Locus 12436

Sequence ID dm3.chrXHet
Location 176,208 – 176,361
Length 153
Max. P 0.980405
window17092 window17093

overview

Window 2

Location 176,208 – 176,361
Length 153
Sequences 4
Columns 160
Reading direction forward
Mean pairwise identity 52.87
Shannon entropy 0.78589
G+C content 0.48764
Mean single sequence MFE -51.51
Consensus MFE -18.51
Energy contribution -20.26
Covariance contribution 1.75
Combinations/Pair 1.63
Mean z-score -1.20
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.81
SVM RNA-class probability 0.822631
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrXHet 176208 153 + 204112
UCGAUAAUCACAGAUCUAGUAGUGAUAUCAACGUGACAAUUGUCAAUGAGGCAGCAUCUUUGUGGGCCACAUAUGAGUGGAGAGUG---GACGAUUGGGAAUUGAGUGACCACAAUAUCAUU---ACUGUUGUGGCCGA-ACAACUACCGCGCCCGCAGU
..((((.((((..........))))))))....((((....))))(((.(((.(((....)))..))).)))....((((.(.(((---(.((((.....))))..((.((((((((.....---..)))))))).)).-.......)))).)))))... ( -40.00, z-score =   0.44, R)
>droVir3.scaffold_12401 104 160 + 1125
UUGCGGGUCCGGUGGGUCAGAGUGACAUUGAUGUUACUCUAGUGAAUGCGGUGGCAAUGAGUAUGUAUGCUUUUCAUUGGUGUGUACUAGGUGGGCUUGGUGUGAGUGACCACAAUCCGAUUGAGAUUGUUGUCACACACACUAUUACGAGGAACGAAAG
...((((((((.(.(((((((((((((....))))))))(((((((.(((...(((.......))).)))..)))))))...)).))).).))))))))(((((.(((((.((((((.......)))))).))))).)))))............(....) ( -53.00, z-score =  -1.71, R)
>droGri2.scaffold_15056 31888 160 - 38174
UUGCGGGCCCGAUGGGUCAGAGUGACAUUGAUGUCACUCUUGCGAAUGUGGCAGCAGCGAGUGUGUUUGGUUUCCAAUGGAGUGUGCUGGGUGGACGCGGUGUGAGUGACCACAAUCCGAUUGAGAUUGUCAUCACUCACACUUCCACCACGCGUGAAAG
((((((((((...)))))(((((((((....))))))))))))))(((((....(((((.......((((...)))).......)))))((((((...(((((((((((..((((((.......))))))..))))))))))))))))).)))))..... ( -69.54, z-score =  -3.28, R)
>triCas2.singleUn_263 2728 152 - 6727
ACUCCGGUCCAGGGGGACAGAGUGAUAUUGACGUCACGCU---GUGUACCGAUGGGUUUUUGGGACUGGUACGCAAAUGGUGUGUGAGAGAUGAGGUUAGUUGUAGCGACCAUAACUUAAUCGA----AUUGGAGUUGGGAU-ACCAUAUUGAUCGGGAU
..(((((((..((.(.((((.(((((......))))).))---)).).)).((((..(((..(..(..(((((((.....)))))....(((.((((((((((...))))..)))))).)))..----))..)..)..))).-.))))...))))))).. ( -43.50, z-score =  -0.27, R)
>consensus
UCGCGGGUCCGAGGGGUCAGAGUGACAUUGACGUCACUCUUGUGAAUGCGGCAGCAUCGAGGGGGUUUGCAUUCCAAUGGAGUGUGCUAGAUGAGCGUGGUGUGAGUGACCACAAUCCGAUUGA_AUUGUUGUCACUCACACUACCACCACGAACGAAAG
..((..(((.........((((((((......))))))))...((((((((...............))))))))...............)))..))...(((((((((((.((((((.......)))))).))))))))))).................. (-18.51 = -20.26 +   1.75)

alignment

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secondary structure

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dotplot

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Window 3

Location 176,208 – 176,361
Length 153
Sequences 4
Columns 160
Reading direction reverse
Mean pairwise identity 52.87
Shannon entropy 0.78589
G+C content 0.48764
Mean single sequence MFE -43.96
Consensus MFE -12.90
Energy contribution -17.53
Covariance contribution 4.63
Combinations/Pair 1.45
Mean z-score -2.25
Structure conservation index 0.29
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.05
SVM RNA-class probability 0.980405
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrXHet 176208 153 - 204112
ACUGCGGGCGCGGUAGUUGU-UCGGCCACAACAGU---AAUGAUAUUGUGGUCACUCAAUUCCCAAUCGUC---CACUCUCCACUCAUAUGUGGCCCACAAAGAUGCUGCCUCAUUGACAAUUGUCACGUUGAUAUCACUACUAGAUCUGUGAUUAUCGA
.....(((.((((((.((((-..(((((((.((..---..)).....((((.(...............).)---)))............))))))).))))...)))))))))..((((....))))..((((((((((..........)))).)))))) ( -43.06, z-score =  -1.34, R)
>droVir3.scaffold_12401 104 160 - 1125
CUUUCGUUCCUCGUAAUAGUGUGUGUGACAACAAUCUCAAUCGGAUUGUGGUCACUCACACCAAGCCCACCUAGUACACACCAAUGAAAAGCAUACAUACUCAUUGCCACCGCAUUCACUAGAGUAACAUCAAUGUCACUCUGACCCACCGGACCCGCAA
..................(((((.(((((.(((((((.....))))))).))))).)))))...((...............((((((.............))))))...(((.......((((((.(((....))).))))))......)))....)).. ( -38.24, z-score =  -2.17, R)
>droGri2.scaffold_15056 31888 160 + 38174
CUUUCACGCGUGGUGGAAGUGUGAGUGAUGACAAUCUCAAUCGGAUUGUGGUCACUCACACCGCGUCCACCCAGCACACUCCAUUGGAAACCAAACACACUCGCUGCUGCCACAUUCGCAAGAGUGACAUCAAUGUCACUCUGACCCAUCGGGCCCGCAA
.......(((.((((((.(((((((((((.(((((((.....))))))).)))))))))))....))))))((((........((((...))))........))))..(((.........(((((((((....))))))))).........))).))).. ( -65.16, z-score =  -4.82, R)
>triCas2.singleUn_263 2728 152 + 6727
AUCCCGAUCAAUAUGGU-AUCCCAACUCCAAU----UCGAUUAAGUUAUGGUCGCUACAACUAACCUCAUCUCUCACACACCAUUUGCGUACCAGUCCCAAAAACCCAUCGGUACAC---AGCGUGACGUCAAUAUCACUCUGUCCCCCUGGACCGGAGU
.............(((.-...)))(((((...----............(((((((...............................))).))))((((.....(((....)))..((---((.((((........)))).))))......)))).))))) ( -29.38, z-score =  -0.66, R)
>consensus
AUUUCGAGCGUGGUAGUAGUGUCAGCGACAACAAU_UCAAUCAGAUUGUGGUCACUCAAACCAAGCCCACCUAGCACACACCAUUGAAAAGCAAACACAAAAAAUGCUGCCGCAUUCACAAGAGUGACAUCAAUAUCACUCUGACCCACCGGACCCGCAA
.........((((.....(((((((((((.(((((((.....))))))).))))))))))).....))))..................................................(((((((((....))))))))).................. (-12.90 = -17.53 +   4.63)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:02:10 2011