Locus 5308

Sequence ID dm3.chr2R
Location 19,373,279 – 19,373,442
Length 163
Max. P 0.704349
window7274 window7275 window7276

overview

Window 4

Location 19,373,279 – 19,373,374
Length 95
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 69.08
Shannon entropy 0.46857
G+C content 0.36129
Mean single sequence MFE -22.28
Consensus MFE -10.24
Energy contribution -11.55
Covariance contribution 1.31
Combinations/Pair 1.25
Mean z-score -1.63
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.06
SVM RNA-class probability 0.525868
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19373279 95 + 21146708
-----UUAA-ACUAAACUACUUUCUUAGUUUAUUGAUCUGUGUGUGA-------GUCAC-UUAGUUAUCGUGGGAUGGUAUAUACCCACAUUUGGGUAUAUCCUUCCUA
-----.(((-(((((.........))))))))..((((((.(((...-------..)))-.)))..))).(((((.((.(((((((((....))))))))))).))))) ( -27.70, z-score =  -3.29, R)
>droSim1.chr2R 17954967 91 + 19596830
-----UUAA-GCUAAACUACUUUCUUAGUUUAUUAAUCUGUGUGUGG-------GUCAC-UUAGUCAUC-CGAACUAGGGUAUAUCC---UUUGGGUAUAUCCUUCUUA
-----.(((-(((((.........)))))))).........((.(((-------((.((-...)).)))-)).)).(((((((((((---...)))))))))))..... ( -20.40, z-score =  -1.58, R)
>droSec1.super_9 2662045 91 + 3197100
-----UUAA-ACUAAACUACUUUCUUAGUUUAUUGAUCUGUGUGUGA-------GUCAC-UUAGUCAUC-CGAACUAGGGUAUAUCC---UUUGGGUAUAUCCGUCUUA
-----....-...............((((((..(((.(((.(((...-------..)))-.))))))..-.))))))((((((((((---...))))))))))...... ( -22.70, z-score =  -2.47, R)
>droEre2.scaffold_4845 20739709 109 + 22589142
UCACAUCAGCAGUUAAAUACUUUUUUAAUUUAUGGGUCUGUGAGUAUCUAAGUUGUCAUGCUGGCGAUCCCCCUAUGAUAUAUACCUCCAUCUGGGCAACUCCUUACUU
((((((((..(((((((......)))))))..)))...)))))(((....(((((((....(((.(...................).)))....)))))))...))).. ( -18.31, z-score =   0.81, R)
>consensus
_____UUAA_ACUAAACUACUUUCUUAGUUUAUUGAUCUGUGUGUGA_______GUCAC_UUAGUCAUC_CGAAAUAGGAUAUACCC___UUUGGGUAUAUCCUUCCUA
............(((((((......))))))).....(((...((((........))))..))).............((((((((((......))))))))))...... (-10.24 = -11.55 +   1.31)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,373,338 – 19,373,442
Length 104
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 69.07
Shannon entropy 0.48339
G+C content 0.34189
Mean single sequence MFE -23.25
Consensus MFE -11.50
Energy contribution -11.62
Covariance contribution 0.12
Combinations/Pair 1.33
Mean z-score -1.56
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.36
SVM RNA-class probability 0.657914
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19373338 104 + 21146708
GAUGGUAUAUACCCACAUUUGGGUAUAUCCUUCCUAAGUUUA---------UUUCAGUUGUAAUAAAUUGCAUUUGAAAUGGGGUUUUCCAUUA--ACAAA-AAAGCGAAUCUGUU
((.((.(((((((((....))))))))))).))....((((.---------..((((.(((((....))))).))))((((((....)))))).--.....-.))))......... ( -25.00, z-score =  -2.16, R)
>droSim1.chr2R 17955025 104 + 19596830
ACUAGGGUAUAUCC---UUUGGGUAUAUCCUUCUUAAAUUUA---------UUUCACUUGUUAUAAAUUGCGUUUGAAAUGGGUUUUCCCACUAAAACAAAUAAAGCGAAUCAGUG
(((.((((((((((---...))))))))))(((...((((((---------(..(....)..)))))))..((((....((((....))))...)))).........)))..))). ( -22.80, z-score =  -2.21, R)
>droSec1.super_9 2662103 104 + 3197100
ACUAGGGUAUAUCC---UUUGGGUAUAUCCGUCUUAAAUUUA---------CUUCACUUGUAAUAGAUUGCGUUUGAAAUGGGUUUUCCCACUAAAACAAAUAAAGCGAAUAGGUG
....((((((((((---...)))))))))).......(((((---------.(((.(((((((....))))((((....((((....))))...)))).....))).)))))))). ( -24.90, z-score =  -1.92, R)
>droEre2.scaffold_4845 20739783 106 + 22589142
-AUGAUAUAUACCUCCAUCUGGGCAACUCCUUACUUAGUUUAAGGUACAUACUGCAGUAGCAAUAAAUGCCCUUUAAAAUGGGUUUUCCCUCUGAUGCAAAUAAGCC---------
-..............((((.(((((...(((((.......))))).......(((....))).....)))))........(((....)))...))))..........--------- ( -20.30, z-score =   0.05, R)
>consensus
AAUAGGAUAUACCC___UUUGGGUAUAUCCUUCCUAAAUUUA_________CUUCACUUGUAAUAAAUUGCGUUUGAAAUGGGUUUUCCCACUAAAACAAAUAAAGCGAAUC_GUG
....((((((((((......))))))))))...........................((((..((((.....))))....(((....)))......))))................ (-11.50 = -11.62 +   0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,373,338 – 19,373,442
Length 104
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 69.07
Shannon entropy 0.48339
G+C content 0.34189
Mean single sequence MFE -23.83
Consensus MFE -9.79
Energy contribution -13.48
Covariance contribution 3.69
Combinations/Pair 1.19
Mean z-score -1.99
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.46
SVM RNA-class probability 0.704349
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19373338 104 - 21146708
AACAGAUUCGCUUU-UUUGU--UAAUGGAAAACCCCAUUUCAAAUGCAAUUUAUUACAACUGAAA---------UAAACUUAGGAAGGAUAUACCCAAAUGUGGGUAUAUACCAUC
......(((((...-((((.--.(((((......))))).)))).))............((((..---------.....)))))))(((((((((((....))))))))).))... ( -24.80, z-score =  -2.94, R)
>droSim1.chr2R 17955025 104 - 19596830
CACUGAUUCGCUUUAUUUGUUUUAGUGGGAAAACCCAUUUCAAACGCAAUUUAUAACAAGUGAAA---------UAAAUUUAAGAAGGAUAUACCCAAA---GGAUAUACCCUAGU
......(((((((.((((((((.((((((....))))))..))))).))).......))))))).---------...........(((.((((((....---)).)))).)))... ( -18.30, z-score =  -1.09, R)
>droSec1.super_9 2662103 104 - 3197100
CACCUAUUCGCUUUAUUUGUUUUAGUGGGAAAACCCAUUUCAAACGCAAUCUAUUACAAGUGAAG---------UAAAUUUAAGACGGAUAUACCCAAA---GGAUAUACCCUAGU
.....(((..((((((((((..(((((((....)))).............)))..))))))))))---------..))).......((.((((((....---)).)))).)).... ( -21.41, z-score =  -1.88, R)
>droEre2.scaffold_4845 20739783 106 - 22589142
---------GGCUUAUUUGCAUCAGAGGGAAAACCCAUUUUAAAGGGCAUUUAUUGCUACUGCAGUAUGUACCUUAAACUAAGUAAGGAGUUGCCCAGAUGGAGGUAUAUAUCAU-
---------....(((((.((((...(((....)))........(((((..((((((....))))))....(((((.......)))))...))))).)))).)))))........- ( -30.80, z-score =  -2.07, R)
>consensus
CAC_GAUUCGCUUUAUUUGUUUUAGUGGGAAAACCCAUUUCAAACGCAAUUUAUUACAACUGAAA_________UAAACUUAAGAAGGAUAUACCCAAA___GGAUAUACACCAGU
...........((((((((((..((((((....))))))...............))))))))))......................((((((((((......)))))))))).... ( -9.79 = -13.48 +   3.69)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:45:45 2011