Locus 8486

Sequence ID dm3.chr3L
Location 23,590,095 – 23,590,240
Length 145
Max. P 0.998240
window11656 window11657

overview

Window 6

Location 23,590,095 – 23,590,240
Length 145
Sequences 3
Columns 149
Reading direction forward
Mean pairwise identity 50.00
Shannon entropy 0.70520
G+C content 0.47344
Mean single sequence MFE -30.82
Consensus MFE -16.79
Energy contribution -16.13
Covariance contribution -0.65
Combinations/Pair 1.50
Mean z-score -1.90
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.30
SVM RNA-class probability 0.998240
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 23590095 145 + 24543557
UACACGCUGGCGUUCA--CUACAUUCUCAUCUUUCUCUUACACACUAUUUAUGACAACCCG--AUCGGAUCUCACUCAGCUGCAGGGGCUGUCCGUGCCUCUGCCGCAGAGCUCGACAGAUUUUUACCGCAAUAUUACAAUUUCAUCAG
.....((.((.((...--..))......((((.((.......................((.--...))......(((.((.((((((((.......)))))))).)).)))...)).)))).....))))................... ( -28.50, z-score =  -0.47, R)
>droAna3.scaffold_13099 1780302 126 - 3324263
----CUCUCAAGUUGAGCCUAUGUCGUCAUCUCUUU--------AAACUUUUGGUAACUCGUCAGCGGACCUCACUCACCAGCAGAGACUACCACCGUCUCUGCUGCUAUGACUUUCGCAUGAAUUCUAUAUUCCCUG-----------
----..(((.....))).....((..(((.......--------.......)))..))...((((((((..(((.....((((((((((.......))))))))))...)))..))))).)))...............----------- ( -29.14, z-score =  -2.19, R)
>droVir3.scaffold_13324 1529453 126 - 2960039
AACUCACUCAUGUCGAGUGUAUGUAGCCAUCUCUGUCUUACUCAAGACUCUUGGUAUCUUACCAUCGAACCUUACUCAGCAGCAGAG--CGUCUCUGCCUCUGCUGCCGUG-CUUUCGUUCAAUAUCAG--------------------
.((.(((((.....)))))...)).((((.....(((((....)))))...))))...........((((......(.(((((((((--.((....))))))))))).)..-.....))))........-------------------- ( -34.82, z-score =  -3.05, R)
>consensus
_AC_CACUCAAGUUGAG_CUAUGUAGUCAUCUCUCUCUUAC_CAAAACUUUUGGUAACUCG_CAUCGGACCUCACUCAGCAGCAGAG_CUGUCACUGCCUCUGCUGCAGUG_CUUUCGCAUAAUUUCAG_A_U________________
......(((.....)))........((.........................(((...(((....)))))).......(((((((((((.......)))))))))))..........)).............................. (-16.79 = -16.13 +  -0.65)

alignment

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secondary structure

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dotplot

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Window 7

Location 23,590,095 – 23,590,240
Length 145
Sequences 3
Columns 149
Reading direction reverse
Mean pairwise identity 50.00
Shannon entropy 0.70520
G+C content 0.47344
Mean single sequence MFE -37.70
Consensus MFE -17.30
Energy contribution -18.20
Covariance contribution 0.90
Combinations/Pair 1.36
Mean z-score -1.39
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.76
SVM RNA-class probability 0.965863
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 23590095 145 - 24543557
CUGAUGAAAUUGUAAUAUUGCGGUAAAAAUCUGUCGAGCUCUGCGGCAGAGGCACGGACAGCCCCUGCAGCUGAGUGAGAUCCGAU--CGGGUUGUCAUAAAUAGUGUGUAAGAGAAAGAUGAGAAUGUAG--UGAACGCCAGCGUGUA
...............(((((((......((((.((..((((.((.((((.(((.......))).)))).)).))))(((((((...--.))))).)).................)).)))).....)))))--)).(((....)))... ( -36.20, z-score =   0.35, R)
>droAna3.scaffold_13099 1780302 126 + 3324263
-----------CAGGGAAUAUAGAAUUCAUGCGAAAGUCAUAGCAGCAGAGACGGUGGUAGUCUCUGCUGGUGAGUGAGGUCCGCUGACGAGUUACCAAAAGUUU--------AAAGAGAUGACGACAUAGGCUCAACUUGAGAG----
-----------((((((.......((((((((....)).....((((((((((.......))))))))))))))))....))).))).((((((.((....(((.--------........)))......))...))))))....---- ( -36.60, z-score =  -1.85, R)
>droVir3.scaffold_13324 1529453 126 + 2960039
--------------------CUGAUAUUGAACGAAAG-CACGGCAGCAGAGGCAGAGACG--CUCUGCUGCUGAGUAAGGUUCGAUGGUAAGAUACCAAGAGUCUUGAGUAAGACAGAGAUGGCUACAUACACUCGACAUGAGUGAGUU
--------------------(((.((((((((....(-(.(((((((((((.(......)--))))))))))).))...))))))))......(((((((...)))).)))...)))..(((....))).(((((.....))))).... ( -40.30, z-score =  -2.66, R)
>consensus
________________A_U_CAGAAAUAAUACGAAAG_CACAGCAGCAGAGGCAGAGACAG_CUCUGCUGCUGAGUGAGGUCCGAUG_CGAGUUACCAAAAGUAUUG_GUAAGAAAGAGAUGACAACAUAG_CUCAACAUGAGAG_GU_
........................................(((((((((((((.......))))))))))))).....((((((....)))...)))...................................(((.....)))...... (-17.30 = -18.20 +   0.90)

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 23:46:31 2011