Locus 3226

Sequence ID dm3.chr2R
Location 3,591,089 – 3,591,192
Length 103
Max. P 0.997612
window4438 window4439

overview

Window 8

Location 3,591,089 – 3,591,192
Length 103
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 69.46
Shannon entropy 0.54397
G+C content 0.43187
Mean single sequence MFE -29.12
Consensus MFE -13.91
Energy contribution -14.83
Covariance contribution 0.92
Combinations/Pair 1.24
Mean z-score -2.59
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.76
SVM RNA-class probability 0.995029
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3591089 103 + 21146708
-------------AGUCCACCCGUUUUUCCAGCUCAACCAACGGAUCGGACAACUGCUCCAA--UAAAAACAUCUUGGU-UAAGCUGCCAUAUUCAUUGCUUGACUGCGUUGAGUUGCC-
-------------................((((((((((...(((.(((....))).)))..--............(((-(((((.............))))))))).)))))))))..- ( -26.42, z-score =  -2.07, R)
>droSim1.chr2R 2314705 103 + 19596830
-------------AGUUCACCUGUAUUUCCAGCUCAACCAACGGAUCGGACAACUGCUCCAA--UAAAAACAUCUUGGU-UCAGCUGCCAUAUCACUUGGUUGACUGCCUUGAGAUGCC-
-------------.........((((((((((.((((((((..(((.((.((.(((..((((--..........)))).-.))).))))..)))..)))))))))))....))))))).- ( -29.30, z-score =  -2.65, R)
>droSec1.super_1 1246507 103 + 14215200
-------------AGUUCACCUGUUUUUCCAGCUCAACCAACGGAUCGGACAACUGCUCCAA--UAAAAACCUCUUGGU-UUAGCUGCCAUAUCAAUUGGUUGACUGCCUUGAAUUGCC-
-------------.........((..((((((.((((((((..(((.((.((.(((..((((--..........)))).-.))).))))..)))..)))))))))))....)))..)).- ( -24.70, z-score =  -1.73, R)
>droYak2.chr2L 16263878 116 + 22324452
UGCCUAUUUGAGAAGUUUAACUGUUUUUCUAGCUCAACCAAUGGAUCGGACAACUGCUCCAA--UGAAAAUAUUUUGGU-UCAUCUGCCCUAUUAAUUGGUUGACUGCCUUAAGUUGCC-
.((..(((((((.((.....)).......(((.(((((((((.(((.((.((..((..((((--..........)))).-.))..)).)).))).)))))))))))).))))))).)).- ( -26.70, z-score =  -1.68, R)
>droEre2.scaffold_4929 7624638 104 - 26641161
------------UGCUGUGGUCAGUUCAACAGCUCAACCAAUGGAUCGGACAACUGCUCCAU--UGAAAAAAUGUUGGC-UCAGCUGCCUUAUUAAUUGGUUGACUGACUUGAGUUGCA-
------------.(((..(((((((.((((........(((((((.(((....))).)))))--))....((((..(((-......))).)))).....)))))))))))..)))....- ( -32.10, z-score =  -1.90, R)
>droAna3.scaffold_13266 10096698 102 + 19884421
------------------CACUAUUUUCAAAAGACAACCAAAGACAAUGACUGCUGUUCCAAGGUUCUAUUAUCUUGGGAUCAGUUGUCUUUACCUUUGGUUAGUCCUCUGAAAUUUCCC
------------------......(((((...(((((((((((.....(((.(((((((((((((......))))))))).)))).))).....)))))))).)))...)))))...... ( -35.50, z-score =  -5.52, R)
>consensus
_____________AGUUCACCUGUUUUUCCAGCUCAACCAACGGAUCGGACAACUGCUCCAA__UAAAAACAUCUUGGU_UCAGCUGCCAUAUCAAUUGGUUGACUGCCUUGAGUUGCC_
.............................(((.((((((((..(((.((.((.(((..((((............))))...))).))))..)))..)))))))))))............. (-13.91 = -14.83 +   0.92)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,591,089 – 3,591,192
Length 103
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 69.46
Shannon entropy 0.54397
G+C content 0.43187
Mean single sequence MFE -31.38
Consensus MFE -21.65
Energy contribution -21.52
Covariance contribution -0.13
Combinations/Pair 1.35
Mean z-score -2.18
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.14
SVM RNA-class probability 0.997612
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3591089 103 - 21146708
-GGCAACUCAACGCAGUCAAGCAAUGAAUAUGGCAGCUUA-ACCAAGAUGUUUUUA--UUGGAGCAGUUGUCCGAUCCGUUGGUUGAGCUGGAAAAACGGGUGGACU-------------
-(...((((...((......))...........(((((((-(((((((((....))--))(((.(........).))).)))))))))))).......))))...).------------- ( -25.80, z-score =   0.19, R)
>droSim1.chr2R 2314705 103 - 19596830
-GGCAUCUCAAGGCAGUCAACCAAGUGAUAUGGCAGCUGA-ACCAAGAUGUUUUUA--UUGGAGCAGUUGUCCGAUCCGUUGGUUGAGCUGGAAAUACAGGUGAACU-------------
-..(((((.....(((((((((((..(((..((((((((.-.((((..........--))))..))))))))..)))..)))))))).))).......)))))....------------- ( -34.20, z-score =  -2.19, R)
>droSec1.super_1 1246507 103 - 14215200
-GGCAAUUCAAGGCAGUCAACCAAUUGAUAUGGCAGCUAA-ACCAAGAGGUUUUUA--UUGGAGCAGUUGUCCGAUCCGUUGGUUGAGCUGGAAAAACAGGUGAACU-------------
-.....((((......(((((((((.(((..(((((((..-.((((..........--))))...)))))))..))).))))))))).(((......))).))))..------------- ( -30.00, z-score =  -1.54, R)
>droYak2.chr2L 16263878 116 - 22324452
-GGCAACUUAAGGCAGUCAACCAAUUAAUAGGGCAGAUGA-ACCAAAAUAUUUUCA--UUGGAGCAGUUGUCCGAUCCAUUGGUUGAGCUAGAAAAACAGUUAAACUUCUCAAAUAGGCA
-.((.......(((..(((((((((.....((((((.((.-.((((..........--))))..)).)))))).....))))))))))))...............((........)))). ( -27.30, z-score =  -1.45, R)
>droEre2.scaffold_4929 7624638 104 + 26641161
-UGCAACUCAAGUCAGUCAACCAAUUAAUAAGGCAGCUGA-GCCAACAUUUUUUCA--AUGGAGCAGUUGUCCGAUCCAUUGGUUGAGCUGUUGAACUGACCACAGCA------------
-...............(((((((((..((..((((((((.-.(((...........--.)))..))))))))..))..)))))))))(((((.(......).))))).------------ ( -33.40, z-score =  -2.81, R)
>droAna3.scaffold_13266 10096698 102 - 19884421
GGGAAAUUUCAGAGGACUAACCAAAGGUAAAGACAACUGAUCCCAAGAUAAUAGAACCUUGGAACAGCAGUCAUUGUCUUUGGUUGUCUUUUGAAAAUAGUG------------------
......(((((((((((.((((((((..((.(((..(((...(((((..........)))))..)))..))).))..)))))))))))))))))))......------------------ ( -37.60, z-score =  -5.26, R)
>consensus
_GGCAACUCAAGGCAGUCAACCAAUUAAUAUGGCAGCUGA_ACCAAGAUGUUUUUA__UUGGAGCAGUUGUCCGAUCCGUUGGUUGAGCUGGAAAAACAGGUGAACU_____________
.............((((((((((((..((..((((((((...((((............))))..))))))))..))..))))))))).)))............................. (-21.65 = -21.52 +  -0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:06:13 2011