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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|6015230|gb|AC011522.1|AC011522 Homo sapiens chromosome 1... 264 1e-68
gi|5923636|gb|AC010184.4|AC010184 Homo sapiens clone RPCI11... 38 1.2
gi|5922244|gb|AW055533.1|AW055533 614083A09.x1 614 - root c... 36 4.6
gi|6015256|gb|AC011496.1|AC011496 Homo sapiens chromosome 1... 36 4.6
gi|5868919|gb|AC009512.3|AC009512 Drosophila melanogaster c... 36 4.6
gi|5918010|emb|AL117694.1|CNS01DRQ Homo sapiens chromosome ... 36 4.6
gi|6015230|gb|AC011522.1|AC011522 Homo sapiens chromosome 19 clone LLNL-F_208A9, WORKING DRAFT SEQUENCE,
111 unordered pieces
Length = 121479
Score = 264 bits (133), Expect = 1e-68
Identities = 133/133 (100%)
Strand = Plus / Minus
Query: 1 gatcttctggtcgttgaaacattgatgtctctgtagcaacataggggtaatcttactgac 60
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Sbjct: 36942 gatcttctggtcgttgaaacattgatgtctctgtagcaacataggggtaatcttactgac 36883
Query: 61 aacagatagttacccgtcattatgcaatttaatatccctacgttgcttacactgttccgt 120
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Sbjct: 36882 aacagatagttacccgtcattatgcaatttaatatccctacgttgcttacactgttccgt 36823
Query: 121 gtcatccttatcc 133
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Sbjct: 36822 gtcatccttatcc 36810
gi|5923636|gb|AC010184.4|AC010184 Homo sapiens clone RPCI11-438D8, WORKING DRAFT SEQUENCE, 40 unordered
pieces
Length = 193453
Score = 38.2 bits (19), Expect = 1.2
Identities = 19/19 (100%)
Strand = Plus / Minus
Query: 446 ccgtctcctggattgggaa 464
|||||||||||||||||||
Sbjct: 115099 ccgtctcctggattgggaa 115081
gi|5922244|gb|AW055533.1|AW055533 614083A09.x1 614 - root cDNA library from Walbot Lab Zea mays cDNA,
mRNA sequence
Length = 331
Score = 36.2 bits (18), Expect = 4.6
Identities = 18/18 (100%)
Strand = Plus / Plus
Query: 696 aggtaagtagaatgcaac 713
||||||||||||||||||
Sbjct: 314 aggtaagtagaatgcaac 331
gi|6015256|gb|AC011496.1|AC011496 Homo sapiens chromosome 19 clone CIT978SKB_3M11, WORKING DRAFT
SEQUENCE, 78 unordered pieces
Length = 152803
Score = 36.2 bits (18), Expect = 4.6
Identities = 18/18 (100%)
Strand = Plus / Minus
Query: 634 tttcggcgtaattttcag 651
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Sbjct: 31333 tttcggcgtaattttcag 31316
gi|5868919|gb|AC009512.3|AC009512 Drosophila melanogaster chromosome 3 clone BACR01F13 (D831) RPCI-98
01.F.13 map 85B-85B strain y; cn bw sp, WORKING DRAFT
SEQUENCE, 58 unordered pieces
Length = 101290
Score = 36.2 bits (18), Expect = 4.6
Identities = 18/18 (100%)
Strand = Plus / Plus
Query: 200 gcgtcgcggcggtgactg 217
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Sbjct: 81590 gcgtcgcggcggtgactg 81607
gi|5918010|emb|AL117694.1|CNS01DRQ Homo sapiens chromosome 14 clone R-226F19, WORKING DRAFT SEQUENCE, in
ordered pieces
Length = 179076
Score = 36.2 bits (18), Expect = 4.6
Identities = 18/18 (100%)
Strand = Plus / Plus
Query: 336 ttatcacagctggtgggt 353
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Sbjct: 114196 ttatcacagctggtgggt 114213
CPU time: 0.11 user secs. 0.05 sys. secs 0.16 total secs.
Database: Non-redundant GenBank+EMBL+DDBJ+PDB sequences released in
the last month
Posted date: Oct 8, 1999 6:43 PM
Number of letters in database: 386,601,334
Number of sequences in database: 126,425
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: 142386
Number of Sequences: 126425
Number of extensions: 142386
Number of successful extensions: 9171
Number of sequences better than 10.0: 6
length of query: 956
length of database: 386,601,334
effective HSP length: 20
effective length of query: 936
effective length of database: 384,072,834
effective search space: 359492172624
effective search space used: 359492172624
T: 0
A: 0
X1: 6 (11.9 bits)
X2: 25 (49.6 bits)
S1: 12 (24.3 bits)
S2: 18 (36.2 bits)