Locus 2884

Sequence ID dm3.chr2RHet
Location 1,482,653 – 1,482,771
Length 118
Max. P 0.976414
window3973 window3974 window3975 window3976

overview

Window 3

Location 1,482,653 – 1,482,768
Length 115
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 56.81
Shannon entropy 0.60031
G+C content 0.48116
Mean single sequence MFE -33.67
Consensus MFE -16.59
Energy contribution -15.60
Covariance contribution -0.99
Combinations/Pair 1.44
Mean z-score -1.80
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.95
SVM RNA-class probability 0.976414
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 1482653 115 + 3288761
UGAUAGACCAGCACUCGUGCGUGUGGAUAAUGGAACAGCCAUCCACGUCAAAGGAACGCACCUAAUAACAUUCAUUGUGAGUGCCAUGGUCAAUGAGACCGUCUUCACAAACCAC
(((.((((..(((((((((((((((((...(((.....)))))))).((....))))))))......(((.....)))))))))...((((.....)))))))))))........ ( -37.50, z-score =  -3.10, R)
>droEre2.scaffold_4784 2404465 115 - 25762168
CGAUAGAUCAGCACUUGUGCGCGUGGAUAAUGGAACGACCAUCCACAUUAGAGGCACGCACCUGAUAACAUUUACUGAGAGUGCUAUGGUCAAUGAGACCGUAUUUGUAAAUCAU
.(((.....(((((((...(..(((((...(((.....))))))))(((((..(....)..)))))..........).)))))))((((((.....))))))........))).. ( -30.50, z-score =  -1.34, R)
>dp4.Unknown_group_128 8950 115 + 26480
CGCCGCACAUGCCUUCGUAACCAUUGACAAUGGCCCGGAACGCCGAAUUACGGGAAAGUACCUGGUGAAUUUUGACCAGGUAGCCUGCAUGAAGGGUUCUACGAACACCAACUUC
.......(((((...(((((((((.....))))..(((....)))..)))))((....((((((((........)))))))).)).)))))..((((((...)))).))...... ( -33.00, z-score =  -0.97, R)
>consensus
CGAUAGACCAGCACUCGUGCGCGUGGAUAAUGGAACGGCCAUCCACAUUAAAGGAACGCACCUGAUAACAUUUAAUGAGAGUGCCAUGGUCAAUGAGACCGUAUUCACAAACCAC
.....(((((((((((..............((((.......))))......(((......)))...............))))))..)))))........................ (-16.59 = -15.60 +  -0.99)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,482,653 – 1,482,768
Length 115
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 56.81
Shannon entropy 0.60031
G+C content 0.48116
Mean single sequence MFE -35.50
Consensus MFE -16.85
Energy contribution -15.76
Covariance contribution -1.10
Combinations/Pair 1.42
Mean z-score -1.49
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.18
SVM RNA-class probability 0.905071
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 1482653 115 - 3288761
GUGGUUUGUGAAGACGGUCUCAUUGACCAUGGCACUCACAAUGAAUGUUAUUAGGUGCGUUCCUUUGACGUGGAUGGCUGUUCCAUUAUCCACACGCACGAGUGCUGGUCUAUCA
........(((((((((((.....))))..(((((((.(((.((((((........))))))..)))..((((((((........))))))))......))))))).)))).))) ( -38.90, z-score =  -1.75, R)
>droEre2.scaffold_4784 2404465 115 + 25762168
AUGAUUUACAAAUACGGUCUCAUUGACCAUAGCACUCUCAGUAAAUGUUAUCAGGUGCGUGCCUCUAAUGUGGAUGGUCGUUCCAUUAUCCACGCGCACAAGUGCUGAUCUAUCG
..(((..........((((.....)))).(((((((....(((..((....))..)))((((......((((((((((......)))))))))).)))).)))))))....))). ( -33.00, z-score =  -2.25, R)
>dp4.Unknown_group_128 8950 115 - 26480
GAAGUUGGUGUUCGUAGAACCCUUCAUGCAGGCUACCUGGUCAAAAUUCACCAGGUACUUUCCCGUAAUUCGGCGUUCCGGGCCAUUGUCAAUGGUUACGAAGGCAUGUGCGGCG
((((..(((.........)))))))....(((.((((((((........)))))))))))..(((((.....((.(((..((((((.....))))))..))).))...))))).. ( -34.60, z-score =  -0.46, R)
>consensus
GUGGUUUGUGAACACGGUCUCAUUGACCAUGGCACUCUCAAUAAAUGUUAUCAGGUGCGUUCCUCUAAUGUGGAUGGCCGUUCCAUUAUCCACGCGCACGAGUGCUGGUCUAUCG
.....................((.(((((..((((((.((.....)).......((((((.........(((((.......))))).......))))))))))))))))).)).. (-16.85 = -15.76 +  -1.10)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,482,657 – 1,482,771
Length 114
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 57.02
Shannon entropy 0.59752
G+C content 0.47661
Mean single sequence MFE -32.77
Consensus MFE -16.59
Energy contribution -15.60
Covariance contribution -0.99
Combinations/Pair 1.44
Mean z-score -1.70
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.90
SVM RNA-class probability 0.974215
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 1482657 114 + 3288761
AGACCAGCACUCGUGCGUGUGGAUAAUGGAACAGCCAUCCACGUCAAAGGAACGCACCUAAUAACAUUCAUUGUGAGUGCCAUGGUCAAUGAGACCGUCUUCACAAACCACGAC
((((..(((((((((((((((((...(((.....)))))))).((....))))))))......(((.....)))))))))...((((.....)))))))).............. ( -35.50, z-score =  -2.41, R)
>droEre2.scaffold_4784 2404469 114 - 25762168
AGAUCAGCACUUGUGCGCGUGGAUAAUGGAACGACCAUCCACAUUAGAGGCACGCACCUGAUAACAUUUACUGAGAGUGCUAUGGUCAAUGAGACCGUAUUUGUAAAUCAUGAC
.(((.(((((((...(..(((((...(((.....))))))))(((((..(....)..)))))..........).)))))))((((((.....))))))........)))..... ( -29.80, z-score =  -1.16, R)
>dp4.Unknown_group_128 8954 114 + 26480
GCACAUGCCUUCGUAACCAUUGACAAUGGCCCGGAACGCCGAAUUACGGGAAAGUACCUGGUGAAUUUUGACCAGGUAGCCUGCAUGAAGGGUUCUACGAACACCAACUUCAAU
...(((((...(((((((((.....))))..(((....)))..)))))((....((((((((........)))))))).)).)))))..((((((...)))).))......... ( -33.00, z-score =  -1.52, R)
>consensus
AGACCAGCACUCGUGCGCGUGGAUAAUGGAACGGCCAUCCACAUUAAAGGAACGCACCUGAUAACAUUUAAUGAGAGUGCCAUGGUCAAUGAGACCGUAUUCACAAACCACGAC
.(((((((((((..............((((.......))))......(((......)))...............))))))..)))))........................... (-16.59 = -15.60 +  -0.99)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,482,657 – 1,482,771
Length 114
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 57.02
Shannon entropy 0.59752
G+C content 0.47661
Mean single sequence MFE -34.73
Consensus MFE -16.66
Energy contribution -16.22
Covariance contribution -0.43
Combinations/Pair 1.38
Mean z-score -1.40
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.07
SVM RNA-class probability 0.885132
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 1482657 114 - 3288761
GUCGUGGUUUGUGAAGACGGUCUCAUUGACCAUGGCACUCACAAUGAAUGUUAUUAGGUGCGUUCCUUUGACGUGGAUGGCUGUUCCAUUAUCCACACGCACGAGUGCUGGUCU
..(((((((.((((........)))).)))))))((((((.(((.((((((........))))))..)))..((((((((........))))))))......))))))...... ( -38.40, z-score =  -1.44, R)
>droEre2.scaffold_4784 2404469 114 + 25762168
GUCAUGAUUUACAAAUACGGUCUCAUUGACCAUAGCACUCUCAGUAAAUGUUAUCAGGUGCGUGCCUCUAAUGUGGAUGGUCGUUCCAUUAUCCACGCGCACAAGUGCUGAUCU
.....(((..........((((.....)))).(((((((....(((..((....))..)))((((......((((((((((......)))))))))).)))).)))))))))). ( -32.70, z-score =  -2.05, R)
>dp4.Unknown_group_128 8954 114 - 26480
AUUGAAGUUGGUGUUCGUAGAACCCUUCAUGCAGGCUACCUGGUCAAAAUUCACCAGGUACUUUCCCGUAAUUCGGCGUUCCGGGCCAUUGUCAAUGGUUACGAAGGCAUGUGC
..........((.((((((((((((....(((.((.((((((((........))))))))....)).)))....)).))))...(((((.....))))))))))).))...... ( -33.10, z-score =  -0.70, R)
>consensus
GUCGUGGUUUGUGAACACGGUCUCAUUGACCAUGGCACUCUCAAUAAAUGUUAUCAGGUGCGUUCCUCUAAUGUGGAUGGCCGUUCCAUUAUCCACGCGCACGAGUGCUGGUCU
...........................(((((..((((((.((.....)).......((((((.........(((((.......))))).......))))))))))))))))). (-16.66 = -16.22 +  -0.43)

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 21:59:50 2011