Locus 13000

Sequence ID dm3.chrX
Location 3,808,494 – 3,808,587
Length 93
Max. P 0.822341
window17870 window17871

overview

Window 0

Location 3,808,494 – 3,808,587
Length 93
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 72.90
Shannon entropy 0.43041
G+C content 0.44569
Mean single sequence MFE -23.46
Consensus MFE -13.36
Energy contribution -14.48
Covariance contribution 1.12
Combinations/Pair 1.07
Mean z-score -1.40
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.14
SVM RNA-class probability 0.564180
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3808494 93 + 22422827
AAUUUCGGUAGCAAAC-GCACUUCCCUUGUCUCGCCUAUCCAUCAUUUUGGUUAGGCGCACAGUCGCGGUUACCAUAUUAGUGAAAUCUUGUUA--------------------------
......((((((...(-(((((......((..((((((.(((......))).)))))).))))).)))))))))....................-------------------------- ( -24.00, z-score =  -2.50, R)
>droSim1.chrX 2803973 91 + 17042790
AAUUUCAGUUGCAAAC-GCACUCCCGUU--UUGGCCUAUCCAUCAUUUUGGUUAGGCGCACAGUCGCGGUUACCAUAUUAGUGAAAUCUUGUAA--------------------------
.((((((..(((....-)))...((((.--.(((((((.(((......))).))))).)).....))))............)))))).......-------------------------- ( -20.60, z-score =  -1.08, R)
>droSec1.super_4 3278956 91 - 6179234
AAUUUCAGUUGCAAAC-GCACUCCCCUU--UUCGCCCAUCCAUUAUUUUGGUUAGGCGCACAGUCGCGGUUACCAUAUUAGUGCAAUCUUGUAA--------------------------
........((((((..-(((((......--...(((...(((......)))...)))((......))............)))))....))))))-------------------------- ( -18.40, z-score =  -1.21, R)
>droYak2.chrX 17164110 119 - 21770863
AAUUUCAGUAGCAAAUUGCACUCCCCUU-UCUCGCCUAUCCAUCAUUUUGGUUAGGCGCACAGUCGCGGUUACAAUAUUAGAGACGCAUGGCACCGAAAUCUGAAUUGAAACUGUUGUAA
......(((.((.....)))))......-...((((((.(((......))).)))))).(((...((((((.((((.(((((..((........))...))))))))).))))))))).. ( -27.40, z-score =  -0.75, R)
>droEre2.scaffold_4690 1192840 110 + 18748788
UAUUUUAGUGGCAAACUGCACUCCCCCU-UCUCGCCCAUCCCUCAUUUUGGUUAGACGCACAGCCGCGGUUACAAUAUUAGUGACGCGUGAAACCGAAAUCUGUGCCACAA---------
.......((((((....((.........-....)).........(((((((((..((((.(......)(((((.......)))))))))..)))))))))...))))))..--------- ( -26.92, z-score =  -1.49, R)
>consensus
AAUUUCAGUAGCAAAC_GCACUCCCCUU_UCUCGCCUAUCCAUCAUUUUGGUUAGGCGCACAGUCGCGGUUACCAUAUUAGUGAAAUCUUGUAA__________________________
.......(((((.....................(((((.(((......))).)))))((......)).)))))............................................... (-13.36 = -14.48 +   1.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,808,494 – 3,808,587
Length 93
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.90
Shannon entropy 0.43041
G+C content 0.44569
Mean single sequence MFE -27.84
Consensus MFE -16.10
Energy contribution -15.94
Covariance contribution -0.16
Combinations/Pair 1.16
Mean z-score -1.69
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.80
SVM RNA-class probability 0.822341
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3808494 93 - 22422827
--------------------------UAACAAGAUUUCACUAAUAUGGUAACCGCGACUGUGCGCCUAACCAAAAUGAUGGAUAGGCGAGACAAGGGAAGUGC-GUUUGCUACCGAAAUU
--------------------------......((((((.......((((((.((((.((((.((((((.(((......))).))))))..)).)).....)))-).))))))..)))))) ( -24.60, z-score =  -2.18, R)
>droSim1.chrX 2803973 91 - 17042790
--------------------------UUACAAGAUUUCACUAAUAUGGUAACCGCGACUGUGCGCCUAACCAAAAUGAUGGAUAGGCCAA--AACGGGAGUGC-GUUUGCAACUGAAAUU
--------------------------......((((((((......)((((.((((.((((..(((((.(((......))).)))))...--.))))...)))-).))))...))))))) ( -25.80, z-score =  -2.63, R)
>droSec1.super_4 3278956 91 + 6179234
--------------------------UUACAAGAUUGCACUAAUAUGGUAACCGCGACUGUGCGCCUAACCAAAAUAAUGGAUGGGCGAA--AAGGGGAGUGC-GUUUGCAACUGAAAUU
--------------------------.....((.(((((((.....)))((((((..((.(.((((((.(((......))).))))))..--.).))..))).-))).))))))...... ( -24.90, z-score =  -1.99, R)
>droYak2.chrX 17164110 119 + 21770863
UUACAACAGUUUCAAUUCAGAUUUCGGUGCCAUGCGUCUCUAAUAUUGUAACCGCGACUGUGCGCCUAACCAAAAUGAUGGAUAGGCGAGA-AAGGGGAGUGCAAUUUGCUACUGAAAUU
...................(((((((((((..((((.((((....((((....))))((...((((((.(((......))).))))))...-.)).))))))))....)).))))))))) ( -32.90, z-score =  -1.52, R)
>droEre2.scaffold_4690 1192840 110 - 18748788
---------UUGUGGCACAGAUUUCGGUUUCACGCGUCACUAAUAUUGUAACCGCGGCUGUGCGUCUAACCAAAAUGAGGGAUGGGCGAGA-AGGGGGAGUGCAGUUUGCCACUAAAAUA
---------..((((((..((((.((.(..(.((((..((.......))...)))).((...((((((.((........)).))))))...-)).)..).)).))))))))))....... ( -31.00, z-score =  -0.16, R)
>consensus
__________________________UUACAAGAUUUCACUAAUAUGGUAACCGCGACUGUGCGCCUAACCAAAAUGAUGGAUAGGCGAGA_AAGGGGAGUGC_GUUUGCAACUGAAAUU
...............................................((((.(((..((.(.((((((.(((......))).)))))).....).))..)))....)))).......... (-16.10 = -15.94 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:12:47 2011