Locus 6309

Sequence ID dm3.chr3L
Location 5,433,865 – 5,433,962
Length 97
Max. P 0.907427
window8675 window8676

overview

Window 5

Location 5,433,865 – 5,433,962
Length 97
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 79.47
Shannon entropy 0.37092
G+C content 0.51822
Mean single sequence MFE -32.70
Consensus MFE -20.98
Energy contribution -23.66
Covariance contribution 2.68
Combinations/Pair 1.15
Mean z-score -1.97
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.17
SVM RNA-class probability 0.903186
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5433865 97 + 24543557
UGUCCAAUUUAUUGGCCAUAACUCAUGCCCGGGAUCGACCAAGGACUGAGUGAGAAGGAUUCCGGAUCC-AGGAAGCAGAAACCAGGAUCCAUGGCCA
............(((((((.(((((..((..((.....))..))..)))))............((((((-.((.........)).))))))))))))) ( -32.10, z-score =  -1.52, R)
>droSim1.chr3L 4950780 98 + 22553184
UGUCCAAUUUAUUGGCCAUAACUCAUGCCCGGGAUCGACCAAGGAGUGAGUGAGAAGGAUUCCGGAUCCCAGGAAGCAGGAACCAGGAUCCAUGGCCA
............(((((((.((((((.((..((.....))..)).)))))).....((((((.((.(((..(....).))).)).))))))))))))) ( -36.60, z-score =  -2.31, R)
>droSec1.super_2 5378990 98 + 7591821
UGUCCAAUUUAUUGGCCAUAACUCAUGCCCGGGAUCGACCAAGGAGUGAGUGAGAAGGAUUCCGGAUCCCAGGAAGCAGGAACCAGGAUCCAUGGCCA
............(((((((.((((((.((..((.....))..)).)))))).....((((((.((.(((..(....).))).)).))))))))))))) ( -36.60, z-score =  -2.31, R)
>droEre2.scaffold_4784 8127257 97 + 25762168
UGUCCAAUUUAUUGGCCAUAACUCAUGCCCGGGAUCGACCAAGGAGUGAGUGAGAAGGAUCCAGGAUCC-AGGAAGCAGGAACCAGGAUCCAUGGCCA
............(((((((.((((((.((..((.....))..)).)))))).....((((((.((.(((-.(....).))).)).))))))))))))) ( -39.80, z-score =  -3.55, R)
>droWil1.scaffold_180698 4200799 88 + 11422946
UGUCCAAUUUAUUGGUCAUAACUCAUGACA-----UGGCUGCAGAGAAAAUGACAGAGACGGAGAGACGUAGGGGGAGGGAGACGUAGUCGGU-----
...((.........(((((.....))))).-----.((((((...........(....(((......)))....)...(....))))))))).----- ( -18.40, z-score =  -0.16, R)
>consensus
UGUCCAAUUUAUUGGCCAUAACUCAUGCCCGGGAUCGACCAAGGAGUGAGUGAGAAGGAUUCCGGAUCC_AGGAAGCAGGAACCAGGAUCCAUGGCCA
.............((((((.((((((.((..((.....))..)).)))))).....((((((.((.(((.........))).)).)))))))))))). (-20.98 = -23.66 +   2.68)

alignment

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secondary structure

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dotplot

Postscript

Window 6

Location 5,433,865 – 5,433,962
Length 97
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 79.47
Shannon entropy 0.37092
G+C content 0.51822
Mean single sequence MFE -32.38
Consensus MFE -21.10
Energy contribution -23.22
Covariance contribution 2.12
Combinations/Pair 1.21
Mean z-score -1.95
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.19
SVM RNA-class probability 0.907427
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5433865 97 - 24543557
UGGCCAUGGAUCCUGGUUUCUGCUUCCU-GGAUCCGGAAUCCUUCUCACUCAGUCCUUGGUCGAUCCCGGGCAUGAGUUAUGGCCAAUAAAUUGGACA
(((((((((((((.((.........)).-))))))............(((((((((..((.....)).)))).))))).)))))))............ ( -34.90, z-score =  -1.67, R)
>droSim1.chr3L 4950780 98 - 22553184
UGGCCAUGGAUCCUGGUUCCUGCUUCCUGGGAUCCGGAAUCCUUCUCACUCACUCCUUGGUCGAUCCCGGGCAUGAGUUAUGGCCAAUAAAUUGGACA
(((((((((((.((((.((((.......)))).)))).)))).....(((((..(((.((.....)).)))..))))).)))))))............ ( -37.20, z-score =  -2.08, R)
>droSec1.super_2 5378990 98 - 7591821
UGGCCAUGGAUCCUGGUUCCUGCUUCCUGGGAUCCGGAAUCCUUCUCACUCACUCCUUGGUCGAUCCCGGGCAUGAGUUAUGGCCAAUAAAUUGGACA
(((((((((((.((((.((((.......)))).)))).)))).....(((((..(((.((.....)).)))..))))).)))))))............ ( -37.20, z-score =  -2.08, R)
>droEre2.scaffold_4784 8127257 97 - 25762168
UGGCCAUGGAUCCUGGUUCCUGCUUCCU-GGAUCCUGGAUCCUUCUCACUCACUCCUUGGUCGAUCCCGGGCAUGAGUUAUGGCCAAUAAAUUGGACA
(((((((((((((.((.(((........-))).)).)))))).....(((((..(((.((.....)).)))..))))).)))))))............ ( -39.60, z-score =  -3.27, R)
>droWil1.scaffold_180698 4200799 88 - 11422946
-----ACCGACUACGUCUCCCUCCCCCUACGUCUCUCCGUCUCUGUCAUUUUCUCUGCAGCCA-----UGUCAUGAGUUAUGACCAAUAAAUUGGACA
-----...(((...))).............((((..........(((((...(((((((....-----)).)).)))..))))).........)))). ( -13.01, z-score =  -0.67, R)
>consensus
UGGCCAUGGAUCCUGGUUCCUGCUUCCU_GGAUCCGGAAUCCUUCUCACUCACUCCUUGGUCGAUCCCGGGCAUGAGUUAUGGCCAAUAAAUUGGACA
(((((((((((.((((.(((.........))).)))).)))).....(((((..(((.((.....)).)))..))))).)))))))............ (-21.10 = -23.22 +   2.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:05:12 2011