Locus 4405

Sequence ID X_DroMel_CAF1
Location 11,625,896 – 11,626,043
Length 147
Max. P 0.809108
window7233 window7234 window7235 window7236

overview

Window 3

Location 11,625,896 – 11,626,004
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 78.86
Mean single sequence MFE -26.20
Consensus MFE -19.52
Energy contribution -21.50
Covariance contribution 1.98
Combinations/Pair 1.07
Mean z-score -1.31
Structure conservation index 0.75
SVM decision value -0.04
SVM RNA-class probability 0.514190
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11625896 108 + 22224390
CAAAAUAACGUGUGUUUUGAAAAUAAACGGUAAU-AUAGCGCAGAAUAUAACAAAACAAUCGUACGCCCUGAGCGAGUUGAAGCGAUAAGGCC--UUG---------CUCUCGCUUUUUC
.......(((..(((((((...(((....((...-.....))....)))..)))))))..))).......(((((((....(((((.......--)))---------))))))))).... ( -19.20)
>DroSec_CAF1 56302 107 + 1
----------UGUGCUUUGAAAAUAAACGGUAAUUAAAGCACAGGAUACAAAAAAACAA---UGCGCUCUGAGCGAGUUGAAGCGAUAAAGCAGGUUGCAAACUGCUCUCUCGCCUUGUC
----------((((((((((..((.....))..))))))))))....((((.....(((---(.(((.....))).))))..((((.(.(((((........))))).).)))).)))). ( -29.80)
>DroSim_CAF1 55873 110 + 1
----------UGUGCUUUGAAAAUAAACGGUAAUUAAAGCACAGGAUACAAAAAAACAAUCGUGCGCUCUGAGCGAGUUGAAGCGAUAAAGCAGGUUGCAAACUGCUCUCUCGCUUUGUC
----------((((((((((..((.....))..)))))))))).((((........((((....(((.....))).))))((((((.(.(((((........))))).).)))))))))) ( -29.60)
>consensus
__________UGUGCUUUGAAAAUAAACGGUAAUUAAAGCACAGGAUACAAAAAAACAAUCGUGCGCUCUGAGCGAGUUGAAGCGAUAAAGCAGGUUGCAAACUGCUCUCUCGCUUUGUC
..........((((((((((..((.....))..)))))))))).....................(((.....)))....(((((((.(.(((((........))))).).)))))))... (-19.52 = -21.50 +   1.98)

alignment

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secondary structure

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Window 4

Location 11,625,896 – 11,626,004
Length 108
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.86
Mean single sequence MFE -25.94
Consensus MFE -19.36
Energy contribution -20.57
Covariance contribution 1.21
Combinations/Pair 1.21
Mean z-score -1.30
Structure conservation index 0.75
SVM decision value -0.05
SVM RNA-class probability 0.507951
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11625896 108 - 22224390
GAAAAAGCGAGAG---------CAA--GGCCUUAUCGCUUCAACUCGCUCAGGGCGUACGAUUGUUUUGUUAUAUUCUGCGCUAU-AUUACCGUUUAUUUUCAAAACACACGUUAUUUUG
(((((((((((..---------..(--(((......))))...))))))...((((((.((.(((......))).))))))))..-...........))))).................. ( -22.60)
>DroSec_CAF1 56302 107 - 1
GACAAGGCGAGAGAGCAGUUUGCAACCUGCUUUAUCGCUUCAACUCGCUCAGAGCGCA---UUGUUUUUUUGUAUCCUGUGCUUUAAUUACCGUUUAUUUUCAAAGCACA----------
.(((((((((.(((((((........))))))).))))).(((..(((.....)))..---))).....)))).....(((((((.................))))))).---------- ( -27.63)
>DroSim_CAF1 55873 110 - 1
GACAAAGCGAGAGAGCAGUUUGCAACCUGCUUUAUCGCUUCAACUCGCUCAGAGCGCACGAUUGUUUUUUUGUAUCCUGUGCUUUAAUUACCGUUUAUUUUCAAAGCACA----------
....((((((.(((((((........))))))).))))))......(((.((((((((.(((...........))).)))))))).......(........)..)))...---------- ( -27.60)
>consensus
GACAAAGCGAGAGAGCAGUUUGCAACCUGCUUUAUCGCUUCAACUCGCUCAGAGCGCACGAUUGUUUUUUUGUAUCCUGUGCUUUAAUUACCGUUUAUUUUCAAAGCACA__________
....((((((.(((((((........))))))).))))))..........((((((((.(((...........))).)))))))).......((((.......))))............. (-19.36 = -20.57 +   1.21)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,625,935 – 11,626,043
Length 108
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 83.75
Mean single sequence MFE -33.20
Consensus MFE -25.45
Energy contribution -27.53
Covariance contribution 2.09
Combinations/Pair 1.06
Mean z-score -2.09
Structure conservation index 0.77
SVM decision value 0.64
SVM RNA-class probability 0.809108
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11625935 108 + 22224390
GCAGAAUAUAACAAAACAAUCGUACGCCCUGAGCGAGUUGAAGCGAUAAGGCC--UUG---------CUCUCGCUUUUUCGCUUAAGCUCGCAACUCGCUUCGCUCUCACUCUGACAUC
.((((..........((....))..((...((((((((((((((((.(((((.--...---------.....))))).)))))).......)))))))))).))......))))..... ( -28.81)
>DroSec_CAF1 56332 116 + 1
ACAGGAUACAAAAAAACAA---UGCGCUCUGAGCGAGUUGAAGCGAUAAAGCAGGUUGCAAACUGCUCUCUCGCCUUGUCACCUGAGCUCGCAACUCGCUUCGCUCUCACUCUGACAAC
...................---.(((....((((((((((.(((.......(((((.((((...((......)).)))).))))).)))..)))))))))))))............... ( -31.30)
>DroSim_CAF1 55903 119 + 1
ACAGGAUACAAAAAAACAAUCGUGCGCUCUGAGCGAGUUGAAGCGAUAAAGCAGGUUGCAAACUGCUCUCUCGCUUUGUCGCCUGAGCUCGCAACUCGCUUUGCUCUCACUCUGACAAC
.((((((...........)))(((.((...((((((((((..(((((((((((((..((.....))..))).))))))))))..(....).)))))))))).))...))).)))..... ( -39.50)
>consensus
ACAGGAUACAAAAAAACAAUCGUGCGCUCUGAGCGAGUUGAAGCGAUAAAGCAGGUUGCAAACUGCUCUCUCGCUUUGUCGCCUGAGCUCGCAACUCGCUUCGCUCUCACUCUGACAAC
.((((..........((....))..((...((((((((((..((((((((((.((..((.....))...)).)))))))))).........)))))))))).))......))))..... (-25.45 = -27.53 +   2.09)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,625,935 – 11,626,043
Length 108
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 83.75
Mean single sequence MFE -38.17
Consensus MFE -33.09
Energy contribution -32.97
Covariance contribution -0.12
Combinations/Pair 1.19
Mean z-score -1.56
Structure conservation index 0.87
SVM decision value 0.46
SVM RNA-class probability 0.746829
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11625935 108 - 22224390
GAUGUCAGAGUGAGAGCGAAGCGAGUUGCGAGCUUAAGCGAAAAAGCGAGAG---------CAA--GGCCUUAUCGCUUCAACUCGCUCAGGGCGUACGAUUGUUUUGUUAUAUUCUGC
.....(((((((..((((((((((..((((..(((.(((((..(((((((((---------...--...))).))))))....))))).))).))))...)))))))))).))))))). ( -35.60)
>DroSec_CAF1 56332 116 - 1
GUUGUCAGAGUGAGAGCGAAGCGAGUUGCGAGCUCAGGUGACAAGGCGAGAGAGCAGUUUGCAACCUGCUUUAUCGCUUCAACUCGCUCAGAGCGCA---UUGUUUUUUUGUAUCCUGU
((..((.((((((((((((((((.((((((((((..(....)...((......)))))))))))).))))...)))))....))))))).))..)).---................... ( -38.90)
>DroSim_CAF1 55903 119 - 1
GUUGUCAGAGUGAGAGCAAAGCGAGUUGCGAGCUCAGGCGACAAAGCGAGAGAGCAGUUUGCAACCUGCUUUAUCGCUUCAACUCGCUCAGAGCGCACGAUUGUUUUUUUGUAUCCUGU
.....(((..((.(((.(((((.(((((.(.((((.(((((..((((((.(((((((........))))))).))))))....)))))..)))).).))))))))))))).))..))). ( -40.00)
>consensus
GUUGUCAGAGUGAGAGCGAAGCGAGUUGCGAGCUCAGGCGACAAAGCGAGAGAGCAGUUUGCAACCUGCUUUAUCGCUUCAACUCGCUCAGAGCGCACGAUUGUUUUUUUGUAUCCUGU
.....(((.((....))(((((((..(((..((((.(((((..((((((.(((((((........))))))).))))))....)))))..)))))))...)))))))........))). (-33.09 = -32.97 +  -0.12)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:12 2006