Locus 574

Sequence ID X_DroMel_CAF1
Location 1,633,155 – 1,633,395
Length 240
Max. P 0.838637
window908 window909 window910 window911

overview

Window 8

Location 1,633,155 – 1,633,275
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.64
Mean single sequence MFE -36.85
Consensus MFE -34.21
Energy contribution -34.02
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -2.07
Structure conservation index 0.93
SVM decision value 0.74
SVM RNA-class probability 0.838637
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1633155 120 - 22224390
CCUACAGCAUGAACGAAUUUACAUUAAAAUUUGGAUGUCGGUGGAGCGGUUAUUGCUGCAGCAGCUGCAGCACAAACUCAGAGAUGCAUGAGUUGCAUUGGCGUAUCAAAAUCUGCAGUA
..(((.(((.((.(((((((......))))))).(((((((((.(((.(((..((((((((...))))))))..)))(((........)))))).))))))))).......))))).))) ( -35.00)
>DroSim_CAF1 44852 120 - 1
CCCACAGCAUGAACGAAAUUACAUUAAAAUUUGGAUGCCGGUGGAGCGGUUAUUGCUGCAGCAGCUGCAGCACAAACUCAGAGAUGCAUGAGUUGCAUUGGCGUAUCAAAAUCUGCACUA
......(((.((.(.(((((.......))))).)(((((((((.(((.(((..((((((((...))))))))..)))(((........)))))).))))))))).......))))).... ( -35.20)
>DroEre_CAF1 29442 120 - 1
CCCACUGCAUGAACGAAAUUACAUUAAAAUUUGGAUGCCGGUGGAGCGGUUAUUGCUGCAGCAGCUGCAGCACAAACUCAGAGAUGCAUGAGUUGCAUUGGCGUAUCAAAAUCUGCAGUA
...((((((.((.(.(((((.......))))).)(((((((((.(((.(((..((((((((...))))))))..)))(((........)))))).))))))))).......)))))))). ( -40.20)
>DroYak_CAF1 32747 120 - 1
CCCACGGCAUGAACGAAAUUACAUUAAAAUUUGGAUGCCGGUGGAGCGGUUAUUGCUGCAGCAGCUGCAGCACAAACUCAGAGAUGCAUGAGUUGCAUUGGCGUAUCAAAAUCUGCAGUA
.(((((((((...(.(((((.......))))).)))))).)))).(((((....)))))....(((((((....((((((........))))))((....))..........))))))). ( -37.00)
>consensus
CCCACAGCAUGAACGAAAUUACAUUAAAAUUUGGAUGCCGGUGGAGCGGUUAUUGCUGCAGCAGCUGCAGCACAAACUCAGAGAUGCAUGAGUUGCAUUGGCGUAUCAAAAUCUGCAGUA
......(((.((..(......).......((((((((((((((.(((.(((..((((((((...))))))))..)))(((........)))))).))))))))).))))).))))).... (-34.21 = -34.02 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,633,195 – 1,633,315
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 97.08
Mean single sequence MFE -32.27
Consensus MFE -29.08
Energy contribution -30.45
Covariance contribution 1.37
Combinations/Pair 1.02
Mean z-score -1.68
Structure conservation index 0.90
SVM decision value 0.07
SVM RNA-class probability 0.568529
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1633195 120 + 22224390
UGAGUUUGUGCUGCAGCUGCUGCAGCAAUAACCGCUCCACCGACAUCCAAAUUUUAAUGUAAAUUCGUUCAUGCUGUAGGGUUGGUAAUGUCUUUCUGACAUUUUGACUUCAUUAAUUCG
.(((((.((((((((((((.((.(((.......))).)).))((((..........))))............)))))))(((..(.((((((.....)))))))..))).))).))))). ( -28.30)
>DroSim_CAF1 44892 120 + 1
UGAGUUUGUGCUGCAGCUGCUGCAGCAAUAACCGCUCCACCGGCAUCCAAAUUUUAAUGUAAUUUCGUUCAUGCUGUGGGGUUGGUAAUGUCUUUCUGACAUUUUGACUUCAUUAAUUCG
.(((((..((((((((...))))))))...((((((((((.((((((.(((((.......))))).)...))))))))))).))))((((((.....))))))...........))))). ( -36.30)
>DroEre_CAF1 29482 120 + 1
UGAGUUUGUGCUGCAGCUGCUGCAGCAAUAACCGCUCCACCGGCAUCCAAAUUUUAAUGUAAUUUCGUUCAUGCAGUGGGGUUGGUAAUGCCUUUCUGACAUUUUGACUUCAUUAAUUCA
.(((((((((((((((...))))))))......(((.....)))...)))))))(((((.....(((...((((((..((((.......))))..))).)))..)))...)))))..... ( -30.50)
>DroYak_CAF1 32787 120 + 1
UGAGUUUGUGCUGCAGCUGCUGCAGCAAUAACCGCUCCACCGGCAUCCAAAUUUUAAUGUAAUUUCGUUCAUGCCGUGGGGUUGGUAAUGCCUUUCUGACAUUUUGACUUCAUUAAUUCG
.(((((..((((((((...))))))))...((((((((((.((((((.(((((.......))))).)...))))))))))).))))............................))))). ( -34.00)
>consensus
UGAGUUUGUGCUGCAGCUGCUGCAGCAAUAACCGCUCCACCGGCAUCCAAAUUUUAAUGUAAUUUCGUUCAUGCUGUGGGGUUGGUAAUGCCUUUCUGACAUUUUGACUUCAUUAAUUCG
.(((((..((((((((...))))))))...((((((((((.((((((.(((((.......))))).)...))))))))))).))))((((((.....))))))...........))))). (-29.08 = -30.45 +   1.37)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,633,195 – 1,633,315
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.08
Mean single sequence MFE -29.70
Consensus MFE -26.92
Energy contribution -26.30
Covariance contribution -0.62
Combinations/Pair 1.09
Mean z-score -1.62
Structure conservation index 0.91
SVM decision value 0.00
SVM RNA-class probability 0.535731
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1633195 120 - 22224390
CGAAUUAAUGAAGUCAAAAUGUCAGAAAGACAUUACCAACCCUACAGCAUGAACGAAUUUACAUUAAAAUUUGGAUGUCGGUGGAGCGGUUAUUGCUGCAGCAGCUGCAGCACAAACUCA
.................((((((.....))))))...((((((((.((((...(((((((......))))))).))))..))))...))))..((((((((...))))))))........ ( -28.50)
>DroSim_CAF1 44892 120 - 1
CGAAUUAAUGAAGUCAAAAUGUCAGAAAGACAUUACCAACCCCACAGCAUGAACGAAAUUACAUUAAAAUUUGGAUGCCGGUGGAGCGGUUAUUGCUGCAGCAGCUGCAGCACAAACUCA
.................((((((.....))))))...((((((((.((((...(.(((((.......))))).)))))..))))...))))..((((((((...))))))))........ ( -28.90)
>DroEre_CAF1 29482 120 - 1
UGAAUUAAUGAAGUCAAAAUGUCAGAAAGGCAUUACCAACCCCACUGCAUGAACGAAAUUACAUUAAAAUUUGGAUGCCGGUGGAGCGGUUAUUGCUGCAGCAGCUGCAGCACAAACUCA
.................((((((.....))))))...(((((((((((((...(.(((((.......))))).)))).))))))...))))..((((((((...))))))))........ ( -29.60)
>DroYak_CAF1 32787 120 - 1
CGAAUUAAUGAAGUCAAAAUGUCAGAAAGGCAUUACCAACCCCACGGCAUGAACGAAAUUACAUUAAAAUUUGGAUGCCGGUGGAGCGGUUAUUGCUGCAGCAGCUGCAGCACAAACUCA
.................((((((.....))))))...(((((((((((((...(.(((((.......))))).)))))).))))...))))..((((((((...))))))))........ ( -31.80)
>consensus
CGAAUUAAUGAAGUCAAAAUGUCAGAAAGACAUUACCAACCCCACAGCAUGAACGAAAUUACAUUAAAAUUUGGAUGCCGGUGGAGCGGUUAUUGCUGCAGCAGCUGCAGCACAAACUCA
.................((((((.....))))))...((((((((.((((...((((.((......)).)))).))))..))))...))))..((((((((...))))))))........ (-26.92 = -26.30 +  -0.62)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,633,275 – 1,633,395
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.28
Mean single sequence MFE -30.90
Consensus MFE -26.05
Energy contribution -25.93
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -2.03
Structure conservation index 0.84
SVM decision value 0.51
SVM RNA-class probability 0.762730
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1633275 120 - 22224390
AGAAAGCACGGUGCAUGUCGAAAAUUGAGAUGCUUUGGCGCUGAUAAAACUUUCGCAGACGCCCAGAAGGCAGAUUUCGUCGAAUUAAUGAAGUCAAAAUGUCAGAAAGACAUUACCAAC
.........((((.(((((.....((((.((((((((((((((............))).))))...))))).((((((((.......))))))))...)).))))...)))))))))... ( -32.60)
>DroSim_CAF1 44972 120 - 1
AGAAAGCACGGUGCAUGUCGAAAAUUGAGAUGCUUUGGCGCUGAUAAAACUUUCGCAGACGGCCAGAAGGCAGAUUUCGUCGAAUUAAUGAAGUCAAAAUGUCAGAAAGACAUUACCAAC
....(((.(((.((((.((((...)))).)))).)))..))).......(((((...(((((((....))).((((((((.......))))))))....)))).)))))........... ( -31.40)
>DroEre_CAF1 29562 120 - 1
AAAAAGCACGGUGCAUGUCGAAAAUCGAGAUGCUUUGGUGCUGAUAAAACUUUCGCAGACGGCCAGAAAGCAGAUUUCGUUGAAUUAAUGAAGUCAAAAUGUCAGAAAGGCAUUACCAAC
....(((((.(.((((.(((.....))).))))..).))))).......(((((...((((((......)).((((((((((...))))))))))....)))).)))))........... ( -34.90)
>DroYak_CAF1 32867 120 - 1
AAAAAGCACGGUGCAUGACGAAAAUUGAGAUGCUUUGGUGCUGAUAAAACUUUCGCAGACGGACAGAAAGCAGAUUUUGUCGAAUUAAUGAAGUCAAAAUGUCAGAAAGGCAUUACCAAC
....(((((.(.((((..(((...)))..))))..).))))).......(((((...(((((((((((......))))))).......((....))...)))).)))))........... ( -24.70)
>consensus
AAAAAGCACGGUGCAUGUCGAAAAUUGAGAUGCUUUGGCGCUGAUAAAACUUUCGCAGACGGCCAGAAAGCAGAUUUCGUCGAAUUAAUGAAGUCAAAAUGUCAGAAAGACAUUACCAAC
....(((((.(.((((.((((...)))).))))..).))))).......(((((...........)))))..((((((((.......))))))))..((((((.....))))))...... (-26.05 = -25.93 +  -0.12)

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 09:48:13 2006