Locus 176

Sequence ID dm3.chr2L
Location 1,262,236 – 1,262,326
Length 90
Max. P 0.770794
window248 window249

overview

Window 8

Location 1,262,236 – 1,262,326
Length 90
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 77.91
Shannon entropy 0.38377
G+C content 0.45061
Mean single sequence MFE -24.30
Consensus MFE -16.70
Energy contribution -18.70
Covariance contribution 2.00
Combinations/Pair 1.20
Mean z-score -1.46
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.64
SVM RNA-class probability 0.770794
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1262236 90 + 23011544
----------------GGCAGAGAGUGCAGCUGACAAA-CUCAAAUUGAAGGGGGCACAAAAGUUUUCCCUUCGGUGCAUUUGGAUUGGCUAAAUAAACGGAGCUGC
----------------..........((((((......-.....(((((((((((.((....)).)))))))))))..((((((.....))))))......)))))) ( -25.50, z-score =  -0.98, R)
>droSim1.chr2L 1234252 90 + 22036055
----------------GGCAGAGACUGCAGCUGACAAA-CUCAAAUUGAAGGGGGCACAAAAGUUUUCCCUUCGUUGCAUUUGGAUUGGCUAAAUAAACGGAGCUGC
----------------..........((((((......-........((((((((.((....)).))))))))(((..((((((.....)))))).)))..)))))) ( -25.90, z-score =  -1.37, R)
>droSec1.super_14 1212827 90 + 2068291
----------------GGCAGAGACUGCAGCUGACAAA-CUCAAAUUGAAGGGGGCACAAAAGUUUUCCCUUCGUUGCAUUUGGAUUGGCUAAAUAAACGGAGCUGC
----------------..........((((((......-........((((((((.((....)).))))))))(((..((((((.....)))))).)))..)))))) ( -25.90, z-score =  -1.37, R)
>droYak2.chr2L 1237346 90 + 22324452
----------------GGCAGACAGUGCAGCUGACAAA-CUCAAAUUGAAGGGGGCACAAAAGUUUUCCCUUCAGUGCAUUUGGAUUGGCUAAAUAAACGGAGCUGC
----------------.((((.(((.....))).....-(((..(((((((((((.((....)).)))))))))))..((((((.....)))))).....))))))) ( -26.40, z-score =  -1.39, R)
>droEre2.scaffold_4929 1302851 90 + 26641161
----------------GGCAGAGAGUACAGCUGACAAA-CUCAAAUUGAAGGGGGCACGAAAGUUUUCCCUUCAGUGCAUUUGGAUUGGCUAAAUAAACGGAGCUGC
----------------.((((...((..(((..(((((-.....(((((((((((.((....)).)))))))))))...))))..)..)))......))....)))) ( -27.80, z-score =  -2.31, R)
>dp4.chr4_group3 9730799 103 + 11692001
AGUAGGGACAAGAAAGGACCACAGCUGCAGCUGACAAAACUGAAAUUAAAGAAGGAGCUAAAGGGGU----UUAAGGAAAUAUUAUAGUAUAAAGAAAAAGAAGGAU
.((.((..(......)..)).((((....))))))...((((.(((........(((((.....)))----))........))).)))).................. ( -14.29, z-score =  -1.36, R)
>consensus
________________GGCAGAGACUGCAGCUGACAAA_CUCAAAUUGAAGGGGGCACAAAAGUUUUCCCUUCAGUGCAUUUGGAUUGGCUAAAUAAACGGAGCUGC
..........................((((((............(((((((((((.((....)).)))))))))))..((((((.....))))))......)))))) (-16.70 = -18.70 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 1,262,236 – 1,262,326
Length 90
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 77.91
Shannon entropy 0.38377
G+C content 0.45061
Mean single sequence MFE -19.93
Consensus MFE -13.32
Energy contribution -13.88
Covariance contribution 0.56
Combinations/Pair 1.29
Mean z-score -1.40
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.39
SVM RNA-class probability 0.676487
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1262236 90 - 23011544
GCAGCUCCGUUUAUUUAGCCAAUCCAAAUGCACCGAAGGGAAAACUUUUGUGCCCCCUUCAAUUUGAG-UUUGUCAGCUGCACUCUCUGCC----------------
((((((..(((.....)))(((.((((((.....((((((...((....))...)))))).))))).)-.)))..))))))..........---------------- ( -22.30, z-score =  -1.77, R)
>droSim1.chr2L 1234252 90 - 22036055
GCAGCUCCGUUUAUUUAGCCAAUCCAAAUGCAACGAAGGGAAAACUUUUGUGCCCCCUUCAAUUUGAG-UUUGUCAGCUGCAGUCUCUGCC----------------
((((((..(((.....))).....(((((.(((.((((((...((....))...))))))...))).)-))))..))))))..........---------------- ( -23.20, z-score =  -1.78, R)
>droSec1.super_14 1212827 90 - 2068291
GCAGCUCCGUUUAUUUAGCCAAUCCAAAUGCAACGAAGGGAAAACUUUUGUGCCCCCUUCAAUUUGAG-UUUGUCAGCUGCAGUCUCUGCC----------------
((((((..(((.....))).....(((((.(((.((((((...((....))...))))))...))).)-))))..))))))..........---------------- ( -23.20, z-score =  -1.78, R)
>droYak2.chr2L 1237346 90 - 22324452
GCAGCUCCGUUUAUUUAGCCAAUCCAAAUGCACUGAAGGGAAAACUUUUGUGCCCCCUUCAAUUUGAG-UUUGUCAGCUGCACUGUCUGCC----------------
((((((..(((.....))).....(((((.((.(((((((...((....))...)))))))...)).)-))))..))))))..........---------------- ( -23.70, z-score =  -1.77, R)
>droEre2.scaffold_4929 1302851 90 - 26641161
GCAGCUCCGUUUAUUUAGCCAAUCCAAAUGCACUGAAGGGAAAACUUUCGUGCCCCCUUCAAUUUGAG-UUUGUCAGCUGUACUCUCUGCC----------------
((((((..(((.....))).....(((((.((.(((((((...((....))...)))))))...)).)-))))..))))))..........---------------- ( -20.70, z-score =  -1.51, R)
>dp4.chr4_group3 9730799 103 - 11692001
AUCCUUCUUUUUCUUUAUACUAUAAUAUUUCCUUAA----ACCCCUUUAGCUCCUUCUUUAAUUUCAGUUUUGUCAGCUGCAGCUGUGGUCCUUUCUUGUCCCUACU
....................................----..................................((((....)))).((..(......)..)).... (  -6.50, z-score =   0.22, R)
>consensus
GCAGCUCCGUUUAUUUAGCCAAUCCAAAUGCACCGAAGGGAAAACUUUUGUGCCCCCUUCAAUUUGAG_UUUGUCAGCUGCACUCUCUGCC________________
((((((..(((.....)))...............((((((...((....))...))))))...............)))))).......................... (-13.32 = -13.88 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:08:06 2011