Locus 1741

Sequence ID X_DroMel_CAF1
Location 4,857,729 – 4,857,838
Length 109
Max. P 0.989217
window2851 window2852 window2853 window2854

overview

Window 1

Location 4,857,729 – 4,857,821
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 89.47
Mean single sequence MFE -23.83
Consensus MFE -21.59
Energy contribution -21.78
Covariance contribution 0.20
Combinations/Pair 1.05
Mean z-score -2.30
Structure conservation index 0.91
SVM decision value 2.15
SVM RNA-class probability 0.989217
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4857729 92 + 22224390
----------------------------CAGCUGCUGUUGGCAAUUUAUAAACGAAAUAAAUUCAAUUGACUUGUUUGCCGCAGCAUUUACAGUUGGCAACAAUUGCAGCAAUGCCAUAA
----------------------------..((((((((.(((((.........(((.....)))...........)))))))))).....((((((....)))))).))).......... ( -23.45)
>DroSec_CAF1 9661 92 + 1
----------------------------CAGCUGCUGUUGGCAAUUUAUAAACGAAAUAAAUUCAAUUGACUUGUUUGCCGCAGCAUUUACAGUUGGCAACAAUUGCAGCAAUGCCAUAA
----------------------------..((((((((.(((((.........(((.....)))...........)))))))))).....((((((....)))))).))).......... ( -23.45)
>DroSim_CAF1 9628 92 + 1
----------------------------CAGCUGCUGUUGGCAAUUUAUAAACGAAAUAAAUUCAAUUGACUUGUUUGCCGCAGCAUUUACAGUUGGCAACAAUUGCAGCAAUGCCAUAA
----------------------------..((((((((.(((((.........(((.....)))...........)))))))))).....((((((....)))))).))).......... ( -23.45)
>DroEre_CAF1 11145 92 + 1
----------------------------CAGCUGCUGUUGGCAAUUUAUAAACGAAAUAAAUUCAAUUGACUUGUUUGCCGCAGCAUUUACAGUUGGCAACAAUUGCAGCAAUGCCAUAA
----------------------------..((((((((.(((((.........(((.....)))...........)))))))))).....((((((....)))))).))).......... ( -23.45)
>DroYak_CAF1 9834 92 + 1
----------------------------CAGCUGCUGUUGGCAAUUUAUAAACGAAAUAAAUUCAAUUGACUUGUUUGCCGCAGCAUUUACAGUUGGCAACAAUUGCAGCAAUGCCAUAA
----------------------------..((((((((.(((((.........(((.....)))...........)))))))))).....((((((....)))))).))).......... ( -23.45)
>DroAna_CAF1 61366 120 + 1
CACCGUCGACUCCACACCGUCGAUUCCACUGAUUCUGCUGGCAAUUUAUAAACGAAAUAAAUUCAAUUGACUUGUUUGCCGCAGCAUUUACAGUUGGCAACAAUUGCAGCAAUGCCAUAA
....((((((........))))))....(((...((((.(((((.........(((.....)))...........)))))))))......((((((....)))))))))........... ( -25.75)
>consensus
____________________________CAGCUGCUGUUGGCAAUUUAUAAACGAAAUAAAUUCAAUUGACUUGUUUGCCGCAGCAUUUACAGUUGGCAACAAUUGCAGCAAUGCCAUAA
..............................((((((((.(((((.........(((.....)))...........)))))))))).....((((((....)))))).))).......... (-21.59 = -21.78 +   0.20)

alignment

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secondary structure

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Window 2

Location 4,857,729 – 4,857,821
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 89.47
Mean single sequence MFE -22.53
Consensus MFE -21.20
Energy contribution -21.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.12
Structure conservation index 0.94
SVM decision value 0.22
SVM RNA-class probability 0.639307
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4857729 92 - 22224390
UUAUGGCAUUGCUGCAAUUGUUGCCAACUGUAAAUGCUGCGGCAAACAAGUCAAUUGAAUUUAUUUCGUUUAUAAAUUGCCAACAGCAGCUG----------------------------
...((((.((((((((....((((.....))))....))))))))............(((((((.......)))))))))))..........---------------------------- ( -21.20)
>DroSec_CAF1 9661 92 - 1
UUAUGGCAUUGCUGCAAUUGUUGCCAACUGUAAAUGCUGCGGCAAACAAGUCAAUUGAAUUUAUUUCGUUUAUAAAUUGCCAACAGCAGCUG----------------------------
...((((.((((((((....((((.....))))....))))))))............(((((((.......)))))))))))..........---------------------------- ( -21.20)
>DroSim_CAF1 9628 92 - 1
UUAUGGCAUUGCUGCAAUUGUUGCCAACUGUAAAUGCUGCGGCAAACAAGUCAAUUGAAUUUAUUUCGUUUAUAAAUUGCCAACAGCAGCUG----------------------------
...((((.((((((((....((((.....))))....))))))))............(((((((.......)))))))))))..........---------------------------- ( -21.20)
>DroEre_CAF1 11145 92 - 1
UUAUGGCAUUGCUGCAAUUGUUGCCAACUGUAAAUGCUGCGGCAAACAAGUCAAUUGAAUUUAUUUCGUUUAUAAAUUGCCAACAGCAGCUG----------------------------
...((((.((((((((....((((.....))))....))))))))............(((((((.......)))))))))))..........---------------------------- ( -21.20)
>DroYak_CAF1 9834 92 - 1
UUAUGGCAUUGCUGCAAUUGUUGCCAACUGUAAAUGCUGCGGCAAACAAGUCAAUUGAAUUUAUUUCGUUUAUAAAUUGCCAACAGCAGCUG----------------------------
...((((.((((((((....((((.....))))....))))))))............(((((((.......)))))))))))..........---------------------------- ( -21.20)
>DroAna_CAF1 61366 120 - 1
UUAUGGCAUUGCUGCAAUUGUUGCCAACUGUAAAUGCUGCGGCAAACAAGUCAAUUGAAUUUAUUUCGUUUAUAAAUUGCCAGCAGAAUCAGUGGAAUCGACGGUGUGGAGUCGACGGUG
...((((....(..((.(((((((((.(((......(((((((...(((.....)))(((((((.......)))))))))).))))...))))))...))))))))..).))))...... ( -29.20)
>consensus
UUAUGGCAUUGCUGCAAUUGUUGCCAACUGUAAAUGCUGCGGCAAACAAGUCAAUUGAAUUUAUUUCGUUUAUAAAUUGCCAACAGCAGCUG____________________________
...((((.((((((((....((((.....))))....))))))))............(((((((.......)))))))))))...................................... (-21.20 = -21.20 +  -0.00)

alignment

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secondary structure

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Window 3

Location 4,857,741 – 4,857,838
Length 97
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.04
Mean single sequence MFE -20.03
Consensus MFE -18.52
Energy contribution -18.52
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.27
Structure conservation index 0.92
SVM decision value 0.68
SVM RNA-class probability 0.819954
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4857741 97 + 22224390
GCAAUUUAUAAACGAAAUAAAUUCAAUUGACUUGUUUGCCGCAGCAUUUACAGUUGGCAACAAUUGCAGCAAUGCCAUAAAUCGUUGGACAAGCAUU-----------------------
(.(((((((.......))))))))........((((((.(.(((((((((.(((((....)))))(((....)))..))))).))))).))))))..----------------------- ( -20.20)
>DroSec_CAF1 9673 97 + 1
GCAAUUUAUAAACGAAAUAAAUUCAAUUGACUUGUUUGCCGCAGCAUUUACAGUUGGCAACAAUUGCAGCAAUGCCAUAAAUCGUUGGACAAGCAUU-----------------------
(.(((((((.......))))))))........((((((.(.(((((((((.(((((....)))))(((....)))..))))).))))).))))))..----------------------- ( -20.20)
>DroSim_CAF1 9640 97 + 1
GCAAUUUAUAAACGAAAUAAAUUCAAUUGACUUGUUUGCCGCAGCAUUUACAGUUGGCAACAAUUGCAGCAAUGCCAUAAAUCGUUGGACAAGCAUU-----------------------
(.(((((((.......))))))))........((((((.(.(((((((((.(((((....)))))(((....)))..))))).))))).))))))..----------------------- ( -20.20)
>DroEre_CAF1 11157 97 + 1
GCAAUUUAUAAACGAAAUAAAUUCAAUUGACUUGUUUGCCGCAGCAUUUACAGUUGGCAACAAUUGCAGCAAUGCCAUAAAUCGUUGGACAAGCAUU-----------------------
(.(((((((.......))))))))........((((((.(.(((((((((.(((((....)))))(((....)))..))))).))))).))))))..----------------------- ( -20.20)
>DroYak_CAF1 9846 97 + 1
GCAAUUUAUAAACGAAAUAAAUUCAAUUGACUUGUUUGCCGCAGCAUUUACAGUUGGCAACAAUUGCAGCAAUGCCAUAAAUCGUUGGACAAGCAUU-----------------------
(.(((((((.......))))))))........((((((.(.(((((((((.(((((....)))))(((....)))..))))).))))).))))))..----------------------- ( -20.20)
>DroAna_CAF1 61406 120 + 1
GCAAUUUAUAAACGAAAUAAAUUCAAUUGACUUGUUUGCCGCAGCAUUUACAGUUGGCAACAAUUGCAGCAAUGCCAUAAAUCGUUGGACAAGAAAUAUAUACAUACAUACAUGUCCCCU
(.(((((((.......))))))))......(((((((..((..(((((..((((((....))))))....))))).......))..)))))))........((((......))))..... ( -19.20)
>consensus
GCAAUUUAUAAACGAAAUAAAUUCAAUUGACUUGUUUGCCGCAGCAUUUACAGUUGGCAACAAUUGCAGCAAUGCCAUAAAUCGUUGGACAAGCAUU_______________________
(.(((((((.......))))))))......(((((((..((..(((((..((((((....))))))....))))).......))..)))))))........................... (-18.52 = -18.52 +   0.00)

alignment

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secondary structure

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Window 4

Location 4,857,741 – 4,857,838
Length 97
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 92.04
Mean single sequence MFE -21.75
Consensus MFE -20.00
Energy contribution -20.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.02
Structure conservation index 0.92
SVM decision value -0.04
SVM RNA-class probability 0.513849
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4857741 97 - 22224390
-----------------------AAUGCUUGUCCAACGAUUUAUGGCAUUGCUGCAAUUGUUGCCAACUGUAAAUGCUGCGGCAAACAAGUCAAUUGAAUUUAUUUCGUUUAUAAAUUGC
-----------------------...(((((((((........)))..((((((((....((((.....))))....))))))))))))))......(((((((.......))))))).. ( -20.20)
>DroSec_CAF1 9673 97 - 1
-----------------------AAUGCUUGUCCAACGAUUUAUGGCAUUGCUGCAAUUGUUGCCAACUGUAAAUGCUGCGGCAAACAAGUCAAUUGAAUUUAUUUCGUUUAUAAAUUGC
-----------------------...(((((((((........)))..((((((((....((((.....))))....))))))))))))))......(((((((.......))))))).. ( -20.20)
>DroSim_CAF1 9640 97 - 1
-----------------------AAUGCUUGUCCAACGAUUUAUGGCAUUGCUGCAAUUGUUGCCAACUGUAAAUGCUGCGGCAAACAAGUCAAUUGAAUUUAUUUCGUUUAUAAAUUGC
-----------------------...(((((((((........)))..((((((((....((((.....))))....))))))))))))))......(((((((.......))))))).. ( -20.20)
>DroEre_CAF1 11157 97 - 1
-----------------------AAUGCUUGUCCAACGAUUUAUGGCAUUGCUGCAAUUGUUGCCAACUGUAAAUGCUGCGGCAAACAAGUCAAUUGAAUUUAUUUCGUUUAUAAAUUGC
-----------------------...(((((((((........)))..((((((((....((((.....))))....))))))))))))))......(((((((.......))))))).. ( -20.20)
>DroYak_CAF1 9846 97 - 1
-----------------------AAUGCUUGUCCAACGAUUUAUGGCAUUGCUGCAAUUGUUGCCAACUGUAAAUGCUGCGGCAAACAAGUCAAUUGAAUUUAUUUCGUUUAUAAAUUGC
-----------------------...(((((((((........)))..((((((((....((((.....))))....))))))))))))))......(((((((.......))))))).. ( -20.20)
>DroAna_CAF1 61406 120 - 1
AGGGGACAUGUAUGUAUGUAUAUAUUUCUUGUCCAACGAUUUAUGGCAUUGCUGCAAUUGUUGCCAACUGUAAAUGCUGCGGCAAACAAGUCAAUUGAAUUUAUUUCGUUUAUAAAUUGC
...(((((.((((((....))))))....)))))..(((((((((((.((((((((....((((.....))))....))))))))...........(((.....)))).)))))))))). ( -29.50)
>consensus
_______________________AAUGCUUGUCCAACGAUUUAUGGCAUUGCUGCAAUUGUUGCCAACUGUAAAUGCUGCGGCAAACAAGUCAAUUGAAUUUAUUUCGUUUAUAAAUUGC
....................................(((((((((((.((((((((....((((.....))))....))))))))...........(((.....)))).)))))))))). (-20.00 = -20.00 +   0.00)

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 10:17:54 2006