Locus 11909

Sequence ID dm3.chr3R
Location 24,500,532 – 24,500,629
Length 97
Max. P 0.995003
window16366 window16367

overview

Window 6

Location 24,500,532 – 24,500,629
Length 97
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 70.44
Shannon entropy 0.55935
G+C content 0.34526
Mean single sequence MFE -15.08
Consensus MFE -10.52
Energy contribution -10.44
Covariance contribution -0.08
Combinations/Pair 1.50
Mean z-score -1.82
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.76
SVM RNA-class probability 0.995003
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24500532 97 + 27905053
GAUAUUUCACUGCUCCAUGUGCAUGACUAAAGCCAUGCAUGUUUAUCUAUGUGAACAAA---CUAUAUCAACAUCGUAUAAAAAACAAUCUCUCUCUUCC
((((((((((......(((((((((........)))))))))........)))))....---..)))))............................... ( -15.14, z-score =  -2.18, R)
>droSim1.chr3R 24197959 97 + 27517382
GAUAUUUCACUGCUCCAUGUGCAUGACUAAAGCCAUGCAUGUUUAUCUAUGUGAAAAAA---CUAUAUCAACAUCGUAUAAAAUACAAUCACUCUCUUCC
(((.((((((......(((((((((........)))))))))........))))))...---.............((((...)))).))).......... ( -15.94, z-score =  -2.30, R)
>droYak2.chr3R 6842571 91 - 28832112
GAUAUUUCACUGCCUCAUGUGCAUGACUAAAGCCAUGCAUGUUUAGCCAUGUGAAAAAA---CUAUAUCAACAUCGUAUAAAAUACAAUCUCUC------
((((((((((.((...(((((((((........)))))))))...))...)))))....---..)))))......((((...))))........------ ( -18.10, z-score =  -2.53, R)
>droEre2.scaffold_4820 6943562 91 - 10470090
AAUAUUUCACUGCCCCAUGUGCAUGACUAAAGCCAUGCAUGUUUAUCCAUGUGAAAAAA---CUAUAUCAACAUCGUAUAAAAUACAAUCUCUC------
....((((((((....(((((((((........))))))))).....)).))))))...---.............((((...))))........------ ( -15.50, z-score =  -2.64, R)
>droAna3.scaffold_13340 17306561 93 + 23697760
GAUUUUCAGCAGCUCCAAGUGCAUGCCUAGAGCCGUGCAUGUUUAUCUAUAGAAAAAAAUAACUAUAUCAACAUCGAAUUAAACACAGACUCU-------
....(((.(((((((...((....))...))))..)))(((((....(((((..........)))))..))))).)))...............------- ( -10.80, z-score =   0.71, R)
>droWil1.scaffold_181089 9211306 96 + 12369635
CAAUUUUUACCGACGCUUGUACAUAUGCAUGUACAUGUACAACUGCAU-UGCAUGAUUGUUUUUCUAUCAAC-UAAACUAAACAAUCUUCUCUUAUUG--
..........(((.((((((((((.((....)).))))))))..)).)-))...((((((((..........-......))))))))...........-- ( -14.99, z-score =  -1.97, R)
>consensus
GAUAUUUCACUGCCCCAUGUGCAUGACUAAAGCCAUGCAUGUUUAUCUAUGUGAAAAAA___CUAUAUCAACAUCGUAUAAAAUACAAUCUCUC______
....((((((......(((((((((.(....).)))))))))........))))))............................................ (-10.52 = -10.44 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 24,500,532 – 24,500,629
Length 97
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 70.44
Shannon entropy 0.55935
G+C content 0.34526
Mean single sequence MFE -22.02
Consensus MFE -10.48
Energy contribution -11.07
Covariance contribution 0.59
Combinations/Pair 1.50
Mean z-score -1.61
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.12
SVM RNA-class probability 0.895819
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24500532 97 - 27905053
GGAAGAGAGAGAUUGUUUUUUAUACGAUGUUGAUAUAG---UUUGUUCACAUAGAUAAACAUGCAUGGCUUUAGUCAUGCACAUGGAGCAGUGAAAUAUC
...........((((((((((((...((((.((((...---..)))).))))..)))))..((((((((....))))))))....)))))))........ ( -21.50, z-score =  -1.31, R)
>droSim1.chr3R 24197959 97 - 27517382
GGAAGAGAGUGAUUGUAUUUUAUACGAUGUUGAUAUAG---UUUUUUCACAUAGAUAAACAUGCAUGGCUUUAGUCAUGCACAUGGAGCAGUGAAAUAUC
....(((((.(((((((((............)))))))---))))))).....((((....((((((((....))))))))(((......)))...)))) ( -19.70, z-score =  -0.63, R)
>droYak2.chr3R 6842571 91 + 28832112
------GAGAGAUUGUAUUUUAUACGAUGUUGAUAUAG---UUUUUUCACAUGGCUAAACAUGCAUGGCUUUAGUCAUGCACAUGAGGCAGUGAAAUAUC
------..(((((((((((............)))))))---))))(((((.((.((.....((((((((....))))))))....)).)))))))..... ( -25.70, z-score =  -2.82, R)
>droEre2.scaffold_4820 6943562 91 + 10470090
------GAGAGAUUGUAUUUUAUACGAUGUUGAUAUAG---UUUUUUCACAUGGAUAAACAUGCAUGGCUUUAGUCAUGCACAUGGGGCAGUGAAAUAUU
------..(((((((((((............)))))))---))))((((((((......)))(((((((....)))))))..........)))))..... ( -21.90, z-score =  -2.04, R)
>droAna3.scaffold_13340 17306561 93 - 23697760
-------AGAGUCUGUGUUUAAUUCGAUGUUGAUAUAGUUAUUUUUUUCUAUAGAUAAACAUGCACGGCUCUAGGCAUGCACUUGGAGCUGCUGAAAAUC
-------((((.((((((........(((((..(((((..(....)..)))))....))))))))))))))).((((.((.......))))))....... ( -21.50, z-score =  -0.84, R)
>droWil1.scaffold_181089 9211306 96 - 12369635
--CAAUAAGAGAAGAUUGUUUAGUUUA-GUUGAUAGAAAAACAAUCAUGCA-AUGCAGUUGUACAUGUACAUGCAUAUGUACAAGCGUCGGUAAAAAUUG
--...........((((((((..((((-.....)))).)))))))).(((.-((((..((((((((((......))))))))))))))..)))....... ( -21.80, z-score =  -2.01, R)
>consensus
______GAGAGAUUGUAUUUUAUACGAUGUUGAUAUAG___UUUUUUCACAUAGAUAAACAUGCAUGGCUUUAGUCAUGCACAUGGAGCAGUGAAAUAUC
........((.((((((.....)))))).)).............((((((...........((((((((....)))))))).........)))))).... (-10.48 = -11.07 +   0.59)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:51:59 2011