Locus 4492

Sequence ID 2R_DroMel_CAF1
Location 14,763,207 – 14,763,406
Length 199
Max. P 0.949916
window7189 window7190 window7191 window7192 window7193

overview

Window 9

Location 14,763,207 – 14,763,326
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.43
Mean single sequence MFE -33.00
Consensus MFE -29.69
Energy contribution -30.13
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -2.37
Structure conservation index 0.90
SVM decision value 0.94
SVM RNA-class probability 0.886182
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14763207 119 + 20766785
GGUCAGCAUUACAAAUGGAGCACCUCCCAACCAUCCAUCCAAUCCGGUAAUUUUGGGCCU-UUGUGCGAUUGACACACGCAUGUCAGGCCCCAUUACUGGAUCUCCAUCAGGCAUUACCU
(((..((.......((((((.....................((((((((((...((((((-.((((((.........))))))..)))))).))))))))))))))))...))...))). ( -36.09)
>DroSim_CAF1 4157 119 + 1
GGUCAGCAUUACAAAUAGAGCACCUCCCAACCAUCCAUCCAAUCCGGUAAUUUCGGGCCU-UUGUGCGAUUGACACACGCAUGUCAGGCCCCAUUACUGGAUCUCCAUCAGGCAUUACCU
(((..((..........(((...)))...............((((((((((...((((((-.((((((.........))))))..)))))).)))))))))).........))...))). ( -32.20)
>DroYak_CAF1 5015 117 + 1
GGUCAGCAGUACAAAUAGAGCACCUACCAACC---GAUCCAAUCCGGUAAUUUCGGGCCUUUUGUGCGAUUGACACACGCAUGUCAGGCCCCAUUACUGAAUCUCCAUCAGGCAUUACCU
((....(((((..................(((---(........))))......((((((..((((((.........))))))..))))))...))))).....))...(((.....))) ( -30.70)
>consensus
GGUCAGCAUUACAAAUAGAGCACCUCCCAACCAUCCAUCCAAUCCGGUAAUUUCGGGCCU_UUGUGCGAUUGACACACGCAUGUCAGGCCCCAUUACUGGAUCUCCAUCAGGCAUUACCU
.(((.((.(((....))).))....................((((((((((...((((((...(((((.........)))))...)))))).))))))))))........)))....... (-29.69 = -30.13 +   0.45)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,763,207 – 14,763,326
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.43
Mean single sequence MFE -39.40
Consensus MFE -36.94
Energy contribution -36.50
Covariance contribution -0.44
Combinations/Pair 1.05
Mean z-score -1.49
Structure conservation index 0.94
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14763207 119 - 20766785
AGGUAAUGCCUGAUGGAGAUCCAGUAAUGGGGCCUGACAUGCGUGUGUCAAUCGCACAA-AGGCCCAAAAUUACCGGAUUGGAUGGAUGGUUGGGAGGUGCUCCAUUUGUAAUGCUGACC
.((((.(((..(((((((..((..((((.((((((....((((.........))))...-))))))...))))((.(((((......))))).)).))..))))))).))).)))).... ( -39.80)
>DroSim_CAF1 4157 119 - 1
AGGUAAUGCCUGAUGGAGAUCCAGUAAUGGGGCCUGACAUGCGUGUGUCAAUCGCACAA-AGGCCCGAAAUUACCGGAUUGGAUGGAUGGUUGGGAGGUGCUCUAUUUGUAAUGCUGACC
.((((.(((..(((((((..((.......((((((....((((.........))))...-)))))).......((.(((((......))))).)).))..))))))).))).)))).... ( -36.90)
>DroYak_CAF1 5015 117 - 1
AGGUAAUGCCUGAUGGAGAUUCAGUAAUGGGGCCUGACAUGCGUGUGUCAAUCGCACAAAAGGCCCGAAAUUACCGGAUUGGAUC---GGUUGGUAGGUGCUCUAUUUGUACUGCUGACC
(((.....)))(((...(((((.(((((.((((((....((((.........))))....))))))...))))).)))))..)))---(((..((((.(((.......)))))))..))) ( -41.50)
>consensus
AGGUAAUGCCUGAUGGAGAUCCAGUAAUGGGGCCUGACAUGCGUGUGUCAAUCGCACAA_AGGCCCGAAAUUACCGGAUUGGAUGGAUGGUUGGGAGGUGCUCUAUUUGUAAUGCUGACC
.((((.(((..(((((((((((.(((((.((((((....((((.........))))....))))))...))))).))))(.(((.....))).)......))))))).))).)))).... (-36.94 = -36.50 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,763,247 – 14,763,366
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 92.11
Mean single sequence MFE -36.25
Consensus MFE -30.69
Energy contribution -31.03
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.48
Structure conservation index 0.85
SVM decision value 1.40
SVM RNA-class probability 0.949916
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14763247 119 + 20766785
AAUCCGGUAAUUUUGGGCCU-UUGUGCGAUUGACACACGCAUGUCAGGCCCCAUUACUGGAUCUCCAUCAGGCAUUACCUCCUCCUUACCCUACAUCGCCAGUUAAUUCCAUUGGAAAUU
.((((((((((...((((((-.((((((.........))))))..)))))).)))))))))).((((...((.((((.((....................)).)))).))..)))).... ( -33.45)
>DroSim_CAF1 4197 115 + 1
AAUCCGGUAAUUUCGGGCCU-UUGUGCGAUUGACACACGCAUGUCAGGCCCCAUUACUGGAUCUCCAUCAGGCAUUACCUCCG----GCCCCGCUUCGCCAGUUAAUUCCUUCGGAAAUU
.((((((((((...((((((-.((((((.........))))))..)))))).)))))))))).(((...(((.((((.((..(----((........))))).)))).)))..))).... ( -38.60)
>DroYak_CAF1 5052 116 + 1
AAUCCGGUAAUUUCGGGCCUUUUGUGCGAUUGACACACGCAUGUCAGGCCCCAUUACUGAAUCUCCAUCAGGCAUUACCUCCG----GCCCCACAUCGCCAGUUAAUUCCUUUGGAAAUU
....(((((((...((((((..((((((.........))))))..)))))).)))))))....((((..(((.((((.((..(----((........))))).)))).))).)))).... ( -36.70)
>consensus
AAUCCGGUAAUUUCGGGCCU_UUGUGCGAUUGACACACGCAUGUCAGGCCCCAUUACUGGAUCUCCAUCAGGCAUUACCUCCG____GCCCCACAUCGCCAGUUAAUUCCUUUGGAAAUU
.((((((((((...((((((...(((((.........)))))...)))))).))))))))))........(((........................)))......((((...))))... (-30.69 = -31.03 +   0.33)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,763,247 – 14,763,366
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.11
Mean single sequence MFE -39.47
Consensus MFE -33.86
Energy contribution -33.20
Covariance contribution -0.66
Combinations/Pair 1.10
Mean z-score -2.37
Structure conservation index 0.86
SVM decision value 0.70
SVM RNA-class probability 0.826256
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14763247 119 - 20766785
AAUUUCCAAUGGAAUUAACUGGCGAUGUAGGGUAAGGAGGAGGUAAUGCCUGAUGGAGAUCCAGUAAUGGGGCCUGACAUGCGUGUGUCAAUCGCACAA-AGGCCCAAAAUUACCGGAUU
..((((((..........((.((........)).))....(((.....)))..))))))(((.(((((.((((((....((((.........))))...-))))))...))))).))).. ( -34.80)
>DroSim_CAF1 4197 115 - 1
AAUUUCCGAAGGAAUUAACUGGCGAAGCGGGGC----CGGAGGUAAUGCCUGAUGGAGAUCCAGUAAUGGGGCCUGACAUGCGUGUGUCAAUCGCACAA-AGGCCCGAAAUUACCGGAUU
..((((((.(((.((((.(((((........))----)))...)))).)))..))))))(((.(((((.((((((....((((.........))))...-))))))...))))).))).. ( -42.70)
>DroYak_CAF1 5052 116 - 1
AAUUUCCAAAGGAAUUAACUGGCGAUGUGGGGC----CGGAGGUAAUGCCUGAUGGAGAUUCAGUAAUGGGGCCUGACAUGCGUGUGUCAAUCGCACAAAAGGCCCGAAAUUACCGGAUU
..((((((.(((.((((.(((((........))----)))...)))).)))..))))))(((.(((((.((((((....((((.........))))....))))))...))))).))).. ( -40.90)
>consensus
AAUUUCCAAAGGAAUUAACUGGCGAUGUGGGGC____CGGAGGUAAUGCCUGAUGGAGAUCCAGUAAUGGGGCCUGACAUGCGUGUGUCAAUCGCACAA_AGGCCCGAAAUUACCGGAUU
..((((((..........((.((...)).)).........(((.....)))..))))))(((.(((((.((((((....((((.........))))....))))))...))))).))).. (-33.86 = -33.20 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,763,286 – 14,763,406
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.13
Mean single sequence MFE -38.07
Consensus MFE -32.67
Energy contribution -32.23
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.95
Structure conservation index 0.86
SVM decision value 0.17
SVM RNA-class probability 0.617697
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14763286 120 - 20766785
UGGUGCGUCAGGUGCAAGGAAAAUCCAAACGGCAAUGCGCAAUUUCCAAUGGAAUUAACUGGCGAUGUAGGGUAAGGAGGAGGUAAUGCCUGAUGGAGAUCCAGUAAUGGGGCCUGACAU
......(((((((..........((((...((((.(((..((((((....))))))..((.((........)).))......))).))))...))))..((((....))))))))))).. ( -32.60)
>DroSim_CAF1 4236 116 - 1
UGGUGCGUCAGGUGCAAGGAAAAUCCAAACGGCAAUGCGCAAUUUCCGAAGGAAUUAACUGGCGAAGCGGGGC----CGGAGGUAAUGCCUGAUGGAGAUCCAGUAAUGGGGCCUGACAU
......(((((((..........((((...((((.(((..((((((....))))))..(((((........))----)))..))).))))...))))..((((....))))))))))).. ( -39.90)
>DroYak_CAF1 5092 116 - 1
UGGUGCGUCAGGUGCAAGGAAAAUCCAACUGGCAAUGCGCAAUUUCCAAAGGAAUUAACUGGCGAUGUGGGGC----CGGAGGUAAUGCCUGAUGGAGAUUCAGUAAUGGGGCCUGACAU
......(((((((.(..((.....)).((((((.....))((((((((.(((.((((.(((((........))----)))...)))).)))..))))))))))))....).))))))).. ( -41.70)
>consensus
UGGUGCGUCAGGUGCAAGGAAAAUCCAAACGGCAAUGCGCAAUUUCCAAAGGAAUUAACUGGCGAUGUGGGGC____CGGAGGUAAUGCCUGAUGGAGAUCCAGUAAUGGGGCCUGACAU
......(((((((..........((((...((((.(((..((((((....))))))..((.((...)).))...........))).))))...))))..((((....))))))))))).. (-32.67 = -32.23 +  -0.44)

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 11:21:13 2006