Locus 1124

Sequence ID 2R_DroMel_CAF1
Location 4,507,195 – 4,507,286
Length 91
Max. P 0.939424
window1982 window1983

overview

Window 2

Location 4,507,195 – 4,507,286
Length 91
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 78.07
Mean single sequence MFE -24.25
Consensus MFE -16.25
Energy contribution -16.62
Covariance contribution 0.36
Combinations/Pair 1.10
Mean z-score -2.02
Structure conservation index 0.67
SVM decision value 1.30
SVM RNA-class probability 0.939424
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4507195 91 + 20766785
----CA--GUCCGA----UGAUGCUGGCUCAAGGCCAGCGUUUAGCCUUCAAAUUGAAUUUAAUGGCCACGCACG-UUGGCUUUGUCUUAUGGCCAAAGUCA
----..--......----((((..(((((((((((((((((...(((.................))).....)))-)))))))))......)))))..)))) ( -29.93)
>DroVir_CAF1 51534 94 + 1
CAGACA--GUCAGACACAAAGUUCUUGCUCAAGGCCAAUGUUCAGCCUUCAAAUUGAAUUUAAUGGCCACGCAU------CUUUGUCUUAUGGCCAAAGUCU
.((((.--((((...((((((....(((....(((((..((((((........))))))....)))))..))).------))))))....))))....)))) ( -24.70)
>DroPse_CAF1 54206 83 + 1
-----A--CUCU------------GGGCUCAAGGCCAACGUUUAGCCUUCAAAUUGAAUUUAAUGGCCACGCAUGCUUGGCUUUGUCUUAUGACCAAAGUCU
-----.--....------------((((....(((((..((((((........))))))....)))))......))))(((((((((....)).))))))). ( -19.40)
>DroMoj_CAF1 53606 89 + 1
-----A--GUCAGACAUAAAGUUCUUACUCAAGGCCAAUGUUCAGCCUUCAAAUUGAAUUUAAUGGCCACGCAU------CUUUGUCUUAUGGCCAAAGUCU
-----.--...((((...((((((......(((((.........)))))......))))))..((((((.(((.------...)))....))))))..)))) ( -22.30)
>DroAna_CAF1 40428 90 + 1
----CUUGGCUC-------GAUGCUGGCUCAAGGCCAGCGGUUAGCCUUCAAAUUGAAUUUAAUGGCCACGCACG-UUGGCUUUGUCUUAUGACCAAAGUCA
----...((((.-------..(((((((.....)))))))...))))..............((((((...)).))-))(((((((((....)).))))))). ( -29.80)
>DroPer_CAF1 57317 83 + 1
-----A--CUCU------------GGGCUCAAGGCCAACGUUUAGCCUUCAAAUUGAAUUUAAUGGCCACGCAUGCUUGGCUUUGUCUUAUGACCAAAGUCU
-----.--....------------((((....(((((..((((((........))))))....)))))......))))(((((((((....)).))))))). ( -19.40)
>consensus
_____A__GUCA_________U_CUGGCUCAAGGCCAACGUUUAGCCUUCAAAUUGAAUUUAAUGGCCACGCAUG_UUGGCUUUGUCUUAUGACCAAAGUCU
................................(((((..((((((........))))))....)))))..........(((((((((....)).))))))). (-16.25 = -16.62 +   0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,507,195 – 4,507,286
Length 91
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 78.07
Mean single sequence MFE -24.72
Consensus MFE -17.78
Energy contribution -16.64
Covariance contribution -1.14
Combinations/Pair 1.18
Mean z-score -1.72
Structure conservation index 0.72
SVM decision value 1.10
SVM RNA-class probability 0.915657
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4507195 91 - 20766785
UGACUUUGGCCAUAAGACAAAGCCAA-CGUGCGUGGCCAUUAAAUUCAAUUUGAAGGCUAAACGCUGGCCUUGAGCCAGCAUCA----UCGGAC--UG----
.....(((((...........)))))-.((.(((((((.((((((...)))))).)))))...((((((.....))))))....----.)).))--..---- ( -27.40)
>DroVir_CAF1 51534 94 - 1
AGACUUUGGCCAUAAGACAAAG------AUGCGUGGCCAUUAAAUUCAAUUUGAAGGCUGAACAUUGGCCUUGAGCAAGAACUUUGUGUCUGAC--UGUCUG
((((..(((((((.........------....))))))).(((((((...((.(((((..(...)..))))).))...))).)))).))))...--...... ( -21.92)
>DroPse_CAF1 54206 83 - 1
AGACUUUGGUCAUAAGACAAAGCCAAGCAUGCGUGGCCAUUAAAUUCAAUUUGAAGGCUAAACGUUGGCCUUGAGCCC------------AGAG--U-----
..(((((((.(.((((.....((((...(((..(((((.((((((...)))))).)))))..))))))))))).).))------------))))--)----- ( -24.50)
>DroMoj_CAF1 53606 89 - 1
AGACUUUGGCCAUAAGACAAAG------AUGCGUGGCCAUUAAAUUCAAUUUGAAGGCUGAACAUUGGCCUUGAGUAAGAACUUUAUGUCUGAC--U-----
((((..(((((((.........------....))))))).(((((((...((.(((((..(...)..))))).))...))).)))).))))...--.----- ( -22.92)
>DroAna_CAF1 40428 90 - 1
UGACUUUGGUCAUAAGACAAAGCCAA-CGUGCGUGGCCAUUAAAUUCAAUUUGAAGGCUAACCGCUGGCCUUGAGCCAGCAUC-------GAGCCAAG----
(((.(((((((....)))...((((.-(....)))))...)))).))).......((((....((((((.....))))))...-------.))))...---- ( -27.10)
>DroPer_CAF1 57317 83 - 1
AGACUUUGGUCAUAAGACAAAGCCAAGCAUGCGUGGCCAUUAAAUUCAAUUUGAAGGCUAAACGUUGGCCUUGAGCCC------------AGAG--U-----
..(((((((.(.((((.....((((...(((..(((((.((((((...)))))).)))))..))))))))))).).))------------))))--)----- ( -24.50)
>consensus
AGACUUUGGCCAUAAGACAAAGCCAA_CAUGCGUGGCCAUUAAAUUCAAUUUGAAGGCUAAACGUUGGCCUUGAGCCAG_A_________AGAC__U_____
...(((.(((((................(((..(((((.((((((...)))))).)))))..))))))))..)))........................... (-17.78 = -16.64 +  -1.14)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:06 2006