Locus 6160

Sequence ID dm3.chr3L
Location 4,213,560 – 4,213,738
Length 178
Max. P 0.967218
window8471 window8472

overview

Window 1

Location 4,213,560 – 4,213,738
Length 178
Sequences 3
Columns 178
Reading direction forward
Mean pairwise identity 83.27
Shannon entropy 0.22042
G+C content 0.40644
Mean single sequence MFE -40.00
Consensus MFE -30.55
Energy contribution -32.00
Covariance contribution 1.45
Combinations/Pair 1.07
Mean z-score -1.63
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.06
SVM RNA-class probability 0.525482
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 4213560 178 + 24543557
UUUGGCGAACAUACUUCAAUCAAUAUUUGAAUAUGUAAUUGAAAUGCCUGCUGUUAAGUUAUGCCGAUUAUCACUCACACGCCAUGUUGUCCAAACGCAAGCAAAUUUCGCUUGGUUUGCGUGACGUGCGAGUAAUCUUCAUAGUAACAUACAUGUCCAAUGUGCCCACCCAAAGUGC
...((((.(((((.(((((.......)))))))))).((((..(((.....(((((...((((..((((...((((.((((.((((.....(((((.(((((.......)))))))))))))).)))).))))))))..)))).)))))..)))...)))).))))(((.....))). ( -43.70, z-score =  -1.09, R)
>droSec1.super_2 4210418 152 + 7591821
--------------------------AUGAAUGAGUAAUUUAUAUGCCUCCUGUUUAGUUAUGCCAAUUAUUACUCACACGCCAUGUUGUCCAAACGCAAGCAAAUUUCGUUUGGUUUACGUGACGUGCGGGUAAUCUUCAUGGUAACAUUCAUGUCUAAAGUGCCCACCCAAAGUGC
--------------------------(((((((.((((((.(((.......)))..))))))((((...(((((((.((((.(((((...(((((((.((.....)).)))))))...))))).)))).))))))).....))))..)))))))............(((.....))). ( -39.80, z-score =  -2.09, R)
>droSim1.chr3L 3755016 152 + 22553184
--------------------------AUGAAUGAGUAAUUUAUAUGCCUCCUGUUUAGUUAUGCCAAUUAUUACUCACACGCCAUGUUGUCCAAACGCAAGCAAAUUUCGUUUGGUUUACGUGACGUGCGUGUAAUCUUCAUGGUAACAUUCAUGUCUAAAGUGCCCACCCAAAGUGC
--------------------------(((((((.((((((.(((.......)))..))))))((((...(((((.(.((((.(((((...(((((((.((.....)).)))))))...))))).)))).).))))).....))))..)))))))............(((.....))). ( -36.50, z-score =  -1.72, R)
>consensus
__________________________AUGAAUGAGUAAUUUAUAUGCCUCCUGUUUAGUUAUGCCAAUUAUUACUCACACGCCAUGUUGUCCAAACGCAAGCAAAUUUCGUUUGGUUUACGUGACGUGCGAGUAAUCUUCAUGGUAACAUUCAUGUCUAAAGUGCCCACCCAAAGUGC
...........................((((((.((((((.....((.....))..))))))((((...(((((((.((((.(((((...(((((((.((.....)).)))))))...))))).)))).))))))).....))))..)))))).............(((.....))). (-30.55 = -32.00 +   1.45)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,213,560 – 4,213,738
Length 178
Sequences 3
Columns 178
Reading direction reverse
Mean pairwise identity 83.27
Shannon entropy 0.22042
G+C content 0.40644
Mean single sequence MFE -46.03
Consensus MFE -36.93
Energy contribution -36.93
Covariance contribution 0.01
Combinations/Pair 1.08
Mean z-score -2.45
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.78
SVM RNA-class probability 0.967218
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 4213560 178 - 24543557
GCACUUUGGGUGGGCACAUUGGACAUGUAUGUUACUAUGAAGAUUACUCGCACGUCACGCAAACCAAGCGAAAUUUGCUUGCGUUUGGACAACAUGGCGUGUGAGUGAUAAUCGGCAUAACUUAACAGCAGGCAUUUCAAUUACAUAUUCAAAUAUUGAUUGAAGUAUGUUCGCCAAA
........((((((((.........(((..((((...(((..(((((((((((((((.(((((((((((((...))))))).))))).....).)))))))))))))))..)))...))))...)))......((((((((((.((((....)))))))))))))).))))))))... ( -57.80, z-score =  -3.53, R)
>droSec1.super_2 4210418 152 - 7591821
GCACUUUGGGUGGGCACUUUAGACAUGAAUGUUACCAUGAAGAUUACCCGCACGUCACGUAAACCAAACGAAAUUUGCUUGCGUUUGGACAACAUGGCGUGUGAGUAAUAAUUGGCAUAACUAAACAGGAGGCAUAUAAAUUACUCAUUCAU--------------------------
......((((((((....(((....)))((((..((.((...(((((.(((((((((.((...(((((((...........)))))))...)).))))))))).)))))..((((.....)))).))))..))))........)))))))).-------------------------- ( -40.20, z-score =  -1.73, R)
>droSim1.chr3L 3755016 152 - 22553184
GCACUUUGGGUGGGCACUUUAGACAUGAAUGUUACCAUGAAGAUUACACGCACGUCACGUAAACCAAACGAAAUUUGCUUGCGUUUGGACAACAUGGCGUGUGAGUAAUAAUUGGCAUAACUAAACAGGAGGCAUAUAAAUUACUCAUUCAU--------------------------
......((((((((....(((....)))((((..((.((...(((((.(((((((((.((...(((((((...........)))))))...)).))))))))).)))))..((((.....)))).))))..))))........)))))))).-------------------------- ( -40.10, z-score =  -2.09, R)
>consensus
GCACUUUGGGUGGGCACUUUAGACAUGAAUGUUACCAUGAAGAUUACACGCACGUCACGUAAACCAAACGAAAUUUGCUUGCGUUUGGACAACAUGGCGUGUGAGUAAUAAUUGGCAUAACUAAACAGGAGGCAUAUAAAUUACUCAUUCAU__________________________
((.((((.(((..((........((((........))))...(((((.(((((((((.((...(((((((...........)))))))...)).))))))))).))))).....))...))).....))))))............................................. (-36.93 = -36.93 +   0.01)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:02:22 2011