Locus 11660

Sequence ID dm3.chr3R
Location 22,861,963 – 22,862,073
Length 110
Max. P 0.723529
window16020 window16021

overview

Window 0

Location 22,861,963 – 22,862,072
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 74.24
Shannon entropy 0.46040
G+C content 0.38458
Mean single sequence MFE -24.72
Consensus MFE -14.37
Energy contribution -14.98
Covariance contribution 0.62
Combinations/Pair 1.47
Mean z-score -1.18
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.537303
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 22861963 109 + 27905053
GCCAAAGUCUUACGCUUCAAGUUUUUUUUUUAACGUGUAGCCAUACACAACAUAGUGAUAUUACCAUCACGC---AGUCAUUGAGAAAAUCAAUGAGGCUGCUCAUUAAUGU--------
(((..........((...................(((((....)))))......(((((......)))))))---..(((((((.....)))))))))).............-------- ( -24.40, z-score =  -2.22, R)
>droAna3.scaffold_12911 3777340 115 + 5364042
ACCAAUAAACCAUUUAAAGAAUUUUCUC-----UGUGUAUCCACGCAUAACUGGGAGGUGUUCUCGCCUCGCCUGGGUUAUUCGGUUCAUCAAUGACUUGGCUCACUAAUGAGGUUUGCU
.....((((((.................-----(((((....)))))....(((((((((....))))))(((.((((((((.((....)))))))))))))...)))....)))))).. ( -28.40, z-score =  -0.91, R)
>droEre2.scaffold_4820 5294956 106 - 10470090
GCCAAAGUAUUAUGUUUAGAGAUUUGUU--UAACGUGUAGCCAAGCACAACAUAGUAAUAUUACCUUCUCGC---AGUCAUUGAGCAAGUCAAUG-GACUGCUCAUUAAUGU--------
.......(((((((((((((......))--))..((((......))))))))))))).............((---(((((((((.....))))).-))))))..........-------- ( -22.20, z-score =  -0.87, R)
>droYak2.chr3R 5200431 107 - 28832112
ACCAAGGUAUUAUGCUUAAAGUUUUUUU--UAACGUGUAGCCAUGCACAACCUAGUGAUAUUACCAUCUCGC---AGUCAUUGAGCAAAUCAGUGGGGCUGCUCAUUAAUGU--------
.....((((.((((((....(((.....--.)))(((((....))))).....))).))).)))).....((---(((((((((.....))))))..)))))..........-------- ( -25.00, z-score =  -0.75, R)
>droSec1.super_13 1625669 107 + 2104621
GCCAAGAAAUUAUGGUAAAAGUUUUUUU--UAACGUGUAGCCAUACACAACCUAGUUGUAUUACCAUGACGC---AGUCAUUGAGCAAAUCAAUGGGGCUGCUCAUUAAUGU--------
.....((..(((((((((..(((.....--.)))(((((....)))))............))))))))).((---(((((((((.....))))))..)))))))........-------- ( -27.70, z-score =  -1.99, R)
>droSim1.chr3R 22687639 105 + 27517382
GCCAAGAAAUUAUGCUUAAUGUUUUUU----AACGUGUAGCCAUACACAACCUAGUUAUAUUACCAUCACGC---AGUCAUUGAGCAAAUCAAUGGGGCUGCUCAUUAAUGU--------
.............((((((((......----...(((((....)))))......................((---(((((((((.....))))))..))))).)))))).))-------- ( -20.60, z-score =  -0.34, R)
>consensus
GCCAAGAAAUUAUGCUUAAAGUUUUUUU__UAACGUGUAGCCAUACACAACCUAGUGAUAUUACCAUCACGC___AGUCAUUGAGCAAAUCAAUGGGGCUGCUCAUUAAUGU________
..................................(.((((((............(((((......))))).......(((((((.....))))))))))))).)................ (-14.37 = -14.98 +   0.62)

alignment

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secondary structure

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dotplot

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Window 1

Location 22,861,964 – 22,862,073
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 74.61
Shannon entropy 0.45593
G+C content 0.37833
Mean single sequence MFE -24.75
Consensus MFE -14.37
Energy contribution -14.98
Covariance contribution 0.62
Combinations/Pair 1.47
Mean z-score -1.41
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.51
SVM RNA-class probability 0.723529
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 22861964 109 + 27905053
CCAAAGUCUUACGCUUCAAGUUUUUUUUUUAACGUGUAGCCAUACACAACAUAGUGAUAUUACCAUCACGC---AGUCAUUGAGAAAAUCAAUGAGGCUGCUCAUUAAUGUU--------
...................(((........)))(((((....)))))(((((.(((((......)))))((---(((((((((.....))))))..)))))......)))))-------- ( -24.50, z-score =  -2.54, R)
>droAna3.scaffold_12911 3777341 115 + 5364042
CCAAUAAACCAUUUAAAGAAUUUUCUCU-----GUGUAUCCACGCAUAACUGGGAGGUGUUCUCGCCUCGCCUGGGUUAUUCGGUUCAUCAAUGACUUGGCUCACUAAUGAGGUUUGCUU
....((((((.................(-----((((....)))))....(((((((((....))))))(((.((((((((.((....)))))))))))))...)))....))))))... ( -28.40, z-score =  -0.95, R)
>droEre2.scaffold_4820 5294957 106 - 10470090
CCAAAGUAUUAUGUUUAGAGAUUUGUUU--AACGUGUAGCCAAGCACAACAUAGUAAUAUUACCUUCUCGC---AGUCAUUGAGCAAGUCAAUG-GACUGCUCAUUAAUGUU--------
......(((((((((((((......)))--)..((((......))))))))))))).............((---(((((((((.....))))).-))))))...........-------- ( -22.20, z-score =  -1.15, R)
>droYak2.chr3R 5200432 107 - 28832112
CCAAGGUAUUAUGCUUAAAGUUUUUUUU--AACGUGUAGCCAUGCACAACCUAGUGAUAUUACCAUCUCGC---AGUCAUUGAGCAAAUCAGUGGGGCUGCUCAUUAAUGUU--------
....((((.((((((....(((......--)))(((((....))))).....))).))).)))).....((---(((((((((.....))))))..)))))...........-------- ( -25.00, z-score =  -0.83, R)
>droSec1.super_13 1625670 107 + 2104621
CCAAGAAAUUAUGGUAAAAGUUUUUUUU--AACGUGUAGCCAUACACAACCUAGUUGUAUUACCAUGACGC---AGUCAUUGAGCAAAUCAAUGGGGCUGCUCAUUAAUGUU--------
....((..(((((((((..(((......--)))(((((....)))))............))))))))).((---(((((((((.....))))))..))))))).........-------- ( -27.70, z-score =  -2.30, R)
>droSim1.chr3R 22687640 105 + 27517382
CCAAGAAAUUAUGCUUAAUGUUUUUU----AACGUGUAGCCAUACACAACCUAGUUAUAUUACCAUCACGC---AGUCAUUGAGCAAAUCAAUGGGGCUGCUCAUUAAUGUU--------
............((((((((......----...(((((....)))))......................((---(((((((((.....))))))..))))).)))))).)).-------- ( -20.70, z-score =  -0.67, R)
>consensus
CCAAGAAAUUAUGCUUAAAGUUUUUUUU__AACGUGUAGCCAUACACAACCUAGUGAUAUUACCAUCACGC___AGUCAUUGAGCAAAUCAAUGGGGCUGCUCAUUAAUGUU________
.................................(.((((((............(((((......))))).......(((((((.....))))))))))))).)................. (-14.37 = -14.98 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:47:08 2011