Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402406.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5486.0, 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, 620
Length: 1034
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.30
Warning! 160 characters in sequence are not A, C, G, or T
Found at i:299 original size:171 final size:163
Alignment explanation
Indices: 3--452 Score: 445
Period size: 171 Copynumber: 2.7 Consensus size: 163
1 GT
*
3 CTTAAGAAACATGAAGAAACAAGCATTCATTGATAAGAAAAGTCCATATATAGCCACCCATTCCT
1 CTTAAGAAACATGAAGAAACAAGCATTCATTGATAAGAAAAGTCCAT-TATAGCCACTCATTCCT
****
68 TAAAAAGACTTATTACTCGCTTTAAATTGTTTTATAATCTNNNNNNNNNNTTTAAGTTGAATTTT
65 TAAAAAGACTTATTACTCGCTTTAAA-TGTTTTATAATCT------CATATTTAAGTTGAA-TTT
**
133 TTTAA-ATTTTTGATTAAAACAGAGTATAATTGAATGTCGAC
122 TTTAATATTTTTGATTAAAACAGACCATAATTGAATGTCGAC
*
174 CTTAAGAAATATGAAGAAACAAGCATTCATTGATAAGAAAAGTCCATTCATAGCCACTCATTCCT
1 CTTAAGAAACATGAAGAAACAAGCATTCATTGATAAGAAAAGTCCATT-ATAGCCACTCATTCCT
****
239 TAAAAAGACTTATTACAT-GCTTTAAATGATTTTATAATCTCATANNNNNNNNNNAGTTGAATTT
65 TAAAAAGACTTATTAC-TCGCTTTAAATG-TTTTATAATCTCATA------TTTAAGTTGAATTT
* * * *
303 TTTAATATTTTTTATTAAAATAGACCATGATTGAATGTCTAC
122 TTTAATATTTTTGATTAAAACAGACCATAATTGAATGTCGAC
* * * * * * * * *
345 CTTGAGAAACCTGATGAAACAAACATCCATTGACAAGAAAAGTCTATTTATAGTCACTCATTCGT
1 CTTAAGAAACATGAAGAAACAAGCATTCATTGATAAGAAAAGTCCA-TTATAGCCACTCATTCCT
* * * *
410 TCAAAAGGCTTATTGCTCGCCTTAAATGGTTTTATAATCTCAT
65 TAAAAAGACTTATTACTCGCTTTAAAT-GTTTTATAATCTCAT
453 NNNNNNNNNN
Statistics
Matches: 236, Mismatches: 30, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
170 12 0.05
171 220 0.93
172 4 0.02
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.34
Consensus pattern (163 bp):
CTTAAGAAACATGAAGAAACAAGCATTCATTGATAAGAAAAGTCCATTATAGCCACTCATTCCTT
AAAAAGACTTATTACTCGCTTTAAATGTTTTATAATCTCATATTTAAGTTGAATTTTTTAATATT
TTTGATTAAAACAGACCATAATTGAATGTCGAC
Found at i:865 original size:170 final size:170
Alignment explanation
Indices: 583--900 Score: 460
Period size: 170 Copynumber: 1.9 Consensus size: 170
573 NNNNNNNNNN
* * * *
583 ATAATTGAATGTCTACCTCAAGAAACATTAAGAAAGAAGTATTCATTGACAAGAGAAGTCTATTT
1 ATAATTGAATGTCTACCTCAAGAAACATGAAGAAAGAAGTATTCATTGACAAGAAAAATCCATTT
* *
648 ATAGTCACCTATTACTTCAAAAGCCTTATTACACACTTTAAATGGTTTTATAATCTGATAAT-TG
66 ATAGTCACCCATTACTTCAAAAGCCTTATTACACACTTTAAATGGTTTTATAATCTCATAATAT-
*
712 ATTTTAAGTTGTATTTTTTGGGTTTTTGGTTTAATCATACC
130 ATTTTAAGTTGAATTTTTTGGGTTTTTGGTTTAATCATACC
* * * *
753 ATAATTGAATGTCTACCTTAAGAAACGTGAAGAAA-AATTCATTTATTGACAAGAAAAATCCATT
1 ATAATTGAATGTCTACCTCAAGAAACATGAAGAAAGAAGT-ATTCATTGACAAGAAAAATCCATT
* * ** *
817 TATAGTCACCCATTCCTTCAAGAGCCTTATTAGTCAGTTTAAATGGTTTTATAATCTCATAATAT
65 TATAGTCACCCATTACTTCAAAAGCCTTATTACACACTTTAAATGGTTTTATAATCTCATAATAT
882 ATTTTAAGTTGAATTTTTT
130 ATTTTAAGTTGAATTTTTT
901 AACATNNNNN
Statistics
Matches: 130, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
169 3 0.02
170 126 0.97
171 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (170 bp):
ATAATTGAATGTCTACCTCAAGAAACATGAAGAAAGAAGTATTCATTGACAAGAAAAATCCATTT
ATAGTCACCCATTACTTCAAAAGCCTTATTACACACTTTAAATGGTTTTATAATCTCATAATATA
TTTTAAGTTGAATTTTTTGGGTTTTTGGTTTAATCATACC
Done.