Locus 7805

Sequence ID dm3.chr3L
Location 17,446,551 – 17,446,689
Length 138
Max. P 0.999530
window10734 window10735

overview

Window 4

Location 17,446,551 – 17,446,689
Length 138
Sequences 5
Columns 140
Reading direction forward
Mean pairwise identity 76.53
Shannon entropy 0.41669
G+C content 0.39794
Mean single sequence MFE -40.81
Consensus MFE -30.88
Energy contribution -31.20
Covariance contribution 0.32
Combinations/Pair 1.21
Mean z-score -3.68
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.98
SVM RNA-class probability 0.999530
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17446551 138 + 24543557
CGGGAUUGGGAUACUCUAGAGAAAACUUUUCUUCUUUCGAAUCAAUUUCUGUCUUUAACUC-GUAGGUAUGCAUAAUACUUUAAACAUUUUGAAGAAUACAGGAAAUCCUUGAGUGUUCCGAUCCCAGGGACUCCCAAA-
.(((((((((((((((.((((((........))))))........(((((((((((((...-((((((((.....))))))...))...)))))))...))))))......))))))))))))))).(((...)))...- ( -43.20, z-score =  -3.81, R)
>droEre2.scaffold_4784 9361095 124 - 25762168
CGGGAUUGGAGCACUCUAAA--AAACGUGCGUUCUUUUCAAUCCAUUUCUGUCUUAAAUUC-CA------------UACCUUAAACGUUUUUAGGAUUAACGCAAAUUCUUGAGUGUUCCGAUCCCAGGAACUACCAGA-
.(((((((((((((((....--.....((((((.................((((((((..(-..------------..........)..)))))))).)))))).......))))))))))))))).((.....))...- ( -38.16, z-score =  -4.62, R)
>droYak2.chr3L 7578039 137 - 24197627
CGGGAUUGGGACACUCUAAAG-AAACUUUUGCUCUUUUAAAUCAAUUUCUGUCUUAAACUC-CAAGAUAUGCAAUGUACUUUCAGCGUUUUUAAGAUGAAAGCAAAUCCAUGAGUGUUCCGAUCCCAGGUACUCCCACA-
.(((((((((((((((....(-(....((((((.(((((((........((((((......-.))))))...(((((.......))))))))))))....))))))))...))))))))))))))).((.....))...- ( -37.70, z-score =  -3.32, R)
>droSec1.super_0 9499237 140 + 21120651
CGGGAUUGGGACACUCUAGAGAAAACUUUCGUUCUUUCGAAUCCAUUUCUGUCUUUAGCUCCGAAGGUAUGCAUAAUACUUUAAAUACUUUGAAGAUUACAGGAAAUCCUUGAGUGUUUCGAUCCCAGGAACUCCCAGAC
.(((((((..((((((.((.((.....((((......))))....(((((((((((((.....(((((((.....))))))).......)))))))...)))))).)))).))))))..))))))).((.....)).... ( -44.50, z-score =  -3.54, R)
>droSim1.chr3L 16786903 118 + 22553184
CGGGAUUGGAACACUCUAGAGAAAACUUUCGUUCUUUCGAUUCAAUUUCUGUCUUUAGCUC-GAAGGUAUG---------------------AAGAUUACAGGAAAUCCUUGAGUGUUUCGAUCCCAGGAACUCCCAGAC
.(((((((((((((((.((.((......(((......))).....((((((((((((...(-....)..))---------------------))))...)))))).)))).))))))))))))))).((.....)).... ( -40.50, z-score =  -3.14, R)
>consensus
CGGGAUUGGGACACUCUAGAGAAAACUUUCGUUCUUUCGAAUCAAUUUCUGUCUUUAACUC_GAAGGUAUGCA___UACUUUAAACAUUUUGAAGAUUACAGGAAAUCCUUGAGUGUUCCGAUCCCAGGAACUCCCAGA_
.(((((((((((((((..((((.(((....))).))))......((((((((((((((...............................))))))))....))))))....))))))))))))))).((.....)).... (-30.88 = -31.20 +   0.32)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,446,551 – 17,446,689
Length 138
Sequences 5
Columns 140
Reading direction reverse
Mean pairwise identity 76.53
Shannon entropy 0.41669
G+C content 0.39794
Mean single sequence MFE -34.96
Consensus MFE -21.10
Energy contribution -22.50
Covariance contribution 1.40
Combinations/Pair 1.11
Mean z-score -1.74
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.91
SVM RNA-class probability 0.849302
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17446551 138 - 24543557
-UUUGGGAGUCCCUGGGAUCGGAACACUCAAGGAUUUCCUGUAUUCUUCAAAAUGUUUAAAGUAUUAUGCAUACCUAC-GAGUUAAAGACAGAAAUUGAUUCGAAAGAAGAAAAGUUUUCUCUAGAGUAUCCCAAUCCCG
-...(((...))).(((((.((...((((.(((....)))...((((((...((((.(((....))).)))).....(-(((((((.........))))))))...))))))............))))...)).))))). ( -33.30, z-score =  -1.25, R)
>droEre2.scaffold_4784 9361095 124 + 25762168
-UCUGGUAGUUCCUGGGAUCGGAACACUCAAGAAUUUGCGUUAAUCCUAAAAACGUUUAAGGUA------------UG-GAAUUUAAGACAGAAAUGGAUUGAAAAGAACGCACGUUU--UUUAGAGUGCUCCAAUCCCG
-...((.....)).(((((.(((.(((((((((((.((((((..(((......(......)...------------.)-)).(((((..((....))..)))))...)))))).))))--))..))))).))).))))). ( -38.40, z-score =  -3.55, R)
>droYak2.chr3L 7578039 137 + 24197627
-UGUGGGAGUACCUGGGAUCGGAACACUCAUGGAUUUGCUUUCAUCUUAAAAACGCUGAAAGUACAUUGCAUAUCUUG-GAGUUUAAGACAGAAAUUGAUUUAAAAGAGCAAAAGUUU-CUUUAGAGUGUCCCAAUCCCG
-...((.....)).(((((.((.((((((..(((..((((((((.(........).))))))))..((((...((((.-.((.((((........)))).))..)))))))).....)-))...)))))).)).))))). ( -35.50, z-score =  -1.59, R)
>droSec1.super_0 9499237 140 - 21120651
GUCUGGGAGUUCCUGGGAUCGAAACACUCAAGGAUUUCCUGUAAUCUUCAAAGUAUUUAAAGUAUUAUGCAUACCUUCGGAGCUAAAGACAGAAAUGGAUUCGAAAGAACGAAAGUUUUCUCUAGAGUGUCCCAAUCCCG
....(((....)))(((((.(..((((((..((((((.((((...((((((.((((.((........)).)))).)).))))......))))....))))))((.(((((....))))).))..))))))..).))))). ( -34.80, z-score =  -0.81, R)
>droSim1.chr3L 16786903 118 - 22553184
GUCUGGGAGUUCCUGGGAUCGAAACACUCAAGGAUUUCCUGUAAUCUU---------------------CAUACCUUC-GAGCUAAAGACAGAAAUUGAAUCGAAAGAACGAAAGUUUUCUCUAGAGUGUUCCAAUCCCG
....(((....)))(((((.(.(((((((...((((((.(((....((---------------------(........-)))......))))))))).....((.(((((....))))).))..))))))).).))))). ( -32.80, z-score =  -1.50, R)
>consensus
_UCUGGGAGUUCCUGGGAUCGGAACACUCAAGGAUUUCCUGUAAUCUUAAAAACGUUUAAAGUA___UGCAUACCUUC_GAGUUAAAGACAGAAAUUGAUUCGAAAGAACGAAAGUUUUCUCUAGAGUGUCCCAAUCCCG
....((.....)).(((((.((.((((((.((((((......))))))......................................................((.(((((....))))).))..)))))).)).))))). (-21.10 = -22.50 +   1.40)

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 23:33:44 2011