Locus 9639

Sequence ID dm3.chr3R
Location 7,915,627 – 7,915,721
Length 94
Max. P 0.995584
window13220 window13221

overview

Window 0

Location 7,915,627 – 7,915,721
Length 94
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 62.89
Shannon entropy 0.63802
G+C content 0.34501
Mean single sequence MFE -18.35
Consensus MFE -11.86
Energy contribution -12.90
Covariance contribution 1.04
Combinations/Pair 1.08
Mean z-score -0.56
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.876683
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7915627 94 + 27905053
--CAAAAGUGCAGCCUCAGUGCUGGCACUUUUGUUUUCGG-UUUCCAUCA-CUAUUAUUUUAGGCUAAUAUAAAUUCAUUGAAUUCUUUCUA-UAGUUA-------------------
--((((((((((((......))).))))))))).......-.........-...........(((((..(..(((((...)))))..)....-))))).------------------- ( -16.00, z-score =  -0.89, R)
>droEre2.scaffold_4770 4038359 107 - 17746568
CAAGACAAGGCAGCAUCAGUGCUGGCACUUUUGGCUUCGCUUUUCUUUUC--CCUAAAUUUACGCUUUUAAGUGUCUUA--AAUUCUGUUUA-UAAAAAUACUUACUCAUUA------
.(((((..(.(((((....))))).)((((..(((...............--...........)))...))))))))).--...........-...................------ ( -16.67, z-score =  -0.14, R)
>droYak2.chr3R 12226100 114 + 28832112
--CAAAAGUGCAGCAUCAGUGCUGGCACCUUUGGCUCCGCUUUUCUUUUUAUUUUUCAUUUGCGUUUGUAUAUGCUUUC--AAUUCUGGCUAUGGUCAACAAAGACACCGAUUUAUUA
--((((.((((((((....)))).)))).))))....((....(((((.............((((......))))....--.....((((....))))..)))))...))........ ( -20.20, z-score =   0.69, R)
>droSec1.super_0 7060100 106 - 21120651
--CAAAAGUGCAGCAUCAGUGCUGGCACUUUUGUUUGCGGGUUUCCAUUU-CUUUUCAUUUAGGUUUAUAUAGCUUUA---AAUUUUUUCUAACACAUAUACUGACAUGUUA------
--(((((((((((((....)))).))))))))).....((....))....-......(((((((((.....))).)))---)))............................------ ( -18.30, z-score =  -0.38, R)
>droSim1.chr3R 14040269 96 - 27517382
--CAAAAGUGCAGCAUCAGUGCUGGCACUUUUGUCUGCGGGUUUCCAUUU-CUUUCUAUUUAGGUUUAUAUAGAUUUA---AAUUCUUUUUAACACAUGUUA----------------
--(((((((((((((....)))).))))))))).....((....))....-......((((((((((....)))))))---)))......((((....))))---------------- ( -20.60, z-score =  -2.09, R)
>consensus
__CAAAAGUGCAGCAUCAGUGCUGGCACUUUUGUCUGCGGGUUUCCAUUU_CUUUUAAUUUAGGUUUAUAUAGAUUUA___AAUUCUUUCUA_CACAUAUAA__AC____________
..(((((((((((((....)))).)))))))))..................................................................................... (-11.86 = -12.90 +   1.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 7,915,627 – 7,915,721
Length 94
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 62.89
Shannon entropy 0.63802
G+C content 0.34501
Mean single sequence MFE -19.86
Consensus MFE -12.32
Energy contribution -12.80
Covariance contribution 0.48
Combinations/Pair 1.17
Mean z-score -1.65
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.82
SVM RNA-class probability 0.995584
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7915627 94 - 27905053
-------------------UAACUA-UAGAAAGAAUUCAAUGAAUUUAUAUUAGCCUAAAAUAAUAG-UGAUGGAAA-CCGAAAACAAAAGUGCCAGCACUGAGGCUGCACUUUUG--
-------------------...(((-(.....((((((...)))))).(((((........))))).-..))))...-.......(((((((((.(((......))))))))))))-- ( -18.80, z-score =  -2.53, R)
>droEre2.scaffold_4770 4038359 107 + 17746568
------UAAUGAGUAAGUAUUUUUA-UAAACAGAAUU--UAAGACACUUAAAAGCGUAAAUUUAGG--GAAAAGAAAAGCGAAGCCAAAAGUGCCAGCACUGAUGCUGCCUUGUCUUG
------......(((((....))))-)..........--((((((.((((((........))))))--........(((.(.(((....((((....))))...))).)))))))))) ( -16.20, z-score =   0.78, R)
>droYak2.chr3R 12226100 114 - 28832112
UAAUAAAUCGGUGUCUUUGUUGACCAUAGCCAGAAUU--GAAAGCAUAUACAAACGCAAAUGAAAAAUAAAAAGAAAAGCGGAGCCAAAGGUGCCAGCACUGAUGCUGCACUUUUG--
.......((((((((......)))....)))......--...............(((.....................)))))..(((((((((.((((....)))))))))))))-- ( -21.80, z-score =  -0.13, R)
>droSec1.super_0 7060100 106 + 21120651
------UAACAUGUCAGUAUAUGUGUUAGAAAAAAUU---UAAAGCUAUAUAAACCUAAAUGAAAAG-AAAUGGAAACCCGCAAACAAAAGUGCCAGCACUGAUGCUGCACUUUUG--
------...(((.....(((((((.(((((.....))---))).)).))))).......))).....-....((....)).....(((((((((.((((....)))))))))))))-- ( -21.00, z-score =  -2.38, R)
>droSim1.chr3R 14040269 96 + 27517382
----------------UAACAUGUGUUAAAAAGAAUU---UAAAUCUAUAUAAACCUAAAUAGAAAG-AAAUGGAAACCCGCAGACAAAAGUGCCAGCACUGAUGCUGCACUUUUG--
----------------.....((((.........(((---(...(((((.((....)).)))))...-))))(....).))))..(((((((((.((((....)))))))))))))-- ( -21.50, z-score =  -4.00, R)
>consensus
____________GU__GUAUAUGUA_UAGAAAGAAUU___UAAACAUAUAUAAACCUAAAUGAAAAG_AAAUGGAAAACCGAAGACAAAAGUGCCAGCACUGAUGCUGCACUUUUG__
.....................................................................................(((((((((.(((......)))))))))))).. (-12.32 = -12.80 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:08:13 2011