Locus 4764

Sequence ID dm3.chr2R
Location 15,548,794 – 15,548,885
Length 91
Max. P 0.999328
window6542 window6543

overview

Window 2

Location 15,548,794 – 15,548,885
Length 91
Sequences 13
Columns 108
Reading direction forward
Mean pairwise identity 85.23
Shannon entropy 0.30940
G+C content 0.41513
Mean single sequence MFE -27.23
Consensus MFE -23.06
Energy contribution -23.09
Covariance contribution 0.04
Combinations/Pair 1.13
Mean z-score -4.12
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.80
SVM RNA-class probability 0.999328
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15548794 91 + 21146708
CACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAC----CGGAAAAAUCACC--UAAGGCUGGACGACCAAAGAAACUAAUUGCAACCG-CUCCAUAA----------
..........(((..(((((((((((((((((((.----........)))..--))))))))))))))))..))).......((....)-).......---------- ( -25.00, z-score =  -4.15, R)
>droSim1.chr2R 14254228 91 + 19596830
CACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAU----CGGAAAAGUCACC--UAAGGCUGGACGACCAAAGAAACUAAUUGCAACCG-CCACAGAA----------
..........(((..((((((((((((((((((((----.......))))..--))))))))))))))))..))).......((....)-).......---------- ( -26.60, z-score =  -3.71, R)
>droSec1.super_1 13063523 91 + 14215200
CACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAU----CGGAAAAGUCACC--UAAGGCUGGACGACCAAAGAAACUAAUUGCAACCG-CCACAGAA----------
..........(((..((((((((((((((((((((----.......))))..--))))))))))))))))..))).......((....)-).......---------- ( -26.60, z-score =  -3.71, R)
>droYak2.chr2R 7515224 91 - 21139217
CACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAU----CAGAAAAGUCACC--UAAGGCUGGACGACCAAAGAAACUAAUUGCAACUG-CCCCAGUA----------
..........(((..((((((((((((((((((((----.......))))..--))))))))))))))))..)))..........((((-...)))).---------- ( -27.70, z-score =  -3.98, R)
>droEre2.scaffold_4845 9749045 91 + 22589142
CACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAU----CAGAAAAGUCACC--UAAGGCUGGACGACCAAAGAAACUAAUUGCAACCG-CUACAGUA----------
..........(((..((((((((((((((((((((----.......))))..--))))))))))))))))..)))(((....((....)-)...))).---------- ( -27.90, z-score =  -4.31, R)
>droAna3.scaffold_13266 10152819 94 - 19884421
CACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAU----CAGAGAAGUCACC--UAAGGCUGGACGACCAAAGAAACUAAUUGCAACCU-UUAUAUUGGUA-------
..........(((..((((((((((((((((((((----.......))))..--))))))))))))))))..)))..........(((.-.......))).------- ( -28.90, z-score =  -4.12, R)
>dp4.chr3 12677418 91 + 19779522
CACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAU----CAGAGAAAUCACC--UAAGGCUGGACGACCAAAGAAACUAAUUGCAACCA-CAAUAAGG----------
..........(((..((((((((((((((((((((----.......))))..--))))))))))))))))..))).((.((((......-)))).)).---------- ( -28.20, z-score =  -5.44, R)
>droPer1.super_2 130065 91 - 9036312
CACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAU----CAGAGAAAUCACC--UAAGGCUGGACGACCAAAGAAACUAAUUGCAACCA-CAAUAAGG----------
..........(((..((((((((((((((((((((----.......))))..--))))))))))))))))..))).((.((((......-)))).)).---------- ( -28.20, z-score =  -5.44, R)
>droWil1.scaffold_180701 1651610 100 + 3904529
CACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAU----CAGAGAAAUCACC--UAAGGCUGGACGACCAAAGAAACUAAUUGCAACC--CGCCAUUUGGUUAAAGUU
.......(((((...((((((((((((((((((((----.......))))..--))))))))))))))))....((((((..((....--.))...)))))).))))) ( -31.00, z-score =  -4.35, R)
>droVir3.scaffold_12875 16499190 91 - 20611582
CACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAU----CAGAGAAAUCACC--UAAGGCUGGACGACCAAAGAAACUAAUUGCAACCU-CUAUAUGA----------
..........(((..((((((((((((((((((((----.......))))..--))))))))))))))))..)))..............-........---------- ( -26.20, z-score =  -4.44, R)
>droMoj3.scaffold_6496 20936627 91 + 26866924
CACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAU----CAGAGAAAUCACC--UAAGGCUGGACGACCAAAGAAACUAAUUGCAACCU-CUAUACGA----------
..........(((..((((((((((((((((((((----.......))))..--))))))))))))))))..)))..............-........---------- ( -26.20, z-score =  -4.57, R)
>droGri2.scaffold_15112 2108672 91 + 5172618
CACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAU----CAGAGAAAUCACC--UAAGGCUGGACGACCAAAGAAACUAAUUGCAACCU-CUAUAAAA----------
..........(((..((((((((((((((((((((----.......))))..--))))))))))))))))..)))..............-........---------- ( -26.20, z-score =  -4.94, R)
>anoGam1.chr3R 43698209 107 + 53272125
CACACCUAUCUGCAGUGAUGGUCUAGCUUUAUGAUGUUCCAGCACAGUAAUCAGUAAGGUAGAAC-ACCAAAGUAGUUAGCUGCAGCGGACAAUAAGCCGCUCAAAUA
..((.(((.((((..((.((.((((.(((..((((..............))))..))).)))).)-).))..)))).))).)).(((((........)))))...... ( -25.34, z-score =  -0.39, R)
>consensus
CACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAU____CAGAGAAAUCACC__UAAGGCUGGACGACCAAAGAAACUAAUUGCAACCG_CUAUAAGA__________
..........(((..((((((((((((((((((((...........))))....))))))))))))))))..)))................................. (-23.06 = -23.09 +   0.04)

alignment

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secondary structure

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dotplot

Postscript

Window 3

Location 15,548,794 – 15,548,885
Length 91
Sequences 13
Columns 108
Reading direction reverse
Mean pairwise identity 85.23
Shannon entropy 0.30940
G+C content 0.41513
Mean single sequence MFE -24.30
Consensus MFE -17.94
Energy contribution -18.05
Covariance contribution 0.11
Combinations/Pair 1.20
Mean z-score -1.85
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.878324
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15548794 91 - 21146708
----------UUAUGGAG-CGGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUA--GGUGAUUUUUCCG----GUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUG
----------........-.....(((((.(..(((..((((.(((.(((....--.((((((.....)----)))))...))).))).))))..)))..).))))). ( -23.80, z-score =  -1.69, R)
>droSim1.chr2R 14254228 91 - 19596830
----------UUCUGUGG-CGGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUA--GGUGACUUUUCCG----AUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUG
----------........-.....(((((.(..(((..((((.(((.(((....--.(((((......)----.))))...))).))).))))..)))..).))))). ( -21.80, z-score =  -0.86, R)
>droSec1.super_1 13063523 91 - 14215200
----------UUCUGUGG-CGGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUA--GGUGACUUUUCCG----AUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUG
----------........-.....(((((.(..(((..((((.(((.(((....--.(((((......)----.))))...))).))).))))..)))..).))))). ( -21.80, z-score =  -0.86, R)
>droYak2.chr2R 7515224 91 + 21139217
----------UACUGGGG-CAGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUA--GGUGACUUUUCUG----AUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUG
----------.((((...-)))).(((((.(..(((..((((.(((.(((....--.(((((......)----.))))...))).))).))))..)))..).))))). ( -22.90, z-score =  -0.82, R)
>droEre2.scaffold_4845 9749045 91 - 22589142
----------UACUGUAG-CGGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUA--GGUGACUUUUCUG----AUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUG
----------........-.....(((((.(..(((..((((.(((.(((....--.(((((......)----.))))...))).))).))))..)))..).))))). ( -22.40, z-score =  -1.22, R)
>droAna3.scaffold_13266 10152819 94 + 19884421
-------UACCAAUAUAA-AGGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUA--GGUGACUUCUCUG----AUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUG
-------.(((.......-.))).(((((.(..(((..((((.(((.(((....--.(((((......)----.))))...))).))).))))..)))..).))))). ( -23.60, z-score =  -2.15, R)
>dp4.chr3 12677418 91 - 19779522
----------CCUUAUUG-UGGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUA--GGUGAUUUCUCUG----AUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUG
----------........-.....(((((.(..(((..((((.(((.(((....--.((((((.....)----)))))...))).))).))))..)))..).))))). ( -25.00, z-score =  -2.93, R)
>droPer1.super_2 130065 91 + 9036312
----------CCUUAUUG-UGGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUA--GGUGAUUUCUCUG----AUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUG
----------........-.....(((((.(..(((..((((.(((.(((....--.((((((.....)----)))))...))).))).))))..)))..).))))). ( -25.00, z-score =  -2.93, R)
>droWil1.scaffold_180701 1651610 100 - 3904529
AACUUUAACCAAAUGGCG--GGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUA--GGUGAUUUCUCUG----AUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUG
......((((........--))))(((((.(..(((..((((.(((.(((....--.((((((.....)----)))))...))).))).))))..)))..).))))). ( -27.60, z-score =  -2.26, R)
>droVir3.scaffold_12875 16499190 91 + 20611582
----------UCAUAUAG-AGGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUA--GGUGAUUUCUCUG----AUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUG
----------........-.....(((((.(..(((..((((.(((.(((....--.((((((.....)----)))))...))).))).))))..)))..).))))). ( -25.00, z-score =  -2.59, R)
>droMoj3.scaffold_6496 20936627 91 - 26866924
----------UCGUAUAG-AGGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUA--GGUGAUUUCUCUG----AUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUG
----------........-.....(((((.(..(((..((((.(((.(((....--.((((((.....)----)))))...))).))).))))..)))..).))))). ( -25.00, z-score =  -2.57, R)
>droGri2.scaffold_15112 2108672 91 - 5172618
----------UUUUAUAG-AGGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUA--GGUGAUUUCUCUG----AUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUG
----------........-.....(((((.(..(((..((((.(((.(((....--.((((((.....)----)))))...))).))).))))..)))..).))))). ( -25.00, z-score =  -2.77, R)
>anoGam1.chr3R 43698209 107 - 53272125
UAUUUGAGCGGCUUAUUGUCCGCUGCAGCUAACUACUUUGGU-GUUCUACCUUACUGAUUACUGUGCUGGAACAUCAUAAAGCUAGACCAUCACUGCAGAUAGGUGUG
......((((((.....).)))))(((.(((.((.(..((((-(.((((.(((..(((....(((......))))))..))).)))).)))))..).)).))).))). ( -27.00, z-score =  -0.39, R)
>consensus
__________UCAUAUAG_CGGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUA__GGUGAUUUCUCUG____AUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUG
........................(((((.((((((..((((.(((.(((.......((((.............))))...))).))).))))..)))))).))))). (-17.94 = -18.05 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:35:32 2011