Locus 5337

Sequence ID dm3.chr2R
Location 19,605,676 – 19,605,771
Length 95
Max. P 0.986741
window7318 window7319

overview

Window 8

Location 19,605,676 – 19,605,771
Length 95
Sequences 7
Columns 105
Reading direction forward
Mean pairwise identity 70.94
Shannon entropy 0.50265
G+C content 0.48404
Mean single sequence MFE -27.83
Consensus MFE -9.88
Energy contribution -11.42
Covariance contribution 1.53
Combinations/Pair 1.12
Mean z-score -2.01
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.15
SVM RNA-class probability 0.567164
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19605676 95 + 21146708
AGCGCAAUCGCCGUUCGUCAUCGCGCUGCUACUGCAGCUGCCGCACAAUGGCG-AAUAAUAAAAUUAGCCACAAUGACGAACAAAGAAGCGCUGGC---------
(((((..((...(((((((((.(((((((....))))).)).......((((.-(((......))).))))..)))))))))...)).)))))...--------- ( -36.40, z-score =  -2.99, R)
>droSim1.chr2R 18171979 95 + 19596830
AGCACAAUCGCCGUUCGUCAUCGCGCUGCUACUGCAGCUACCGCACAAUGGCG-AAUAAUAAAAUUAGCCACAAUGACGAACAAAGAAGCGCUGGC---------
(((.(..((...(((((((((.(((((((....)))))....))....((((.-(((......))).))))..)))))))))...)).).)))...--------- ( -29.70, z-score =  -2.10, R)
>droSec1.super_9 2886443 95 + 3197100
AGCACAAUCGCCGUUCGUCAUCGCGCUGCUACUGCAGCUACCGCACAAUGGCG-AAUAAUAAAAUUAGCCACAAUGACGAACAAAGAAGCGCUGGC---------
(((.(..((...(((((((((.(((((((....)))))....))....((((.-(((......))).))))..)))))))))...)).).)))...--------- ( -29.70, z-score =  -2.10, R)
>droYak2.chr2R 19583540 91 + 21139217
AGCACAAUCGCCGUUCGUCAUCGCGCUGCUACUGCA----CCGCACAAUGGCG-AAUAAUAAAAUUAGCCACAAUGACGAACAAAGAAGCGCUGGC---------
(((.(..((...(((((((((.(((.(((....)))----.)))....((((.-(((......))).))))..)))))))))...)).).)))...--------- ( -29.10, z-score =  -2.49, R)
>droEre2.scaffold_4845 20967848 91 + 22589142
AGCACAAUCGCCGUUCGUCAUCGCGCUGCUACUGCA----CCGCACAAUGGCG-AAUAAUAAAAUUAGCCACAAUGACGAACAAAGAAGCGUUGGC---------
.((.(((.(((.(((((((((.(((.(((....)))----.)))....((((.-(((......))).))))..)))))))))......))))))))--------- ( -30.30, z-score =  -2.95, R)
>dp4.chr3 10384393 97 - 19779522
----GGCUAAUGAUUCGUCAUCGACUUGGGGCCCCC---AACAAACAAUGGGGCAAUGAUGAAAUUGGCAGCAAUGUGACACACAAA-GAAUGAAAUACGAAUAC
----.((((((..((((((((...(....)(((((.---..........))))).)))))))))))))).....((((...))))..-................. ( -21.90, z-score =  -0.85, R)
>droPer1.super_4 2445281 98 - 7162766
----GGCUAAUGAUUCGUCAUCGACUUGGGGCCCCC---AACAAACAAUGAAACAAUGAUGAAAUUGGCAGCAAUGUGACACACAAAAGAAUGAAAUACGAAUAC
----.((((((..((((((((.(..(((((...)))---))((.....))...).)))))))))))))).....((((...)))).................... ( -17.70, z-score =  -0.61, R)
>consensus
AGCACAAUCGCCGUUCGUCAUCGCGCUGCUACUGCA___ACCGCACAAUGGCG_AAUAAUAAAAUUAGCCACAAUGACGAACAAAGAAGCGCUGGC_________
............(((((((((.(....((....)).............((((...............))))).)))))))))....................... ( -9.88 = -11.42 +   1.53)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,605,676 – 19,605,771
Length 95
Sequences 7
Columns 105
Reading direction reverse
Mean pairwise identity 70.94
Shannon entropy 0.50265
G+C content 0.48404
Mean single sequence MFE -34.04
Consensus MFE -17.30
Energy contribution -18.53
Covariance contribution 1.23
Combinations/Pair 1.23
Mean z-score -2.37
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.25
SVM RNA-class probability 0.986741
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19605676 95 - 21146708
---------GCCAGCGCUUCUUUGUUCGUCAUUGUGGCUAAUUUUAUUAUU-CGCCAUUGUGCGGCAGCUGCAGUAGCAGCGCGAUGACGAACGGCGAUUGCGCU
---------...(((((.((.(((((((((((((((((.(((......)))-.)))...........(((((....))))))))))))))))))).))..))))) ( -42.60, z-score =  -3.33, R)
>droSim1.chr2R 18171979 95 - 19596830
---------GCCAGCGCUUCUUUGUUCGUCAUUGUGGCUAAUUUUAUUAUU-CGCCAUUGUGCGGUAGCUGCAGUAGCAGCGCGAUGACGAACGGCGAUUGUGCU
---------...(((((.((.(((((((((((((((((.(((......)))-.)))...........(((((....))))))))))))))))))).))..))))) ( -40.70, z-score =  -3.45, R)
>droSec1.super_9 2886443 95 - 3197100
---------GCCAGCGCUUCUUUGUUCGUCAUUGUGGCUAAUUUUAUUAUU-CGCCAUUGUGCGGUAGCUGCAGUAGCAGCGCGAUGACGAACGGCGAUUGUGCU
---------...(((((.((.(((((((((((((((((.(((......)))-.)))...........(((((....))))))))))))))))))).))..))))) ( -40.70, z-score =  -3.45, R)
>droYak2.chr2R 19583540 91 - 21139217
---------GCCAGCGCUUCUUUGUUCGUCAUUGUGGCUAAUUUUAUUAUU-CGCCAUUGUGCGG----UGCAGUAGCAGCGCGAUGACGAACGGCGAUUGUGCU
---------...(((((.((.(((((((((((((((((.(((......)))-.)))))...(((.----(((....))).))))))))))))))).))..))))) ( -39.50, z-score =  -3.66, R)
>droEre2.scaffold_4845 20967848 91 - 22589142
---------GCCAACGCUUCUUUGUUCGUCAUUGUGGCUAAUUUUAUUAUU-CGCCAUUGUGCGG----UGCAGUAGCAGCGCGAUGACGAACGGCGAUUGUGCU
---------(((((((((.....(((((((((((((((.(((......)))-.)))))...(((.----(((....))).))))))))))))))))).))).)). ( -38.00, z-score =  -3.61, R)
>dp4.chr3 10384393 97 + 19779522
GUAUUCGUAUUUCAUUC-UUUGUGUGUCACAUUGCUGCCAAUUUCAUCAUUGCCCCAUUGUUUGUU---GGGGGCCCCAAGUCGAUGACGAAUCAUUAGCC----
(.((((((...((....-..((((...))))(((..((((((......))))(((((........)---))))))..)))...))..))))))).......---- ( -18.70, z-score =   0.57, R)
>droPer1.super_4 2445281 98 + 7162766
GUAUUCGUAUUUCAUUCUUUUGUGUGUCACAUUGCUGCCAAUUUCAUCAUUGUUUCAUUGUUUGUU---GGGGGCCCCAAGUCGAUGACGAAUCAUUAGCC----
(.((((((...((.......((((...))))..(((.(((((..((............))...)))---)).)))........))..))))))).......---- ( -18.10, z-score =   0.30, R)
>consensus
_________GCCAGCGCUUCUUUGUUCGUCAUUGUGGCUAAUUUUAUUAUU_CGCCAUUGUGCGGU___UGCAGUAGCAGCGCGAUGACGAACGGCGAUUGUGCU
..................((.(((((((((((((((................(((......)))......((....))..))))))))))))))).))....... (-17.30 = -18.53 +   1.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:46:20 2011