Locus 3221

Sequence ID dm3.chr2R
Location 3,556,527 – 3,556,650
Length 123
Max. P 0.641740
window4431 window4432

overview

Window 1

Location 3,556,527 – 3,556,650
Length 123
Sequences 6
Columns 123
Reading direction forward
Mean pairwise identity 57.57
Shannon entropy 0.81563
G+C content 0.38599
Mean single sequence MFE -27.57
Consensus MFE -9.03
Energy contribution -10.62
Covariance contribution 1.59
Combinations/Pair 1.45
Mean z-score -1.07
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.32
SVM RNA-class probability 0.641740
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3556527 123 + 21146708
GUUAUAUCGAUAAGUCGAUGACUCGAUUAUAUGUAGUCAUCUAUGGGCGUACCAAUGCUGGGCAGCACUGGUGAAUUGGCGGUUAUGAAUUUAUGAAAUUGAUUAGUACUUUUUAUAUCCUAG
....((((((....))))))..((((((.((((...((((..((.(.(((((((.((((....)))).)))))...)).).)).))))...)))).))))))..................... ( -26.60, z-score =   0.23, R)
>droSim1.chr2R 2283474 121 + 19596830
GUUAUAUCGAUACGUCGAUGACUCGAUUAUAUUUAGUCAUCGAUGGUCGUACUAAUGCUGGGCAGCACUGGUGGAUUGGCGCUUAUUAAUUUAUGAAAUGGAUUAGUACUUUUUAUAGCCU--
((((((..(((.(((((((((((.(((...))).))))))))))))))(((((((((((....)))..(.(((((((((......))))))))).).....))))))))....))))))..-- ( -35.80, z-score =  -2.88, R)
>droSec1.super_1 1212673 121 + 14215200
GUUAUAUCGAUACGUCGAUGACUCGAUUAUAUUUAGUCAUCGAUGGUCGUACUAAUGCUGGGCAGCACUGGUGGAUUGGCGCUUAUUAAUUUAUGAAAUGGAUUAGUACUUUUUAUAGUCU--
.......((((.(((((((((((.(((...))).)))))))))))))))(((((.((((....)))).)))))(((((.....(((((((((((...))))))))))).......))))).-- ( -34.20, z-score =  -2.52, R)
>droYak2.chr2L 16227713 109 + 22324452
GUUGUAUCGAUAGAUCGAUGACU-CGCCAUG--UAGUUAUCGAUUCAUGUA-CCAUGCUGUGCAGCACUGGUGGAUUGUCGCUAAUUUUUUGACGUUAUGCCGCCAAGAUUCC----------
(((((((.(...(((((((((((-.......--.)))))))))))((((..-.))))).)))))))..((((((..(((((.........))))).....)))))).......---------- ( -30.70, z-score =  -1.31, R)
>droEre2.scaffold_4929 7590155 94 - 26641161
GUUAUAUCGAUAGGUCUAUGACUAUGCCAU---CAUUCAUCGAUAAAUGUAACUAAGCUGGGCCGCACUGGUGGAUUGGCGGUCAAUUUUUGACGUU--------------------------
(((((((..((.(((..((((........)---)))..))).))..)))))))...((..(.((((....)))).)..)).((((.....))))...-------------------------- ( -22.70, z-score =  -0.38, R)
>droMoj3.scaffold_6496 10086653 108 + 26866924
------ACAGCUAACAGCUGUCUCAAUAUGGUUUAGUAUUUUUUUGUUGCAUCUACUGGUUGCUGUUCUUG-AUUUUAACAUAUCUAUGUUAACAUAUAACAUAUUUGCUCCUCA--------
------(((((.....)))))........((...((((..(...(((((((((....)).)))........-...(((((((....))))))).....)))).)..))))))...-------- ( -15.40, z-score =   0.41, R)
>consensus
GUUAUAUCGAUAAGUCGAUGACUCGAUUAUAUUUAGUCAUCGAUGGUCGUACCAAUGCUGGGCAGCACUGGUGGAUUGGCGCUUAUUAAUUUACGAAAUGGAUUAGUACUUUUUA________
............(((((((((((...........)))))))))))..(((.....((((((......)))))).....))).......................................... ( -9.03 = -10.62 +   1.59)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,556,527 – 3,556,650
Length 123
Sequences 6
Columns 123
Reading direction reverse
Mean pairwise identity 57.57
Shannon entropy 0.81563
G+C content 0.38599
Mean single sequence MFE -21.54
Consensus MFE -5.07
Energy contribution -7.52
Covariance contribution 2.44
Combinations/Pair 1.07
Mean z-score -1.53
Structure conservation index 0.24
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.08
SVM RNA-class probability 0.535731
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3556527 123 - 21146708
CUAGGAUAUAAAAAGUACUAAUCAAUUUCAUAAAUUCAUAACCGCCAAUUCACCAGUGCUGCCCAGCAUUGGUACGCCCAUAGAUGACUACAUAUAAUCGAGUCAUCGACUUAUCGAUAUAAC
.....((((...((((...................................(((((((((....))))))))).........(((((((.(........)))))))).))))....))))... ( -24.30, z-score =  -2.42, R)
>droSim1.chr2R 2283474 121 - 19596830
--AGGCUAUAAAAAGUACUAAUCCAUUUCAUAAAUUAAUAAGCGCCAAUCCACCAGUGCUGCCCAGCAUUAGUACGACCAUCGAUGACUAAAUAUAAUCGAGUCAUCGACGUAUCGAUAUAAC
--....((((....((((((((..................(((((..........)))))((...)))))))))).....(((((((((...........)))))))))........)))).. ( -23.60, z-score =  -2.37, R)
>droSec1.super_1 1212673 121 - 14215200
--AGACUAUAAAAAGUACUAAUCCAUUUCAUAAAUUAAUAAGCGCCAAUCCACCAGUGCUGCCCAGCAUUAGUACGACCAUCGAUGACUAAAUAUAAUCGAGUCAUCGACGUAUCGAUAUAAC
--.((.(((.....((((((((..................(((((..........)))))((...)))))))))).....(((((((((...........))))))))).)))))........ ( -23.70, z-score =  -3.03, R)
>droYak2.chr2L 16227713 109 - 22324452
----------GGAAUCUUGGCGGCAUAACGUCAAAAAAUUAGCGACAAUCCACCAGUGCUGCACAGCAUGG-UACAUGAAUCGAUAACUA--CAUGGCG-AGUCAUCGAUCUAUCGAUACAAC
----------.((.((((((((......)))))).......((........((((.((((....)))))))-).((((............--)))))))-).))(((((....)))))..... ( -24.50, z-score =  -0.70, R)
>droEre2.scaffold_4929 7590155 94 + 26641161
--------------------------AACGUCAAAAAUUGACCGCCAAUCCACCAGUGCGGCCCAGCUUAGUUACAUUUAUCGAUGAAUG---AUGGCAUAGUCAUAGACCUAUCGAUAUAAC
--------------------------(((((((.....)))).(((.((......))..)))........))).....((((((((....---(((((...))))).....)))))))).... ( -16.00, z-score =  -0.14, R)
>droMoj3.scaffold_6496 10086653 108 - 26866924
--------UGAGGAGCAAAUAUGUUAUAUGUUAACAUAGAUAUGUUAAAAU-CAAGAACAGCAACCAGUAGAUGCAACAAAAAAAUACUAAACCAUAUUGAGACAGCUGUUAGCUGU------
--------.....(((.((((((((.((((....)))))))))))).....-....((((((..((((((.........................))))).)...)))))).)))..------ ( -17.11, z-score =  -0.49, R)
>consensus
________UAAAAAGUACUAAUCCAUUACAUAAAUAAAUAAGCGCCAAUCCACCAGUGCUGCCCAGCAUUGGUACAACCAUCGAUGACUAAAUAUAAUCGAGUCAUCGACCUAUCGAUAUAAC
.......................................................(((((....)))))...........(((((((((...........))))))))).............. ( -5.07 =  -7.52 +   2.44)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:06:07 2011