Locus 4546

Sequence ID dm3.chr2R
Location 13,890,645 – 13,890,761
Length 116
Max. P 0.979915
window6228 window6229

overview

Window 8

Location 13,890,645 – 13,890,761
Length 116
Sequences 8
Columns 117
Reading direction forward
Mean pairwise identity 71.15
Shannon entropy 0.54630
G+C content 0.54897
Mean single sequence MFE -38.61
Consensus MFE -19.75
Energy contribution -20.06
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -1.56
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.16
SVM RNA-class probability 0.902593
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13890645 116 + 21146708
CAUUGGUAAUGGGACGGGGAAGGGGAA-GGGGACCACGCCCACGUGGCGCUGCAUUUGUAACAGGUGAGCUUUAUGGCUCUGUUACCGUUGCAACGCAUUGCAUUCAACGUGGUGUG
.....((((((((((((((..((((..-(....)..).))).(((((.(((.((((((...))))))))).))))).))))))).)))))))..(((((..(.......)..))))) ( -41.20, z-score =  -1.09, R)
>droSim1.chr2R 12628446 109 + 19596830
CAUUGGCAAUGGGAAGGGUAAGGGUAA-GGG-ACCACGCCCACGUGGCGCUGCAUUUGUAACAGGUGAGCUUUAUGGCUCUGUUACCGUUGCAACGCAUUGCAUUCAACGU------
.....((((((.(....((((.(((((-.((-((((.(((.....)))(((.((((((...)))))))))....))).))).))))).))))..).)))))).........------ ( -39.10, z-score =  -1.51, R)
>droSec1.super_1 11385061 109 + 14215200
CAUUGGCAAUGGGAAGGAAAAGGGUAA-GGG-ACCACGCCCACGUGGCGCUUCAUUUGUAACAGGUGAGCUUUAUGGCGCUGUUACCGUUGCAACGCAUUGCAUUCAACGU------
.....((((((.(..........(.((-(.(-.(((((....)))))).))))..(((((((.((((((((....)))....))))))))))))).)))))).........------ ( -32.90, z-score =  -0.09, R)
>droYak2.chr2R 5850551 97 - 21139217
------------CAUCGGCAAUGGGGC-GGA-GCCACGCCCACGUGGCGCUGCAUUUGUAACAGGUGAGCUUUAUGGCUCUGUUACCGUUGCAACGCGUUGCAUUCAACGU------
------------.....((((((((((-(((-((((.(((.....)))(((.((((((...)))))))))....)))))))))).)))))))...((((((....))))))------ ( -42.70, z-score =  -2.75, R)
>droEre2.scaffold_4845 8119211 95 + 22589142
------------CAUCGGCUA-GGGGA-GGG-GCCACGCCCACGUGGCGCUGCAUUUGUAACAGGUGAGCUUUAUGGCUCUGUUACCGUUGCAAC-CGUUGCAUUCAACGU------
------------.....((.(-.((..-((.-((((((....)))))).))(((...((((((...(((((....)))))))))))...)))..)-).).)).........------ ( -34.10, z-score =  -0.66, R)
>droAna3.scaffold_13266 9589025 97 - 19884421
CCGCAGCCACGGGAUGGGUCAUGGCAG-GC---CCACGCCCACGUGGCGCUGCAUUUGUAACAGGUGAGCUUUAUGGCUCUGUUACCGUUGCAUU-UGCCGU---------------
..((.((((((((.((((((......)-))---)))...)).)))))))).(((..((((((.((((((((....)))))....)))))))))..-)))...--------------- ( -44.70, z-score =  -2.36, R)
>dp4.chr3 6356039 100 + 19779522
-CAAGACCAGGCCAGAGGCAGCCCUGGCAGGACCCACGUCCAUGUGGUGUUGCAUUUGUAACAGGUGAGCUUUAUGGCUAUGUUACCGUUGCAUU-UACCGC---------------
-.........(((((.((...))))))).((((....))))..((((((.((((...((((((....((((....)))).))))))...))))..-))))))--------------- ( -37.10, z-score =  -1.87, R)
>droPer1.super_2 6572448 100 + 9036312
-CAAGACCAGGCCAGAGGCAUCCCUGGCAGGACCCACGUCCAUGUGGUGUUGCAUUUGUAACAGGUGAGCUUUAUGGCUAUGUUACCGUUGCAUU-UACCGC---------------
-.........(((((.((...))))))).((((....))))..((((((.((((...((((((....((((....)))).))))))...))))..-))))))--------------- ( -37.10, z-score =  -2.16, R)
>consensus
_AUUGGCAAUGGCAUGGGCAAGGGUAA_GGG_ACCACGCCCACGUGGCGCUGCAUUUGUAACAGGUGAGCUUUAUGGCUCUGUUACCGUUGCAAC_CAUUGCAUUCAACGU______
.................................(((((....)))))...((((...(((((((...((((....)))))))))))...))))........................ (-19.75 = -20.06 +   0.31) 

alignment

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secondary structure

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dotplot

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Window 9

Location 13,890,645 – 13,890,761
Length 116
Sequences 8
Columns 117
Reading direction reverse
Mean pairwise identity 71.15
Shannon entropy 0.54630
G+C content 0.54897
Mean single sequence MFE -35.33
Consensus MFE -18.76
Energy contribution -19.51
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.94
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.03
SVM RNA-class probability 0.979915
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13890645 116 - 21146708
CACACCACGUUGAAUGCAAUGCGUUGCAACGGUAACAGAGCCAUAAAGCUCACCUGUUACAAAUGCAGCGCCACGUGGGCGUGGUCCCC-UUCCCCUUCCCCGUCCCAUUACCAAUG
.......(((((........((((((((...((((((((((......))))...))))))...))))))))...(((((((.((.....-........)).)).)))))...))))) ( -36.82, z-score =  -3.12, R)
>droSim1.chr2R 12628446 109 - 19596830
------ACGUUGAAUGCAAUGCGUUGCAACGGUAACAGAGCCAUAAAGCUCACCUGUUACAAAUGCAGCGCCACGUGGGCGUGGU-CCC-UUACCCUUACCCUUCCCAUUGCCAAUG
------.(((((...((((((.((((((...((((((((((......))))...))))))...))))))((((((....))))))-...-................))))))))))) ( -37.40, z-score =  -3.18, R)
>droSec1.super_1 11385061 109 - 14215200
------ACGUUGAAUGCAAUGCGUUGCAACGGUAACAGCGCCAUAAAGCUCACCUGUUACAAAUGAAGCGCCACGUGGGCGUGGU-CCC-UUACCCUUUUCCUUCCCAUUGCCAAUG
------.(((((...((((((.(((.((...(((((((.((......))....)))))))...)).)))((((((....))))))-...-................))))))))))) ( -28.80, z-score =  -0.59, R)
>droYak2.chr2R 5850551 97 + 21139217
------ACGUUGAAUGCAACGCGUUGCAACGGUAACAGAGCCAUAAAGCUCACCUGUUACAAAUGCAGCGCCACGUGGGCGUGGC-UCC-GCCCCAUUGCCGAUG------------
------.(((((...(((..((((((((...((((((((((......))))...))))))...))))))))...(((((.(((..-..)-)))))))))))))))------------ ( -39.40, z-score =  -2.89, R)
>droEre2.scaffold_4845 8119211 95 - 22589142
------ACGUUGAAUGCAACG-GUUGCAACGGUAACAGAGCCAUAAAGCUCACCUGUUACAAAUGCAGCGCCACGUGGGCGUGGC-CCC-UCCCC-UAGCCGAUG------------
------.(((((....)))))-((((((...((((((((((......))))...))))))...))))))((((((....))))))-...-.....-.........------------ ( -35.50, z-score =  -2.46, R)
>droAna3.scaffold_13266 9589025 97 + 19884421
---------------ACGGCA-AAUGCAACGGUAACAGAGCCAUAAAGCUCACCUGUUACAAAUGCAGCGCCACGUGGGCGUGG---GC-CUGCCAUGACCCAUCCCGUGGCUGCGG
---------------.(.(((-..((((...((((((((((......))))...))))))...))))..(((((((((((((((---..-...))))).))))...))))))))).) ( -41.80, z-score =  -2.30, R)
>dp4.chr3 6356039 100 - 19779522
---------------GCGGUA-AAUGCAACGGUAACAUAGCCAUAAAGCUCACCUGUUACAAAUGCAACACCACAUGGACGUGGGUCCUGCCAGGGCUGCCUCUGGCCUGGUCUUG-
---------------(.(((.-..((((...((((((.(((......)))....))))))...))))..))).)..((((....)))).((((((.(.......).))))))....- ( -31.40, z-score =  -0.36, R)
>droPer1.super_2 6572448 100 - 9036312
---------------GCGGUA-AAUGCAACGGUAACAUAGCCAUAAAGCUCACCUGUUACAAAUGCAACACCACAUGGACGUGGGUCCUGCCAGGGAUGCCUCUGGCCUGGUCUUG-
---------------......-..((((...((((((.(((......)))....))))))...))))...((((......))))(.((.(((((((....)))))))..)).)...- ( -31.50, z-score =  -0.64, R)
>consensus
______ACGUUGAAUGCAAUG_GUUGCAACGGUAACAGAGCCAUAAAGCUCACCUGUUACAAAUGCAGCGCCACGUGGGCGUGGU_CCC_UCACCCUUGCCCAUCCCAUGGCCAAG_
........................((((...((((((((((......)))...)))))))...))))...(((((....)))))................................. (-18.76 = -19.51 +   0.75) 

alignment

Postscript

secondary structure

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dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:31:13 2011