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 513 0.0 0.0 0.0 A05E03_CONSENSUS 1 57 (494) + (TC)n Simple_repeat 1 57 (0) 203 10.0 0.0 2.5 A05E03_CONSENSUS 188 227 (324) + (CCA)n Simple_repeat 2 40 (0) 348 29.5 1.7 1.7 A05E03_CONSENSUS 247 419 (132) + (CCA)n Simple_repeat 2 174 (0)Alignments:
513 0.00 0.00 0.00 A05E03_CONSENSUS 1 57 (494) C (GA)n#Simple_repeat (123) 57 1 0 A05E03_CONSENSU 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 C (GA)n#Simple_re 57 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 8 A05E03_CONSENSU 51 CTCTCTC 57 C (GA)n#Simple_re 7 CTCTCTC 1 Transitions / transversions = 1.00 (0 / 0) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.00 (0 / 0) 203 10.00 0.00 2.50 A05E03_CONSENSUS 188 227 (324) C (TGG)n#Simple_repeat (140) 40 2 5 A05E03_CONSENSU 188 ACCACTCACCACCACCACCACCATCCCCATCTCCACCACC 227 i v i v C (TGG)n#Simple_r 40 ACCAC-CACCACCACCACCACCACCACCACCACCACCACC 2 Transitions / transversions = 1.00 (2 / 2) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 348 29.48 1.73 1.73 A05E03_CONSENSUS 247 419 (132) C (TGG)n#Simple_repeat (6) 174 2 5 A05E03_CONSENSU 247 CCTCCACCACCATCCCCTTCTCCTCCTCC-CCCCTACTAYTATCACTCTC 295 v i v vi v v v v i i ?i i v C (TGG)n#Simple_r 174 CCACCACCACCACCACCACCACCACCACCACCACCACCACCACCAC-CAC 126 A05E03_CONSENSU 296 CACCACCACCATCTCCTTCTYYTYTTNC-TCNCTACTACTACCACTCTCC 344 i v vi v??v?iv? i ? i i i v C (TGG)n#Simple_r 125 CACCACCACCACCACCACCACCACCACCACCACCACCACCACCAC-CACC 77 A05E03_CONSENSU 345 ACCACCACCATCCCCATCACCGCCGTCTCCAT-ATTATTANAAATCCCCT 393 i v i i ii v i ii ii ?v i v v C (TGG)n#Simple_r 76 ACCACCACCACCACCACCACCACCACCACCACCACCACCACCA-CCACCA 28 A05E03_CONSENSU 394 CCACCTCCATCTCCATCTCCACCACC 419 v i v i v C (TGG)n#Simple_r 27 CCACCACCACCACCACCACCACCACC 2 Transitions / transversions = 1.36 (30 / 22) Gap_init rate = 0.03 (6 / 173), avg. gap size = 1.00 (6 / 6)Masked Sequence:
>A05E03_CONSENSUS NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNCTCGTGCCGAATTCGGCACGAGCTCCTTACTATTATAAATCTC CCCCACCACCTTCACCATCCCCACCACCACCTTATTATTATCATTCCCCA CCTCCACCTAAAGAGCATGTACACCCTCCCTACTATTNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNTCCTTATTATTATAAATCCNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNTCNTTAMTAMTATCAAAGTCCTCCTCCACCA TCTCCCACTTCTCATCCTCCCTATTACTANCAAATCYCCTCCANACCAAC GTCATATCCTCCAKCTCCTTAYCATTACGTGAGCCCTCACMAACTTTTTC CSummary:
================================================== file name: /repeatmasker/tmp/RM2seq sequences: 1 total length: 551 bp GC level: 49.91 % bases masked: 270 bp ( 49.00 %) ================================================== 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: 3 270 bp 49.00 % 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