Locus 2282

Sequence ID dm3.chr2L
Location 17,588,235 – 17,588,307
Length 72
Max. P 0.963834
window3149 window3150

overview

Window 9

Location 17,588,235 – 17,588,307
Length 72
Sequences 12
Columns 88
Reading direction forward
Mean pairwise identity 81.69
Shannon entropy 0.37789
G+C content 0.39307
Mean single sequence MFE -20.93
Consensus MFE -12.00
Energy contribution -12.23
Covariance contribution 0.22
Combinations/Pair 1.20
Mean z-score -2.32
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.42
SVM RNA-class probability 0.938179
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17588235 72 + 23011544
---------GAAAAUAUUUGGCAUGUGCCAUUUA-UGGCAUUGUUCCAGC-UUUGAACAAU-GCGAUACCAUAAUUUCCAGGCA----
---------(((((((..((((....))))..))-).(((((((((....-...)))))))-))..........))))......---- ( -20.00, z-score =  -1.81, R)
>droSim1.chr2L 17291952 72 + 22036055
---------GAAAAUAUUUGGCAUGUGCCAUUUA-UGGCAUUGUUCCAGC-UUUGAACAAU-GCGAUACCAUAAUUUCCAGGCA----
---------(((((((..((((....))))..))-).(((((((((....-...)))))))-))..........))))......---- ( -20.00, z-score =  -1.81, R)
>droSec1.super_7 1229551 72 + 3727775
---------GAAAAUAUUUGGCAUGUGCCAUUUA-UGGCAUUGUUCCAGC-UUUGAACAAU-GCGAUACCAUAAUUUCCAGGCA----
---------(((((((..((((....))))..))-).(((((((((....-...)))))))-))..........))))......---- ( -20.00, z-score =  -1.81, R)
>droYak2.chr2R 17628663 72 - 21139217
---------GAAAAUAUUUGGCAUGUGCCAUUUA-UGGCAUUGUUCCAGC-UUUGAACAAU-GCGAUACCAUAAUUUCCAGGCA----
---------(((((((..((((....))))..))-).(((((((((....-...)))))))-))..........))))......---- ( -20.00, z-score =  -1.81, R)
>droEre2.scaffold_4845 15926676 72 - 22589142
---------GAAAAUAUUUGGCAUGUGCCAUUUA-UGGCAUUGUUCCAGC-UUUGAACAAU-GCGAUACCAUAAUUUUCAGGCA----
---------((((((...((((....))))..((-(.(((((((((....-...)))))))-)).))).....)))))).....---- ( -22.70, z-score =  -2.94, R)
>droAna3.scaffold_12916 12891571 72 - 16180835
---------GAAAAUAUUUGGCAUGUGCCAUUUA-UGGCAUUGUUCCAAG-UUGGAACAAU-GCGAUACCAUAGUUUCCAGGCA----
---------((((.(((.((((....))))..((-(.((((((((((...-..))))))))-)).)))..))).))))......---- ( -24.50, z-score =  -3.15, R)
>dp4.chr4_group3 847368 73 - 11692001
--------GAAAUAUAUUUGGCAUGUGCCAUUUA-UGGCAUUGUUCCAAC-UUUGAACAAU-GCGAUACCAUAAUUUCCAGGCA----
--------(((((.....((((....))))..((-(.(((((((((....-...)))))))-)).))).....)))))......---- ( -20.90, z-score =  -2.59, R)
>droPer1.super_8 1910752 73 - 3966273
--------GAAAUAUAUUUGGCAUGUGCCAUUUA-UGGCAUUGUUCCAAC-UUUGAACAAU-GCGAUACCAUAAUUUCCAGGCA----
--------(((((.....((((....))))..((-(.(((((((((....-...)))))))-)).))).....)))))......---- ( -20.90, z-score =  -2.59, R)
>droWil1.scaffold_180764 3040729 74 - 3949147
---------GAAAAUAUUUGGCAUGUGCCAUUUA-UGGCAUUGUUCCAACAUCUGAACAAUUGCGAUACCAUAAUUUUCAGGCA----
---------((((((...((((....))))..((-(.(((((((((........)))))).))).))).....)))))).....---- ( -19.20, z-score =  -1.95, R)
>droVir3.scaffold_12963 16521758 61 + 20206255
---------AAAAAUGUUUGGCAUGUGCCAUUCGCUGGCAUUGUGCCCAC-UUUAAACAAU-GCGAUGC-ACA---------------
---------......(..((((....))))..)(((.(((((((......-.....)))))-)).).))-...--------------- ( -18.00, z-score =  -1.09, R)
>droMoj3.scaffold_6500 21449344 77 + 32352404
---------GAAAAUGUUUGGCAUGUGCCAAACGCUGGCAUUGUUUUCAC-UUUGAACAAU-GCGAUACCAUAAUUUGCAGCACAACA
---------......(((((((....)))))))(((((((((((((....-...)))))))-)).....((.....))))))...... ( -26.10, z-score =  -3.44, R)
>droGri2.scaffold_15252 13932840 83 + 17193109
UACAACACUGGCCCCGUUGAAACAACGCCAUUGCCUGGCAUUGUUCCCAACUUUGAACAAU-GCGAUAACAUAAUUUACAGACA----
..((.((.((((...((((...)))))))).))..))(((((((((........)))))))-))....................---- ( -18.90, z-score =  -2.84, R)
>consensus
_________GAAAAUAUUUGGCAUGUGCCAUUUA_UGGCAUUGUUCCAAC_UUUGAACAAU_GCGAUACCAUAAUUUCCAGGCA____
..............((..((((....))))..))...(((((((((........))))))).))........................ (-12.00 = -12.23 +   0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 17,588,235 – 17,588,307
Length 72
Sequences 12
Columns 88
Reading direction reverse
Mean pairwise identity 81.69
Shannon entropy 0.37789
G+C content 0.39307
Mean single sequence MFE -20.92
Consensus MFE -14.35
Energy contribution -14.81
Covariance contribution 0.46
Combinations/Pair 1.18
Mean z-score -2.09
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.73
SVM RNA-class probability 0.963834
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17588235 72 - 23011544
----UGCCUGGAAAUUAUGGUAUCGC-AUUGUUCAAA-GCUGGAACAAUGCCA-UAAAUGGCACAUGCCAAAUAUUUUC---------
----((((..........))))..((-(((((((...-....)))))))))..-....((((....)))).........--------- ( -19.70, z-score =  -1.81, R)
>droSim1.chr2L 17291952 72 - 22036055
----UGCCUGGAAAUUAUGGUAUCGC-AUUGUUCAAA-GCUGGAACAAUGCCA-UAAAUGGCACAUGCCAAAUAUUUUC---------
----((((..........))))..((-(((((((...-....)))))))))..-....((((....)))).........--------- ( -19.70, z-score =  -1.81, R)
>droSec1.super_7 1229551 72 - 3727775
----UGCCUGGAAAUUAUGGUAUCGC-AUUGUUCAAA-GCUGGAACAAUGCCA-UAAAUGGCACAUGCCAAAUAUUUUC---------
----((((..........))))..((-(((((((...-....)))))))))..-....((((....)))).........--------- ( -19.70, z-score =  -1.81, R)
>droYak2.chr2R 17628663 72 + 21139217
----UGCCUGGAAAUUAUGGUAUCGC-AUUGUUCAAA-GCUGGAACAAUGCCA-UAAAUGGCACAUGCCAAAUAUUUUC---------
----((((..........))))..((-(((((((...-....)))))))))..-....((((....)))).........--------- ( -19.70, z-score =  -1.81, R)
>droEre2.scaffold_4845 15926676 72 + 22589142
----UGCCUGAAAAUUAUGGUAUCGC-AUUGUUCAAA-GCUGGAACAAUGCCA-UAAAUGGCACAUGCCAAAUAUUUUC---------
----((((..........))))..((-(((((((...-....)))))))))..-....((((....)))).........--------- ( -19.70, z-score =  -2.26, R)
>droAna3.scaffold_12916 12891571 72 + 16180835
----UGCCUGGAAACUAUGGUAUCGC-AUUGUUCCAA-CUUGGAACAAUGCCA-UAAAUGGCACAUGCCAAAUAUUUUC---------
----((((.(....)...))))..((-((((((((..-...))))))))))..-....((((....)))).........--------- ( -26.70, z-score =  -4.92, R)
>dp4.chr4_group3 847368 73 + 11692001
----UGCCUGGAAAUUAUGGUAUCGC-AUUGUUCAAA-GUUGGAACAAUGCCA-UAAAUGGCACAUGCCAAAUAUAUUUC--------
----((((..........))))..((-(((((((...-....)))))))))..-....((((....))))..........-------- ( -19.70, z-score =  -1.90, R)
>droPer1.super_8 1910752 73 + 3966273
----UGCCUGGAAAUUAUGGUAUCGC-AUUGUUCAAA-GUUGGAACAAUGCCA-UAAAUGGCACAUGCCAAAUAUAUUUC--------
----((((..........))))..((-(((((((...-....)))))))))..-....((((....))))..........-------- ( -19.70, z-score =  -1.90, R)
>droWil1.scaffold_180764 3040729 74 + 3949147
----UGCCUGAAAAUUAUGGUAUCGCAAUUGUUCAGAUGUUGGAACAAUGCCA-UAAAUGGCACAUGCCAAAUAUUUUC---------
----.....((((((..((((((....(((((((........)))))))((((-....))))..))))))...))))))--------- ( -19.60, z-score =  -1.89, R)
>droVir3.scaffold_12963 16521758 61 - 20206255
---------------UGU-GCAUCGC-AUUGUUUAAA-GUGGGCACAAUGCCAGCGAAUGGCACAUGCCAAACAUUUUU---------
---------------(((-((.((((-(((......)-)).(((.....))).))))...)))))..............--------- ( -16.20, z-score =  -0.27, R)
>droMoj3.scaffold_6500 21449344 77 - 32352404
UGUUGUGCUGCAAAUUAUGGUAUCGC-AUUGUUCAAA-GUGAAAACAAUGCCAGCGUUUGGCACAUGCCAAACAUUUUC---------
......((((((.....)).....((-(((((((...-..))..)))))))))))(((((((....)))))))......--------- ( -22.40, z-score =  -1.61, R)
>droGri2.scaffold_15252 13932840 83 - 17193109
----UGUCUGUAAAUUAUGUUAUCGC-AUUGUUCAAAGUUGGGAACAAUGCCAGGCAAUGGCGUUGUUUCAACGGGGCCAGUGUUGUA
----................(((.((-((((..(...(((((.((((((((((.....)))))))))))))))..)..)))))).))) ( -28.20, z-score =  -3.11, R)
>consensus
____UGCCUGGAAAUUAUGGUAUCGC_AUUGUUCAAA_GUUGGAACAAUGCCA_UAAAUGGCACAUGCCAAAUAUUUUC_________
.................((((((....(((((((........)))))))((((.....))))..)))))).................. (-14.35 = -14.81 +   0.46)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:48:22 2011