Locus 8496

Sequence ID X_DroMel_CAF1
Location 21,062,285 – 21,062,475
Length 190
Max. P 0.963574
window13980 window13981 window13982

overview

Window 0

Location 21,062,285 – 21,062,405
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 92.13
Mean single sequence MFE -22.17
Consensus MFE -19.34
Energy contribution -18.90
Covariance contribution -0.44
Combinations/Pair 1.10
Mean z-score -1.88
Structure conservation index 0.87
SVM decision value 0.18
SVM RNA-class probability 0.622073
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21062285 120 + 22224390
CUUUGCCCCCUAUUUUUUCCUCUAUUUCCUUGACUUUUUCUGUUUUAGUUUUCUUCUAUUUCCCAUUUUGGUGUCAAGUGUUGCGUAUCAUUUAAUGUGACACACUUAGCCGGAAAAUGC
..............((((((.(((.....(((((...........(((.......)))....((.....)).)))))((((..(((........)))..))))...)))..))))))... ( -19.90)
>DroEre_CAF1 33412 116 + 1
CUUUGCCCCCCU--UUUUCCUCCAUUUCCUUGGCUU--UCUGUUUUAGUUUUCUUCUUUUGCCCAUUUUGGUGUCAAGUGUUGCGUAUCAUUUAAUGUGACACACUUAGCCGGAAAAUGC
............--..........(((((..((((.--...((...............((((((.....)).).)))((((..(((........)))..))))))..))))))))).... ( -21.40)
>DroYak_CAF1 36419 116 + 1
CUUUGCCCCCCA--UUUUCCUCUAUUUCCUUGGCUU--UCAGUUCAAGCUUUCUUCUUUUGCCCAUUUUGGUGUCAAGUGUUGCGUAUCAUUUAAUGUGACACACUUAGCCGGAAAAUGC
..........((--((((((...........(((((--.......)))))...................(((.....((((..(((........)))..)))).....))))))))))). ( -25.20)
>consensus
CUUUGCCCCCCA__UUUUCCUCUAUUUCCUUGGCUU__UCUGUUUUAGUUUUCUUCUUUUGCCCAUUUUGGUGUCAAGUGUUGCGUAUCAUUUAAUGUGACACACUUAGCCGGAAAAUGC
..............((((((...........((((...........))))...................(((.....((((..(((........)))..)))).....)))))))))... (-19.34 = -18.90 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 21,062,285 – 21,062,405
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.13
Mean single sequence MFE -26.53
Consensus MFE -20.72
Energy contribution -20.83
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -2.72
Structure conservation index 0.78
SVM decision value 0.48
SVM RNA-class probability 0.750921
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21062285 120 - 22224390
GCAUUUUCCGGCUAAGUGUGUCACAUUAAAUGAUACGCAACACUUGACACCAAAAUGGGAAAUAGAAGAAAACUAAAACAGAAAAAGUCAAGGAAAUAGAGGAAAAAAUAGGGGGCAAAG
...((((((..(((.((((((((.......))))))))....((((((.((.....))....(((.......)))...........))))))....))).)))))).............. ( -26.40)
>DroEre_CAF1 33412 116 - 1
GCAUUUUCCGGCUAAGUGUGUCACAUUAAAUGAUACGCAACACUUGACACCAAAAUGGGCAAAAGAAGAAAACUAAAACAGA--AAGCCAAGGAAAUGGAGGAAAA--AGGGGGGCAAAG
.(((((((.((((..((((((((.......))))))))....(((....((.....))....))).................--.))))..)))))))........--............ ( -24.10)
>DroYak_CAF1 36419 116 - 1
GCAUUUUCCGGCUAAGUGUGUCACAUUAAAUGAUACGCAACACUUGACACCAAAAUGGGCAAAAGAAGAAAGCUUGAACUGA--AAGCCAAGGAAAUAGAGGAAAA--UGGGGGGCAAAG
.((((((((..(((.((((((((.......))))))))....((((...((.....)).............((((.......--))))))))....))).))))))--)).......... ( -29.10)
>consensus
GCAUUUUCCGGCUAAGUGUGUCACAUUAAAUGAUACGCAACACUUGACACCAAAAUGGGCAAAAGAAGAAAACUAAAACAGA__AAGCCAAGGAAAUAGAGGAAAA__UGGGGGGCAAAG
....(((((((((..((((((((.......))))))))....(((....((.....))....)))....................))))..)))))........................ (-20.72 = -20.83 +   0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,062,365 – 21,062,475
Length 110
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 91.04
Mean single sequence MFE -32.10
Consensus MFE -30.67
Energy contribution -30.23
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -2.27
Structure conservation index 0.96
SVM decision value 1.55
SVM RNA-class probability 0.963574
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21062365 110 - 22224390
CGCUUGGCACAGCAAAUUAGCAUUCAGCCAACAUAUGUGCUCAGCUGUCAGUCUGGAAAAGUUCCUCC----------CCGCAUUUUCCGGCUAAGUGUGUCACAUUAAAUGAUACGCAA
.(((.((((((........((.....)).......)))))).)))....((.((((((((((......----------..)).))))))))))..((((((((.......)))))))).. ( -31.96)
>DroEre_CAF1 33488 118 - 1
CGCUUAGCACAGCAAAUUAGCAUUCAGCCAACA--UGUGCUCAGCUGUCAGUCGGGAAAAGCCCCUCCCCUGUUUUCCCCGCAUUUUCCGGCUAAGUGUGUCACAUUAAAUGAUACGCAA
.(((.((((((........((.....)).....--)))))).)))....((((((((((.((..................)).))))))))))..((((((((.......)))))))).. ( -34.69)
>DroYak_CAF1 36495 117 - 1
CGCUUAGCACAGCAAAUUAGCAUUCAGCCAACA--UGUGCUCAGCUGUCAGUCUGGAAAAGUCCCUCCCCUGUUUUC-CCGCAUUUUCCGGCUAAGUGUGUCACAUUAAAUGAUACGCAA
.(((.((((((........((.....)).....--)))))).)))....((.((((((((((...............-..)).))))))))))..((((((((.......)))))))).. ( -29.65)
>consensus
CGCUUAGCACAGCAAAUUAGCAUUCAGCCAACA__UGUGCUCAGCUGUCAGUCUGGAAAAGUCCCUCCCCUGUUUUC_CCGCAUUUUCCGGCUAAGUGUGUCACAUUAAAUGAUACGCAA
.(((.((((((........((.....)).......)))))).)))....((((.((((((((..................)).))))))))))..((((((((.......)))))))).. (-30.67 = -30.23 +  -0.44)

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 13:05:47 2006