Locus 12246

Sequence ID dm3.chr3R
Location 26,740,474 – 26,740,566
Length 92
Max. P 0.950889
window16843 window16844

overview

Window 3

Location 26,740,474 – 26,740,566
Length 92
Sequences 12
Columns 118
Reading direction forward
Mean pairwise identity 78.25
Shannon entropy 0.41836
G+C content 0.38807
Mean single sequence MFE -23.94
Consensus MFE -13.12
Energy contribution -13.46
Covariance contribution 0.34
Combinations/Pair 1.09
Mean z-score -2.14
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.33
SVM RNA-class probability 0.927628
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26740474 92 + 27905053
-------------CUAUUAUU--AUUGCUGUUGAACAACCGCAAAUGGAUUUAACAUUACAGCCGCACUAAUCCACUGGGGAUCAAGUGGAGAUCAAGCGGCAUUAU-----------
-------------........--..(((.(((....))).)))((((.......))))...(((((.....((((((........))))))......))))).....----------- ( -25.00, z-score =  -2.54, R)
>droSim1.chr3R 26383621 92 + 27517382
-------------CUAUUAUU--AUUGCUGUUGAACAACCGCAAAUGGAUUUAACAUUACAGCCGCACUAAUCCACUGGGGAUCAAGUGGAGAUCAAGCGGCAUUAU-----------
-------------........--..(((.(((....))).)))((((.......))))...(((((.....((((((........))))))......))))).....----------- ( -25.00, z-score =  -2.54, R)
>droSec1.super_4 5566630 92 + 6179234
-------------CUAUUAUU--AUUGCUGUUGAACAACCGCAAAUGGAUUUAACAUUACAGCCGCACUAAUCCACUGGGGAUCAAGUGGAGAUCAAGCGGCAUUAU-----------
-------------........--..(((.(((....))).)))((((.......))))...(((((.....((((((........))))))......))))).....----------- ( -25.00, z-score =  -2.54, R)
>droYak2.chr3R 27665557 105 + 28832112
CUAUUAUUAUUGCUGGCUAUU--AUUAUUGUUGAACAACCGCAAAUGGAUUUAACAUUACAGCCGCACUAAUCCACUGGGGAUCAAGUGGAGAUCAAGCGGCAUUAU-----------
.....................--.....(((((((...(((....))).))))))).....(((((.....((((((........))))))......))))).....----------- ( -24.10, z-score =  -1.15, R)
>droEre2.scaffold_4820 9222342 97 - 10470090
--------CUAUUAUAUUAUU--AUUGCUGUUGAACAACCGCAAAUGGAUUUAACAUUACAGCCGCACUAAUCCACUGGGGAUCAAGUGGAGAUCAAGCGGCAUUAU-----------
--------.............--..(((.(((....))).)))((((.......))))...(((((.....((((((........))))))......))))).....----------- ( -25.00, z-score =  -2.41, R)
>droAna3.scaffold_12911 1156559 104 - 5364042
-----------CGUUAUUAUUGUAUUAUUGUUGAACAACCGCAAAUGGAUUUAAUAUUACAGCCGCACUAAUCCACUGGGGAUCAAGUGGAGAUCAAGCGGCAUUAUCAAGCAUG---
-----------.(((.....((((....(((((((...(((....))).))))))).))))(((((.....((((((........))))))......))))).......)))...--- ( -25.70, z-score =  -1.72, R)
>dp4.chr2 30367923 93 - 30794189
----------------AUGUU---U-GUGG--GGACAACCGCAAAUGGAUUUAAUAUUACAGCCGCACUAAUCCACUGGGGAUCAAGUGGAGAUCAAGCGGCAUUAUCAAGUAUA---
----------------..(((---(-((((--......))))))))...............(((((.....((((((........))))))......))))).............--- ( -29.50, z-score =  -3.09, R)
>droPer1.super_7 1234359 94 - 4445127
----------------AUGUU---UUGUGG--GGACAACCGCAAAUGGAUUUAAUAUUACAGCCGCACUAAUCCACUGGGGAUCAAGUGGAGAUCAAGCGGCAUUAUCAAGUAUA---
----------------....(---((((((--......)))))))................(((((.....((((((........))))))......))))).............--- ( -28.00, z-score =  -2.57, R)
>droWil1.scaffold_181130 10330123 102 + 16660200
--------------UAUUAUU--GUUAUUAAAAUAUAACCGCAAAGCGAUUUAAUAUUACAGUCAGACUAAUCCACUUGGGAUCAAGUGGAGAUCAAGCAGGAUAUAUGAAUAUAUUC
--------------.......--..((((...(((((.((((.....((((.........)))).((....((((((((....))))))))..))..)).)).))))).))))..... ( -19.80, z-score =  -1.76, R)
>droMoj3.scaffold_6540 3969556 98 - 34148556
-------------UUAUUAUU--GUUAUUAAAACA--ACCGCAAGGCAAUUUAAUAUUACAGCCACACUAAUCCACUGGGGAUCAAGUGCAGAUCAUGCGGCUUUAUCAAGUAUA---
-------------......((--(((.....))))--)(((((.(((..............))).((((.((((.....))))..)))).......)))))..............--- ( -18.94, z-score =  -1.12, R)
>droGri2.scaffold_14624 1643538 98 + 4233967
-------------UUAUUAUU--GUUAUUAAAACA--ACCGCAAGGCAAUUUAAUAUUACAGCCGCACUAAUCCACUAGGGAUCAAGUGCAGAUCAAGCGGCAUUAUCAAGUAUA---
-------------......((--(((.....))))--)((((..(((..............)))(((((.((((.....))))..))))).......))))..............--- ( -22.64, z-score =  -3.11, R)
>droVir3.scaffold_13047 11589644 98 + 19223366
-------------UUAUUAUU--GUUAUUAAAACA--ACCACAAGGCAAUUUAAUAUUACAGCCGCACUAAUCCACUGGGGAUCAAGUGCAGAUCAAGCGGCAUUAUCAGGUAUA---
-------------.......(--(((((((((...--.((....))...)))))))..)))(((((......((....))((((.......))))..))))).............--- ( -18.60, z-score =  -1.16, R)
>consensus
_____________UUAUUAUU__AUUAUUGUUGAACAACCGCAAAUGGAUUUAAUAUUACAGCCGCACUAAUCCACUGGGGAUCAAGUGGAGAUCAAGCGGCAUUAUCAAGUAUA___
.............................................................(((((......((....))((((.......))))..)))))................ (-13.12 = -13.46 +   0.34)

alignment

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secondary structure

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dotplot

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Window 4

Location 26,740,474 – 26,740,566
Length 92
Sequences 12
Columns 118
Reading direction reverse
Mean pairwise identity 78.25
Shannon entropy 0.41836
G+C content 0.38807
Mean single sequence MFE -23.46
Consensus MFE -14.95
Energy contribution -14.99
Covariance contribution 0.04
Combinations/Pair 1.14
Mean z-score -1.95
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.57
SVM RNA-class probability 0.950889
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26740474 92 - 27905053
-----------AUAAUGCCGCUUGAUCUCCACUUGAUCCCCAGUGGAUUAGUGCGGCUGUAAUGUUAAAUCCAUUUGCGGUUGUUCAACAGCAAU--AAUAAUAG-------------
-----------.....(((((((((..((((((.(....).)))))))))).))))).................((((.(((....))).)))).--........------------- ( -23.00, z-score =  -1.71, R)
>droSim1.chr3R 26383621 92 - 27517382
-----------AUAAUGCCGCUUGAUCUCCACUUGAUCCCCAGUGGAUUAGUGCGGCUGUAAUGUUAAAUCCAUUUGCGGUUGUUCAACAGCAAU--AAUAAUAG-------------
-----------.....(((((((((..((((((.(....).)))))))))).))))).................((((.(((....))).)))).--........------------- ( -23.00, z-score =  -1.71, R)
>droSec1.super_4 5566630 92 - 6179234
-----------AUAAUGCCGCUUGAUCUCCACUUGAUCCCCAGUGGAUUAGUGCGGCUGUAAUGUUAAAUCCAUUUGCGGUUGUUCAACAGCAAU--AAUAAUAG-------------
-----------.....(((((((((..((((((.(....).)))))))))).))))).................((((.(((....))).)))).--........------------- ( -23.00, z-score =  -1.71, R)
>droYak2.chr3R 27665557 105 - 28832112
-----------AUAAUGCCGCUUGAUCUCCACUUGAUCCCCAGUGGAUUAGUGCGGCUGUAAUGUUAAAUCCAUUUGCGGUUGUUCAACAAUAAU--AAUAGCCAGCAAUAAUAAUAG
-----------.....(((((((((..((((((.(....).)))))))))).))))).................(((((((((((..........--))))))).))))......... ( -26.50, z-score =  -2.19, R)
>droEre2.scaffold_4820 9222342 97 + 10470090
-----------AUAAUGCCGCUUGAUCUCCACUUGAUCCCCAGUGGAUUAGUGCGGCUGUAAUGUUAAAUCCAUUUGCGGUUGUUCAACAGCAAU--AAUAAUAUAAUAG--------
-----------.....(((((((((..((((((.(....).)))))))))).)))))(((.((((((.......((((.(((....))).)))).--..)))))).))).-------- ( -24.30, z-score =  -2.06, R)
>droAna3.scaffold_12911 1156559 104 + 5364042
---CAUGCUUGAUAAUGCCGCUUGAUCUCCACUUGAUCCCCAGUGGAUUAGUGCGGCUGUAAUAUUAAAUCCAUUUGCGGUUGUUCAACAAUAAUACAAUAAUAACG-----------
---..((.(((((((((((((((((..((((((.(....).)))))))))).)))))(((((............))))))))).)))))).................----------- ( -22.00, z-score =  -0.97, R)
>dp4.chr2 30367923 93 + 30794189
---UAUACUUGAUAAUGCCGCUUGAUCUCCACUUGAUCCCCAGUGGAUUAGUGCGGCUGUAAUAUUAAAUCCAUUUGCGGUUGUCC--CCAC-A---AACAU----------------
---.....((((((..(((((((((..((((((.(....).)))))))))).))))).....)))))).....((((.((......--)).)-)---))...---------------- ( -22.60, z-score =  -1.90, R)
>droPer1.super_7 1234359 94 + 4445127
---UAUACUUGAUAAUGCCGCUUGAUCUCCACUUGAUCCCCAGUGGAUUAGUGCGGCUGUAAUAUUAAAUCCAUUUGCGGUUGUCC--CCACAA---AACAU----------------
---.....((((((..(((((((((..((((((.(....).)))))))))).))))).....)))))).....((((.((......--)).)))---)....---------------- ( -22.90, z-score =  -2.06, R)
>droWil1.scaffold_181130 10330123 102 - 16660200
GAAUAUAUUCAUAUAUCCUGCUUGAUCUCCACUUGAUCCCAAGUGGAUUAGUCUGACUGUAAUAUUAAAUCGCUUUGCGGUUAUAUUUUAAUAAC--AAUAAUA--------------
((((((.................(((.((((((((....))))))))...))).((((((((............)))))))))))))).......--.......-------------- ( -19.20, z-score =  -1.74, R)
>droMoj3.scaffold_6540 3969556 98 + 34148556
---UAUACUUGAUAAAGCCGCAUGAUCUGCACUUGAUCCCCAGUGGAUUAGUGUGGCUGUAAUAUUAAAUUGCCUUGCGGU--UGUUUUAAUAAC--AAUAAUAA-------------
---.....((((...(((((((.(..(..((((.(((((.....)))))))))..)..(((((.....)))))).))))))--)...))))....--........------------- ( -24.80, z-score =  -2.21, R)
>droGri2.scaffold_14624 1643538 98 - 4233967
---UAUACUUGAUAAUGCCGCUUGAUCUGCACUUGAUCCCUAGUGGAUUAGUGCGGCUGUAAUAUUAAAUUGCCUUGCGGU--UGUUUUAAUAAC--AAUAAUAA-------------
---.....((((....(((((..(..(((((((.(((((.....))))))))))))..(((((.....))))))..)))))--....))))....--........------------- ( -25.40, z-score =  -2.69, R)
>droVir3.scaffold_13047 11589644 98 - 19223366
---UAUACCUGAUAAUGCCGCUUGAUCUGCACUUGAUCCCCAGUGGAUUAGUGCGGCUGUAAUAUUAAAUUGCCUUGUGGU--UGUUUUAAUAAC--AAUAAUAA-------------
---.............(((((((((((..(............)..)))))).)))))(((..(((((((..(((....)))--...)))))))))--).......------------- ( -24.80, z-score =  -2.48, R)
>consensus
___UAUACUUGAUAAUGCCGCUUGAUCUCCACUUGAUCCCCAGUGGAUUAGUGCGGCUGUAAUAUUAAAUCCAUUUGCGGUUGUUCAACAACAAU__AAUAAUAA_____________
................(((((((((((..((((.(....).)))))))))).)))))(((((............)))))....................................... (-14.95 = -14.99 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:58:35 2011