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
processing output: cycle 1 cycle 2 cycle 3 cycle 4Repeat 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) ID 202 20.2 1.3 1.3 A12F08_CONSENSUS 30 108 (492) + (CCA)n Simple_repeat 2 80 (0)Alignments:
202 20.25 1.27 1.27 A12F08_CONSENSUS 30 108 (492) C (TGG)n#Simple_repeat (100) 80 2 5 A12F08_CONSENSU 30 CACCCCCACCACCATCTCCATCACCACCACCACC-CTATTACTACAAATC 78 v i v i i ii i v i C (TGG)n#Simple_r 80 CACCACCACCACCACCACCACCACCACCACCACCACCACCACCACCA-CC 32 A12F08_CONSENSU 79 ACCTCCACCCCCATCACCTTCTCCACCACC 108 v v i vi v C (TGG)n#Simple_r 31 ACCACCACCACCACCACCACCACCACCACC 2 Transitions / transversions = 1.29 (9 / 7) Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2)Masked Sequence:
>A12F08_CONSENSUS GCACGAGCCACCTCCTTACTATTACAAGTNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNTCCTTACTACTACAAGAGTCCTCCTCCACCATCTCCCGTTTC TCATCCTCCCTACTACTACAAATCTCCTCCACCCCCAACGTCGTCTCCCC CACCTCCTTATCACTACGTGAGCCCTCCACCACCAACCAAGTCTCCACCA CCACCAGTTTACATTTATGCTTCCCCTCCACCACCCATCTACAAGTAAGC TTGGAATTAAGAAGCAGCAACAATAATAAGTCATGTTCTAGTATTCATTG TGGAATAAATTTCCGTTCCATTTGGAGCAGAGTTAAGCATATAATTTGTT ATACAAGTTCTTTGAATAAGAGTCTGAGTGTATCACCTCTAAGCTACGAT CTTCATGANTCATATGAGGTGCTTCTATTTATTTGGTGGCAATTTTCAAG TGTTGTCTTACTAAGTTCCAGGGAGCGACAATCNAAAGATCNAGANCAGG AAGCAAGATTAGAATGTTGATTCAATTCCGGNGNCTTTAAACTTTCTTATSummary:
================================================== file name: /repeatmasker/tmp/RM2seq sequences: 1 total length: 600 bp GC level: 44.11 % bases masked: 79 bp ( 13.17 %) ================================================== 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 % L3/CR1 0 0 bp 0.00 % LTR elements: 0 0 bp 0.00 % MaLRs 0 0 bp 0.00 % ERVL 0 0 bp 0.00 % ERV_classI 0 0 bp 0.00 % ERV_classII 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 % 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 79 bp 13.17 % Low complexity: 0 0 bp 0.00 % ================================================== * 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 07/16/2000 default ProcessRepeats version 07/16/2000 Repbase version 03/31/2000