Locus 11317

Sequence ID dm3.chr3R
Location 20,292,304 – 20,292,476
Length 172
Max. P 0.786081
window15568 window15569

overview

Window 8

Location 20,292,304 – 20,292,383
Length 79
Sequences 7
Columns 91
Reading direction reverse
Mean pairwise identity 69.98
Shannon entropy 0.58190
G+C content 0.49592
Mean single sequence MFE -22.71
Consensus MFE -12.08
Energy contribution -11.76
Covariance contribution -0.32
Combinations/Pair 1.65
Mean z-score -0.90
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.36
SVM RNA-class probability 0.658534
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 20292304 79 - 27905053
---------GAGCUGAAAUGAG-AUUGA-GGAGC-AGGUUGGAGCAGCUGCUUACUGGAGUGUGCUGAUAAGACUCGGGAUCAGCUUAAAA
---------(((((((......-.....-.((((-((.(((...))))))))).((.((((.(.......).)))).)).))))))).... ( -24.20, z-score =  -1.87, R)
>droSim1.chr3R 20133233 79 - 27517382
---------GAGCUGAGAUGAG-GUUGA-GGAGC-AGGUUGGGGCAGCUGCUUACUGGAGUGUGCUGAUAAGACUCGGGAUCAGCUUAAAA
---------(((((((......-.....-.((((-((.(((...))))))))).((.((((.(.......).)))).)).))))))).... ( -24.20, z-score =  -1.36, R)
>droSec1.super_0 20628615 79 - 21120651
---------GAGCUGAGAUGAG-GUUGA-GGAGC-AGGUUGGAGCAGCUGCUUACUGGAGUGUGCUGAUAAGACUCGGGAUCAGCUUAAAA
---------(((((((......-.....-.((((-((.(((...))))))))).((.((((.(.......).)))).)).))))))).... ( -24.20, z-score =  -1.38, R)
>droYak2.chr3R 2622199 83 + 28832112
------GAUGAGCUGCGAUGAG-GACGAUGUGGC-AGGUUGAAGCAGCUGCUUACUGGAGUGUGCUGAUAAGACUCGGGAUCAGCUUAAAA
------.....((..((.((..-..)).))..))-((((((((((....)))..((.((((.(.......).)))).)).))))))).... ( -22.00, z-score =  -0.33, R)
>droEre2.scaffold_4820 2703000 79 + 10470090
---------GAACUGCGAUGGG-G-CGGUUGGGC-AGGUUGAAGCAGCUGCUUACUGGAGUGUGCUGAUAAGACUGGGGAUCAGCUUAAAA
---------..(((.((...((-(-((((((..(-.....)...)))))))))..)).)))..((((((..........))))))...... ( -20.70, z-score =  -0.07, R)
>droAna3.scaffold_13088 333342 91 - 569066
AGGUGGAGGAGGCUUUUGUGGGUGGCCAUGGAGCUUUGUUCGGGUUCCCGCUUACUGGAGUGUGCUGAUAAGGCUUGGGAUCAGCUUAAAA
(((((((.((((((.(..(((....)))..))))))).))).(((((((((((....))))).(((.....)))..)))))).)))).... ( -28.90, z-score =  -0.36, R)
>droGri2.scaffold_14906 314793 65 - 14172833
--------------------------AAAUUUAUGGUGCUGUGAGUAAUUUUCAUUGGGGUGUGCUGAUAAGCCCCCGAAUAAGCUUAAGA
--------------------------...........(((.((((.....))))((((((...(((....)))))))))...)))...... ( -14.80, z-score =  -0.95, R)
>consensus
_________GAGCUGAGAUGAG_GUCGA_GGAGC_AGGUUGGAGCAGCUGCUUACUGGAGUGUGCUGAUAAGACUCGGGAUCAGCUUAAAA
.........((((((..........................((((....)))).((.((((.(.......).)))).))..)))))).... (-12.08 = -11.76 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,292,383 – 20,292,476
Length 93
Sequences 8
Columns 119
Reading direction reverse
Mean pairwise identity 78.98
Shannon entropy 0.37416
G+C content 0.35107
Mean single sequence MFE -22.86
Consensus MFE -14.57
Energy contribution -15.34
Covariance contribution 0.77
Combinations/Pair 1.13
Mean z-score -1.70
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.68
SVM RNA-class probability 0.786081
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20292383 93 - 27905053
---------------------UUUUGUAUUGUGUACAUCUUCAAUAUUUUAUAAUAAAGUGAAAUUCCAGGAAGAGGAAUACAAAAAUGUGCAGCUAAAGUUGCGCCAGUGGGC-----
---------------------.......((((((.(.(((((...(((((((......))))))).....))))).).))))))....(((((((....)))))))........----- ( -22.70, z-score =  -2.29, R)
>droPer1.super_3 6135752 119 + 7375914
UGUUUUUUUUGUUUUUUGUUUUGUUUCUUCCUGUACAUCUUCAAUAUUUUAUAAUAAAGCGAAAUUCCAGGAAGAGGAAUACAAAAAUGUGCAGCAACAGCGGCAACAGCGGCAUCGGG
((((....(((((((((((....((((((((((...........((((....))))...........))))))))))...)))))))...)))).))))((.((....)).))...... ( -24.25, z-score =  -0.44, R)
>dp4.chr2 12290286 117 + 30794189
--UGUUUUUUUGUUUUUGUUUUGUUUCUUCCUGUACAUCUUCAAUAUUUUAUAAUAAAGCGAAAUUCCAGGAAGAGGAAUACAAAAAUGUGUAGCAACAGCGGCAACAGCGGCAUCGGG
--((((....(((((((((....((((((((((...........((((....))))...........))))))))))...)))))))))...))))...((.((....)).))...... ( -26.35, z-score =  -1.37, R)
>droAna3.scaffold_13088 333433 94 - 569066
--------------------UUGGUGUAUUGUGAACAUCUUCAAUAUUUUAUAAUAAAGCGAAAUUCCAGGAAGAGAAGUACAAAAAUGUGCAGCCAAAGUUGAGCCAGGAGGG-----
--------------------(((((...(((((....(((((...((((..(......)..)))).....)))))....))))).......((((....)))).))))).....----- ( -15.80, z-score =   0.03, R)
>droEre2.scaffold_4820 2703079 98 + 10470090
----------------CCUUUUUUUGUAUUGUGUACAUCUUCAAUAUUUUAUAAUAAAGUGAAAUUCCAGGAAGAGGAAUACAAAAAUGUGCAGCUAAAGUUGCGCCACUGGAC-----
----------------((..((((((((((.(.....(((((...(((((((......))))))).....)))))).)))))))))).(((((((....)))))))....))..----- ( -24.60, z-score =  -2.70, R)
>droYak2.chr3R 2622282 98 + 28832112
----------------ACUUAUUUUGUAUUGUGUACAUCUUCAAUAUUUUAUAAUAAAGUGAAAUUCCUGGAAGAGGAAUACAAAAAUGUGCAGCCAAAGUUGCGCCAGCGGAC-----
----------------......(((((.((((((.(.(((((...(((((((......))))))).....))))).).))))))....(((((((....)))))))..))))).----- ( -23.80, z-score =  -2.24, R)
>droSec1.super_0 20628694 93 - 21120651
---------------------UUUUGUAUUGUGUACAUCUUCAAUAUUUUAUAAUAAAGUGAAAUUCCAGGAAGAGGAAUACAAAAAUGUGCAGCUAAAGUUGCGCCAGUGGGC-----
---------------------.......((((((.(.(((((...(((((((......))))))).....))))).).))))))....(((((((....)))))))........----- ( -22.70, z-score =  -2.29, R)
>droSim1.chr3R 20133312 93 - 27517382
---------------------UUUUGUAUUGUGUACAUCUUCAAUAUUUUAUAAUAAAGUGAAAUUCCAGGAAGAGGAAUACAAAAAUGUGCAGCUAAAGUUGCGCCAGUGGGC-----
---------------------.......((((((.(.(((((...(((((((......))))))).....))))).).))))))....(((((((....)))))))........----- ( -22.70, z-score =  -2.29, R)
>consensus
____________________UUUUUGUAUUGUGUACAUCUUCAAUAUUUUAUAAUAAAGUGAAAUUCCAGGAAGAGGAAUACAAAAAUGUGCAGCUAAAGUUGCGCCAGUGGGC_____
............................((((((...(((((...(((((..........))))).....)))))...))))))....(((((((....)))))))............. (-14.57 = -15.34 +   0.77)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:40:47 2011