Locus 2278

Sequence ID dm3.chr2L
Location 17,566,376 – 17,566,471
Length 95
Max. P 0.999179
window3141 window3142

overview

Window 1

Location 17,566,376 – 17,566,471
Length 95
Sequences 15
Columns 114
Reading direction forward
Mean pairwise identity 81.68
Shannon entropy 0.38201
G+C content 0.45846
Mean single sequence MFE -32.22
Consensus MFE -28.57
Energy contribution -28.52
Covariance contribution -0.06
Combinations/Pair 1.21
Mean z-score -3.70
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.69
SVM RNA-class probability 0.999179
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17566376 95 + 23011544
GUACGUUUUUCUCCUGGUAUCCACUGUAGGCCUAUAUGUAUU---UCCAC------CAUAAGGCACGCGGUGAAUGCCAAGAGCGAACGCAGUUCUACAAAUUA----------
...(((((..(((.((((((.((((((..((((.((((....---.....------))))))))..)))))).)))))).))).)))))...............---------- ( -31.30, z-score =  -3.63, R)
>droSim1.chr2L 17270511 95 + 22036055
GUACGUUUUUCUCCUGGUAUCCACUGUAGGCCUAUAUGUAUU---UCCAC------CAUAAGGCACGCGGUGAAUGCCAAGAGCGAACGCAGUUCUACAAAUUA----------
...(((((..(((.((((((.((((((..((((.((((....---.....------))))))))..)))))).)))))).))).)))))...............---------- ( -31.30, z-score =  -3.63, R)
>droSec1.super_7 1207326 95 + 3727775
GUACGUUUUUCUCCUGGUAUCCACUGUAGGCCUAUAUGUAUU---UCCAC------CAUAAGGCACGCGGUGAAUGCCAAGAGCGAACGCAGUUCUACAAAUUA----------
...(((((..(((.((((((.((((((..((((.((((....---.....------))))))))..)))))).)))))).))).)))))...............---------- ( -31.30, z-score =  -3.63, R)
>droYak2.chr2R 17605945 95 - 21139217
GUACGUUUUUCUCCUGGUAUCCACUGUAGGCCUAUAUGUAUU---UCCAC------CAUAAGGCACGCGGUGAAUGCCAAGAGCGAACGCAGUUCUACAAAUUU----------
...(((((..(((.((((((.((((((..((((.((((....---.....------))))))))..)))))).)))))).))).)))))...............---------- ( -31.30, z-score =  -3.75, R)
>droEre2.scaffold_4845 15905082 95 - 22589142
GUACGUUUUUCUCCUGGUAUCCACUGUAGGCCUAUAUGUAUU---UCCAC------CAUAAGGCACGCGGUGAAUGCCAAGAGCGAACGCAGUUCUACAAAUUA----------
...(((((..(((.((((((.((((((..((((.((((....---.....------))))))))..)))))).)))))).))).)))))...............---------- ( -31.30, z-score =  -3.63, R)
>droAna3.scaffold_12916 12871051 95 - 16180835
GUACGUUUUUCUCCUGGUAUCCACUGUAGGCCUAUAUGUAUU---UCGAC------CAUAAGGCACGCGGUGAAUGCCAAGAGCGAACGAAACUCUACAAACUA----------
...(((((..(((.((((((.((((((..((((.((((....---.....------))))))))..)))))).)))))).))).)))))...............---------- ( -32.00, z-score =  -4.04, R)
>dp4.chr4_group3 824283 94 - 11692001
GUACGUUUUUCUCCUGGUAUCCACUGUAGGCCUAUAUGUAUU---UCGAC------CAUAAGGCACGCGGUGAAUGCCAAGAGCGGACGAAACUCUACUAUCA-----------
...(((((..(((.((((((.((((((..((((.((((....---.....------))))))))..)))))).)))))).))).)))))..............----------- ( -31.60, z-score =  -3.32, R)
>droPer1.super_8 1887458 94 - 3966273
GUACGUUUUUCUCCUGGUAUCCACUGUAGGCCUAUAUGUAUU---UCGAC------CAUAAGGCACGCGGUGAAUGCCAAGAGCGGACGAAACUCUACUAUCA-----------
...(((((..(((.((((((.((((((..((((.((((....---.....------))))))))..)))))).)))))).))).)))))..............----------- ( -31.60, z-score =  -3.32, R)
>droWil1.scaffold_180764 3008858 94 - 3949147
GUACGUUUUUCUCCUGGUAUCCACUGCAGGCCUAUAUGUUAU---UUGAC------CAUAAGGCACGCGGUGAAUGCCAAGAGCGAACGAAAUUCUACAAAAA-----------
...(((((..(((.((((((.((((((..((((.((((....---.....------))))))))..)))))).)))))).))).)))))..............----------- ( -33.30, z-score =  -4.63, R)
>droVir3.scaffold_12963 16493169 97 + 20206255
GUACGUUUUUCUCCUGGUAUCCACUGUAGGCCUCUAUGAAUU---UUGAC------CAUAAGGCACGCGGUGAAUGCCAAGAGCGAACGAAACUCUACAAUUAACA--------
...(((((..(((.((((((.((((((..((((.((((....---.....------))))))))..)))))).)))))).))).))))).................-------- ( -32.50, z-score =  -4.34, R)
>droMoj3.scaffold_6500 21419493 91 + 32352404
GUACGUUUUUCUCCUGGUAUCCACUGUAGGCCUCUAUGAAUU---UUGAC------CAUAAGGCACGCGGUGAAUGCCAAGAGCGAACGAAACUCUACAA--------------
...(((((..(((.((((((.((((((..((((.((((....---.....------))))))))..)))))).)))))).))).)))))...........-------------- ( -32.50, z-score =  -4.48, R)
>droGri2.scaffold_15252 13906834 104 + 17193109
GUACGUUUUUCUCCUGGUAUCCACUGUAGGCCUCUAUGUUUU---UUGAC------CAUAAGGCACGCGGUGAAUGCCAAGAGCGAACGAAACUCUACACUUC-CAUUCAAAUA
...(((((..(((.((((((.((((((..((((.((((((..---..)).------))))))))..)))))).)))))).))).)))))..............-.......... ( -32.30, z-score =  -3.89, R)
>anoGam1.chr3R 29342229 100 + 53272125
GCACGUUUUUCUCCUGGUGUUCACUGUAGGCCUGUAUGUUCU---AUUGCGGAUUUCAUAAGGCACGCGGUGAAUGCCAAGAGCGAACGAUACCCAUCGUGAA-----------
.(((((((..(((.(((((((((((((..((((.((((.(((---.....)))...))))))))..))))))))))))).))).))))(((....))))))..----------- ( -39.20, z-score =  -3.93, R)
>triCas2.ChLG5 1908647 93 - 18847211
----GUCAUUCUCCUAGUGUUCACUGUUGGCCUGUAUGUUUU--UGUAACG-----CAUAAGGCACGCGGUGAAUGCCAAGAGCAGACUUUUGUCAACGAAUCA----------
----.((...(((...(((((((((((..((((.(((((...--......)-----))))))))..)))))))))))...)))..(((....)))...))....---------- ( -28.00, z-score =  -1.85, R)
>apiMel3.Group11 8130434 92 - 12576330
------UGUGCUCCUUGCGUUCACUGCGGGCUUCCAUGUGCCAACUUUUCAAAAUUCAUAAGGCACGCGGUGAAUGCCAAGAGCGGACCAAAUUCAAC----------------
------..(((((...(((((((((((((....))..(((((...................))))))))))))))))...))))).............---------------- ( -33.81, z-score =  -3.37, R)
>consensus
GUACGUUUUUCUCCUGGUAUCCACUGUAGGCCUAUAUGUAUU___UCGAC______CAUAAGGCACGCGGUGAAUGCCAAGAGCGAACGAAACUCUACAAAUU___________
...(((((..(((.((((((.((((((..((((.((((..................))))))))..)))))).)))))).))).)))))......................... (-28.57 = -28.52 +  -0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 17,566,376 – 17,566,471
Length 95
Sequences 15
Columns 114
Reading direction reverse
Mean pairwise identity 81.68
Shannon entropy 0.38201
G+C content 0.45846
Mean single sequence MFE -29.48
Consensus MFE -21.39
Energy contribution -21.61
Covariance contribution 0.22
Combinations/Pair 1.16
Mean z-score -2.40
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.42
SVM RNA-class probability 0.990449
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17566376 95 - 23011544
----------UAAUUUGUAGAACUGCGUUCGCUCUUGGCAUUCACCGCGUGCCUUAUG------GUGGA---AAUACAUAUAGGCCUACAGUGGAUACCAGGAGAAAAACGUAC
----------.............((((((..(((((((.((((((.(...((((((((------((...---.)).)))).))))...).)))))).)))))))...)))))). ( -31.30, z-score =  -2.99, R)
>droSim1.chr2L 17270511 95 - 22036055
----------UAAUUUGUAGAACUGCGUUCGCUCUUGGCAUUCACCGCGUGCCUUAUG------GUGGA---AAUACAUAUAGGCCUACAGUGGAUACCAGGAGAAAAACGUAC
----------.............((((((..(((((((.((((((.(...((((((((------((...---.)).)))).))))...).)))))).)))))))...)))))). ( -31.30, z-score =  -2.99, R)
>droSec1.super_7 1207326 95 - 3727775
----------UAAUUUGUAGAACUGCGUUCGCUCUUGGCAUUCACCGCGUGCCUUAUG------GUGGA---AAUACAUAUAGGCCUACAGUGGAUACCAGGAGAAAAACGUAC
----------.............((((((..(((((((.((((((.(...((((((((------((...---.)).)))).))))...).)))))).)))))))...)))))). ( -31.30, z-score =  -2.99, R)
>droYak2.chr2R 17605945 95 + 21139217
----------AAAUUUGUAGAACUGCGUUCGCUCUUGGCAUUCACCGCGUGCCUUAUG------GUGGA---AAUACAUAUAGGCCUACAGUGGAUACCAGGAGAAAAACGUAC
----------.............((((((..(((((((.((((((.(...((((((((------((...---.)).)))).))))...).)))))).)))))))...)))))). ( -31.30, z-score =  -3.03, R)
>droEre2.scaffold_4845 15905082 95 + 22589142
----------UAAUUUGUAGAACUGCGUUCGCUCUUGGCAUUCACCGCGUGCCUUAUG------GUGGA---AAUACAUAUAGGCCUACAGUGGAUACCAGGAGAAAAACGUAC
----------.............((((((..(((((((.((((((.(...((((((((------((...---.)).)))).))))...).)))))).)))))))...)))))). ( -31.30, z-score =  -2.99, R)
>droAna3.scaffold_12916 12871051 95 + 16180835
----------UAGUUUGUAGAGUUUCGUUCGCUCUUGGCAUUCACCGCGUGCCUUAUG------GUCGA---AAUACAUAUAGGCCUACAGUGGAUACCAGGAGAAAAACGUAC
----------...............((((..(((((((.((((((.(...((((((((------.....---....)))).))))...).)))))).)))))))...))))... ( -28.00, z-score =  -2.02, R)
>dp4.chr4_group3 824283 94 + 11692001
-----------UGAUAGUAGAGUUUCGUCCGCUCUUGGCAUUCACCGCGUGCCUUAUG------GUCGA---AAUACAUAUAGGCCUACAGUGGAUACCAGGAGAAAAACGUAC
-----------..............(((...(((((((.((((((.(...((((((((------.....---....)))).))))...).)))))).)))))))....)))... ( -26.70, z-score =  -1.57, R)
>droPer1.super_8 1887458 94 + 3966273
-----------UGAUAGUAGAGUUUCGUCCGCUCUUGGCAUUCACCGCGUGCCUUAUG------GUCGA---AAUACAUAUAGGCCUACAGUGGAUACCAGGAGAAAAACGUAC
-----------..............(((...(((((((.((((((.(...((((((((------.....---....)))).))))...).)))))).)))))))....)))... ( -26.70, z-score =  -1.57, R)
>droWil1.scaffold_180764 3008858 94 + 3949147
-----------UUUUUGUAGAAUUUCGUUCGCUCUUGGCAUUCACCGCGUGCCUUAUG------GUCAA---AUAACAUAUAGGCCUGCAGUGGAUACCAGGAGAAAAACGUAC
-----------..............((((..(((((((.((((((.(((.((((((((------.....---....)))).)))).))).)))))).)))))))...))))... ( -33.70, z-score =  -4.35, R)
>droVir3.scaffold_12963 16493169 97 - 20206255
--------UGUUAAUUGUAGAGUUUCGUUCGCUCUUGGCAUUCACCGCGUGCCUUAUG------GUCAA---AAUUCAUAGAGGCCUACAGUGGAUACCAGGAGAAAAACGUAC
--------.................((((..(((((((.((((((.(...((((((((------(....---...)))).)))))...).)))))).)))))))...))))... ( -28.80, z-score =  -2.34, R)
>droMoj3.scaffold_6500 21419493 91 - 32352404
--------------UUGUAGAGUUUCGUUCGCUCUUGGCAUUCACCGCGUGCCUUAUG------GUCAA---AAUUCAUAGAGGCCUACAGUGGAUACCAGGAGAAAAACGUAC
--------------...........((((..(((((((.((((((.(...((((((((------(....---...)))).)))))...).)))))).)))))))...))))... ( -28.80, z-score =  -2.73, R)
>droGri2.scaffold_15252 13906834 104 - 17193109
UAUUUGAAUG-GAAGUGUAGAGUUUCGUUCGCUCUUGGCAUUCACCGCGUGCCUUAUG------GUCAA---AAAACAUAGAGGCCUACAGUGGAUACCAGGAGAAAAACGUAC
.....(((((-(((.(....).)))))))).(((((((.((((((.(...((((((((------.....---....))).)))))...).)))))).))))))).......... ( -32.10, z-score =  -2.68, R)
>anoGam1.chr3R 29342229 100 - 53272125
-----------UUCACGAUGGGUAUCGUUCGCUCUUGGCAUUCACCGCGUGCCUUAUGAAAUCCGCAAU---AGAACAUACAGGCCUACAGUGAACACCAGGAGAAAAACGUGC
-----------..((((((....)))(((..(((((((..(((((.(...((((((((...........---....)))).))))...).)))))..)))))))...)))))). ( -26.26, z-score =  -0.91, R)
>triCas2.ChLG5 1908647 93 + 18847211
----------UGAUUCGUUGACAAAAGUCUGCUCUUGGCAUUCACCGCGUGCCUUAUG-----CGUUACA--AAAACAUACAGGCCAACAGUGAACACUAGGAGAAUGAC----
----------....((((((((....)))..(((((((..(((((.(...((((((((-----.......--....)))).))))...).)))))..)))))))))))).---- ( -24.10, z-score =  -1.44, R)
>apiMel3.Group11 8130434 92 + 12576330
----------------GUUGAAUUUGGUCCGCUCUUGGCAUUCACCGCGUGCCUUAUGAAUUUUGAAAAGUUGGCACAUGGAAGCCCGCAGUGAACGCAAGGAGCACA------
----------------..............((((((.((.(((((.(((((((...................)))))..((....)))).))))).)).))))))...------ ( -30.51, z-score =  -1.43, R)
>consensus
___________AAUUUGUAGAAUUUCGUUCGCUCUUGGCAUUCACCGCGUGCCUUAUG______GUCGA___AAUACAUAUAGGCCUACAGUGGAUACCAGGAGAAAAACGUAC
.........................((((..(((((((..(((((.(...((((((((..................)))).))))...).)))))..)))))))...))))... (-21.39 = -21.61 +   0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:48:16 2011