WU-BLAST 2.0 search of the National Center for Biotechnology Information's NR Protein Database.
BEAUTY post-processing provided by the Human Genome Sequencing Center, Baylor College of Medicine.
BEAUTY Reference:
Worley KC, Culpepper P, Wiese BA, Smith RF. BEAUTY-X: enhanced BLAST searches for DNA queries. Bioinformatics 1998;14(10):890-1. Abstract
Worley KC, Wiese BA, Smith RF. BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results. Genome Res 1995 Sep;5(2):173-84 Abstract
Repeat sequence:
SW perc perc perc query position in query matching repeat position in repeat score div. del. ins. sequence begin end (left) repeat class/family begin end (left) 24 3.9 0.0 0.0 A01g19 224 249 (697) + AT_rich Low_complexity 1 26 (0) 215 4.0 0.0 0.0 A01g19 479 503 (443) + (TTCTCC)n Simple_repeat 4 28 (0)Alignments:
24 3.85 0.00 0.00 A01g19 224 249 (673) AT_rich#Low_complexity 1 26 (274) 3 A01g19 224 TTTTATTTTNTATTAAATTATTTAAT 249 vvvv vvv? vvv vvvvv AT_rich#Low_com 1 AAAAATAAAATAAATAATATAAAAAT 26 Transitions / transversions = 0.00 (0 / 15) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.00 (0 / 0) 215 4.00 0.00 0.00 A01g19 479 503 (443) C (GGAGAA)n#Simple_repeat (152) 28 4 A01g19 479 CTCCTTCTCCNTCTCCTTCTCCTTC 503 ? C (GGAGAA)n#Simpl 28 CTCCTTCTCCTTCTCCTTCTCCTTC 4 Transitions / transversions = 1.00 (0 / 0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.00 (0 / 0)Masked Sequence:
>A01g19 GNGGCGGNNGCNCNANAATANTGGATCCCCCGGGCTGCAGGAATTCGGCA CGAGGCGAGAGAGAGAGAACTAGTCTGAGTTNTNTTTGTNTTTTTTTTTT TTNGATTTAAAGATACNTTTTATNCTCCTCTCGAACAAACATACAGAAAA TGAAATGCTTTCANATNGTTACAACNAATTAACATACACTGTTTTACNCG TGCAANATGGATCNCACAANATGNNNNNNNNNNNNNNNNNNNNNNNNNNG CNTTTTNGTGGCAAACTTGCAAGGGTNATTTTTGGTGGATATATTTTAGT ANAAAGCCATAATGACGGACTGCACAGCATGAATGGGTTTGACAGTGTAT GAGCTANATCCTGCCATTTTGATGACATATTCCCACTCTTTGGANTGTGG GCNCTTTGCCGAAGTTANTGTGCGCCANCATTACCATGTCCAGNATNAAT CCCACATCCTTNAATCCGTCATGCTTCNNNNNNNNNNNNNNNNNNNNNNN NNNAATCACCGCCTCCAAANTAATAACCCTTCCGTTTTCCTTTGAATTTG ATATGGCTTCCCTACACTTCTTNAATATTTGGATGCACTCTTCGTCTGAC CAATCGTGCAAAACCCACATAANAAAAGCAGCATCAGCTTTANGAACACT TAAAAACATGTCGNCNNACACNTGTTGGANGCCATCGCCNTCNCCATCGC NNAAGGCNTGACTTGAAGAAGATCNAAATTGATGGGTCNAATGGAAGGGC AAGCCTTAACCANATGCGCNTGGCGGTGCCGTTGCCCCACCNACTCNNCC AAGGATTGAGGCNTGAAATGCCNCCNGCCACTTTGAATGAAGANAGGCNA ACAGCCTANCNCCCNNCCNTTGCTCCTTGAAAAGTGCTGTGAANAAATTG CGGAGGTTNCCCNCCTCTCCCCGNAACCTTGNAATGANGGTGCNTGSummary:
================================================== file name: /repeatmasker/tmp/RM2seq sequences: 1 total length: 946 bp GC level: 43.87 % bases masked 51 bp ( 5.39 %) ================================================== number of length percentage elements* occupied of sequence -------------------------------------------------- SINEs: 0 0 bp 0.00 % ALUs 0 0 bp 0.00 % MIRs 0 0 bp 0.00 % LINEs: 0 0 bp 0.00 % LINE1 0 0 bp 0.00 % LINE2 0 0 bp 0.00 % LTR elements: 0 0 bp 0.00 % MaLRs 0 0 bp 0.00 % Retrov. 0 0 bp 0.00 % MER4_group 0 0 bp 0.00 % DNA elements: 0 0 bp 0.00 % MER1_type 0 0 bp 0.00 % MER2_type 0 0 bp 0.00 % Mariners 0 0 bp 0.00 % Unclassified: 0 0 bp 0.00 % Total interspersed repeats: 0 bp 0.00 % Small RNA: 0 0 bp 0.00 % Satellites: 0 0 bp 0.00 % Simple repeats: 1 25 bp 2.64 % Low complexity: 1 26 bp 2.75 % ================================================== * most repeats fragmented by insertions or deletions have been counted as one element The sequence(s) were assumed to be of primate origin. RepeatMasker version 05/05/99 default ProcessRepeats version 05/05/99 Repbase version 3.04