Locus 14071

Sequence ID dm3.chrX
Location 10,939,737 – 10,939,886
Length 149
Max. P 0.995884
window19351 window19352

overview

Window 1

Location 10,939,737 – 10,939,886
Length 149
Sequences 7
Columns 165
Reading direction forward
Mean pairwise identity 80.92
Shannon entropy 0.36801
G+C content 0.42814
Mean single sequence MFE -49.19
Consensus MFE -28.84
Energy contribution -30.31
Covariance contribution 1.48
Combinations/Pair 1.32
Mean z-score -3.18
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.86
SVM RNA-class probability 0.995884
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10939737 149 + 22422827
GAUUGGGGUGGUG-UGAUGCCACAUUGUUAUGUUUUGUUUUAUUUAUAACGAAACG--------CAAUGUGUGCUCGG--CGAUUUUCAAAAGAGUCGCCGCCUAUAAAUAAGUCGGAUAU----GAAUGAAUCCGAUAUGCA-GCCGUUGAGAGAAGCCAGAAG
..((((((((((.-.((.((((((((((...((((((((........)))))))))--------))))))).))))((--((((((......))))))))))).........(((((((..----......))))))).....-))).((....))..))))... ( -49.30, z-score =  -3.76, R)
>droAna3.scaffold_13417 5984378 153 - 6960332
GGUUGGG-CGGUU-CUCUGCCGCAUUGUUGUGUUUUGUUUUAUUUAUAACGGAGCGGGAC-GCUCGAUGUGUGUGCGGAGCGAUAUUCAAAAGCGUCGCCGCCUAUAAAUAAAUCGGAUAU----GAAUGAAUCCGAUAUGCA-GGCGUCGAAAGACAGCG----
...((((-((((.-(((((((((((((..(((((((((((..(.....)..)))))))))-)).)))))))...)))))).(((..........))))))))))).......(((((((..----......))))))).....-.(((((....))).)).---- ( -55.70, z-score =  -2.49, R)
>droEre2.scaffold_4690 14564586 149 - 18748788
GAUUGGGGUGGUG-CGAUGCCACAUUGUUAUGUUUUGCUUUAUUUAUAACGAAACG--------CAAUGUGUGCUCGG--CGAUUUUCAAAAGAGUCGCCGCCUAUAAAUAAGUCGGAUAU----GAAUGAAUCCGAUAUGCA-GGCGUUGAGAGAAACCAGAAG
..((((.(((((.-....))))).((((((((..(......)..))))))))..(.--------((((((.(((.(((--((((((......)))))))))...........(((((((..----......)))))))..)))-.)))))).).....))))... ( -48.70, z-score =  -3.21, R)
>droYak2.chrX 10592795 149 - 21770863
GAUUGGGGUGGUG-CGAUGCCACAUUGUUAUGUUUUGUUUUAUUUAUAACGAAACG--------CAAUGUGUGCUCGG--CGAUUUUCAAAAGAGUCGCCGCCUAUAAAUAAGUCGGAUAU----GAAUGAAUCCGAUAUGCA-GGCGUUGAGAGAAGCCAGAAG
..(((..((((.(-(((.((((((((((...((((((((........)))))))))--------))))))).))))((--((((((......))))))))))))))...)))(((((((..----......))))))).....-(((.((....)).)))..... ( -52.60, z-score =  -4.29, R)
>droSec1.super_15 1651506 149 + 1954846
GAUUGGGGUGGUG-UGAUGCCACAUUGUUAUGUUUUGUUUUAUUUAUAACGAAACG--------CAAUGUGUGCUCGG--CGAUUUUCAAAAGAGUCGCCGCCUAUAAAUAAGUCGGAUAU----GAAUGAAUCCGAUAUGCA-GGCGUUGAGAGAAGCCAGAAG
.(((.((((....-.((.((((((((((...((((((((........)))))))))--------))))))).))))((--((((((......))))))))))))...)))..(((((((..----......))))))).....-(((.((....)).)))..... ( -51.00, z-score =  -4.14, R)
>droSim1.chrX 8493875 149 + 17042790
GAUUGGGGUGGUG-UGAUGCCACAUUGUUAUGUUUUGUUUUAUUUAUAACGGAACG--------CAAUGUGUGCUCGG--CGAUUUUCAAAAGAGUCGCCGCCUAUAAAUAAGUCGGAUAU----GAAUGAAUCCGAUAUGCA-GGCGUUGAGAGAAGCCAGAAG
.(((.((((....-.((.((((((((((...((((((((........)))))))))--------))))))).))))((--((((((......))))))))))))...)))..(((((((..----......))))))).....-(((.((....)).)))..... ( -50.60, z-score =  -3.79, R)
>droWil1.scaffold_180702 996571 153 + 4511350
GGCUGGGGCGGUGGCCAGGCGGCAU--UUGUUUUGUGUUUUCUAUAUACCUAUUUAUUUUUAACCAAAACGCAAUGGGUGUGAGAU--GAAAUGAAAGCAUCCUAUAAAUAAGUCGGAUAUAUAUGAAUAAAUCUGAUAUGCAAGACGAUGGAAGAA--------
.((((.(((....)))...))))..--(((((((((((((((..((((((((((...((((....))))...))))))))))....--.....)))))).............(((((((.(((....))).)))))))..)))))))))........-------- ( -36.40, z-score =  -0.55, R)
>consensus
GAUUGGGGUGGUG_CGAUGCCACAUUGUUAUGUUUUGUUUUAUUUAUAACGAAACG________CAAUGUGUGCUCGG__CGAUUUUCAAAAGAGUCGCCGCCUAUAAAUAAGUCGGAUAU____GAAUGAAUCCGAUAUGCA_GGCGUUGAGAGAAGCCAGAAG
.....(((((((..(((.(((((((((...(((((((((........)))))))))........))))))).)))))....(((((......))))))))))))........(((((((............)))))))........................... (-28.84 = -30.31 +   1.48)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,939,737 – 10,939,886
Length 149
Sequences 7
Columns 165
Reading direction reverse
Mean pairwise identity 80.92
Shannon entropy 0.36801
G+C content 0.42814
Mean single sequence MFE -34.98
Consensus MFE -15.76
Energy contribution -15.46
Covariance contribution -0.30
Combinations/Pair 1.24
Mean z-score -2.68
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.07
SVM RNA-class probability 0.886417
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10939737 149 - 22422827
CUUCUGGCUUCUCUCAACGGC-UGCAUAUCGGAUUCAUUC----AUAUCCGACUUAUUUAUAGGCGGCGACUCUUUUGAAAAUCG--CCGAGCACACAUUG--------CGUUUCGUUAUAAAUAAAACAAAACAUAACAAUGUGGCAUCA-CACCACCCCAAUC
....(((............((-..(((.((((((......----..)))))).((((((((((.((((((.((....))...)))--))).(((.....))--------)......))))))))))..............)))..))....-.......)))... ( -34.60, z-score =  -2.80, R)
>droAna3.scaffold_13417 5984378 153 + 6960332
----CGCUGUCUUUCGACGCC-UGCAUAUCGGAUUCAUUC----AUAUCCGAUUUAUUUAUAGGCGGCGACGCUUUUGAAUAUCGCUCCGCACACACAUCGAGC-GUCCCGCUCCGUUAUAAAUAAAACAAAACACAACAAUGCGGCAGAG-AACCG-CCCAACC
----.((.((.((((...(((-.((((.((((((......----..))))))(((((((((((((((.(((((((.........((...)).........))))-))))))))....)))))))))).............))))))).)))-))).)-)...... ( -45.17, z-score =  -3.66, R)
>droEre2.scaffold_4690 14564586 149 + 18748788
CUUCUGGUUUCUCUCAACGCC-UGCAUAUCGGAUUCAUUC----AUAUCCGACUUAUUUAUAGGCGGCGACUCUUUUGAAAAUCG--CCGAGCACACAUUG--------CGUUUCGUUAUAAAUAAAGCAAAACAUAACAAUGUGGCAUCG-CACCACCCCAAUC
....((((..........(((-((.(((((((((......----..))))))..)))...)))))(((((.((....))...)))--))((((.(((((((--------.((((.(((........))).))))....))))))))).)).-.))))........ ( -37.60, z-score =  -3.11, R)
>droYak2.chrX 10592795 149 + 21770863
CUUCUGGCUUCUCUCAACGCC-UGCAUAUCGGAUUCAUUC----AUAUCCGACUUAUUUAUAGGCGGCGACUCUUUUGAAAAUCG--CCGAGCACACAUUG--------CGUUUCGUUAUAAAUAAAACAAAACAUAACAAUGUGGCAUCG-CACCACCCCAAUC
......((..........(((-((.(((((((((......----..))))))..)))...)))))(((((.((....))...)))--))((((.(((((((--------.((((.(((........))).))))....))))))))).)))-)............ ( -36.60, z-score =  -3.29, R)
>droSec1.super_15 1651506 149 - 1954846
CUUCUGGCUUCUCUCAACGCC-UGCAUAUCGGAUUCAUUC----AUAUCCGACUUAUUUAUAGGCGGCGACUCUUUUGAAAAUCG--CCGAGCACACAUUG--------CGUUUCGUUAUAAAUAAAACAAAACAUAACAAUGUGGCAUCA-CACCACCCCAAUC
....(((...........(((-((.(((((((((......----..))))))..)))...)))))(((((.((....))...)))--))((((.(((((((--------.((((.(((........))).))))....))))))))).)).-.......)))... ( -36.50, z-score =  -3.79, R)
>droSim1.chrX 8493875 149 - 17042790
CUUCUGGCUUCUCUCAACGCC-UGCAUAUCGGAUUCAUUC----AUAUCCGACUUAUUUAUAGGCGGCGACUCUUUUGAAAAUCG--CCGAGCACACAUUG--------CGUUCCGUUAUAAAUAAAACAAAACAUAACAAUGUGGCAUCA-CACCACCCCAAUC
....(((...........(((-((.(((((((((......----..))))))..)))...)))))(((((.((....))...)))--))((((.(((((((--------.(((..(((........)))..)))....))))))))).)).-.......)))... ( -34.80, z-score =  -3.19, R)
>droWil1.scaffold_180702 996571 153 - 4511350
--------UUCUUCCAUCGUCUUGCAUAUCAGAUUUAUUCAUAUAUAUCCGACUUAUUUAUAGGAUGCUUUCAUUUC--AUCUCACACCCAUUGCGUUUUGGUUAAAAAUAAAUAGGUAUAUAGAAAACACAAAACAA--AUGCCGCCUGGCCACCGCCCCAGCC
--------...............((((....(((.(((....))).)))..((((((((((.(((((.........)--)))).....(((........)))......))))))))))....................--)))).((..(((....)))...)). ( -19.60, z-score =   1.11, R)
>consensus
CUUCUGGCUUCUCUCAACGCC_UGCAUAUCGGAUUCAUUC____AUAUCCGACUUAUUUAUAGGCGGCGACUCUUUUGAAAAUCG__CCGAGCACACAUUG________CGUUUCGUUAUAAAUAAAACAAAACAUAACAAUGUGGCAUCG_CACCACCCCAAUC
..................(((..((((.((((((............)))))).((((((((((.(((.(((.......................................))))))))))))))))..............))))))).................. (-15.76 = -15.46 +  -0.30)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:33:04 2011