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
CGTCTA
Summary:
==================================================
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
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 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)
Database: BCM Human Transcript Database
19,242 sequences; 35,825,453 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
dbj|D26361|HUMORFW Human mRNA for KIAA0042 gene, complete cds 36 0.43
dbj|D86479|D86479 Homo sapiens mRNA for AEBP1, complete cds 34 1.7
gb|AF053944|AF053944 Homo sapiens aortic carboxypeptidase-like ... 34 1.7
dbj|AB012192|AB012192 Homo sapiens mRNA for chondroitin 6-sulfo... 34 1.7
>dbj|D26361|HUMORFWHuman mRNA for KIAA0042 gene, complete cds
Length = 6586
Score = 36.2 bits (18), Expect = 0.43
Identities = 18/18 (100%), Positives = 18/18 (100%)
Query: 384 tgaaattattatttctgc 401
||||||||||||||||||
Sbjct: 4981 tgaaattattatttctgc 4998
>dbj|D86479|D86479Homo sapiens mRNA for AEBP1, complete cds
Length = 2839
Score = 34.2 bits (17), Expect = 1.7
Identities = 17/17 (100%), Positives = 17/17 (100%)
Query: 482 agatggtggcgttggca 498
|||||||||||||||||
Sbjct: 1837 agatggtggcgttggca 1821
>gb|AF053944|AF053944Homo sapiens aortic carboxypeptidase-like
protein ACLP mRNA, complete cds
Length = 3935
Score = 34.2 bits (17), Expect = 1.7
Identities = 17/17 (100%), Positives = 17/17 (100%)
Query: 482 agatggtggcgttggca 498
|||||||||||||||||
Sbjct: 2915 agatggtggcgttggca 2899
>dbj|AB012192|AB012192Homo sapiens mRNA for chondroitin
6-sulfotransferase, complete cds
Length = 2731
Score = 34.2 bits (17), Expect = 1.7
Identities = 17/17 (100%), Positives = 17/17 (100%)
Query: 887 tctggctgaaaggcctg 903
|||||||||||||||||
Sbjct: 1925 tctggctgaaaggcctg 1941
Lambda K H
1.37 0.711 1.31
Gapped
Lambda K H
1.37 0.711 1.31
Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 13869
Number of Sequences: 19242
Number of extensions: 13869
Number of successful extensions: 938
Number of sequences better than 10: 5
length of query: 956
length of database: 35825453
effective HSP length: 18
effective length of query: 938
effective length of database: 35479097
effective search space: 33279392986
T: 0
A: 0
X1: 6 (11.9 bits)
X2: 25 (49.6 bits)
S1: 0 ( 0.5 bits)
S2: 16 (32.2 bits)
