
1913 NNNNNNNNNN
Statistics
Matches: 666, Mismatches: 189, Indels: 57
0.73 0.21 0.06
Matches are distributed among these distances:
169 1 0.00
170 139 0.21
171 394 0.59
172 126 0.19
173 6 0.01
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.38
Consensus pattern (168 bp):
GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTGGTTAAAATAGAATATAT
TTGAATGTCTACCTTGAGAAACATGAAGAAAAAGCCATCCATTAGCAAGAAAAGTCCATTATAGT
CACTCATGCCTTCGAAAGCTTTATTACTGCCTTAAATA
Done.