Locus 6046

Sequence ID 3R_DroMel_CAF1
Location 15,915,254 – 15,915,433
Length 179
Max. P 0.812964
window9862 window9863

overview

Window 2

Location 15,915,254 – 15,915,353
Length 99
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.79
Mean single sequence MFE -32.27
Consensus MFE -16.44
Energy contribution -17.33
Covariance contribution 0.89
Combinations/Pair 1.09
Mean z-score -2.69
Structure conservation index 0.51
SVM decision value 0.65
SVM RNA-class probability 0.812964
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15915254 99 + 27905053
UUUGAAAUUGGAAGCGCAAAUGAAAAUGUGCAAAAAGGCUUU-GCCAGCAGGUGGAAGUGUAGGACUAGGACAUGUCCUCAGCC--------------------UAGCCAAAGCCGAAAA
.......((((..(((((........))))).....(((((.-.((....))..))....((((.((((((....)))).))))--------------------)))))....))))... ( -29.60)
>DroSec_CAF1 32896 99 + 1
UUUGAAAUUGGAAGCGCAAAUGAAAAUGUGCAAAAAGGCUUU-GCCAGCAGGUGGAAGUGUAGGACUAGUACAUGUCCUCAGCC--------------------UGGCCAGAGCCGAAAA
.............(((((........))))).....((((((-(((((...(.(((.(((((.......))))).))).)...)--------------------))).)))))))..... ( -32.50)
>DroSim_CAF1 22685 99 + 1
UUUGAAAUUGGAAGCGCAAAUGAAAAUGUGCAAAAAGGCUUU-GCCAGCAGGUGGAAGUGUAGGACUAGGACAUGUCCUCAGCC--------------------UGGCCAGAGCCGAAAA
.............(((((........))))).....((((((-(((((...(.(((.((((.........)))).))).)...)--------------------))).)))))))..... ( -31.10)
>DroEre_CAF1 22216 119 + 1
UUUGAAAUUGGAAGCGCAAAUGAAAAUGUGCAAAAAGGCUUU-GCCAGCAGGUGGAAGUGUAGCACCAGGACAUGUCCUCAGCCAGAGCCAGGACCCCCAAGCAUGGGCAAAGCCGAAAA
.............(((((........))))).....((((((-(((.((.((((.........)))).((....(((((..((....)).)))))..))..))...)))))))))..... ( -38.90)
>DroYak_CAF1 23646 117 + 1
UGUGAAAUUGGAAGCGUAAAUGAAAAUGUGCAAAAA-GCUUU-GCCAGCAGGUGGAAGUGUAGGACCAGGACAUGUCCUCAGCCAGAGCCUGGGCC-CAAAGCAUGGGCAAAGCCGAAAA
.......(((.....(((.((....)).))).....-(((((-(((..(((((....((..(((((........)))))..))....))))).((.-....))...)))))))))))... ( -32.10)
>DroAna_CAF1 16006 94 + 1
UUUGAAAUUAGAAGCCCGAAUGAAAAUGUGCGAAAAGGCUGUGGCCAGCAGGUGGAAGUGUAGG------GAAUGUCCUGACGC--------------------UGAGCCUGGGCGAAAA
.............((((............((.....(((....))).))((((...(((((.((------(.....))).))))--------------------)..))))))))..... ( -29.40)
>consensus
UUUGAAAUUGGAAGCGCAAAUGAAAAUGUGCAAAAAGGCUUU_GCCAGCAGGUGGAAGUGUAGGACUAGGACAUGUCCUCAGCC____________________UGGCCAAAGCCGAAAA
.......((((..(((((........)))))....(.(((((.(((....))).))))).)(((((........)))))..................................))))... (-16.44 = -17.33 +   0.89)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,915,333 – 15,915,433
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.18
Mean single sequence MFE -35.75
Consensus MFE -21.83
Energy contribution -22.33
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.86
Structure conservation index 0.61
SVM decision value -0.01
SVM RNA-class probability 0.530267
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15915333 100 + 27905053
AGCC--------------------UAGCCAAAGCCGAAAAUUCUCGUUACAUGCAAACUGGCUCAGCCUCGGGGCUUGUCACUUGAGCUGAGCUGAGGCUGACACAAACAUGUCUGCAUG
((((--------------------(.((......(((......)))......)).....((((((((.(((((........))))))))))))).)))))((((......))))...... ( -31.70)
>DroSec_CAF1 32975 100 + 1
AGCC--------------------UGGCCAGAGCCGAAAAUUCUCGUUACAUGCAAACUGGCUCAGCCUCGGGGCUUGUCACUUGAGCUGAGCUGAGGCUGACACAAACAUGUCUGCAUG
....--------------------((((....)))).............((((((.((((..((((((((((((((((.....))))))...))))))))))..)).....)).)))))) ( -34.20)
>DroSim_CAF1 22764 100 + 1
AGCC--------------------UGGCCAGAGCCGAAAAUUCUCGUUACAUGCAAACUGGCUCAGCCUCGGGGCUUGUCACUUGAGCUGAGCUGAGGCUGACACAAACAUGUCUGCAUG
....--------------------((((....)))).............((((((.((((..((((((((((((((((.....))))))...))))))))))..)).....)).)))))) ( -34.20)
>DroEre_CAF1 22295 115 + 1
AGCCAGAGCCAGGACCCCCAAGCAUGGGCAAAGCCGAAAAUUCUCGUUACAUGCAAACUGGCUCAGCCUCGGGGCUUGUCACUUGAG-----CUGAGGCUGACACAAACAUGUCUGCAUA
.((..((((((((.....)..((((((((...)))((......))....)))))...)))))))((((((..((((((.....))))-----))))))))((((......)))).))... ( -40.40)
>DroYak_CAF1 23724 114 + 1
AGCCAGAGCCUGGGCC-CAAAGCAUGGGCAAAGCCGAAAAUUCUCGUUACAUGCAAACUGGCUCAGCCUCGGGGCUUGUCACUUGAG-----CUGAGGCUGACACAAACAUGUCUGCAUA
.(((((.((....)).-....((((((((...)))((......))....)))))...)))))((((((((..((((((.....))))-----)))))))))).......(((....))). ( -40.00)
>DroAna_CAF1 16080 95 + 1
ACGC--------------------UGAGCCUGGGCGAAAAUUCUCGUUACAAGCAAACUGGCUCAGCCUCGGGCCUUGUCACUUGAG-----CUGUGGCUGACACAAACAUGUCUGCCCU
..((--------------------((((((..(((((......)))))...........))))))))...((((...(((((.....-----..))))).((((......)))).)))). ( -34.02)
>consensus
AGCC____________________UGGCCAAAGCCGAAAAUUCUCGUUACAUGCAAACUGGCUCAGCCUCGGGGCUUGUCACUUGAG_____CUGAGGCUGACACAAACAUGUCUGCAUG
..................................(((......)))....(((((.((((..((((((((((......((....))......))))))))))..)).....)).))))). (-21.83 = -22.33 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:16 2006