Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399158.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2431.0, 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: 2889
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.27
Warning! 837 characters in sequence are not A, C, G, or T
Found at i:685 original size:169 final size:171
Alignment explanation
Indices: 313--690 Score: 383
Period size: 171 Copynumber: 2.2 Consensus size: 171
303 NNNNNNNNNN
* *
313 ATGATATCCATTGGCAAGAGAAGTACATTTAT-TGTCACCCATGCCTTCGAAAGCCTTATTACTC
1 ATGATATCCATTGGCAAGAGAAGTCCATTTATAT-TCACCCATGCCTTCGAAAGCCTTATTACAC
*********
377 GCATTAAAAAGTTTTGTAATCACATAATTAGTTTTAAGTTGANNNNNNNNNNATTTTTTATTAAA
65 GCATTAAAAAGTTTTGTAATCACATAATTAGTTTTAAGTTGA-AACTTTTTTATTTTTTATTAAA
** ** * * * *
442 ACAGATTATAACTGTATGTTTACCTCGAGAAATGTGAAGAAAA
129 ACAGATTATAACTAAATGGCTACCTCAAAAAACGTGAAAAAAA
* * *
485 A-GATATCCATT-CCGAAGAAAAGTCAATTTATATTCACCCATGCCTTCGAAAGCCTTATTACAC
1 ATGATATCCATTGGC-AAGAGAAGTCCATTTATATTCACCCATGCCTTCGAAAGCCTTATTACAC
** * * * *
548 GC-TTGCAATGCTTTTTTAATCTCATGATTAG-TTTAAGTTG-AACTTTTTTATATTTTTATTAA
65 GCATTAAAAAG-TTTTGTAATCACATAATTAGTTTTAAGTTGAAACTTTTTTAT-TTTTTATTAA
* *
610 AACAGATTATAATTAAATGGCTGCCTCAAAAAACGT-AAAAAAA
128 AACAGATTATAACTAAATGGCTACCTCAAAAAACGTGAAAAAAA
*
653 ATGATATCCATTGGCAAGAGAAGTCCATTTATAATCAC
1 ATGATATCCATTGGCAAGAGAAGTCCATTTATATTCAC
691 NNNNNNNNNN
Statistics
Matches: 166, Mismatches: 34, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
168 9 0.05
169 67 0.40
170 16 0.10
171 72 0.43
172 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.34
Consensus pattern (171 bp):
ATGATATCCATTGGCAAGAGAAGTCCATTTATATTCACCCATGCCTTCGAAAGCCTTATTACACG
CATTAAAAAGTTTTGTAATCACATAATTAGTTTTAAGTTGAAACTTTTTTATTTTTTATTAAAAC
AGATTATAACTAAATGGCTACCTCAAAAAACGTGAAAAAAA
Found at i:2353 original size:170 final size:170
Alignment explanation
Indices: 1991--2514 Score: 482
Period size: 170 Copynumber: 3.1 Consensus size: 170
1981 TAGTTTTAAG
* * ** * * * * *
1991 TTGAACTTTTTT-ATATTTATTGTTAAAACATATTATAATTGTTTATTTATCTCAAGAAACGTGA
1 TTGAA-TTTTTTAATATTT-TTATTAAAACAGATTATAATTGAATGTCTACCTGAAGAAACATGA
* * * *
2055 AGAAAAAGATATCCATTAGCAA-AAAAATTCTATTTATAGTCACCCATGCCTTCAAAAGCCTTAT
64 AGAAAAAGATATCCATTGGCAAGAAAAA-TCCATTTATAGTAACTCATGCCTTCAAAAGCCTTAT
********** *
2119 TACTCACTNNNNNNNNNNTTATAACCTCATAATTGATTTTAAT
128 TACTCACTTTAAATGATTTTATAACCTCATAATTGATTTTAGT
** * *
2162 TTGAATTTTTTTGTATTTTTATTAGAATAGATTATAATTGAATGTCTACCTGAAGAAACATGAAG
1 TTGAATTTTTTAATATTTTTATTAAAACAGATTATAATTGAATGTCTACCTGAAGAAACATGAAG
* * * ** *
2227 AAAAATATATCCATTGGTAAGAAAAGTCCATTTATAGTCGC-CATGCCTTCAAAAGCCTTGTTAC
66 AAAAAGATATCCATTGGCAAGAAAAATCCATTTATAGTAACTCATGCCTTCAAAAGCCTTATTAC
*
2291 TCATTTTAAATGATTTTATAACCTCATAATTGATTTTAGT
131 TCACTTTAAATGATTTTATAACCTCATAATTGATTTTAGT
**********
2331 TTGAATTTTTTAATATTTTTTATTAAAACAGATTATAATTGAATGTNNNNNNNNNNAAACATGAA
1 TTGAATTTTTTAATA-TTTTTATTAAAACAGATTATAATTGAATGTCTACCTGAAGAAACATGAA
*
2396 GAAAAAGATATCCATTGGCAAGAAAAATCCATTTATTGTAACTCATGCCTTCAAAAGCCTTATTA
65 GAAAAAGATATCCATTGGCAAGAAAAATCCATTTATAGTAACTCATGCCTTCAAAAGCCTTATTA
** * * * *
2461 CTTGCTTTAAATGTTTTTTTAATCTCATGATTTG-TTTTAAG-
130 CTCACTTTAAATGATTTTATAACCTCAT-AATTGATTTT-AGT
2502 TTGAACTTTTTTA
1 TTGAA-TTTTTTA
2515 TATNNNNNNN
Statistics
Matches: 287, Mismatches: 59, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
169 63 0.22
170 145 0.51
171 66 0.23
172 13 0.05
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.39
Consensus pattern (170 bp):
TTGAATTTTTTAATATTTTTATTAAAACAGATTATAATTGAATGTCTACCTGAAGAAACATGAAG
AAAAAGATATCCATTGGCAAGAAAAATCCATTTATAGTAACTCATGCCTTCAAAAGCCTTATTAC
TCACTTTAAATGATTTTATAACCTCATAATTGATTTTAGT
Done.