Locus 4490

Sequence ID 2R_DroMel_CAF1
Location 14,761,876 – 14,762,026
Length 150
Max. P 0.900102
window7180 window7181 window7182

overview

Window 0

Location 14,761,876 – 14,761,987
Length 111
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 88.00
Mean single sequence MFE -31.67
Consensus MFE -23.32
Energy contribution -23.43
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -2.23
Structure conservation index 0.74
SVM decision value 0.18
SVM RNA-class probability 0.620648
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14761876 111 + 20766785
AGUUAUUAUUCCCAUG-----UUUUCGUU-UUGU---GGGGUGGAACAUAUGGCCUUUUUUUCAGGUGGGUCAUUCCAUGGCCCAUUUAUGGAAUUAUGCCAUGGCAUAAAAAUUUGAUG
.(((.....(((((((-----........-.)))---))))...))).((((((..(..(((((.(((((((((...)))))))))...)))))..).))))))................ ( -30.60)
>DroSim_CAF1 2304 110 + 1
AGUUAUUUUU-CCAUG-----UUUUCGUUUUUGG---GGGGUGGAACAUAUGGCCUUU-UUUCAGGUGGGUCAUUCCAUGGCCCAUUUAUGGAAUUAUGCCAUGGCAUAAAAAUUUGAUG
.(((((..((-((((.-----((..((....)).---.))))))))...)))))....-(((((.(((((((((...)))))))))...)))))((((((....)))))).......... ( -31.70)
>DroYak_CAF1 3619 117 + 1
AGUUAUUUUUCCGGUUUUGGUUUUUGGUU-UUUUGGGGGGUUGGAACAUAUGGCCCU--UUUCAGGUGGGUCAUUCCAUGGCCCAUUUAUGGAAUUAUGCCAUGGCAUAAAAAUUUGAUG
.((((..(((...((..((((...(((((-(..((((((((((((....(((((((.--........)))))))))))..)))).))))..)))))).))))..))....)))..)))). ( -32.70)
>consensus
AGUUAUUUUUCCCAUG_____UUUUCGUU_UUGU___GGGGUGGAACAUAUGGCCUUU_UUUCAGGUGGGUCAUUCCAUGGCCCAUUUAUGGAAUUAUGCCAUGGCAUAAAAAUUUGAUG
.....................................((((((((....(((((((...........))))))))))))..)))..........((((((....)))))).......... (-23.32 = -23.43 +   0.11)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,761,876 – 14,761,987
Length 111
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.00
Mean single sequence MFE -23.67
Consensus MFE -17.49
Energy contribution -17.27
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -3.20
Structure conservation index 0.74
SVM decision value 1.01
SVM RNA-class probability 0.900102
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14761876 111 - 20766785
CAUCAAAUUUUUAUGCCAUGGCAUAAUUCCAUAAAUGGGCCAUGGAAUGACCCACCUGAAAAAAAGGCCAUAUGUUCCACCCC---ACAA-AACGAAAA-----CAUGGGAAUAAUAACU
..........((((((....))))))((((((...((((...((((((......(((.......)))......)))))).)))---)(..-...)....-----.))))))......... ( -22.90)
>DroSim_CAF1 2304 110 - 1
CAUCAAAUUUUUAUGCCAUGGCAUAAUUCCAUAAAUGGGCCAUGGAAUGACCCACCUGAAA-AAAGGCCAUAUGUUCCACCCC---CCAAAAACGAAAA-----CAUGG-AAAAAUAACU
..........((((((....))))))((((((...((((...((((((......(((....-..)))......))))))...)---))).....(....-----)))))-))........ ( -24.90)
>DroYak_CAF1 3619 117 - 1
CAUCAAAUUUUUAUGCCAUGGCAUAAUUCCAUAAAUGGGCCAUGGAAUGACCCACCUGAAA--AGGGCCAUAUGUUCCAACCCCCCAAAA-AACCAAAAACCAAAACCGGAAAAAUAACU
..........((((((....)))))).........((((...((((((......(((....--))).......))))))....))))...-.........((......)).......... ( -23.22)
>consensus
CAUCAAAUUUUUAUGCCAUGGCAUAAUUCCAUAAAUGGGCCAUGGAAUGACCCACCUGAAA_AAAGGCCAUAUGUUCCACCCC___ACAA_AACGAAAA_____CAUGGGAAAAAUAACU
..........((((((....))))))..........(((...((((((......(((.......)))......)))))).)))..................................... (-17.49 = -17.27 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,761,907 – 14,762,026
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.09
Mean single sequence MFE -33.63
Consensus MFE -30.77
Energy contribution -30.77
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.09
Structure conservation index 0.91
SVM decision value 0.62
SVM RNA-class probability 0.802652
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14761907 119 + 20766785
GUGGAACAUAUGGCCUUUUUUUCAGGUGGGUCAUUCCAUGGCCCAUUUAUGGAAUUAUGCCAUGGCAUAAAAAUUUGAUGAGCUUCAACUUCACAAGUGCCUGGAUCCCA-AUGAAAAGU
.................(((((((..((((....((((.((((((....)))..((((((....))))))..(((((.((((.......)))))))))))))))).))))-.))))))). ( -32.40)
>DroSim_CAF1 2335 119 + 1
GUGGAACAUAUGGCCUUU-UUUCAGGUGGGUCAUUCCAUGGCCCAUUUAUGGAAUUAUGCCAUGGCAUAAAAAUUUGAUGAGCUUCAACUUCACAAGUGCCUGGAUCCCAAAUGAAAAGU
................((-(((((..((((....((((.((((((....)))..((((((....))))))..(((((.((((.......)))))))))))))))).))))..))))))). ( -34.00)
>DroYak_CAF1 3658 117 + 1
UUGGAACAUAUGGCCCU--UUUCAGGUGGGUCAUUCCAUGGCCCAUUUAUGGAAUUAUGCCAUGGCAUAAAAAUUUGAUGAGCUUCCACUUCACAAGUGCCAGGAUCCCA-AUGAAAAGU
...............((--(((((..((((....(((.(((((((....)))..((((((....))))))..(((((.((((.......)))))))))))))))).))))-.))))))). ( -34.50)
>consensus
GUGGAACAUAUGGCCUUU_UUUCAGGUGGGUCAUUCCAUGGCCCAUUUAUGGAAUUAUGCCAUGGCAUAAAAAUUUGAUGAGCUUCAACUUCACAAGUGCCUGGAUCCCA_AUGAAAAGU
..(((.(..(((((.....(((((.(((((((((...)))))))))...)))))....)))))(((((......(((.((((.......))))))))))))..).)))............ (-30.77 = -30.77 +   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 11:21:03 2006