Locus 4947

Sequence ID dm3.chr2R
Location 16,619,648 – 16,619,739
Length 91
Max. P 0.939354
window6800 window6801

overview

Window 0

Location 16,619,648 – 16,619,739
Length 91
Sequences 12
Columns 114
Reading direction forward
Mean pairwise identity 79.01
Shannon entropy 0.40323
G+C content 0.41345
Mean single sequence MFE -21.92
Consensus MFE -15.56
Energy contribution -15.21
Covariance contribution -0.35
Combinations/Pair 1.17
Mean z-score -1.75
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.45
SVM RNA-class probability 0.939354
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16619648 91 + 21146708
-GUCGAGUUUU--GGCCAA-GUCUAAAGUCU---CUCUUGGUUAGAGACGCAGAAAAUGCGUCAGCAAAGUUUUUAAUGUAUUUUCGCCAAGUUUUCC----------------
-...(((.(((--(((...-.......((((---((.......))))))...((((((((((.((........)).))))))))))))))))..))).---------------- ( -23.30, z-score =  -2.50, R)
>droGri2.scaffold_15245 15978999 113 + 18325388
AGUUGUGUCCUAAGAACAAAGUCUAAAGUCGGCGUCUU-GGUUAGAGACGCAGAAAAUGCGUCAGCAAAGUUUUUAAUGUAUUUUCGCCAAGUUUGCAACAUACACAAGCACAG
.((((((..((.(((......)))......((((((((-.....)))))...((((((((((.((........)).))))))))))))).))..)))))).............. ( -26.60, z-score =  -1.16, R)
>droMoj3.scaffold_6496 25424994 92 - 26866924
-----GGCUAAAAGUCCAAAGUCUAAAGUCUGCGCCUUUGGUUAGAGACGCAGAAAAUGCGUCAGCAAAGUUUUUAAUGUAUUUUCGCCAAGUUUGC-----------------
-----(((.((((..((((((.(..........).)))))).....((((((.....))))))..................)))).)))........----------------- ( -20.40, z-score =  -0.53, R)
>droVir3.scaffold_12823 364553 89 - 2474545
------UCCCAAAGUCCAAAGUCUAAAGUCUGUGCCUU-GGUUAGAGACGCAGAAAAUGCGUCAGCAAAGUUUUUAAUGUAUUUUCGCCAAGUU-GC-----------------
------.........................((..(((-(((.(((((((((.....)))))).(((..........)))..))).))))))..-))----------------- ( -17.90, z-score =  -1.26, R)
>droWil1.scaffold_181141 4769086 84 + 5303230
--------UCAAGUUUCCUUACCAAAAGACU-----CUUGGUUAGAGACGCAGAAAAUGCGUCAGCAAAGUUUUUAAUGUAUUUUCGCCAAGUUUUC-----------------
--------....(((((...(((((......-----.)))))..)))))((.((((((((((.((........)).)))))))))))).........----------------- ( -18.30, z-score =  -2.03, R)
>droPer1.super_4 4753466 88 - 7162766
-----GUCAAGUGGGGUUGGGUCUAAAGUCU-----UUUGGCUAGAGACGCAGAAAAUGCGUCAGCGAAGUUUUUAAUGUAUUUUCGCCAAGUUUUCC----------------
-----.........(((((.((((..((((.-----...))))..)))).))((((((((((.((........)).))))))))))))).........---------------- ( -22.50, z-score =  -1.39, R)
>dp4.chr3 11253483 88 - 19779522
-----GUCAAGUGGGGUUGGGUCCAAAGUCU-----UUUGGCUAGAGACGCAGAAAAUGCGUCAGCGAAGUUUUUAAUGUAUUUUCGCCAAGUUUUCC----------------
-----((((((.((..(((....)))..)).-----))))))....((((((.....)))))).((((((............))))))..........---------------- ( -23.70, z-score =  -1.68, R)
>droAna3.scaffold_13266 15924589 93 - 19884421
-GUCGGGUUUUUCGGCCAA-GUCUAAAGUCU---CUCUUGGUUAGAGACGCAGAAAAUGCGUCAGCAAAGUUUUUAAUGUAUUUUCGCCAAGUUUUCC----------------
-...((((((((.((((((-(..........---..)))))))))))))...((((((((((.((........)).)))))))))).)).........---------------- ( -21.20, z-score =  -1.45, R)
>droEre2.scaffold_4845 10769171 90 + 22589142
-GUCGAGUUU---GGCCAA-GUCUAAAGUCU---CUCUUGGUUAGAGACGCAGAAAAUGCGUCAGCAAAGUUUUUAAUGUAUUUUCGCCAAGUUUUCC----------------
-...((..((---(((...-.......((((---((.......))))))...((((((((((.((........)).)))))))))))))))..))...---------------- ( -22.60, z-score =  -2.30, R)
>droYak2.chr2R 8565701 90 - 21139217
-----GUCGAGUUUGGCCAAGUCUAAAGUCU---CCCUUGGUUAGAGACGCAGAAAAUGCGUCAGCAAAGUUUUUAAUGUAUUUUCGCCAAGUUUUCC----------------
-----(.((((((((((((((..........---..))))))))))((((((.....))))))....................)))).).........---------------- ( -21.40, z-score =  -2.13, R)
>droSec1.super_1 14172464 90 + 14215200
-GUCGAGUUU---GGCCAA-GUCUAAAGUCU---CUCUUGGUUAGAGACGCAGAAAAUGCGUCAGCAAAGUUUUUAAUGUAUUUUCGCCAAGUUUUCC----------------
-...((..((---(((...-.......((((---((.......))))))...((((((((((.((........)).)))))))))))))))..))...---------------- ( -22.60, z-score =  -2.30, R)
>droSim1.chr2R 15280060 90 + 19596830
-GUCGAGUUU---GGCCAA-GUCUAAAGUCU---CUCUUGGUUAGAGACGCAGAAAAUGCGUCAGCAAAGUUUUUAAUGUAUUUUCGCCAAGUUUUCC----------------
-...((..((---(((...-.......((((---((.......))))))...((((((((((.((........)).)))))))))))))))..))...---------------- ( -22.60, z-score =  -2.30, R)
>consensus
_____GGUUU___GGCCAA_GUCUAAAGUCU___CUCUUGGUUAGAGACGCAGAAAAUGCGUCAGCAAAGUUUUUAAUGUAUUUUCGCCAAGUUUUCC________________
....................................((((((.(((((((((.....)))))).(((..........)))..))).))))))...................... (-15.56 = -15.21 +  -0.35)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 1

Location 16,619,648 – 16,619,739
Length 91
Sequences 12
Columns 114
Reading direction reverse
Mean pairwise identity 79.01
Shannon entropy 0.40323
G+C content 0.41345
Mean single sequence MFE -19.19
Consensus MFE -12.03
Energy contribution -11.89
Covariance contribution -0.14
Combinations/Pair 1.08
Mean z-score -1.77
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.877982
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16619648 91 - 21146708
----------------GGAAAACUUGGCGAAAAUACAUUAAAAACUUUGCUGACGCAUUUUCUGCGUCUCUAACCAAGAG---AGACUUUAGAC-UUGGCC--AAAACUCGAC-
----------------.......(((((.((................(((....)))...((((.((((((.......))---))))..)))).-)).)))--))........- ( -18.00, z-score =  -1.54, R)
>droGri2.scaffold_15245 15978999 113 - 18325388
CUGUGCUUGUGUAUGUUGCAAACUUGGCGAAAAUACAUUAAAAACUUUGCUGACGCAUUUUCUGCGUCUCUAACC-AAGACGCCGACUUUAGACUUUGUUCUUAGGACACAACU
.((((((((.....(((..(((.((((((......................((((((.....))))))(((....-.))))))))).))).)))........)))).))))... ( -24.72, z-score =  -1.12, R)
>droMoj3.scaffold_6496 25424994 92 + 26866924
-----------------GCAAACUUGGCGAAAAUACAUUAAAAACUUUGCUGACGCAUUUUCUGCGUCUCUAACCAAAGGCGCAGACUUUAGACUUUGGACUUUUAGCC-----
-----------------........(((.((((..((..........(((....)))...(((((((((........)))))))))..........))...)))).)))----- ( -19.10, z-score =  -1.04, R)
>droVir3.scaffold_12823 364553 89 + 2474545
-----------------GC-AACUUGGCGAAAAUACAUUAAAAACUUUGCUGACGCAUUUUCUGCGUCUCUAACC-AAGGCACAGACUUUAGACUUUGGACUUUGGGA------
-----------------..-.....((((((..............))))))((((((.....)))))).....((-((((..((((........))))..))))))..------ ( -21.74, z-score =  -2.61, R)
>droWil1.scaffold_181141 4769086 84 - 5303230
-----------------GAAAACUUGGCGAAAAUACAUUAAAAACUUUGCUGACGCAUUUUCUGCGUCUCUAACCAAG-----AGUCUUUUGGUAAGGAAACUUGA--------
-----------------........((((((..............))))))((((((.....))))))....((((((-----(...)))))))(((....)))..-------- ( -19.44, z-score =  -2.22, R)
>droPer1.super_4 4753466 88 + 7162766
----------------GGAAAACUUGGCGAAAAUACAUUAAAAACUUCGCUGACGCAUUUUCUGCGUCUCUAGCCAAA-----AGACUUUAGACCCAACCCCACUUGAC-----
----------------((.......((((((..............))))))((((((.....))))))..........-----...........)).............----- ( -15.44, z-score =  -1.70, R)
>dp4.chr3 11253483 88 + 19779522
----------------GGAAAACUUGGCGAAAAUACAUUAAAAACUUCGCUGACGCAUUUUCUGCGUCUCUAGCCAAA-----AGACUUUGGACCCAACCCCACUUGAC-----
----------------((.......((((((..............))))))((((((.....)))))).....(((((-----....)))))..)).............----- ( -18.44, z-score =  -2.38, R)
>droAna3.scaffold_13266 15924589 93 + 19884421
----------------GGAAAACUUGGCGAAAAUACAUUAAAAACUUUGCUGACGCAUUUUCUGCGUCUCUAACCAAGAG---AGACUUUAGAC-UUGGCCGAAAAACCCGAC-
----------------((.....(((((.((................(((....)))...((((.((((((.......))---))))..)))).-)).))))).....))...- ( -19.10, z-score =  -1.84, R)
>droEre2.scaffold_4845 10769171 90 - 22589142
----------------GGAAAACUUGGCGAAAAUACAUUAAAAACUUUGCUGACGCAUUUUCUGCGUCUCUAACCAAGAG---AGACUUUAGAC-UUGGCC---AAACUCGAC-
----------------.......(((((.((................(((....)))...((((.((((((.......))---))))..)))).-)).)))---)).......- ( -18.00, z-score =  -1.55, R)
>droYak2.chr2R 8565701 90 + 21139217
----------------GGAAAACUUGGCGAAAAUACAUUAAAAACUUUGCUGACGCAUUUUCUGCGUCUCUAACCAAGGG---AGACUUUAGACUUGGCCAAACUCGAC-----
----------------.......(((((.((....................((((((.....))))))(((((....((.---...))))))).)).))))).......----- ( -20.30, z-score =  -2.17, R)
>droSec1.super_1 14172464 90 - 14215200
----------------GGAAAACUUGGCGAAAAUACAUUAAAAACUUUGCUGACGCAUUUUCUGCGUCUCUAACCAAGAG---AGACUUUAGAC-UUGGCC---AAACUCGAC-
----------------.......(((((.((................(((....)))...((((.((((((.......))---))))..)))).-)).)))---)).......- ( -18.00, z-score =  -1.55, R)
>droSim1.chr2R 15280060 90 - 19596830
----------------GGAAAACUUGGCGAAAAUACAUUAAAAACUUUGCUGACGCAUUUUCUGCGUCUCUAACCAAGAG---AGACUUUAGAC-UUGGCC---AAACUCGAC-
----------------.......(((((.((................(((....)))...((((.((((((.......))---))))..)))).-)).)))---)).......- ( -18.00, z-score =  -1.55, R)
>consensus
________________GGAAAACUUGGCGAAAAUACAUUAAAAACUUUGCUGACGCAUUUUCUGCGUCUCUAACCAAGAG___AGACUUUAGAC_UUGGCC___AAACC_____
.........................((((((..............))))))((((((.....)))))).............................................. (-12.03 = -11.89 +  -0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:39:03 2011