Locus 12421

Sequence ID dm3.chr4
Location 1,020,679 – 1,020,822
Length 143
Max. P 0.976260
window17071 window17072

overview

Window 1

Location 1,020,679 – 1,020,786
Length 107
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 59.29
Shannon entropy 0.66329
G+C content 0.53362
Mean single sequence MFE -37.23
Consensus MFE -13.44
Energy contribution -17.75
Covariance contribution 4.31
Combinations/Pair 1.56
Mean z-score -1.29
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.11
SVM RNA-class probability 0.549450
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 1020679 107 + 1351857
---UCGUGGGAGAUCAUGCCGACGACCCAUGGGGGCGCGUCUACAAGAUUUGCCGAGGCCGCAGAAAGUGC------ACGGAGAUUGGAUGCCUCCACGUGAAUGGCGAGCUGAUC
---........(((((.((((.(.(..((((((((.((((((....(((((.(((..((.((.....))))------.)))))))))))))))))).))))..).))).))))))) ( -34.60, z-score =   0.37, R)
>droAna3.scaffold_13278 90558 112 + 130239
CUUUCGUAGAUCGAAAUAAACACGAUCCCUGGGGUCGUGUUUACAAGAUUCUGCGGGAGAAUGGGAAGGAGGGGUCCAGGGAUAUUUGUGCCCUACGGGUUG--AAGGUUGAGA--
((..((((((((....((((((((((((...))))))))))))...)).))))))..)).........(.((((..((((....))))..)))).)......--..........-- ( -39.10, z-score =  -2.24, R)
>droVir3.scaffold_12945 170395 110 - 206789
CUUUCCUGGAGCGCAAUAAGGAUGAUCCCUGGGGUCGUGCUUAUAAAAUAGUUCGAGGUAGAGGCAGGGAA------ACGGAUGUAAGUUGCCUCCGUGCUGGCAACGUUCAGUUA
(((((((.((((...(((((.(((((((...))))))).)))))......)))).))).))))(((.(...------.)...)))..((((((........))))))......... ( -37.30, z-score =  -1.78, R)
>droGri2.scaffold_15040 43474 110 - 162499
CCUUUUUGGAGCGCAAUAAGGACGACCCCUGGGGUCGUGCUUAUAAAGUUGUGAGAGGUAGGCGUAGGGAA------GCGGAUGUAAGUGGCCUCCGUGUCGGUGACGUUCAGUUA
.(((((((.(((...(((((.(((((((...))))))).)))))...))).)))))))(..((((...((.------(((((.((.....)).))))).))....))))..).... ( -37.90, z-score =  -1.49, R)
>consensus
CUUUCGUGGAGCGCAAUAAGGACGACCCCUGGGGUCGUGCUUACAAAAUUGUGCGAGGUAGAGGAAAGGAA______ACGGAUAUAAGUGGCCUCCGUGUUGGUAACGUUCAGAUA
.((((((((((....(((((.(((((((...))))))).)))))....)))))))))).....................((((((((.((((......)))).))))))))..... (-13.44 = -17.75 +   4.31)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,020,716 – 1,020,822
Length 106
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 54.83
Shannon entropy 0.73525
G+C content 0.48859
Mean single sequence MFE -33.52
Consensus MFE -12.74
Energy contribution -12.05
Covariance contribution -0.69
Combinations/Pair 1.83
Mean z-score -1.81
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.95
SVM RNA-class probability 0.976260
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 1020716 106 + 1351857
CUACAAGAUUUGCCGAGGCCGCAGAAAGUGCACG------GAGAUUGGAUGCCUCCACGUGAAUGGCGAGCUGAUCACUGAUUGGGGUGACUGUGCACGAGUGCUCCUCCGC--
...........((.((((..(((....(((((((------(.(((..(.((((...........))))..)..)))(((......)))..))))))))...))).)))).))-- ( -34.00, z-score =  -0.19, R)
>droAna3.scaffold_13278 90598 112 + 130239
UUACAAGAUUCUGCGGGAGAAUGGGAAGGAGGGGUCCAGGGAUAUUUGUGCCCUACGGGUUGAAGGUUGAGACCUUAUAACCUGGAAGGAUUGUGUU-GAAUGUCUU-UUGUCC
.......(((((.....))))).....(((((((..((((....))))..)))).((((((((((((....))))).)))))))(((((((......-....)))))-)).))) ( -30.40, z-score =  -0.06, R)
>droVir3.scaffold_12945 170435 106 - 206789
UUAUAAAAUAGUUCGAGGUAGAGGCAGGGAAACG------GAUGUAAGUUGCCUCCGUGCUGGCAACGUUCAGUUAACAGCAUGGAGGGAUUGUAU--GAAUGUCUUGUUGAAU
..........((((((....((((((.(....).------...(((...(.(((((((((((..(((.....)))..))))))))))).)...)))--...)))))).)))))) ( -36.30, z-score =  -4.25, R)
>droGri2.scaffold_15040 43514 106 - 162499
UUAUAAAGUUGUGAGAGGUAGGCGUAGGGAAGCG------GAUGUAAGUGGCCUCCGUGUCGGUGACGUUCAGUUAACGGCAUGGAGUGACUGCAU--GAAUGUCUUAUUGAAU
..........((((((.((..((........)).------.(((((.((.((.(((((((((.((((.....)))).))))))))))).)))))))--..)).))))))..... ( -33.40, z-score =  -2.74, R)
>consensus
UUACAAAAUUGUGCGAGGUAGAGGAAAGGAAACG______GAUAUAAGUGGCCUCCGUGUUGAUGACGUUCAGUUAACAGCAUGGAGGGACUGUAU__GAAUGUCUU_UUGAAU
.......................(((((.......................(((((((((((.((((.....)))).)))))))))))....((((....)))))))))..... (-12.74 = -12.05 +  -0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:01:50 2011