Locus 7116

Sequence ID 3L_DroMel_CAF1
Location 19,168,157 – 19,168,354
Length 197
Max. P 0.883940
window11543 window11544 window11545

overview

Window 3

Location 19,168,157 – 19,168,277
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.62
Mean single sequence MFE -16.65
Consensus MFE -15.35
Energy contribution -15.35
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.71
Structure conservation index 0.92
SVM decision value 0.93
SVM RNA-class probability 0.883940
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19168157 120 + 23771897
ACACACCCAACCCAAACCCGCCACCCAGAAAAACAAACCGAGGACAAACUCAUAAAUCUUUGCAAGGGACUCCGACUCCCCUUUCUUGCGAAAUCCAAGGAAACAUGCCAUAAAACACAU
.......................................(((......)))..........(((.((((.......)))).(((((((.(....))))))))...)))............ ( -15.30)
>DroSim_CAF1 956 107 + 1
ACACACCCAACC-------------CAGAAAAGCAAACCGAGGACAAACUCAUAAAUCUUUGCAAGGGACUCCGACUCCCCUUUCUUGCGAAAUCCAAGGAAACAUGCCAUAAAACACAU
............-------------.......(((....(((......))).......((((((((..(............)..))))))))......(....).)))............ ( -16.80)
>DroEre_CAF1 670 118 + 1
ACACACCAAAC--GACCCCGCCACCCAGGAAAACAAACCGAGGACAAACUCAUAAAUCUUUGCAAGGGACUCCGACUCCCCUUUCUUGCGAAAUCCAAGGAAACAUGCCAUAAAACACAU
...........--......((......(((.........(((......))).......((((((((..(............)..)))))))).)))..(....)..))............ ( -19.00)
>DroYak_CAF1 2401 118 + 1
ACACACCAAAC--AACCCCGCCACCCAGAAAAACAAACCGAGGACAAACUCAUAAAUCUUAGCAAGGGACUCCGACUCCCCUUUCUUGCGAAAUCCAAGGAAACAUGCCAUAAAACACAU
...........--..........................(((......)))..........(((.((((.......)))).(((((((.(....))))))))...)))............ ( -15.50)
>consensus
ACACACCAAAC__AACCCCGCCACCCAGAAAAACAAACCGAGGACAAACUCAUAAAUCUUUGCAAGGGACUCCGACUCCCCUUUCUUGCGAAAUCCAAGGAAACAUGCCAUAAAACACAU
.......................................(((......)))..........(((.((((.......)))).(((((((.(....))))))))...)))............ (-15.35 = -15.35 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,168,197 – 19,168,316
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 97.91
Mean single sequence MFE -28.93
Consensus MFE -28.95
Energy contribution -28.70
Covariance contribution -0.25
Combinations/Pair 1.04
Mean z-score -1.66
Structure conservation index 1.00
SVM decision value 0.29
SVM RNA-class probability 0.669638
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19168197 119 + 23771897
AGGACAAACUCAUAAAUCUUUGCAAGGGACUCCGACUCCCCUUUCUUGCGAAAUCCAAGGAAACAUGCCAUAAAACACAUGAAGAAGUGUGUAAAUAACAGAAGGAGCCGCAGGAUGAG-
........((((...........(((((..........)))))(((((((...(((..(....)..........((((((......))))))...........)))..)))))))))))- ( -29.40)
>DroSim_CAF1 983 120 + 1
AGGACAAACUCAUAAAUCUUUGCAAGGGACUCCGACUCCCCUUUCUUGCGAAAUCCAAGGAAACAUGCCAUAAAACACAUGAAGAAGUGUGUAAAUAACAGAAGGAGCCGCAGGAUGAGU
.......(((((...........(((((..........)))))(((((((...(((..(....)..........((((((......))))))...........)))..)))))))))))) ( -30.90)
>DroEre_CAF1 708 119 + 1
AGGACAAACUCAUAAAUCUUUGCAAGGGACUCCGACUCCCCUUUCUUGCGAAAUCCAAGGAAACAUGCCAUAAAACACAUGAAGGAGUGUGUAAAUAACAGAAGGAGCUGCAGGAUGAG-
........((((...........(((((..........)))))(((((((...(((..(....)..........((((((......))))))...........)))..)))))))))))- ( -27.70)
>DroYak_CAF1 2439 119 + 1
AGGACAAACUCAUAAAUCUUAGCAAGGGACUCCGACUCCCCUUUCUUGCGAAAUCCAAGGAAACAUGCCAUAAAACACAUGAAGCAGUGUGUAAAUAACAGAAGGAGCUGCAGGAUGAG-
........((((...........(((((..........)))))(((((((...(((..(....)..........((((((......))))))...........)))..)))))))))))- ( -27.70)
>consensus
AGGACAAACUCAUAAAUCUUUGCAAGGGACUCCGACUCCCCUUUCUUGCGAAAUCCAAGGAAACAUGCCAUAAAACACAUGAAGAAGUGUGUAAAUAACAGAAGGAGCCGCAGGAUGAG_
........((((...........(((((..........)))))(((((((...(((..(....)..........((((((......))))))...........)))..))))))))))). (-28.95 = -28.70 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,168,237 – 19,168,354
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.07
Mean single sequence MFE -32.35
Consensus MFE -27.52
Energy contribution -28.03
Covariance contribution 0.50
Combinations/Pair 1.04
Mean z-score -2.26
Structure conservation index 0.85
SVM decision value 0.89
SVM RNA-class probability 0.874392
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19168237 117 + 23771897
CUUUCUUGCGAAAUCCAAGGAAACAUGCCAUAAAACACAUGAAGAAGUGUGUAAAUAACAGAAGGAGCCGCAGGAUGAG---GAAGCCCCAGGAGCAUCGAGAGCACCGAAGGGGAAGUA
((((((((((...(((..(....)..........((((((......))))))...........)))..))))))).)))---....((((.((.((.......)).))...))))..... ( -34.70)
>DroSim_CAF1 1023 120 + 1
CUUUCUUGCGAAAUCCAAGGAAACAUGCCAUAAAACACAUGAAGAAGUGUGUAAAUAACAGAAGGAGCCGCAGGAUGAGUAUGAAGCCCCAGGAGCAUCGAGAGCACCGAAGGGGAAGUA
((((((((((...(((..(....)..........((((((......))))))...........)))..))))))).))).......((((.((.((.......)).))...))))..... ( -34.00)
>DroEre_CAF1 748 116 + 1
CUUUCUUGCGAAAUCCAAGGAAACAUGCCAUAAAACACAUGAAGGAGUGUGUAAAUAACAGAAGGAGCUGCAGGAUGAG---GAUGCCCCAGGAGCAUCGGG-GCACCGAAGAGGAAGUA
...(((((((...(((..(....)..........((((((......))))))...........)))..)))))))...(---(.((((((.........)))-)))))............ ( -34.40)
>DroYak_CAF1 2479 116 + 1
CUUUCUUGCGAAAUCCAAGGAAACAUGCCAUAAAACACAUGAAGCAGUGUGUAAAUAACAGAAGGAGCUGCAGGAUGAG---GAAGCCCCAGGAGCAUCGAG-CCACCGAAGAGGAAGUA
((((((((((...(((..(....)..........((((((......))))))...........)))..))))))).)))---((.(((....).)).))..(-(..((.....))..)). ( -26.30)
>consensus
CUUUCUUGCGAAAUCCAAGGAAACAUGCCAUAAAACACAUGAAGAAGUGUGUAAAUAACAGAAGGAGCCGCAGGAUGAG___GAAGCCCCAGGAGCAUCGAG_GCACCGAAGAGGAAGUA
((((((((((...(((..(....)..........((((((......))))))...........)))..))))))).))).......((((.((.((.......)).))...))))..... (-27.52 = -28.03 +   0.50)

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 12:38:15 2006