Locus 6360

Sequence ID dm3.chr3L
Location 5,909,517 – 5,909,646
Length 129
Max. P 0.994499
window8750 window8751

overview

Window 0

Location 5,909,517 – 5,909,620
Length 103
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 73.14
Shannon entropy 0.50523
G+C content 0.47246
Mean single sequence MFE -32.92
Consensus MFE -15.61
Energy contribution -15.73
Covariance contribution 0.12
Combinations/Pair 1.46
Mean z-score -2.11
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.48
SVM RNA-class probability 0.942526
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5909517 103 - 24543557
-UCUCAUAAUGUUUUUAUUAGCCCGCGGAUGCUGAACGCUCUCCGUGUGGGCGUGAGCCCAUACUUAGCGACAUUUAAUUUGGCAGAC-----GAGAUAAACCCAUUGA
-.....(((((..((((((......((..(((..((((((....((((((((....))))))))..))))........))..)))..)-----).))))))..))))). ( -35.00, z-score =  -3.64, R)
>droSim1.chr3L 5402581 103 - 22553184
-UCCGGGAGUGUUUUUAUUAGCCCGCGGCUGCUGAAGGCCAUCCGUGUGGGCGUGAGCCCGUACUUAGCGACAUUUAAUUUGGCAGAC-----GAGAUAAAACCAUUGA
-...((...((((((.....((((((((((......))))....((((((((....))))))))...)))...........)))....-----))))))...))..... ( -32.20, z-score =  -0.87, R)
>droSec1.super_2 5845184 103 - 7591821
-UCCGGGAGUGUUUUUAUUAGCCCGCGGCAGCUGAAGGCCAUCCGUGUGGGCGUGAGCCCAUACUUAGCGACAUUUAAUUUGGCCGAC-----GAGAUAAACCUAUUGA
-..((((...((....))...))))((((.(((((.((....))((((((((....)))))))))))))..((.......))))))..-----................ ( -35.40, z-score =  -2.03, R)
>droYak2.chr3L 6486962 100 - 24197627
----UUUUAUGCUUUUAUUAGCUCGUGGAUGCUGCAGGGCCUUCGUGUGGGCGUGAGCCCAUAUUUAGCGACAUUUAAUUUGCCGUUC-----GCGAUAAACCCACUGA
----......(((......)))(((((((((..(((((.(((..((((((((....))))))))..)).)........))))))))))-----))))............ ( -31.70, z-score =  -1.78, R)
>droEre2.scaffold_4784 8606589 103 - 25762168
-UUCGGGAGUGUUUUUAUUAGCCCGAAAAUGCUUAAGGGCCUUCGUGUGGGCGUGAGCCCAUAUUUAGCGAAAUUUCAUUUGCCAUUC-----GAGAUAAACCCAUUGA
-...(((..((((((.....((((............))))....((((((((....))))))))...(((((......))))).....-----))))))..)))..... ( -33.00, z-score =  -2.53, R)
>droAna3.scaffold_13337 10688511 104 + 23293914
UUGGGGAUGUAUUUUUAUUAGCCGCAGGACAUU---GGUCCCCAAAAU--GCCACAGACAUUAUUUAGAGGCAUUUAAUUUUGUGGCCUCGCAGAUGUGAACCCAUCGA
.((((...............((((((((((...---.))))...((((--(((.(.((......)).).))))))).....)))))).((((....)))).)))).... ( -30.20, z-score =  -1.80, R)
>consensus
_UCCGGGAGUGUUUUUAUUAGCCCGCGGAUGCUGAAGGCCCUCCGUGUGGGCGUGAGCCCAUACUUAGCGACAUUUAAUUUGGCAGAC_____GAGAUAAACCCAUUGA
.......((((..(((((((((........)))....(((....((((((((....))))))))((((......))))...)))...........))))))..)))).. (-15.61 = -15.73 +   0.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,909,547 – 5,909,646
Length 99
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 73.44
Shannon entropy 0.47957
G+C content 0.49641
Mean single sequence MFE -35.62
Consensus MFE -17.03
Energy contribution -18.65
Covariance contribution 1.62
Combinations/Pair 1.38
Mean z-score -2.90
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.71
SVM RNA-class probability 0.994499
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5909547 99 - 24543557
-----GAAAU-----CCUGCGAUAAAGAGACGCUUUUCUCAUA-AUGUUUUUAUUAGCCCGCGGAUGCUGAACGCUCUCCGUGUGGGCGUGAGCCCAUACUUAGCGACAU
-----...((-----((.(((.....((((......)))).((-(((....)))))...)))))))......((((....((((((((....))))))))..)))).... ( -34.60, z-score =  -3.44, R)
>droSim1.chr3L 5402611 99 - 22553184
-----GAAGU-----CCUGCGAUAAGGAGACCCUUUUCCGGGA-GUGUUUUUAUUAGCCCGCGGCUGCUGAAGGCCAUCCGUGUGGGCGUGAGCCCGUACUUAGCGACAU
-----..(.(-----((((.((.((((....)))).)))))))-.).............(((((((......))))....((((((((....))))))))...))).... ( -37.80, z-score =  -2.18, R)
>droSec1.super_2 5845214 99 - 7591821
-----GAAGU-----CCUGCGAUAAGGAGACCCUUUUCCGGGA-GUGUUUUUAUUAGCCCGCGGCAGCUGAAGGCCAUCCGUGUGGGCGUGAGCCCAUACUUAGCGACAU
-----....(-----((((.((.((((....)))).)))))))-(((((.......(((...))).(((((.((....))((((((((....)))))))))))))))))) ( -40.70, z-score =  -3.36, R)
>droYak2.chr3L 6486992 96 - 24197627
-----GAAGU-----CCUGCGAUAAGAGUACCCUUUUUU---U-AUGCUUUUAUUAGCUCGUGGAUGCUGCAGGGCCUUCGUGUGGGCGUGAGCCCAUAUUUAGCGACAU
-----(((((-----(((((((((((((((.........---.-.))))))))))(((........))))))))).))))((((((((....)))))))).......... ( -39.10, z-score =  -4.39, R)
>droEre2.scaffold_4784 8606619 99 - 25762168
-----GAAGU-----CCUGCGAUAAGGAUACCCUUUUUCGGGA-GUGUUUUUAUUAGCCCGAAAAUGCUUAAGGGCCUUCGUGUGGGCGUGAGCCCAUAUUUAGCGAAAU
-----(((((-----(((......))))..((((((((((((.-..((....))...)))))))......))))).))))((((((((....)))))))).......... ( -36.90, z-score =  -3.55, R)
>droAna3.scaffold_13337 10688546 105 + 23293914
UUUCAAAAGUCUCGGCCAGCGAUAAGUGAACCCUUUUUGGGGAUGUAUUUUUAUUAGCCGCAGGACAUU----GGUCCCCAAAAUGCCACAGACAU-UAUUUAGAGGCAU
........((((((((.((..(.(((((..((((....))))...))))))..)).)))(((((((...----.))))......))).........-......))))).. ( -24.60, z-score =  -0.46, R)
>consensus
_____GAAGU_____CCUGCGAUAAGGAGACCCUUUUCCGGGA_GUGUUUUUAUUAGCCCGCGGAUGCUGAAGGCCCUCCGUGUGGGCGUGAGCCCAUACUUAGCGACAU
..................((((((((((.(((((.....)))..)).)))))))).)).......((((((.........((((((((....)))))))))))))).... (-17.03 = -18.65 +   1.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:06:15 2011