Locus 10109

Sequence ID dm3.chr3R
Location 11,341,384 – 11,341,487
Length 103
Max. P 0.878182
window13902 window13903

overview

Window 2

Location 11,341,384 – 11,341,487
Length 103
Sequences 12
Columns 122
Reading direction forward
Mean pairwise identity 68.90
Shannon entropy 0.59055
G+C content 0.43203
Mean single sequence MFE -24.65
Consensus MFE -12.59
Energy contribution -12.33
Covariance contribution -0.26
Combinations/Pair 1.19
Mean z-score -1.28
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.878182
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 11341384 103 + 27905053
-----GGAGUGGAGCU-GUGACUGUGACUG------CAAGUUGCAUGAAAUUAUGCUUUAAUCUAAUUAGCAUAAUUUGGCUGCCCUGAUGGCGACGACUAUGGGUACAAUGAGG-------
-----.......((((-(..(((((....)------).)))..)...((((((((((...........))))))))))))))((((.(.((....)).)...)))).........------- ( -25.20, z-score =  -0.51, R)
>droSim1.chr3R 17382547 103 - 27517382
-----GGAGUGGAGCU-GUGACUGUGACUG------CAAGUUGCAUGAAAUUAUGCUUUAAUCUAAUUAGCAUAAUUUGGCUGCCCUGAUGGCGACGACUAUGGGUACAAUGAGG-------
-----.......((((-(..(((((....)------).)))..)...((((((((((...........))))))))))))))((((.(.((....)).)...)))).........------- ( -25.20, z-score =  -0.51, R)
>droSec1.super_0 10516970 103 - 21120651
-----GGAGUGGAGCU-GUGACUGUGACUG------CAAGUUGCAUGAAAUUAUGCUUUAAUCUAUUUAGCAUAAUUUGGCUGCCCUGAUGGCGACGACUAUGGGUACAAUGAGG-------
-----.......((((-(..(((((....)------).)))..)...((((((((((...........))))))))))))))((((.(.((....)).)...)))).........------- ( -25.20, z-score =  -0.41, R)
>droYak2.chr3R 13745587 114 - 28832112
GGAGUGGAGUGGAGCU-GUGACUGUGACUGUGACUGCAAGUUGCAUGAAAUUAUGCUUUAAUCUAAUUAGCAUAAUUUGGCUGCCCUGAUGGCGACGACUAUGGCUACAAUGAGG-------
...((((.((((((((-.....((..(((((....)).)))..))..((((((((((...........))))))))))))))(((.....))).....))))..)))).......------- ( -30.10, z-score =  -1.04, R)
>droEre2.scaffold_4770 10868861 103 + 17746568
-----GGAGUGGAGCU-GUGACUGUGACUG------CAAGUUGCAUGAAAUUAUGCUUUAAUCUAAUUAGCAUAAUUUGGCUGCCCUGAUGGCGACGACUAUGGGUACAAUGAGG-------
-----.......((((-(..(((((....)------).)))..)...((((((((((...........))))))))))))))((((.(.((....)).)...)))).........------- ( -25.20, z-score =  -0.51, R)
>droAna3.scaffold_13340 15955157 87 + 23697760
-----CCAGUCAGACU-GCGACUGUAACUG------CGAGUUGCAUGAAAUUAUGCUUUAAUCUAAUUAGCAUAAUUUGGCUGCCCUGCUGGCAAUGAC-----------------------
-----((((.(((..(-((((((((....)------).)))))))(.((((((((((...........)))))))))).).....))))))).......----------------------- ( -25.60, z-score =  -2.38, R)
>dp4.chr2 30333574 79 + 30794189
-----GAAGUGGAACU-GCGACUGCGACUG------UAAGUUGCAUGAAAUUAUGCUUUAAUCUAAUUAGCAUAAUUUGGCUGCCCUCCUG-------------------------------
-----.....(((...-(((.(((((((..------...)))))...((((((((((...........)))))))))))).)))..)))..------------------------------- ( -20.20, z-score =  -2.44, R)
>droPer1.super_6 5725130 79 + 6141320
-----GAAGUGGAACU-GCGACUGCGACUG------UAAGUUGCAUGAAAUUAUGCUUUAAUCUAAUUAGCAUAAUUUGGCUGCCCUCCUG-------------------------------
-----.....(((...-(((.(((((((..------...)))))...((((((((((...........)))))))))))).)))..)))..------------------------------- ( -20.20, z-score =  -2.44, R)
>droWil1.scaffold_181089 2569370 100 + 12369635
---------------GCACAGCUGUAAAUG------UAAGUUGCAUGAAAUUAUGCUUUAAUCUAAUUAGCAUAAUUUGCCAGUCACAA-GACUCCAAAGAGUCAUACAGACACAGUCGGGC
---------------((.(.(((((...((------((.((.((.((((((((((((...........))))))))))..)))).))..-(((((....))))).))))...))))).).)) ( -26.50, z-score =  -2.64, R)
>droMoj3.scaffold_6540 22229865 93 + 34148556
--------GUGGGGCGAACAGACGCAGCCG------UAAGUUGCAUGAAAUUAUGAUUUAAUCUAAUUAGCAUAAUUUGGCGGCAAUGAUGACGAUGGGCGCUGAGA---------------
--------....((((..((..((((..((------(..(((((...((((((((...((((...)))).)))))))).))))).))).)).)).))..))))....--------------- ( -21.60, z-score =  -0.07, R)
>droVir3.scaffold_12855 4923131 93 + 10161210
--------GUUGUGUAAGCAGACACAGCUG------UAAGUUGCAUGAAAUUAUGCUUUAAUCUAAUUAGCAUAAUUUGGCGGCAAUGAUGAUGAUGGGCGCUGAGG---------------
--------(((((((......)))))))..------...(((((...((((((((((...........)))))))))).))))).......................--------------- ( -23.50, z-score =  -0.50, R)
>droGri2.scaffold_14906 4553625 93 - 14172833
--------AUAGUGCAAACAGACACAGCUG------UAAGUUGCAUGAAAUUAUGCUUUAAUCUAAUUAGCAUAAUUUGGCGGCAAUGAUGGCGAUGGGCGCUGAGG---------------
--------.((((((...((......((((------(..(((((...((((((((((...........)))))))))).)))))....)))))..)).))))))...--------------- ( -27.30, z-score =  -1.90, R)
>consensus
_____GGAGUGGAGCU_GCGACUGUGACUG______CAAGUUGCAUGAAAUUAUGCUUUAAUCUAAUUAGCAUAAUUUGGCUGCCCUGAUGGCGACGACUAUGGAUA_______________
.......................((((((.........))))))...((((((((((...........))))))))))............................................ (-12.59 = -12.33 +  -0.26)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,341,384 – 11,341,487
Length 103
Sequences 12
Columns 122
Reading direction reverse
Mean pairwise identity 68.90
Shannon entropy 0.59055
G+C content 0.43203
Mean single sequence MFE -18.44
Consensus MFE -8.62
Energy contribution -8.79
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.08
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.26
SVM RNA-class probability 0.615324
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 11341384 103 - 27905053
-------CCUCAUUGUACCCAUAGUCGUCGCCAUCAGGGCAGCCAAAUUAUGCUAAUUAGAUUAAAGCAUAAUUUCAUGCAACUUG------CAGUCACAGUCAC-AGCUCCACUCC-----
-------....(((((((....(((....(((.....))).((.((((((((((...........))))))))))...)).)))..------..)).)))))...-...........----- ( -17.30, z-score =  -0.68, R)
>droSim1.chr3R 17382547 103 + 27517382
-------CCUCAUUGUACCCAUAGUCGUCGCCAUCAGGGCAGCCAAAUUAUGCUAAUUAGAUUAAAGCAUAAUUUCAUGCAACUUG------CAGUCACAGUCAC-AGCUCCACUCC-----
-------....(((((((....(((....(((.....))).((.((((((((((...........))))))))))...)).)))..------..)).)))))...-...........----- ( -17.30, z-score =  -0.68, R)
>droSec1.super_0 10516970 103 + 21120651
-------CCUCAUUGUACCCAUAGUCGUCGCCAUCAGGGCAGCCAAAUUAUGCUAAAUAGAUUAAAGCAUAAUUUCAUGCAACUUG------CAGUCACAGUCAC-AGCUCCACUCC-----
-------....(((((((....(((....(((.....))).((.((((((((((...........))))))))))...)).)))..------..)).)))))...-...........----- ( -17.30, z-score =  -0.68, R)
>droYak2.chr3R 13745587 114 + 28832112
-------CCUCAUUGUAGCCAUAGUCGUCGCCAUCAGGGCAGCCAAAUUAUGCUAAUUAGAUUAAAGCAUAAUUUCAUGCAACUUGCAGUCACAGUCACAGUCAC-AGCUCCACUCCACUCC
-------....(((((..(...(((....(((.....))).((.((((((((((...........))))))))))...)).)))....)..))))).........-................ ( -18.20, z-score =  -0.21, R)
>droEre2.scaffold_4770 10868861 103 - 17746568
-------CCUCAUUGUACCCAUAGUCGUCGCCAUCAGGGCAGCCAAAUUAUGCUAAUUAGAUUAAAGCAUAAUUUCAUGCAACUUG------CAGUCACAGUCAC-AGCUCCACUCC-----
-------....(((((((....(((....(((.....))).((.((((((((((...........))))))))))...)).)))..------..)).)))))...-...........----- ( -17.30, z-score =  -0.68, R)
>droAna3.scaffold_13340 15955157 87 - 23697760
-----------------------GUCAUUGCCAGCAGGGCAGCCAAAUUAUGCUAAUUAGAUUAAAGCAUAAUUUCAUGCAACUCG------CAGUUACAGUCGC-AGUCUGACUGG-----
-----------------------...(((((.((....(((...((((((((((...........))))))))))..)))..)).)------))))..((((((.-....)))))).----- ( -23.70, z-score =  -1.77, R)
>dp4.chr2 30333574 79 - 30794189
-------------------------------CAGGAGGGCAGCCAAAUUAUGCUAAUUAGAUUAAAGCAUAAUUUCAUGCAACUUA------CAGUCGCAGUCGC-AGUUCCACUUC-----
-------------------------------..((((.((.((.((((((((((...........))))))))))..(((.((...------..)).))))).))-..)))).....----- ( -18.70, z-score =  -2.43, R)
>droPer1.super_6 5725130 79 - 6141320
-------------------------------CAGGAGGGCAGCCAAAUUAUGCUAAUUAGAUUAAAGCAUAAUUUCAUGCAACUUA------CAGUCGCAGUCGC-AGUUCCACUUC-----
-------------------------------..((((.((.((.((((((((((...........))))))))))..(((.((...------..)).))))).))-..)))).....----- ( -18.70, z-score =  -2.43, R)
>droWil1.scaffold_181089 2569370 100 - 12369635
GCCCGACUGUGUCUGUAUGACUCUUUGGAGUC-UUGUGACUGGCAAAUUAUGCUAAUUAGAUUAAAGCAUAAUUUCAUGCAACUUA------CAUUUACAGCUGUGC---------------
((.((.(((((..((((.(((((....)))))-.........((((((((((((...........)))))))))...)))....))------))..))))).)).))--------------- ( -26.80, z-score =  -2.16, R)
>droMoj3.scaffold_6540 22229865 93 - 34148556
---------------UCUCAGCGCCCAUCGUCAUCAUUGCCGCCAAAUUAUGCUAAUUAGAUUAAAUCAUAAUUUCAUGCAACUUA------CGGCUGCGUCUGUUCGCCCCAC--------
---------------...((((((...((((.....((((....((((((((.((((...))))...))))))))...))))...)------)))..))).)))..........-------- ( -13.70, z-score =   0.03, R)
>droVir3.scaffold_12855 4923131 93 - 10161210
---------------CCUCAGCGCCCAUCAUCAUCAUUGCCGCCAAAUUAUGCUAAUUAGAUUAAAGCAUAAUUUCAUGCAACUUA------CAGCUGUGUCUGCUUACACAAC--------
---------------....((((..(((........((((....((((((((((...........))))))))))...))))....------.....)))..))))........-------- ( -15.43, z-score =  -0.83, R)
>droGri2.scaffold_14906 4553625 93 + 14172833
---------------CCUCAGCGCCCAUCGCCAUCAUUGCCGCCAAAUUAUGCUAAUUAGAUUAAAGCAUAAUUUCAUGCAACUUA------CAGCUGUGUCUGUUUGCACUAU--------
---------------.(.((((((.....)).....((((....((((((((((...........))))))))))...))))....------..)))).)..............-------- ( -16.90, z-score =  -0.46, R)
>consensus
_______________UACCCAUAGUCGUCGCCAUCAGGGCAGCCAAAUUAUGCUAAUUAGAUUAAAGCAUAAUUUCAUGCAACUUA______CAGUCACAGUCGC_AGCUCCACUCC_____
.........................................((.((((((((((...........))))))))))...)).......................................... ( -8.62 =  -8.79 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:17:41 2011