Locus 4288

Sequence ID dm3.chr2R
Location 11,962,572 – 11,962,666
Length 94
Max. P 0.859792
window5875 window5876

overview

Window 5

Location 11,962,572 – 11,962,666
Length 94
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 68.74
Shannon entropy 0.54966
G+C content 0.50391
Mean single sequence MFE -28.42
Consensus MFE -15.22
Energy contribution -16.70
Covariance contribution 1.48
Combinations/Pair 1.59
Mean z-score -1.31
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.95
SVM RNA-class probability 0.859792
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11962572 94 + 21146708
--------CUAGAUGAACUGGAGAAGUUGGUCGGU-----UGGCUUGGCCGGCGUGUCCAGAAAUGGACACUGCGACAAUUUGUGGCAAUUACAU--GUGUUAUCCCGC
--------...(((.((((.....)))).))).((-----((((...))))))(((((((....)))))))(((.((.....)).))).......--............ ( -32.80, z-score =  -2.12, R)
>droSim1.chr2R 10700440 82 + 19596830
--------CUAGAUGAACUGGAGAAG-----------------CUUAGCCGGCGUGUCCAGAAAUGGACACUGCGACAAUUUGUGGCAAUUACAU--GUGUUAUCCCGC
--------...(((((((((.....(-----------------((.....)))(((((((....)))))))(((.((.....)).)))....)).--)).))))).... ( -23.80, z-score =  -1.61, R)
>droSec1.super_1 9458495 82 + 14215200
--------CUAGAUGAACUGGAGAAG-----------------CUUAGCCGGCGUGUCCAGAAAUGGACACUGCGACAAUUUGUGGCAAUUACAU--GUGUUAUCCCGC
--------...(((((((((.....(-----------------((.....)))(((((((....)))))))(((.((.....)).)))....)).--)).))))).... ( -23.80, z-score =  -1.61, R)
>droYak2.chr2R 4116788 107 - 21139217
CUACAUACAUAGAUGUACUGGAGCAGCUGGCUAGCUUGACUGGCUUAGCUGGCGUGUCCAGAAAUGGACACUGCGACAAUUUGAGGCAAUUACAU--GUGUUAUCCCGC
.(((((......)))))..((((((((..(((((((.....))).))))..))(((((((....)))))))))).......(((.(((......)--)).))))))... ( -38.80, z-score =  -2.95, R)
>droEre2.scaffold_4845 8694039 97 - 22589142
-CCGGCACACAGACGAACUGGAGAAGCUGGC---------UGGCUUGGUCGGCGUGUCCAGAAGUGGACACUGCGACAAUUUGAGGCAAUUACAU--GUGUUAUCCCGC
-.(((.(((((..((((.((..(..((((((---------(.....)))))))(((((((....)))))))..)..)).)))).(.......).)--))))....))). ( -29.80, z-score =  -0.09, R)
>droVir3.scaffold_12875 17418683 91 + 20611582
--------CAGGAUGUGGCUCGAUGAUUGGC---------CAACGUU-UCGUUUCGGCUCUUAAUGGCCGUUUGGACAGUUUAAAGCAAUUACACCCAUGUCGUCCAGC
--------(..(((((((((........)))---------).)))))-..)...(((((......))))).((((((.((.....))....(((....))).)))))). ( -21.50, z-score =   0.53, R)
>consensus
________CUAGAUGAACUGGAGAAG_UGGC_________UGGCUUAGCCGGCGUGUCCAGAAAUGGACACUGCGACAAUUUGAGGCAAUUACAU__GUGUUAUCCCGC
...........(((((.((((..((((((...........))))))..)))).(((((((....))))))).............................))))).... (-15.22 = -16.70 +   1.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 11,962,572 – 11,962,666
Length 94
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 68.74
Shannon entropy 0.54966
G+C content 0.50391
Mean single sequence MFE -22.80
Consensus MFE -13.91
Energy contribution -14.05
Covariance contribution 0.14
Combinations/Pair 1.28
Mean z-score -0.67
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.586105
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11962572 94 - 21146708
GCGGGAUAACAC--AUGUAAUUGCCACAAAUUGUCGCAGUGUCCAUUUCUGGACACGCCGGCCAAGCCA-----ACCGACCAACUUCUCCAGUUCAUCUAG--------
...(((((((..--.(((.......)))....(((((.(((((((....))))))))).(((...))).-----...)))...........))).))))..-------- ( -21.30, z-score =  -0.83, R)
>droSim1.chr2R 10700440 82 - 19596830
GCGGGAUAACAC--AUGUAAUUGCCACAAAUUGUCGCAGUGUCCAUUUCUGGACACGCCGGCUAAG-----------------CUUCUCCAGUUCAUCUAG--------
((.((.......--.......(((.((.....)).)))(((((((....))))))).)).))....-----------------..................-------- ( -20.20, z-score =  -1.20, R)
>droSec1.super_1 9458495 82 - 14215200
GCGGGAUAACAC--AUGUAAUUGCCACAAAUUGUCGCAGUGUCCAUUUCUGGACACGCCGGCUAAG-----------------CUUCUCCAGUUCAUCUAG--------
((.((.......--.......(((.((.....)).)))(((((((....))))))).)).))....-----------------..................-------- ( -20.20, z-score =  -1.20, R)
>droYak2.chr2R 4116788 107 + 21139217
GCGGGAUAACAC--AUGUAAUUGCCUCAAAUUGUCGCAGUGUCCAUUUCUGGACACGCCAGCUAAGCCAGUCAAGCUAGCCAGCUGCUCCAGUACAUCUAUGUAUGUAG
...(((......--.......(((..(.....)..)))(((((((....)))))))((.((((..((.((.....)).)).))))))))).(((((....))))).... ( -26.70, z-score =  -0.14, R)
>droEre2.scaffold_4845 8694039 97 + 22589142
GCGGGAUAACAC--AUGUAAUUGCCUCAAAUUGUCGCAGUGUCCACUUCUGGACACGCCGACCAAGCCA---------GCCAGCUUCUCCAGUUCGUCUGUGUGCCGG-
.(((.(((.((.--(((.(((((.........((((..(((((((....)))))))..)))).((((..---------....))))...)))))))).))))).))).- ( -29.40, z-score =  -1.20, R)
>droVir3.scaffold_12875 17418683 91 - 20611582
GCUGGACGACAUGGGUGUAAUUGCUUUAAACUGUCCAAACGGCCAUUAAGAGCCGAAACGA-AACGUUG---------GCCAAUCAUCGAGCCACAUCCUG--------
..((((((....((((......)))).....))))))..((((........))))......-...((.(---------(((.......).)))))......-------- ( -19.00, z-score =   0.52, R)
>consensus
GCGGGAUAACAC__AUGUAAUUGCCACAAAUUGUCGCAGUGUCCAUUUCUGGACACGCCGGCUAAGCCA_________GCCA_CUUCUCCAGUUCAUCUAG________
...((((.(((....)))..............((((..(((((((....)))))))..)))).................................)))).......... (-13.91 = -14.05 +   0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:26:17 2011