Locus 4593

Sequence ID dm3.chr2R
Location 14,328,366 – 14,328,441
Length 75
Max. P 0.861627
window6292 window6293

overview

Window 2

Location 14,328,366 – 14,328,441
Length 75
Sequences 4
Columns 86
Reading direction forward
Mean pairwise identity 61.49
Shannon entropy 0.60628
G+C content 0.37417
Mean single sequence MFE -13.85
Consensus MFE -6.15
Energy contribution -5.90
Covariance contribution -0.25
Combinations/Pair 1.45
Mean z-score -1.50
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.96
SVM RNA-class probability 0.861627
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14328366 75 + 21146708
AAAAAAUGAAAUACACUAUCGAUAGCCAAC-------UGUG--CAAUCGAUAGCGUG--UCAUCUCUGACUCAAAUGCACUCGAAU
......(((...((.((((((((.(((...-------.).)--).)))))))).))(--(((....)))))))............. ( -17.30, z-score =  -2.93, R)
>droSim1.chr2R 13034692 75 + 19596830
AAAAACAAAAAUACCCUAUCGAUUGCACAA-------UAUG--AAAUCGAUAGCGUA--UCACCUCUGACUCAAGUGCACUCGAAU
..........((((.(((((((((.((...-------..))--.))))))))).)))--)..........((.((....)).)).. ( -13.30, z-score =  -2.87, R)
>droEre2.scaffold_4845 8535926 82 + 22589142
--CGAUAAAAUUGCACUAUCGAUAGCCAAUCGAAUCGUAUGGUCAAUCGAUAGCGUG--UCACCUCCAGUUCAGAUGCAUUCGAAU
--(((..........((((((((.((((..((...))..))))..)))))))).(((--((............)))))..)))... ( -17.00, z-score =  -0.53, R)
>droAna3.scaffold_13266 15682125 71 - 19884421
AAAAGGGAAAUAACACUAAAUAUGA-------------AUG--CAAAUUGUGACGUUAUUCAACACUGGAUUAUGUGCAAUCGAAU
.........................-------------...--...(((((.((((.(((((....))))).)))))))))..... (  -7.80, z-score =   0.34, R)
>consensus
AAAAAAAAAAAUACACUAUCGAUAGCCAA________UAUG__CAAUCGAUAGCGUG__UCACCUCUGACUCAAAUGCACUCGAAU
...........(((.((((((((......................)))))))).)))............................. ( -6.15 =  -5.90 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 14,328,366 – 14,328,441
Length 75
Sequences 4
Columns 86
Reading direction reverse
Mean pairwise identity 61.49
Shannon entropy 0.60628
G+C content 0.37417
Mean single sequence MFE -18.57
Consensus MFE -6.39
Energy contribution -7.70
Covariance contribution 1.31
Combinations/Pair 1.31
Mean z-score -1.91
Structure conservation index 0.34
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.779869
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14328366 75 - 21146708
AUUCGAGUGCAUUUGAGUCAGAGAUGA--CACGCUAUCGAUUG--CACA-------GUUGGCUAUCGAUAGUGUAUUUCAUUUUUU
(((((((....))))))).((((((((--.(((((((((((.(--(.(.-------...))).)))))))))))...)))))))). ( -24.10, z-score =  -3.29, R)
>droSim1.chr2R 13034692 75 - 19596830
AUUCGAGUGCACUUGAGUCAGAGGUGA--UACGCUAUCGAUUU--CAUA-------UUGUGCAAUCGAUAGGGUAUUUUUGUUUUU
(((((((....)))))))((((...((--(((.(((((((((.--(((.-------..))).))))))))).)))))))))..... ( -23.10, z-score =  -3.44, R)
>droEre2.scaffold_4845 8535926 82 - 22589142
AUUCGAAUGCAUCUGAACUGGAGGUGA--CACGCUAUCGAUUGACCAUACGAUUCGAUUGGCUAUCGAUAGUGCAAUUUUAUCG--
...(((.(((((((.......))))).--))((((((((((.(.(((..((...))..)))).))))))))))........)))-- ( -21.00, z-score =  -1.29, R)
>droAna3.scaffold_13266 15682125 71 + 19884421
AUUCGAUUGCACAUAAUCCAGUGUUGAAUAACGUCACAAUUUG--CAU-------------UCAUAUUUAGUGUUAUUUCCCUUUU
....((.(((((((......))))(((......)))......)--)).-------------))....................... (  -6.10, z-score =   0.39, R)
>consensus
AUUCGAGUGCACUUGAGCCAGAGGUGA__CACGCUAUCGAUUG__CAUA________UUGGCUAUCGAUAGUGUAAUUUUAUUUUU
.........(((((.......)))))....(((((((((((......................)))))))))))............ ( -6.39 =  -7.70 +   1.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:32:07 2011