Locus 2339

Sequence ID 2R_DroMel_CAF1
Location 8,548,955 – 8,549,108
Length 153
Max. P 0.996023
window3856 window3857 window3858

overview

Window 6

Location 8,548,955 – 8,549,071
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.04
Mean single sequence MFE -22.58
Consensus MFE -19.28
Energy contribution -19.92
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -1.31
Structure conservation index 0.85
SVM decision value 0.22
SVM RNA-class probability 0.639014
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8548955 116 - 20766785
ACAAACAAAUACGACGCACACACACUUUUGUGCAUUUAUAUUUGUUCAUAA----UCGUAAUUAUUUCAGGCCAAGCAGUUGGACGCAUUGAUGUAAUGAUAAACAAAGGAAUCAUUUCA
...((((((((..(.(((((........)))))..)..))))))))....(----((((...(((.((((.((((....)))).....)))).))))))))........(((....))). ( -18.60)
>DroSec_CAF1 24480 120 - 1
ACAAACAAAUACGACGCACACACACGUUAGUGCAUUUAUAUUUGUUCAUAUUUGUUCGUAAUUAUUUCAGGCCAAGCAGUUGGACGCAUUGAAGUAAUGAUAAACAAAGGAAUCAUUUCA
...((((((((..(.((((..........))))..)..))))))))....((((((..(.((((((((((.((((....)))).....)))))))))).)..)))))).(((....))). ( -25.50)
>DroSim_CAF1 28119 116 - 1
ACAAACAAAUACGACGCACACACACGUUAGUGCAUUUAUAUUUGUUCAUAA----UCGUAAUUAUUUCAGGCCAAGCAGUUGGACGCAUUGAAGUAAUGAUAAACAAAGGAAUCAUUUCA
...((((((((..(.((((..........))))..)..))))))))....(----((((...((((((((.((((....)))).....)))))))))))))........(((....))). ( -20.10)
>DroEre_CAF1 13651 114 - 1
ACAAACAAAUACGACGCACACA--CUUAUGUGCAUUUAUAUUUGUUCAUAA----UCGUAAUUAUUUCAGGCCAAGCAGUUGGACGCAUUGAAGUAAUGAUAAACAAAGGAAUCAUUUCA
...((((((((..(.(((((..--....)))))..)..))))))))....(----((((...((((((((.((((....)))).....)))))))))))))........(((....))). ( -21.90)
>DroYak_CAF1 27759 114 - 1
ACAAACAAAUACGAGGCACACA--GUUAUGUGCAUUUAUAUUUGUUCAUAA----UCGUAAUUAUUUCAGGCCCAGCAGUUGGACGCACUGAAGUAAUGAUAAACAAAGGAAUCAUUUCA
...((((((((..(((((((..--....))))).))..))))))))....(----((((...((((((((((((((...))))..)).)))))))))))))........(((....))). ( -26.80)
>consensus
ACAAACAAAUACGACGCACACACACUUUUGUGCAUUUAUAUUUGUUCAUAA____UCGUAAUUAUUUCAGGCCAAGCAGUUGGACGCAUUGAAGUAAUGAUAAACAAAGGAAUCAUUUCA
...((((((((..(.(((((........)))))..)..))))))))..............((((((((((.((((....)))).....))))))))))...........(((....))). (-19.28 = -19.92 +   0.64)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,548,995 – 8,549,108
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.21
Mean single sequence MFE -30.40
Consensus MFE -25.22
Energy contribution -26.02
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.53
Structure conservation index 0.83
SVM decision value 2.64
SVM RNA-class probability 0.996023
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8548995 113 + 20766785
ACUGCUUGGCCUGAAAUAAUUACGA----UUAUGAACAAAUAUAAAUGCACAAAAGUGUGUGUGCGUCGUAUUUGUUUGUAAAUACA--CA-AUGCUGGCGAAUGAAGGCCUUUGAAGAU
.((....(((((......(((.((.----(((..(((((((((..(((((((........))))))).)))))))))..))).....--((-....)).)))))..))))).....)).. ( -28.60)
>DroSec_CAF1 24520 117 + 1
ACUGCUUGGCCUGAAAUAAUUACGAACAAAUAUGAACAAAUAUAAAUGCACUAACGUGUGUGUGCGUCGUAUUUGUUUGUAAAUACA--CA-AAGCUGGCGAAUGAAGGCCUUUGAAGAU
.((....(((((.......((((((((((((((((....((((....((((....))))))))...)))))))))))))))).....--((-....))........))))).....)).. ( -32.90)
>DroSim_CAF1 28159 114 + 1
ACUGCUUGGCCUGAAAUAAUUACGA----UUAUGAACAAAUAUAAAUGCACUAACGUGUGUGUGCGUCGUAUUUGUUUGUAAAUACA--AAAAAGCUGGCGAAUGAAGGCCUUUGAAGAU
.((....(((((......(((.((.----(((..(((((((((..((((((..........)))))).)))))))))..)))...((--.......)).)))))..))))).....)).. ( -27.00)
>DroEre_CAF1 13691 111 + 1
ACUGCUUGGCCUGAAAUAAUUACGA----UUAUGAACAAAUAUAAAUGCACAUAAG--UGUGUGCGUCGUAUUUGUUUGUAAAUACA--CA-ACGCUGGCGAAUGAAGGCCUUUGAAGAU
.((....(((((.............----(((..(((((((((..((((((((...--.)))))))).)))))))))..))).....--..-.((....)).....))))).....)).. ( -31.90)
>DroYak_CAF1 27799 113 + 1
ACUGCUGGGCCUGAAAUAAUUACGA----UUAUGAACAAAUAUAAAUGCACAUAAC--UGUGUGCCUCGUAUUUGUUUGUAAAUACACACA-GCGCUGGCGAAUGAAGGCCUUUGAAGAU
.((...((((((.............----(((..(((((((((....((((((...--.))))))...)))))))))..))).........-((....))......))))))....)).. ( -31.60)
>consensus
ACUGCUUGGCCUGAAAUAAUUACGA____UUAUGAACAAAUAUAAAUGCACAAAAGUGUGUGUGCGUCGUAUUUGUUUGUAAAUACA__CA_AAGCUGGCGAAUGAAGGCCUUUGAAGAU
.((....(((((.................(((..(((((((((..(((((((........))))))).)))))))))..)))............(....)......))))).....)).. (-25.22 = -26.02 +   0.80)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,548,995 – 8,549,108
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.21
Mean single sequence MFE -22.36
Consensus MFE -17.94
Energy contribution -18.34
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.37
Structure conservation index 0.80
SVM decision value -0.03
SVM RNA-class probability 0.520697
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8548995 113 - 20766785
AUCUUCAAAGGCCUUCAUUCGCCAGCAU-UG--UGUAUUUACAAACAAAUACGACGCACACACACUUUUGUGCAUUUAUAUUUGUUCAUAA----UCGUAAUUAUUUCAGGCCAAGCAGU
.........(((((..........((((-((--((........((((((((..(.(((((........)))))..)..)))))))))))))----).)).........)))))....... ( -22.11)
>DroSec_CAF1 24520 117 - 1
AUCUUCAAAGGCCUUCAUUCGCCAGCUU-UG--UGUAUUUACAAACAAAUACGACGCACACACACGUUAGUGCAUUUAUAUUUGUUCAUAUUUGUUCGUAAUUAUUUCAGGCCAAGCAGU
.........(((........))).((((-.(--((((.((((.((((((((.((((........)))).(.(((........))).).)))))))).)))).))).....)).))))... ( -21.30)
>DroSim_CAF1 28159 114 - 1
AUCUUCAAAGGCCUUCAUUCGCCAGCUUUUU--UGUAUUUACAAACAAAUACGACGCACACACACGUUAGUGCAUUUAUAUUUGUUCAUAA----UCGUAAUUAUUUCAGGCCAAGCAGU
.........(((((..........((.....--.))..(((..((((((((..(.((((..........))))..)..))))))))..)))----.............)))))....... ( -18.70)
>DroEre_CAF1 13691 111 - 1
AUCUUCAAAGGCCUUCAUUCGCCAGCGU-UG--UGUAUUUACAAACAAAUACGACGCACACA--CUUAUGUGCAUUUAUAUUUGUUCAUAA----UCGUAAUUAUUUCAGGCCAAGCAGU
.........(((((..........((((-((--(((............)))))))))..((.--.(((((.(((........))).)))))----..)).........)))))....... ( -25.30)
>DroYak_CAF1 27799 113 - 1
AUCUUCAAAGGCCUUCAUUCGCCAGCGC-UGUGUGUAUUUACAAACAAAUACGAGGCACACA--GUUAUGUGCAUUUAUAUUUGUUCAUAA----UCGUAAUUAUUUCAGGCCCAGCAGU
.........(((((..........(.((-(...(((((((......))))))).))).)((.--((((((.(((........))).)))))----).)).........)))))....... ( -24.40)
>consensus
AUCUUCAAAGGCCUUCAUUCGCCAGCGU_UG__UGUAUUUACAAACAAAUACGACGCACACACACUUUUGUGCAUUUAUAUUUGUUCAUAA____UCGUAAUUAUUUCAGGCCAAGCAGU
.........(((((...................(((....)))((((((((..(.(((((........)))))..)..))))))))......................)))))....... (-17.94 = -18.34 +   0.40)

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 10:27:21 2006