Locus 13439

Sequence ID dm3.chrX
Location 6,548,653 – 6,548,755
Length 102
Max. P 0.982343
window18508 window18509

overview

Window 8

Location 6,548,653 – 6,548,755
Length 102
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 79.26
Shannon entropy 0.36997
G+C content 0.49009
Mean single sequence MFE -30.70
Consensus MFE -18.76
Energy contribution -17.71
Covariance contribution -1.05
Combinations/Pair 1.42
Mean z-score -2.22
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.43
SVM RNA-class probability 0.939059
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6548653 102 + 22422827
-----------AUCCAUAAUCUCGAAAAAACCAUCG--AUGGCAUCGAAC---CGGCUGGAACUGAACCAUCGAUAUUAUCAGUAGCGCCAUCGAUGGUUUGAUAGCACCUCAGCUCC
-----------................(((((((((--(((((..((...---))(((...(((((.............))))))))))))))))))))))...(((......))).. ( -30.32, z-score =  -2.89, R)
>droEre2.scaffold_4690 15475925 105 + 18748788
---------CGACCCAUAGUCUCGAAAAAACCAUCGG-AUGGCAUCGAAC---CGGCUGGAACUGAACCGUCGAUAGUAUCAGUAGCGCCAUCGAUGGUUUGAUAGCACCUCAGCUCC
---------.(((.....)))......(((((((((.-(((((..((...---))(((...(((((..(.......)..))))))))))))))))))))))...(((......))).. ( -29.30, z-score =  -0.92, R)
>droYak2.chrX 2511258 103 + 21770863
----------ACCCCAUAGUCUCGAAAAAACCAUCG--AUGGCAUCGAAC---CGGCUGGAACUGAACCAUCGAUAUUAUCAGUAGCGCCAUCGAUGGUUUGAUACCACCUCAGCUCC
----------.................(((((((((--(((((..((...---))(((...(((((.............))))))))))))))))))))))................. ( -28.92, z-score =  -2.60, R)
>droSec1.super_4 5922938 102 - 6179234
-----------UCCCAUUGUCUCGAAAAAACCAUCG--AUGGCAUCGAAC---CGGCUGGAACUGAACCAUCGAUAUUAUCAGUAGUGCCAUCGAUGGUUUGAUAGCACAUCAGCUCC
-----------................(((((((((--(((((((....(---(....)).(((((.............))))).))))))))))))))))...(((......))).. ( -31.52, z-score =  -2.81, R)
>droSim1.chrX 5151674 102 + 17042790
-----------UCCCAUAGUCUCGAAAAAACCAUCG--AUGGCAUCGAAC---CGGCUGGAACUGAACCAUCGAUAUUAUCAGUAGUGCCAUCGAUGGUUUGAUAGCACCUCAGCUCC
-----------................(((((((((--(((((((....(---(....)).(((((.............))))).))))))))))))))))...(((......))).. ( -31.52, z-score =  -2.99, R)
>droPer1.super_0 3818545 118 - 11822988
AACCUUGGGCUCGAUAAAAUCUUGGCUAUGUGGUCAGGACGACACCAGGCGUUCCAUCCGAACCAAAAUAUCGAUACUAUCGAUAGUGCCCUCGAUGGUUUGAUACCACUACCGCGCC
.....(((..(((......((((((((....)))))))))))..)))(((((((.....)))).....((((((.((((((((........))))))))))))))..........))) ( -32.60, z-score =  -1.09, R)
>consensus
___________ACCCAUAGUCUCGAAAAAACCAUCG__AUGGCAUCGAAC___CGGCUGGAACUGAACCAUCGAUAUUAUCAGUAGCGCCAUCGAUGGUUUGAUAGCACCUCAGCUCC
.....................((((.....((((....))))..))))......((((((...((((((((((((...............))))))))))))........)))))).. (-18.76 = -17.71 +  -1.05)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,548,653 – 6,548,755
Length 102
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 79.26
Shannon entropy 0.36997
G+C content 0.49009
Mean single sequence MFE -36.43
Consensus MFE -29.67
Energy contribution -29.65
Covariance contribution -0.02
Combinations/Pair 1.29
Mean z-score -2.04
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.10
SVM RNA-class probability 0.982343
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6548653 102 - 22422827
GGAGCUGAGGUGCUAUCAAACCAUCGAUGGCGCUACUGAUAAUAUCGAUGGUUCAGUUCCAGCCG---GUUCGAUGCCAU--CGAUGGUUUUUUCGAGAUUAUGGAU-----------
(((((((((((...)))..((((((((((...(....)....))))))))))))))))))..(((---.(((((.((((.--...))))....)))))....)))..----------- ( -35.30, z-score =  -2.21, R)
>droEre2.scaffold_4690 15475925 105 - 18748788
GGAGCUGAGGUGCUAUCAAACCAUCGAUGGCGCUACUGAUACUAUCGACGGUUCAGUUCCAGCCG---GUUCGAUGCCAU-CCGAUGGUUUUUUCGAGACUAUGGGUCG---------
(((((((((((((((((........)))))))))((((..........))))))))))))....(---((.....)))..-((.((((((((...)))))))).))...--------- ( -36.90, z-score =  -1.79, R)
>droYak2.chrX 2511258 103 - 21770863
GGAGCUGAGGUGGUAUCAAACCAUCGAUGGCGCUACUGAUAAUAUCGAUGGUUCAGUUCCAGCCG---GUUCGAUGCCAU--CGAUGGUUUUUUCGAGACUAUGGGGU----------
.((((((.(.(((.((..(((((((((((...(....)....)))))))))))..)).))).)))---))))...(((..--(.((((((((...)))))))).))))---------- ( -36.20, z-score =  -1.91, R)
>droSec1.super_4 5922938 102 + 6179234
GGAGCUGAUGUGCUAUCAAACCAUCGAUGGCACUACUGAUAAUAUCGAUGGUUCAGUUCCAGCCG---GUUCGAUGCCAU--CGAUGGUUUUUUCGAGACAAUGGGA-----------
((((((((((......)).((((((((((.((....))....))))))))))))))))))..(((---.(((((.((((.--...))))....)))))....)))..----------- ( -35.20, z-score =  -2.33, R)
>droSim1.chrX 5151674 102 - 17042790
GGAGCUGAGGUGCUAUCAAACCAUCGAUGGCACUACUGAUAAUAUCGAUGGUUCAGUUCCAGCCG---GUUCGAUGCCAU--CGAUGGUUUUUUCGAGACUAUGGGA-----------
(((((((((((((((((........)))))))))..((((...)))).....))))))))..(((---.(((((.((((.--...))))....)))))....)))..----------- ( -35.70, z-score =  -2.32, R)
>droPer1.super_0 3818545 118 + 11822988
GGCGCGGUAGUGGUAUCAAACCAUCGAGGGCACUAUCGAUAGUAUCGAUAUUUUGGUUCGGAUGGAACGCCUGGUGUCGUCCUGACCACAUAGCCAAGAUUUUAUCGAGCCCAAGGUU
(((.((((((((((.....))))((...(((..(((((((...)))))))...(((((.(((((..((.....))..))))).)))))....)))..))..)))))).)))....... ( -39.30, z-score =  -1.68, R)
>consensus
GGAGCUGAGGUGCUAUCAAACCAUCGAUGGCACUACUGAUAAUAUCGAUGGUUCAGUUCCAGCCG___GUUCGAUGCCAU__CGAUGGUUUUUUCGAGACUAUGGGA___________
(((((((((((((((((........)))))))))..((((...)))).....))))))))..(((....(((((.(((((....)))))....)))))....)))............. (-29.67 = -29.65 +  -0.02)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:21:28 2011