Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400100.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3319.0, 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: 2164
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.33
Warning! 237 characters in sequence are not A, C, G, or T
Found at i:793 original size:171 final size:172
Alignment explanation
Indices: 265--809 Score: 459
Period size: 171 Copynumber: 3.2 Consensus size: 172
255 ATTGAATATA
* * * * * *
265 AAGAAAAAGGCATTCATTGGTAAGAAAAGTCCATTTAGAGTCACTCATTCTTTCGAAGGCCTTAT
1 AAGAAAAAAGCATTCATTGGTAAGAAAAGTCTATTTATAGTCACTCATTCCTTCAAAAGCCTTAT
* ********** * * * **
330 TACTCACTTTAAANNNNNNNNNNATCTCAAAATTGATTTTAGGTT--GATTTTTTTGATGTTTTT
66 TACTCACTCTAAAACGTTTTACAATCTCAAAATTGATTTTAAGTTCAAACTTTTTT-ACATTTTT
* * * * **
393 GGCT-AGAAGAGATTATAATTGAATGTCTGCC-CTGGGAAACATG
130 AG-TGAAAACAGATTATAATTGAATGTCTACCTC-AAGAAACATG
* ** * * *
436 AAGAAAAAGGTGTTCATTAGTAAGAAGAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTAT
1 AAGAAAAAAGCATTCATTGGTAAGAAAAGTCTATTTATAGTCACTCATTCCTTCAAAAGCCTTAT
* *
501 TACTCACTGTAAAACGTTTTACAATCTCAAAATTGATTTTAAGTTGAAACTTTTTTACATTTTTA
66 TACTCACTCTAAAACGTTTTACAATCTCAAAATTGATTTTAAGTTCAAACTTTTTTACATTTTTA
* * *
566 GTTAAAACAGATTATAATTGGATGTCTACCTTAAG-AA-ATG
131 GTGAAAACAGATTATAATTGAATGTCTACCTCAAGAAACATG
*
606 TAA-AAAAAAGGCATTCATTGGTAAGAAAAGTCTATTTATAGTCAC-CTATTGCTTCAAAAGCCT
1 -AAGAAAAAA-GCATTCATTGGTAAGAAAAGTCTATTTATAGTCACTC-ATTCCTTCAAAAGCCT
* ** *
669 TATTACTCATTCTAAATGGTTTTATAATCTCAAAATT-ACTTTTAAGTTCAAA-TATTTTTACA-
63 TATTACTCACTCTAAAACGTTTTACAATCTCAAAATTGA-TTTTAAGTTCAAACT-TTTTTACAT
* * * * *
731 TTTTGGTGACAACATATTATAATAT-AATG-CATAGCTCGAGAAACATG
126 TTTTAGTGAAAACAGATTATAAT-TGAATGTC-TACCTCAAGAAACATG
*
778 AAGAAAAAAGCATTCATTGGCAAGAAAAGTCT
1 AAGAAAAAAGCATTCATTGGTAAGAAAAGTCT
810 TATTACATAC
Statistics
Matches: 306, Mismatches: 54, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
169 1 0.00
170 39 0.13
171 219 0.72
172 40 0.13
173 7 0.02
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (172 bp):
AAGAAAAAAGCATTCATTGGTAAGAAAAGTCTATTTATAGTCACTCATTCCTTCAAAAGCCTTAT
TACTCACTCTAAAACGTTTTACAATCTCAAAATTGATTTTAAGTTCAAACTTTTTTACATTTTTA
GTGAAAACAGATTATAATTGAATGTCTACCTCAAGAAACATG
Found at i:987 original size:189 final size:189
Alignment explanation
Indices: 640--997 Score: 406
Period size: 189 Copynumber: 1.9 Consensus size: 189
630 GAAAAGTCTA
* * * * *
640 TTTATAGTCACCTATTGCTTCAAAAGCCTTATTACTCATTCTAAATGGTTTTATAATCTCAAAAT
1 TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACACATTCTAAATGATTTGATAATCTCAAAAT
* * * * * * *
705 TACTTTTAAGTTCAAATATTTTTACATTTTGGTGACAACATATTATAATATAATGCATAGCTCGA
66 TAATTTTAAGTTCAAATATTTTTACATTTTGATGACAAAAAACTATAATATAATGCATACCTAGA
* **
770 GAAACATGAAGAAAAAAGCATTCATTGGCA-AGAAAAGTCTTATTACATACTTTAAATGG
131 GAAACATAAAGAAAAAAGCAGCCATTGGCACA-AAAAGTCTTATTACATACTTTAAATGG
*
829 TTTATAGTCACCCATTCCTTTAAAAGCCTTATTACACACTT-TAAATGATTTGATAATCTCAAAA
1 TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACACA-TTCTAAATGATTTGATAATCTCAAAA
* * * *
893 TTAATTTTAAGTT-AAATTTTTTTATATTTTTGATTA-AAAAAAGCTATAAT-TGAATGCTTACC
65 TTAATTTTAAGTTCAAATATTTTTACA-TTTTGATGACAAAAAA-CTATAATAT-AATGCATACC
* *
955 TTAG-GGAACATAAAG-CAAAAGTCAGCCATTGGCACAAAAAGTC
127 -TAGAGAAACATAAAGAAAAAAG-CAGCCATTGGCACAAAAAGTC
998 CATTTATAAT
Statistics
Matches: 140, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
188 21 0.15
189 114 0.81
190 5 0.04
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (189 bp):
TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACACATTCTAAATGATTTGATAATCTCAAAAT
TAATTTTAAGTTCAAATATTTTTACATTTTGATGACAAAAAACTATAATATAATGCATACCTAGA
GAAACATAAAGAAAAAAGCAGCCATTGGCACAAAAAGTCTTATTACATACTTTAAATGG
Done.