Locus 4124

Sequence ID X_DroMel_CAF1
Location 10,853,058 – 10,853,192
Length 134
Max. P 0.901961
window6773 window6774 window6775

overview

Window 3

Location 10,853,058 – 10,853,156
Length 98
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 95.41
Mean single sequence MFE -28.38
Consensus MFE -23.91
Energy contribution -24.48
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -2.65
Structure conservation index 0.84
SVM decision value 1.02
SVM RNA-class probability 0.901961
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10853058 98 + 22224390
CCCCAAUGUGUUAUGCCAAAAGCUAAAAACUUAUGCUUUUGCCAGUUUAUUGUCUUGUUUUGCUU-UGUCUGGUGCGACAGGCAGGCAGCAAAACAAAG
...(((((.....((.(((((((...........))))))).))...)))))..(((((((((((-((((((......)))))))..)))))))))).. ( -30.50)
>DroSec_CAF1 6950 97 + 1
CUCCAAUGUGUUAUGCCAAAAGCUAAAAACUUAUGCUUUUGCCAGUUUAUUGUCUUGUUUUGCUU-UGUCU-GUGCGACAGGCAGGCAGCAAAACAAAG
...(((((.....((.(((((((...........))))))).))...)))))..(((((((((((-(((((-(.....)))))))..)))))))))).. ( -29.80)
>DroSim_CAF1 7058 97 + 1
CCCCAAUGUGUUAUGCCAAAAGCUAAAAACUUAUGCUUUUGCCAGUUUAUUGUCUUGUUUUGCUU-UGUCU-GUGCGACAGGCAGGCGGCAAAACAAAG
...(((((.....((.(((((((...........))))))).))...)))))..(((((((((((-(((((-(.....)))))))..)))))))))).. ( -29.80)
>DroYak_CAF1 7075 94 + 1
CCCCAAUGUGUUAUGCCAAAAGCUAAAAACUUAUGCUUUUGCCAGUUUAUUGUCUUGUUUUGCUUUUGUCU-GUGCG----GCAGGCAGCCAAACAAAG
...(((((.....((.(((((((...........))))))).))...)))))..((((((.(((...((((-(....----.)))))))).)))))).. ( -23.40)
>consensus
CCCCAAUGUGUUAUGCCAAAAGCUAAAAACUUAUGCUUUUGCCAGUUUAUUGUCUUGUUUUGCUU_UGUCU_GUGCGACAGGCAGGCAGCAAAACAAAG
...(((((.....((.(((((((...........))))))).))...)))))..((((((((((..(((((........)))))...)))))))))).. (-23.91 = -24.48 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,853,058 – 10,853,156
Length 98
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 95.41
Mean single sequence MFE -23.75
Consensus MFE -21.42
Energy contribution -22.67
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -1.63
Structure conservation index 0.90
SVM decision value 0.30
SVM RNA-class probability 0.677887
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10853058 98 - 22224390
CUUUGUUUUGCUGCCUGCCUGUCGCACCAGACA-AAGCAAAACAAGACAAUAAACUGGCAAAAGCAUAAGUUUUUAGCUUUUGGCAUAACACAUUGGGG
.(((((((((((...((.(((......))).))-.))))))))))).((((....((.(((((((...........))))))).))......))))... ( -25.40)
>DroSec_CAF1 6950 97 - 1
CUUUGUUUUGCUGCCUGCCUGUCGCAC-AGACA-AAGCAAAACAAGACAAUAAACUGGCAAAAGCAUAAGUUUUUAGCUUUUGGCAUAACACAUUGGAG
.(((((((((((...((.(((.....)-)).))-.))))))))))).((((....((.(((((((...........))))))).))......))))... ( -26.10)
>DroSim_CAF1 7058 97 - 1
CUUUGUUUUGCCGCCUGCCUGUCGCAC-AGACA-AAGCAAAACAAGACAAUAAACUGGCAAAAGCAUAAGUUUUUAGCUUUUGGCAUAACACAUUGGGG
.((((((((((....((.(((.....)-)).))-..)))))))))).((((....((.(((((((...........))))))).))......))))... ( -23.30)
>DroYak_CAF1 7075 94 - 1
CUUUGUUUGGCUGCCUGC----CGCAC-AGACAAAAGCAAAACAAGACAAUAAACUGGCAAAAGCAUAAGUUUUUAGCUUUUGGCAUAACACAUUGGGG
.((((((((((.(....)----.)).)-)))))))............((((....((.(((((((...........))))))).))......))))... ( -20.20)
>consensus
CUUUGUUUUGCUGCCUGCCUGUCGCAC_AGACA_AAGCAAAACAAGACAAUAAACUGGCAAAAGCAUAAGUUUUUAGCUUUUGGCAUAACACAUUGGGG
.(((((((((((.......((((......))))..))))))))))).((((....((.(((((((...........))))))).))......))))... (-21.42 = -22.67 +   1.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,853,098 – 10,853,192
Length 94
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 90.21
Mean single sequence MFE -25.50
Consensus MFE -18.11
Energy contribution -18.68
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -2.23
Structure conservation index 0.71
SVM decision value 0.38
SVM RNA-class probability 0.713844
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10853098 94 + 22224390
GCCAGUUUAUUGUCUUGUUUUGCUU-UGUCUGGUGCGACAGGCAGGCAGCAAAACAAAGUGGAAAACUCUUUUUCCAGCACCCAAAA----AAAUAUUC
((............(((((((((((-((((((......)))))))..))))))))))..(((((((....)))))))))........----........ ( -27.10)
>DroSec_CAF1 6990 97 + 1
GCCAGUUUAUUGUCUUGUUUUGCUU-UGUCU-GUGCGACAGGCAGGCAGCAAAACAAAGUGGAAAACUCUUUUUCCAGCACCCAAAAAAAAAAAUAUUC
((............(((((((((((-(((((-(.....)))))))..))))))))))..(((((((....))))))))).................... ( -26.40)
>DroSim_CAF1 7098 96 + 1
GCCAGUUUAUUGUCUUGUUUUGCUU-UGUCU-GUGCGACAGGCAGGCGGCAAAACAAAGUGGAAAACUCUUUUCCCAGCACCCAAAAA-AAAAAUAUUC
((............(((((((((((-(((((-(.....)))))))..)))))))))).(.(((((.....)))))).)).........-.......... ( -24.40)
>DroYak_CAF1 7115 89 + 1
GCCAGUUUAUUGUCUUGUUUUGCUUUUGUCU-GUGCG----GCAGGCAGCCAAACAAAGUGGGAAACUCUUUUUCGAGCACCCACA-----AAAUAUGC
....((.((((...((((((.(((...((((-(....----.)))))))).)))))).(((((...(((......)))..))))).-----.)))).)) ( -24.10)
>consensus
GCCAGUUUAUUGUCUUGUUUUGCUU_UGUCU_GUGCGACAGGCAGGCAGCAAAACAAAGUGGAAAACUCUUUUUCCAGCACCCAAAA____AAAUAUUC
...(((((.(..(.((((((((((..(((((........)))))...)))))))))).)..).)))))............................... (-18.11 = -18.68 +   0.56)

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 11:16:54 2006