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Links to Entrez and to the Sequence Retrieval System (SRS) provided by the Human Genome Sequencing Center, Baylor College of Medicine:
= Retrieve Entrez links (e.g., Medline abstracts, FASTA-formatted sequence reports).
= Retrieve Entrez links to Related sequences (neighbors).
= Retrieve SRS links (if present).
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) 229 26.8 0.0 0.0 ECOPGSA 789 844 (112) + tRNA-Lys-AAG tRNA 8 63 (13)Alignments:
229 26.79 0.00 0.00 ECOPGSA 789 844 (112) tRNA-Lys-AAG#tRNA 8 63 (13) ECOPGSA 789 TAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCG 838 i i vvi vii vv i i i tRNA-Lys-AAG#tR 8 TAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGTCGTGGGTTCG 57 ECOPGSA 839 AGTCTC 844 i i tRNA-Lys-AAG#tR 58 AGCCCC 63 Transitions / transversions = 2.00 (10 / 5) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.00 (0 / 0)Masked Sequence:
>ECOPGSA GATCTTCTGGTCGTTGAAACATTGATGTCTCTGTAGCAACATAGGGGTAA TCTTACTGACAACAGATAGTTACCCGTCATTATGCAATTTAATATCCCTA CGTTGCTTACACTGTTCCGTGTCATCCTTATCCCATTCTTTGTATTGGTC TTTTATCTGCCTGTCACCTGGTCGCCGTTTGCCGCCGCGCTCATTTTCTG CGTCGCGGCGGTGACTGACTGGTTCGATGGTTTTCTGGCACGCCGCTGGA ACCAGAGTACCCGGTTTGGTGCTTTCCTTGACCCTGTGGCAGATAAAGTT CTCGTGGCTATCGCCATGGTGCTGGTAACCGAGCATTATCACAGCTGGTG GGTGACATTACCGGCGGCAACGATGATCGCCCGTGAAATTATTATTTCTG CGCTACGCGAATGGATGGCGGAGTTGGGTAAACGCAGTAGCGTGGCCGTC TCCTGGATTGGGAAAGTGAAAACCACTGCCCAGATGGTGGCGTTGGCATG GCTGCTGTGGCGTCCGAACATTTGGGTTGAGTACGCCGGTATTGCACTTT TCTTTGTGGCTGCGGTACTGACTCTGTGGTCAATGTTGCAATATTTGAGC GCTGCGCGTGCAGATTTGCTTGATCAGTGATCGTTTCGGCGTAATTTTCA GCAAACGATCAAAAGTGGTGAAAAATATCGTTGACTCATCGCGCCAGGTA AGTAGAATGCAACGCATCGAACGGCGGCACTGATTGCCAGACGATAATAA AATCAAGTGATTAACTGATTGCTTGATGAATGCGGGAANNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTTTCC CGCTCCAGTTTAAAAGACATCGGCGTCAAGCGGATGTCTGGCTGAAAGGC CTGAAGAATTTGGCGCGTTAACAAAGCGGTTATGTAGCGGATTGCAAATC CGTCTASummary:
================================================== file name: /repeatmasker/tmp/RM2seq sequences: 1 total length: 956 bp GC level: 49.90 % bases masked 56 bp ( 5.86 %) ================================================== 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: 1 56 bp 5.86 % Satellites: 0 0 bp 0.00 % Simple repeats: 0 0 bp 0.00 % 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 05/05/99 default ProcessRepeats version 05/05/99 Repbase version 3.04
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Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= ECOPGSA
(956 letters)
If you have any problems or questions with the results of this search
please refer to the BLAST FAQs
Score E
Sequences producing significant alignments: (bits) Value
gi|4631764|dbj|AU047129.1|AU047129 Rattus norvegicus, OTSUK... 38 0.083
gi|5223770|gb|G52593.1|G52593 SHGC-81577 Human Homo sapiens... 36 0.33
gi|308704|gb|L16352|HUMUT904 Human chromosome 8 STS UT904. 34 1.3
gi|720650|gb|G03692|G03692 human STS WI-183. 34 1.3
gi|4492213|gb|G45922.1|G45922 Z5031_1 Zebrafish AB Danio re... 34 1.3
gi|4631764|dbj|AU047129.1|AU047129 Rattus norvegicus, OTSUKA clone, 139g03, microsatellite sequence,
sequence tagged site
Length = 501
Score = 38.2 bits (19), Expect = 0.083
Identities = 19/19 (100%)
Strand = Plus / Minus
Query: 260 cccggtttggtgctttcct 278
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Sbjct: 153 cccggtttggtgctttcct 135
gi|5223770|gb|G52593.1|G52593 SHGC-81577 Human Homo sapiens STS genomic, sequence tagged site
Length = 509
Score = 36.2 bits (18), Expect = 0.33
Identities = 18/18 (100%)
Strand = Plus / Minus
Query: 888 ctggctgaaaggcctgaa 905
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Sbjct: 200 ctggctgaaaggcctgaa 183
gi|308704|gb|L16352|HUMUT904 Human chromosome 8 STS UT904.
Length = 419
Score = 34.2 bits (17), Expect = 1.3
Identities = 20/21 (95%)
Strand = Plus / Plus
Query: 213 gactgactggttcgatggttt 233
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Sbjct: 248 gactgactggttggatggttt 268
gi|720650|gb|G03692|G03692 human STS WI-183.
Length = 138
Score = 34.2 bits (17), Expect = 1.3
Identities = 17/17 (100%)
Strand = Plus / Plus
Query: 659 tcaaaagtggtgaaaaa 675
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Sbjct: 55 tcaaaagtggtgaaaaa 71
gi|4492213|gb|G45922.1|G45922 Z5031_1 Zebrafish AB Danio rerio STS genomic clone Z5031 5',
sequence tagged site
Length = 448
Score = 34.2 bits (17), Expect = 1.3
Identities = 17/17 (100%)
Strand = Plus / Plus
Query: 345 ctggtgggtgacattac 361
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Sbjct: 234 ctggtgggtgacattac 250
CPU time: 0.08 user secs. 0.02 sys. secs 0.10 total secs.
Database: Non-redundant Database of GenBank STS Division
Posted date: Oct 8, 1999 6:16 PM
Number of letters in database: 28,665,134
Number of sequences in database: 80,777
Lambda K H
1.37 0.711 0.00
Gapped
Lambda K H
1.37 0.711 4.94e-324
Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 9785
Number of Sequences: 80777
Number of extensions: 9785
Number of successful extensions: 640
Number of sequences better than 10.0: 5
length of query: 956
length of database: 28,665,134
effective HSP length: 18
effective length of query: 938
effective length of database: 27,211,148
effective search space: 25524056824
effective search space used: 25524056824
T: 0
A: 0
X1: 6 (11.9 bits)
X2: 25 (49.6 bits)
S1: 12 (24.3 bits)
S2: 16 (32.2 bits)