Locus 3764

Sequence ID X_DroMel_CAF1
Location 9,974,279 – 9,974,401
Length 122
Max. P 0.956110
window6182 window6183 window6184

overview

Window 2

Location 9,974,279 – 9,974,383
Length 104
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 83.71
Mean single sequence MFE -25.98
Consensus MFE -21.32
Energy contribution -21.68
Covariance contribution 0.36
Combinations/Pair 1.05
Mean z-score -1.67
Structure conservation index 0.82
SVM decision value 0.38
SVM RNA-class probability 0.712506
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9974279 104 + 22224390
CGUUUCCCGAGAUCGUUUUUUAUGCAUUUAUUAAUUGCGAACGUCCGCAAAGCCAAUUAACUUGGCCAAGGACCAUUUUC------AUUUUCGCUGCAUACUCUCGGGCA-
.....(((((((........((((((..........(((((.((((.....(((((.....)))))...)))).......------...))))))))))).)))))))..- ( -27.10)
>DroSec_CAF1 19650 104 + 1
CGCUGUCCGAGAUCGUUUUUUAUGCAUUUAUUAAUUGCGAACGUCCGCAAAGCCAAUUAACUUGGCCAAGGACCAUUUUC------AUUUUCGCUGCAUACUCUCGGGCA-
....((((((((........((((((..........(((((.((((.....(((((.....)))))...)))).......------...))))))))))).)))))))).- ( -29.00)
>DroEre_CAF1 6966 110 + 1
CGUUAACCGAGAUCGUUUUUUAUGCAUUUAUUAAUUGCGAACGUCCGCAGAGCCAAUUAACUUGGCCAGGGACCAUUUUCAUUUUCAUUUUCGCUGCAUACUCUCGGGCA-
......((((((.(((((.....(((.........))))))))...((((.(((((.....)))))..(..(....)..).............))))....))))))...- ( -24.90)
>DroYak_CAF1 7217 104 + 1
CGUUAACCGAGAUCGUUUUUUAUGCAUUUAUUAAUUGCGAACGUCCGCAAAGCCAAUUAACUUGGCCAAGGACCAUUUUC------AUUUUCGCUGCAUACUCUCGGGCA-
......((((((........((((((..........(((((.((((.....(((((.....)))))...)))).......------...))))))))))).))))))...- ( -25.10)
>DroAna_CAF1 9695 95 + 1
CGUCCGCCGAC----UGCUCUCUGCAUUUAUUAAUUGCGCCACUCCGCAGAGCCAAUUAACUUGGCCGGGAAACAAU------------UCCGUCGCAUACUCUCGGGCCU
.(((((((((.----(((.....)))....(((((((.(((........).))))))))).)))))(((((.....)------------))))............)))).. ( -23.80)
>consensus
CGUUAACCGAGAUCGUUUUUUAUGCAUUUAUUAAUUGCGAACGUCCGCAAAGCCAAUUAACUUGGCCAAGGACCAUUUUC______AUUUUCGCUGCAUACUCUCGGGCA_
......((((((........(((((.........(((((......))))).(((((.....))))).............................))))).)))))).... (-21.32 = -21.68 +   0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,974,279 – 9,974,383
Length 104
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 83.71
Mean single sequence MFE -31.46
Consensus MFE -23.98
Energy contribution -24.42
Covariance contribution 0.44
Combinations/Pair 1.05
Mean z-score -2.34
Structure conservation index 0.76
SVM decision value 1.46
SVM RNA-class probability 0.956110
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9974279 104 - 22224390
-UGCCCGAGAGUAUGCAGCGAAAAU------GAAAAUGGUCCUUGGCCAAGUUAAUUGGCUUUGCGGACGUUCGCAAUUAAUAAAUGCAUAAAAAACGAUCUCGGGAAACG
-..(((((((.(((((((((((.((------....)).((((..((((((.....))))))....)))).)))))..........))))))........)))))))..... ( -35.00)
>DroSec_CAF1 19650 104 - 1
-UGCCCGAGAGUAUGCAGCGAAAAU------GAAAAUGGUCCUUGGCCAAGUUAAUUGGCUUUGCGGACGUUCGCAAUUAAUAAAUGCAUAAAAAACGAUCUCGGACAGCG
-((.((((((.(((((((((((.((------....)).((((..((((((.....))))))....)))).)))))..........))))))........)))))).))... ( -32.40)
>DroEre_CAF1 6966 110 - 1
-UGCCCGAGAGUAUGCAGCGAAAAUGAAAAUGAAAAUGGUCCCUGGCCAAGUUAAUUGGCUCUGCGGACGUUCGCAAUUAAUAAAUGCAUAAAAAACGAUCUCGGUUAACG
-...((((((.(((((((((((.((....)).......(((((.((((((.....))))))..).)))).)))))..........))))))........))))))...... ( -31.70)
>DroYak_CAF1 7217 104 - 1
-UGCCCGAGAGUAUGCAGCGAAAAU------GAAAAUGGUCCUUGGCCAAGUUAAUUGGCUUUGCGGACGUUCGCAAUUAAUAAAUGCAUAAAAAACGAUCUCGGUUAACG
-...((((((.(((((((((((.((------....)).((((..((((((.....))))))....)))).)))))..........))))))........))))))...... ( -31.30)
>DroAna_CAF1 9695 95 - 1
AGGCCCGAGAGUAUGCGACGGA------------AUUGUUUCCCGGCCAAGUUAAUUGGCUCUGCGGAGUGGCGCAAUUAAUAAAUGCAGAGAGCA----GUCGGCGGACG
.(((((....)........(((------------(....)))).))))..((..((((.(((((((.(((......)))......)))))))..))----))..))..... ( -26.90)
>consensus
_UGCCCGAGAGUAUGCAGCGAAAAU______GAAAAUGGUCCUUGGCCAAGUUAAUUGGCUUUGCGGACGUUCGCAAUUAAUAAAUGCAUAAAAAACGAUCUCGGUUAACG
....((((((.((((((...........................((((((.....)))))).((((......)))).........))))))........))))))...... (-23.98 = -24.42 +   0.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,974,310 – 9,974,401
Length 91
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 94.15
Mean single sequence MFE -26.50
Consensus MFE -22.92
Energy contribution -22.93
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 0.86
SVM decision value 0.43
SVM RNA-class probability 0.732250
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9974310 91 - 22224390
UUUUUAUUUUUCCCCAGCUGCCCGAGAGUAUGCAGCGAAAAU------GAAAAUGGUCCUUGGCCAAGUUAAUUGGCUUUGCGGACGUUCGCAAUUA
(((((((((((.....(((((.(....)...)))))))))))------)))))..((((..((((((.....))))))....))))........... ( -26.50)
>DroSec_CAF1 19681 91 - 1
CUUUUAUUUUUCCCCAGCUGCCCGAGAGUAUGCAGCGAAAAU------GAAAAUGGUCCUUGGCCAAGUUAAUUGGCUUUGCGGACGUUCGCAAUUA
.((((((((((.....(((((.(....)...)))))))))))------))))...((((..((((((.....))))))....))))........... ( -25.90)
>DroEre_CAF1 6997 96 - 1
-UUUUAUUUUACCCCAGCUGCCCGAGAGUAUGCAGCGAAAAUGAAAAUGAAAAUGGUCCCUGGCCAAGUUAAUUGGCUCUGCGGACGUUCGCAAUUA
-(((((((((......(((((.(....)...))))).......)))))))))...(((((.((((((.....))))))..).))))........... ( -27.62)
>DroYak_CAF1 7248 91 - 1
GUUUUAUUUUUCCCCAGCUGCCCGAGAGUAUGCAGCGAAAAU------GAAAAUGGUCCUUGGCCAAGUUAAUUGGCUUUGCGGACGUUCGCAAUUA
.((((((((((.....(((((.(....)...)))))))))))------))))...((((..((((((.....))))))....))))........... ( -26.00)
>consensus
_UUUUAUUUUUCCCCAGCUGCCCGAGAGUAUGCAGCGAAAAU______GAAAAUGGUCCUUGGCCAAGUUAAUUGGCUUUGCGGACGUUCGCAAUUA
................(((((.(....)...)))))............(((....((((..((((((.....))))))....)))).)))....... (-22.92 = -22.93 +   0.00)

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 11:07:51 2006