Locus 4256

Sequence ID dm3.chr2R
Location 11,725,387 – 11,725,462
Length 75
Max. P 0.984666
window5830 window5831

overview

Window 0

Location 11,725,387 – 11,725,462
Length 75
Sequences 7
Columns 93
Reading direction forward
Mean pairwise identity 68.21
Shannon entropy 0.53394
G+C content 0.50213
Mean single sequence MFE -23.39
Consensus MFE -13.95
Energy contribution -15.46
Covariance contribution 1.51
Combinations/Pair 1.06
Mean z-score -1.83
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.17
SVM RNA-class probability 0.984666
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11725387 75 + 21146708
CAAAGGCGUCGCAUUCCAAGAUGCGUGCCACCGA---AUCAUUAGGUGGCAUGCUAAGAAGAAAAAAAACGAGGUGAA---------------
.....((.(((..(((......((((((((((..---.......))))))))))......)))......))).))...--------------- ( -23.60, z-score =  -2.99, R)
>droPer1.super_37 297649 93 - 760358
CACAGGCGACGCAUUCCUCGAUGCGUGCCCCCAGCUCAUCAUCAGGAGGCAGCAAGGCUUGGCUUUGGAGGAUCCAAAAAACCAAGACAGUAG
....(((.(((((((....))))))))))((..((((.((.....)).).)))..))(((((.(((((.....)))))...)))))....... ( -27.00, z-score =  -0.42, R)
>dp4.chr3 318675 93 - 19779522
CACAGGCGACGCAUUCCUCGAUGCGUGCCCCCAGCUCAUCAUCAGGAGGCAGCAAGGCUUGGCUUUGGAGGAUCCAAAAAAGCAAGACAGUAG
..(((((.(((((((....)))))))(((.((............)).)))......)))))(((((((.....)))...)))).......... ( -26.70, z-score =  -0.11, R)
>droEre2.scaffold_4845 8454934 67 - 22589142
CAAAGGCGUCGCAUUCCAAGAUGCGUGCCACCGA---AUCAUUAGGUGGGCUGCCAA--------AAAACGAGGUAAA---------------
....(((..((((((....))))))..(((((..---.......)))))...)))..--------.............--------------- ( -19.50, z-score =  -1.27, R)
>droYak2.chr2R 3879393 71 - 21139217
CAAAGGCGUCGCAUUCCAAGAUGCGUGCCACCAA---AUCAUUAGAUGGGAUGCCAACA----AAAAAACGAGGUAAA---------------
....((((.((((((....))))))))))(((..---(((....)))((....))....----.........)))...--------------- ( -17.60, z-score =  -1.74, R)
>droSec1.super_1 9219542 71 + 14215200
CGAAGGCGUCGCAUUCCAAGAUGCGUGCCACCGA---AUCAUUAGGUGGCAUGCUAACA----AAAAAACGAGGUGAA---------------
.....((.(((...........((((((((((..---.......)))))))))).....----......))).))...--------------- ( -24.65, z-score =  -2.98, R)
>droSim1.chr2R 10465073 71 + 19596830
CAAAGGCGUCGCAUUCCAAGAUGCGUGCCACCGA---AUCAUUAGGUGGCAUGCUAACA----AAAAAACGAGGUGAA---------------
.....((.(((...........((((((((((..---.......)))))))))).....----......))).))...--------------- ( -24.65, z-score =  -3.32, R)
>consensus
CAAAGGCGUCGCAUUCCAAGAUGCGUGCCACCGA___AUCAUUAGGUGGCAUGCUAACA____AAAAAACGAGGUAAA_______________
.....((.(((((((....)))))((((((((............))))))))..................)).)).................. (-13.95 = -15.46 +   1.51)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 11,725,387 – 11,725,462
Length 75
Sequences 7
Columns 93
Reading direction reverse
Mean pairwise identity 68.21
Shannon entropy 0.53394
G+C content 0.50213
Mean single sequence MFE -21.14
Consensus MFE -14.70
Energy contribution -14.60
Covariance contribution -0.10
Combinations/Pair 1.17
Mean z-score -1.20
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.55
SVM RNA-class probability 0.949134
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11725387 75 - 21146708
---------------UUCACCUCGUUUUUUUUCUUCUUAGCAUGCCACCUAAUGAU---UCGGUGGCACGCAUCUUGGAAUGCGACGCCUUUG
---------------......((((.....((((.....((.(((((((.......---..))))))).)).....)))).))))........ ( -20.00, z-score =  -2.72, R)
>droPer1.super_37 297649 93 + 760358
CUACUGUCUUGGUUUUUUGGAUCCUCCAAAGCCAAGCCUUGCUGCCUCCUGAUGAUGAGCUGGGGGCACGCAUCGAGGAAUGCGUCGCCUGUG
.......((((((..(((((.....)))))))))))(((.(((.(.((.....)).)))).)))(((((((((......)))))).))).... ( -29.90, z-score =  -0.50, R)
>dp4.chr3 318675 93 + 19779522
CUACUGUCUUGCUUUUUUGGAUCCUCCAAAGCCAAGCCUUGCUGCCUCCUGAUGAUGAGCUGGGGGCACGCAUCGAGGAAUGCGUCGCCUGUG
.(((.((..(((..((((((.....)))))).....(((((((((((((............))))))).)))...)))...)))..))..))) ( -25.50, z-score =   0.70, R)
>droEre2.scaffold_4845 8454934 67 + 22589142
---------------UUUACCUCGUUUU--------UUGGCAGCCCACCUAAUGAU---UCGGUGGCACGCAUCUUGGAAUGCGACGCCUUUG
---------------.............--------..(((.(((.(((.......---..)))))).(((((......)))))..))).... ( -18.10, z-score =  -1.40, R)
>droYak2.chr2R 3879393 71 + 21139217
---------------UUUACCUCGUUUUUU----UGUUGGCAUCCCAUCUAAUGAU---UUGGUGGCACGCAUCUUGGAAUGCGACGCCUUUG
---------------...............----....(((...(((((.......---..)))))..(((((......)))))..))).... ( -15.30, z-score =  -0.61, R)
>droSec1.super_1 9219542 71 - 14215200
---------------UUCACCUCGUUUUUU----UGUUAGCAUGCCACCUAAUGAU---UCGGUGGCACGCAUCUUGGAAUGCGACGCCUUCG
---------------......((((.((((----.....((.(((((((.......---..))))))).)).....)))).))))........ ( -19.60, z-score =  -1.86, R)
>droSim1.chr2R 10465073 71 - 19596830
---------------UUCACCUCGUUUUUU----UGUUAGCAUGCCACCUAAUGAU---UCGGUGGCACGCAUCUUGGAAUGCGACGCCUUUG
---------------......((((.((((----.....((.(((((((.......---..))))))).)).....)))).))))........ ( -19.60, z-score =  -1.98, R)
>consensus
_______________UUUACCUCGUUUUUU____UGUUAGCAUGCCACCUAAUGAU___UCGGUGGCACGCAUCUUGGAAUGCGACGCCUUUG
..........................................(((((((............)))))))(((((......)))))......... (-14.70 = -14.60 +  -0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:25:40 2011