Locus 15262

Sequence ID dm3.chrX
Location 18,175,524 – 18,175,651
Length 127
Max. P 0.946111
window21027 window21028

overview

Window 7

Location 18,175,524 – 18,175,641
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 69.32
Shannon entropy 0.50079
G+C content 0.43248
Mean single sequence MFE -23.16
Consensus MFE -15.94
Energy contribution -14.78
Covariance contribution -1.16
Combinations/Pair 1.53
Mean z-score -0.69
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.25
SVM RNA-class probability 0.613707
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18175524 117 - 22422827
CGAUCUCAUAAAAGUAUCUGUUUAUGGCCACGCCAAGUGAACUACACUCAUCUGGUUAUCUGCAGAUAUUACUGUCCUAUACGAAACUUUCCCGGACACCAAGGAAUUAGCACGUUG
.(((..(.....(((((((((..(((((((.....((((.....))))....)))))))..)))))))))..(((((................)))))....)..)))......... ( -26.29, z-score =  -1.49, R)
>droEre2.scaffold_4690 8502100 117 - 18748788
CGAUCUCAUAAAAGUAUCUGUUUAUGACCAUGCCAAGUGAACUACACUCAUCUGGUUAUCUGCAGAUAUUACUGUCCUAUACGAAACUUUCCCGGACAUCUAGGAAUUAGCACGUUG
............(((((((((..(((((((.....((((.....))))....)))))))..)))))))))..........(((.....((((..(....)..))))......))).. ( -26.90, z-score =  -1.92, R)
>droYak2.chrX 16807380 117 - 21770863
UGAGCUCAUAAAAAUAGCUGUUUAUGAUCACGCCAAGUGAACUACACUCAUCUGGUUAUCUGCAGAUAUUACUGUCCUAUACGAAACUUUCCCGGACACCUAGGAAUUAGCACGUUG
...(((.((...((((.((((..(((((((.....((((.....))))....)))))))..)))).))))..(((((................))))).......)).)))...... ( -20.99, z-score =   0.09, R)
>dp4.chrXL_group3a 142990 104 - 2690836
-CUGUCUGUCAUAAAAUCUUAUUGGAACUGC-CAGAGCGAACUGCGCGUAUCUGGUUCUCUGCAGAUUAUUCCGUCUUGCACAGCCUCCUCC-----------AAAUUAGCACUUUG
-....................(((((...((-(((((((.....)))...)))))).((.(((((((......))).)))).)).....)))-----------))............ ( -20.40, z-score =   0.02, R)
>droPer1.super_39 152979 104 + 745454
-CUGUCUGUCAUAAAAUCUUAUUGGAGCUUC-CAGAGCGAACUGCGCGUAUCUGGUUCUCUGCAGAUUAUUCCGUCUUGCACAGCCUCCUCC-----------AAAUUAGCACUUUG
-....................((((((...(-(((((((.....)))...)))))..((.(((((((......))).)))).))....))))-----------))............ ( -21.20, z-score =  -0.15, R)
>consensus
_GAGCUCAUAAAAAUAUCUGUUUAUGACCACGCCAAGUGAACUACACUCAUCUGGUUAUCUGCAGAUAUUACUGUCCUAUACGAAACUUUCCCGGACA_C_AGGAAUUAGCACGUUG
............(((((((((..(((((((......(((.....))).....)))))))..)))))))))............................................... (-15.94 = -14.78 +  -1.16)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,175,547 – 18,175,651
Length 104
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 67.83
Shannon entropy 0.49964
G+C content 0.46359
Mean single sequence MFE -23.08
Consensus MFE -14.74
Energy contribution -14.46
Covariance contribution -0.28
Combinations/Pair 1.47
Mean z-score -1.51
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.52
SVM RNA-class probability 0.946111
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18175547 104 - 22422827
-------------GCCGCACCUGCGAUCUCAUAAAAGUAUCUGUUUAUGGCCACGCCAAGUGAACUACACUCAUCUGGUUAUCUGCAGAUAUUACUGUCCUAUACGAAACUUUCCCG
-------------..(((....)))..........(((((((((..(((((((.....((((.....))))....)))))))..)))))))))........................ ( -23.90, z-score =  -2.63, R)
>droEre2.scaffold_4690 8502123 104 - 18748788
-------------GCCGCACCUGCGAUCUCAUAAAAGUAUCUGUUUAUGACCAUGCCAAGUGAACUACACUCAUCUGGUUAUCUGCAGAUAUUACUGUCCUAUACGAAACUUUCCCG
-------------..(((....)))..........(((((((((..(((((((.....((((.....))))....)))))))..)))))))))........................ ( -24.40, z-score =  -3.36, R)
>droYak2.chrX 16807403 104 - 21770863
-------------GCCGCACCUGUGAGCUCAUAAAAAUAGCUGUUUAUGAUCACGCCAAGUGAACUACACUCAUCUGGUUAUCUGCAGAUAUUACUGUCCUAUACGAAACUUUCCCG
-------------...(((...((((..(((((((........)))))))))))((((..(((.......)))..))))....))).((((....)))).................. ( -18.20, z-score =  -0.59, R)
>dp4.chrXL_group3a 143004 99 - 2690836
--------------CUACUCCCGCUGUCUGUCAUAAA-AUCUUAUUGGAACUGC-CAGAGCGAACUGCGCGUAUCUGGUUCUCUGCAGAUUAUUCCGUCUUGCACAGCCUCCUCC--
--------------........(((((..........-........(((...((-(((((((.....)))...))))))..)))((((((......))).)))))))).......-- ( -22.30, z-score =  -1.01, R)
>droPer1.super_39 152993 113 + 745454
AGUAGGCAAAGGUUCUACUCCCGCUGUCUGUCAUAAA-AUCUUAUUGGAGCUUC-CAGAGCGAACUGCGCGUAUCUGGUUCUCUGCAGAUUAUUCCGUCUUGCACAGCCUCCUCC--
(((((((....).))))))...(((((..........-........((((...(-(((((((.....)))...)))))..))))((((((......))).)))))))).......-- ( -26.60, z-score =   0.04, R)
>consensus
_____________GCCGCACCUGCGAUCUCAUAAAAAUAUCUGUUUAUGACCACGCCAAGUGAACUACACUCAUCUGGUUAUCUGCAGAUAUUACUGUCCUAUACGAAACUUUCCCG
...................................(((((((((..(((((((......(((.....))).....)))))))..)))))))))........................ (-14.74 = -14.46 +  -0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:56:02 2011