Locus 2437

Sequence ID dm3.chr2L
Location 19,048,262 – 19,048,359
Length 97
Max. P 0.999927
window3353 window3354

overview

Window 3

Location 19,048,262 – 19,048,359
Length 97
Sequences 12
Columns 113
Reading direction forward
Mean pairwise identity 65.85
Shannon entropy 0.69429
G+C content 0.31197
Mean single sequence MFE -19.95
Consensus MFE -12.41
Energy contribution -12.69
Covariance contribution 0.29
Combinations/Pair 1.12
Mean z-score -3.07
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.94
SVM RNA-class probability 0.999927
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19048262 97 + 23011544
----CGUUUGUAAUAUUCAACUUGAACU--GAACCGACUUCAAAUUGAAUACUUUCG---CCAACGUCUCAUCCAC--AUUCUGAUUUUGAGAUUUCAAACUCUCUUU-----
----.(((((...(((((((.(((((..--........))))).)))))))......---.....((((((.....--..........))))))..))))).......----- ( -15.46, z-score =  -1.84, R)
>droGri2.scaffold_15252 423429 94 + 17193109
-----------AAUAUUCCAUUUGAAGUUAAGCUCAACUUCGAAUUGAAUAUUUUUG--CGCAAACACUCAG-AAAGAUGAAUAACAUUGAGAUUUAAAUUUCUUUUU-----
-----------(((((((.((((((((((......)))))))))).)))))))....--...........((-(((..(((((.........)))))..)))))....----- ( -17.50, z-score =  -1.86, R)
>droMoj3.scaffold_6500 23390397 96 - 32352404
---------AUUAUAUUCAAUUUGAAGUCAAACUUCACUCCAAGUUGAAUAUUUUCCAUCCCAAUCACUCAACGCAGAAACUUAA---UGAGAUUUAAAUUUCUUUCU-----
---------...((((((((((((.(((........))).)))))))))))).......................(((((.((((---......)))).)))))....----- ( -15.60, z-score =  -3.06, R)
>droVir3.scaffold_12963 15129209 94 - 20206255
-----------AAUAUUCAACUUGAAGUCAG--UGUACUUCAAUUUGAAUAUUUUUC-CCCUAAUGACUCGACAAAGAAACCUAACAAUGAGAUUUCAAUUUCUUUUU-----
-----------(((((((((.(((((((...--...))))))).)))))))))....-..................((((.((.......)).))))...........----- ( -15.60, z-score =  -1.78, R)
>droWil1.scaffold_180772 747294 94 - 8906247
-----GUUUGUCAUAUUCAAUUUGAAGUU-AAACUAACUUCAAUUUGAAUAUAUACU--UGCAACGUCUGACAGA-----UAGGAUUUCCAAAAACAAAUUUUUCUU------
-----(((((((((((((((.((((((((-(...))))))))).))))))))..((.--......))..))))))-----).((....)).................------ ( -22.20, z-score =  -4.17, R)
>droPer1.super_1 8168306 107 - 10282868
CGUUCUUAUUAAAUAUUCAACUUGAAGUUCAAAUCGACUUCAAAUUGAAUGUUUUUG---CCUACGUUUU-CACAA--AACUUAACUUGAAGAUUUUCCACUUCUCUUCCACU
(((.......((((((((((.((((((((......)))))))).))))))))))...---...)))....-.....--..........(((((...........))))).... ( -20.72, z-score =  -4.09, R)
>dp4.chr4_group3 11053126 107 - 11692001
CGUUCUUAUUAAAUAUUCAACUUGAAGUUCAAAUCGACUUCAAAUUGAAUGUUUUUG---CCAACGUUUU-CACAA--AACUUAACUUGAAGAUUUUCCACUUCUCUUCCACU
((((......((((((((((.((((((((......)))))))).))))))))))...---..))))....-.....--..........(((((...........))))).... ( -21.10, z-score =  -4.04, R)
>droAna3.scaffold_12916 10802256 95 - 16180835
----CAGUUGUAAUAUUCAACUUGAAGUCAAA-UGUACUUCAAUUUGAAUAUUUUUU--ACUGACGUUUUGACAU-----UCUAACUUUGAGAUUCAAAUUACCCUU------
----((((...(((((((((.((((((((...-.).))))))).)))))))))....--))))....(((((..(-----((.......)))..)))))........------ ( -21.80, z-score =  -3.69, R)
>droEre2.scaffold_4845 17366809 97 - 22589142
----CGUUUGUAAUAUUCAACUUGAAGU--GAACAGACUUCAAUUUGAAUAUUUUCG---CCAACGUCCCAUCCAC--AUUCUGAUUUUGAGAUUUUGGACUCUCUUU-----
----((((.(((((((((((.(((((((--......))))))).)))))))))...)---).)))).....((((.--..(((.......)))...))))........----- ( -22.90, z-score =  -3.02, R)
>droYak2.chr2R 5564103 97 + 21139217
----CGUUUGUAAUAUUCAACUUGAAGU--GAACAGACUUCAAUUUGAAUAUUUUCG---CCAACGUCUCAUCCAC--AUUCUGAUUUUGAGAUUUCGAACUCUCUUU-----
----.(((((.(((((((((.(((((((--......))))))).)))))))))....---.....((((((.....--..........))))))..))))).......----- ( -22.56, z-score =  -2.98, R)
>droSec1.super_7 2678253 97 + 3727775
----CGUUUGUAAUAUUCAACUUGAAGU--GAACCGACUUCAAAUUGAAUAUUUUGG---CCAACGUCUCACCCAC--AUUCUGAUUUUGAGAUUUCAAACUCUCUUU-----
----.(((((.(((((((((.(((((((--......))))))).)))))))))....---.....((((((.....--..........))))))..))))).......----- ( -21.96, z-score =  -3.15, R)
>droSim1.chr2L 18742946 97 + 22036055
----CGUUUGUAAUAUUCAACUUGAAGU--GAACCGACUUCAAAUUGAAUAUUUUGG---CCAACGUCUCACCCAC--AUUCUGAUUUUGAGAUUUCAAACUCUCUUU-----
----.(((((.(((((((((.(((((((--......))))))).)))))))))....---.....((((((.....--..........))))))..))))).......----- ( -21.96, z-score =  -3.15, R)
>consensus
____CGUUUGUAAUAUUCAACUUGAAGU__AAACCGACUUCAAAUUGAAUAUUUUCG___CCAACGUCUCACCCAA__AUUCUAAUUUUGAGAUUUCAAACUCUCUUU_____
...........(((((((((.(((((((........))))))).)))))))))............................................................ (-12.41 = -12.69 +   0.29)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,048,262 – 19,048,359
Length 97
Sequences 12
Columns 113
Reading direction reverse
Mean pairwise identity 65.85
Shannon entropy 0.69429
G+C content 0.31197
Mean single sequence MFE -22.80
Consensus MFE -13.24
Energy contribution -13.56
Covariance contribution 0.31
Combinations/Pair 1.30
Mean z-score -2.40
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.15
SVM RNA-class probability 0.999659
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19048262 97 - 23011544
-----AAAGAGAGUUUGAAAUCUCAAAAUCAGAAU--GUGGAUGAGACGUUGG---CGAAAGUAUUCAAUUUGAAGUCGGUUC--AGUUCAAGUUGAAUAUUACAAACG----
-----.......(((((...(((((...(((....--.))).)))))((....---))..(((((((((((((((.(......--).))))))))))))))).))))).---- ( -23.20, z-score =  -2.05, R)
>droGri2.scaffold_15252 423429 94 - 17193109
-----AAAAAGAAAUUUAAAUCUCAAUGUUAUUCAUCUUU-CUGAGUGUUUGCG--CAAAAAUAUUCAAUUCGAAGUUGAGCUUAACUUCAAAUGGAAUAUU-----------
-----........................(((((......-.(((((((((...--...)))))))))....(((((((....))))))).....)))))..----------- ( -16.40, z-score =  -1.23, R)
>droMoj3.scaffold_6500 23390397 96 + 32352404
-----AGAAAGAAAUUUAAAUCUCA---UUAAGUUUCUGCGUUGAGUGAUUGGGAUGGAAAAUAUUCAACUUGGAGUGAAGUUUGACUUCAAAUUGAAUAUAAU---------
-----....((((((((((......---))))))))))...(..(....)..)........((((((((.(((((((........))))))).))))))))...--------- ( -21.00, z-score =  -1.93, R)
>droVir3.scaffold_12963 15129209 94 + 20206255
-----AAAAAGAAAUUGAAAUCUCAUUGUUAGGUUUCUUUGUCGAGUCAUUAGGG-GAAAAAUAUUCAAAUUGAAGUACA--CUGACUUCAAGUUGAAUAUU-----------
-----.....((....(((((((.......)))))))....))............-....(((((((((.(((((((...--...))))))).)))))))))----------- ( -21.00, z-score =  -2.10, R)
>droWil1.scaffold_180772 747294 94 + 8906247
------AAGAAAAAUUUGUUUUUGGAAAUCCUA-----UCUGUCAGACGUUGCA--AGUAUAUAUUCAAAUUGAAGUUAGUUU-AACUUCAAAUUGAAUAUGACAAAC-----
------.......((((((.(((((........-----....)))))....)))--))).(((((((((.(((((((((...)-)))))))).)))))))))......----- ( -19.40, z-score =  -2.22, R)
>droPer1.super_1 8168306 107 + 10282868
AGUGGAAGAGAAGUGGAAAAUCUUCAAGUUAAGUU--UUGUG-AAAACGUAGG---CAAAAACAUUCAAUUUGAAGUCGAUUUGAACUUCAAGUUGAAUAUUUAAUAAGAACG
....(((((....(....).)))))..(((..(((--((((.-...))).)))---)..(((.((((((((((((((........)))))))))))))).)))......))). ( -24.40, z-score =  -2.46, R)
>dp4.chr4_group3 11053126 107 + 11692001
AGUGGAAGAGAAGUGGAAAAUCUUCAAGUUAAGUU--UUGUG-AAAACGUUGG---CAAAAACAUUCAAUUUGAAGUCGAUUUGAACUUCAAGUUGAAUAUUUAAUAAGAACG
....(((((....(....).))))).......(((--((.((-((...(((..---....)))((((((((((((((........)))))))))))))).))))...))))). ( -24.70, z-score =  -2.28, R)
>droAna3.scaffold_12916 10802256 95 + 16180835
------AAGGGUAAUUUGAAUCUCAAAGUUAGA-----AUGUCAAAACGUCAGU--AAAAAAUAUUCAAAUUGAAGUACA-UUUGACUUCAAGUUGAAUAUUACAACUG----
------........(((((...((.......))-----...)))))....((((--....(((((((((.(((((((.(.-...)))))))).)))))))))...))))---- ( -19.40, z-score =  -2.43, R)
>droEre2.scaffold_4845 17366809 97 + 22589142
-----AAAGAGAGUCCAAAAUCUCAAAAUCAGAAU--GUGGAUGGGACGUUGG---CGAAAAUAUUCAAAUUGAAGUCUGUUC--ACUUCAAGUUGAAUAUUACAAACG----
-----.......(.((((..(((((...(((....--.))).)))))..))))---)...(((((((((.(((((((......--))))))).))))))))).......---- ( -23.50, z-score =  -2.35, R)
>droYak2.chr2R 5564103 97 - 21139217
-----AAAGAGAGUUCGAAAUCUCAAAAUCAGAAU--GUGGAUGAGACGUUGG---CGAAAAUAUUCAAAUUGAAGUCUGUUC--ACUUCAAGUUGAAUAUUACAAACG----
-----...((((........))))..........(--((.((((...)))).)---))..(((((((((.(((((((......--))))))).))))))))).......---- ( -22.40, z-score =  -1.68, R)
>droSec1.super_7 2678253 97 - 3727775
-----AAAGAGAGUUUGAAAUCUCAAAAUCAGAAU--GUGGGUGAGACGUUGG---CCAAAAUAUUCAAUUUGAAGUCGGUUC--ACUUCAAGUUGAAUAUUACAAACG----
-----.......(((((...(((((...(((....--.))).)))))......---....(((((((((((((((((......--))))))))))))))))).))))).---- ( -29.10, z-score =  -4.05, R)
>droSim1.chr2L 18742946 97 - 22036055
-----AAAGAGAGUUUGAAAUCUCAAAAUCAGAAU--GUGGGUGAGACGUUGG---CCAAAAUAUUCAAUUUGAAGUCGGUUC--ACUUCAAGUUGAAUAUUACAAACG----
-----.......(((((...(((((...(((....--.))).)))))......---....(((((((((((((((((......--))))))))))))))))).))))).---- ( -29.10, z-score =  -4.05, R)
>consensus
_____AAAGAGAGUUUGAAAUCUCAAAAUCAGAAU__GUGGGUGAGACGUUGG___CAAAAAUAUUCAAUUUGAAGUCGAUUC__ACUUCAAGUUGAAUAUUACAAACG____
........((((........))))....................................(((((((((.(((((((........))))))).)))))))))........... (-13.24 = -13.56 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:51:13 2011