Locus 3841

Sequence ID 3L_DroMel_CAF1
Location 11,098,238 – 11,098,370
Length 132
Max. P 0.872881
window5981 window5982 window5983

overview

Window 1

Location 11,098,238 – 11,098,330
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 85.36
Mean single sequence MFE -19.98
Consensus MFE -13.44
Energy contribution -13.00
Covariance contribution -0.44
Combinations/Pair 1.27
Mean z-score -2.28
Structure conservation index 0.67
SVM decision value 0.66
SVM RNA-class probability 0.814825
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11098238 92 + 23771897
UCCAGUGACUCACAAGCUGGCUUCAAAUAAUGAAGCCUAACUUAAGGCGUCAGUUGCAUCCUUGCAAAUUUUUGUAAAUUCAUUUAAUAAGC
...(((((...((((((((((((((.....))))((((......))))))))))((((....)))).....))))....)))))........ ( -20.80)
>DroSec_CAF1 9251 87 + 1
UCCAGUGACUCACGAGCUGGCUUCGAAAAAUGAAGCCUAACUUAAGGCGUCACUUGCAUCCUUAAAUUUUGUUGGAAAUUCAUUUAG-----
(((((((((.(..(((..(((((((.....)))))))...)))...).)))))..(((...........)))))))...........----- ( -20.80)
>DroSim_CAF1 11674 87 + 1
UCCAGUGACUCACAAGCUGGCUUCAAAAAAUGAAGCCUAACUUAAGGCGUCAGUUGCAUCCUUGAAUUUUGUUGUAAAUUCAUUUAA-----
....(..(((.((..((((((((((.....)))))))........))))).)))..).....(((((((......))))))).....----- ( -21.00)
>DroEre_CAF1 9454 92 + 1
UCCAGUUACUCACUAGCUGGCUUCAAAAAAUGAAGCCUAACUUAAGGCGUCAUUUGCAUCCUUGAAUAUUUUAGUAAAUACUUUUAGUAAAC
.(((((((.....))))))).(((((.((((((.((((......)))).))))))......)))))...((((.((((....)))).)))). ( -21.00)
>DroYak_CAF1 9416 92 + 1
UCCAGUUAUUCACAAGCUGGCUUUAAAAAAUGAAGCCUAACUUAAGGCGCCAUUUGCAUCCUUGAAUUUUUUACUUAAUACUUUUAAUAACC
....((((((...(((..(((((((.....)))))))....((((((.((.....))..))))))...............)))..)))))). ( -16.30)
>consensus
UCCAGUGACUCACAAGCUGGCUUCAAAAAAUGAAGCCUAACUUAAGGCGUCAGUUGCAUCCUUGAAUUUUUUUGUAAAUUCAUUUAAUAA_C
..................(((((((.....)))))))....((((((.((.....))..))))))........................... (-13.44 = -13.00 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,098,238 – 11,098,330
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 85.36
Mean single sequence MFE -23.00
Consensus MFE -15.68
Energy contribution -16.92
Covariance contribution 1.24
Combinations/Pair 1.04
Mean z-score -2.40
Structure conservation index 0.68
SVM decision value 0.88
SVM RNA-class probability 0.872881
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11098238 92 - 23771897
GCUUAUUAAAUGAAUUUACAAAAAUUUGCAAGGAUGCAACUGACGCCUUAAGUUAGGCUUCAUUAUUUGAAGCCAGCUUGUGAGUCACUGGA
.........................(((((....))))).((((....((((((.(((((((.....)))))))))))))...))))..... ( -23.70)
>DroSec_CAF1 9251 87 - 1
-----CUAAAUGAAUUUCCAACAAAAUUUAAGGAUGCAAGUGACGCCUUAAGUUAGGCUUCAUUUUUCGAAGCCAGCUCGUGAGUCACUGGA
-----.....(((((((......)))))))........((((((..(...((((.((((((.......))))))))))...).))))))... ( -21.60)
>DroSim_CAF1 11674 87 - 1
-----UUAAAUGAAUUUACAACAAAAUUCAAGGAUGCAACUGACGCCUUAAGUUAGGCUUCAUUUUUUGAAGCCAGCUUGUGAGUCACUGGA
-----.....(((((((......)))))))..........((((....((((((.(((((((.....)))))))))))))...))))..... ( -24.30)
>DroEre_CAF1 9454 92 - 1
GUUUACUAAAAGUAUUUACUAAAAUAUUCAAGGAUGCAAAUGACGCCUUAAGUUAGGCUUCAUUUUUUGAAGCCAGCUAGUGAGUAACUGGA
.....(((....(((((((((........((((...(....)...))))..(((.(((((((.....)))))))))))))))))))..))). ( -24.10)
>DroYak_CAF1 9416 92 - 1
GGUUAUUAAAAGUAUUAAGUAAAAAAUUCAAGGAUGCAAAUGGCGCCUUAAGUUAGGCUUCAUUUUUUAAAGCCAGCUUGUGAAUAACUGGA
(((((((..((((...........((((.((((.(((.....))))))).)))).(((((.........))))).))))...)))))))... ( -21.30)
>consensus
G_UUAUUAAAUGAAUUUACAAAAAAAUUCAAGGAUGCAAAUGACGCCUUAAGUUAGGCUUCAUUUUUUGAAGCCAGCUUGUGAGUCACUGGA
.............((((((..........((((...(....)...))))(((((.(((((((.....))))))))))))))))))....... (-15.68 = -16.92 +   1.24)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,098,250 – 11,098,370
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.05
Mean single sequence MFE -22.38
Consensus MFE -14.84
Energy contribution -14.16
Covariance contribution -0.68
Combinations/Pair 1.30
Mean z-score -1.64
Structure conservation index 0.66
SVM decision value 0.35
SVM RNA-class probability 0.702254
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11098250 120 + 23771897
CAAGCUGGCUUCAAAUAAUGAAGCCUAACUUAAGGCGUCAGUUGCAUCCUUGCAAAUUUUUGUAAAUUCAUUUAAUAAGCGCUCUAUGGCCCAACAUAUUCCAGUUUCCAAAAGUUUUUA
.((((((((((.....((((((((((......)))).....(((((....)))))...........))))))....))))....((((......))))...))))))............. ( -25.00)
>DroSec_CAF1 9263 109 + 1
CGAGCUGGCUUCGAAAAAUGAAGCCUAACUUAAGGCGUCACUUGCAUCCUUAAAUUUUGUUGGAAAUUCAUUUAG-----------UGACACAACAUAUUCCAGUUUCCAAAAGUUUUUA
.((((((((((((.....)))))))....((((((.((.....))..))))))......(((((((((....(((-----------(......)).))....))))))))).)))))... ( -22.20)
>DroSim_CAF1 11686 109 + 1
CAAGCUGGCUUCAAAAAAUGAAGCCUAACUUAAGGCGUCAGUUGCAUCCUUGAAUUUUGUUGUAAAUUCAUUUAA-----------UGUCCCAACAUAUUCCAGUUUCCAAAAGUUUUUA
.(((((((..........(((.((((......)))).)))(((((((...(((((((......)))))))....)-----------))...)))).....)))))))............. ( -22.60)
>DroEre_CAF1 9466 108 + 1
CUAGCUGGCUUCAAAAAAUGAAGCCUAACUUAAGGCGUCAUUUGCAUCCUUGAAUAUUUUAGUAAAUACUUUUAGUAAACGCCUCAUGAUUCAACAUAUUCUAAUUAC------------
......(((((((.....))))))).......((((((((..........)))....((((.((((....)))).)))))))))........................------------ ( -19.60)
>DroYak_CAF1 9428 120 + 1
CAAGCUGGCUUUAAAAAAUGAAGCCUAACUUAAGGCGCCAUUUGCAUCCUUGAAUUUUUUACUUAAUACUUUUAAUAACCGCUUUAUGGUCCAAUAUAUGCCAGUUUCUAAAAGUUUGUA
.((((((((.............((((......))))(((((..((....(((((................))))).....))...))))).........))))))))............. ( -22.49)
>consensus
CAAGCUGGCUUCAAAAAAUGAAGCCUAACUUAAGGCGUCAGUUGCAUCCUUGAAUUUUUUUGUAAAUUCAUUUAAUAA_CGC___AUGACCCAACAUAUUCCAGUUUCCAAAAGUUUUUA
.((((((((((((.....)))))))....((((((.((.....))..)))))).................................................)))))............. (-14.84 = -14.16 +  -0.68)

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 11:08:07 2006