Locus 129

Sequence ID 2R_DroMel_CAF1
Location 1,389,780 – 1,389,940
Length 160
Max. P 0.997084
window271 window272

overview

Window 1

Location 1,389,780 – 1,389,900
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.68
Mean single sequence MFE -25.72
Consensus MFE -22.64
Energy contribution -22.82
Covariance contribution 0.19
Combinations/Pair 1.07
Mean z-score -2.11
Structure conservation index 0.88
SVM decision value 0.87
SVM RNA-class probability 0.870177
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1389780 120 + 20766785
GGCCAAAUCAGCGGCAAAAAAGCCAAACGAUACGCUGCGCUCAUAAAAAGACCAUAAAAAAGUGACAUUUUGGCCAGUAGCUAUUGGCAUAAACUCAGUCGAGAAAAAAAGUCAACAAGC
.(((((...((((((......))).........((((.(((....((((...(((......)))...))))))))))).))).))))).....(((....)))................. ( -24.20)
>DroSec_CAF1 16784 118 + 1
GGCCAAAUCAGCGGCAAAAAAGCCAAACGAUACGCUGCGCUCAUAAAAAGACCAUAAAAAAGUGACAUUUUGGCCAGCAGCUAUUGGCAUAAACUCAGUCGAGAAAA-A-GUCAACAAGC
.(((((...((((((......))).........((((.(((....((((...(((......)))...))))))))))).))).))))).....(((....)))....-.-.......... ( -26.60)
>DroSim_CAF1 21538 119 + 1
GGCCAAAUCAGCGGCAAAAAAGCCAAACGAUACGCUGCGCUCAUAAAAAGACCAUAAAAAAGUGACAUUUUGGCCAGCAGCUAUUGGCAUAAACUCAGUCCAGAAAA-AGGUCAACAAGC
((((......(((((......)))...(((((.((((((((....((((...(((......)))...)))))))..))))))))))))......((......))...-.))))....... ( -26.40)
>DroEre_CAF1 14941 117 + 1
-GCCAAAUCAGCGGCAAAAAAGCCAAACGAUACGCUGCGCUCAUAAAAACACUAUAAA-AAGUGACAUUUUGGCCAGAAGCUAUUGGCAUAAACUCAGCCGAGAAAA-AAGUCAACAAGC
-(((((...((((((......)))..........(((.((.((......((((.....-.))))......)))))))..))).))))).....(((....)))....-............ ( -25.70)
>consensus
GGCCAAAUCAGCGGCAAAAAAGCCAAACGAUACGCUGCGCUCAUAAAAAGACCAUAAAAAAGUGACAUUUUGGCCAGCAGCUAUUGGCAUAAACUCAGUCGAGAAAA_AAGUCAACAAGC
.(((((...((((((......))).........((((.(((....((((...(((......)))...))))))))))).))).))))).....(((....)))................. (-22.64 = -22.82 +   0.19) 

alignment

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secondary structure

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dotplot

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Window 2

Location 1,389,820 – 1,389,940
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -28.90
Consensus MFE -26.74
Energy contribution -26.98
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.94
Structure conservation index 0.93
SVM decision value 2.80
SVM RNA-class probability 0.997084
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1389820 120 + 20766785
UCAUAAAAAGACCAUAAAAAAGUGACAUUUUGGCCAGUAGCUAUUGGCAUAAACUCAGUCGAGAAAAAAAGUCAACAAGCGCCUGCGAUAAGCGUUGGGGGCGGGUCAAAAUCAAAUCAC
.........((((.........((((.((((.((((((....)))))).....(((....)))..)))).)))).....(((((.((((....)))).)))))))))............. ( -33.50)
>DroSec_CAF1 16824 118 + 1
UCAUAAAAAGACCAUAAAAAAGUGACAUUUUGGCCAGCAGCUAUUGGCAUAAACUCAGUCGAGAAAA-A-GUCAACAAGCGUCUGCGAUAAGCGUUGGGGGCGGGUCAAAAUCAAAUCAC
.........((((.........((((.((((.(((((......))))).....(((....)))))))-.-)))).....(((((.((((....)))).)))))))))............. ( -29.30)
>DroSim_CAF1 21578 119 + 1
UCAUAAAAAGACCAUAAAAAAGUGACAUUUUGGCCAGCAGCUAUUGGCAUAAACUCAGUCCAGAAAA-AGGUCAACAAGCGUCUGCGAUAAGCGUUGGGGGCGGGUCAAAAUCAAAUCAC
.....................((((.(((((((((....(((.(((((......((......))...-..)))))..)))((((.((((....)))).)))).)))))))))....)))) ( -27.00)
>DroEre_CAF1 14980 118 + 1
UCAUAAAAACACUAUAAA-AAGUGACAUUUUGGCCAGAAGCUAUUGGCAUAAACUCAGCCGAGAAAA-AAGUCAACAAGCGUCUGCGAUAAGCGUUGGGGGCGGGUCAAAAUCAAAUCAC
.........((((.....-.))))..(((((((((....(((.(((((.....(((....)))....-..)))))..)))((((.((((....)))).)))).)))))))))........ ( -29.30)
>DroYak_CAF1 12727 119 + 1
UCAUAAAAAGGCUAUAAAAAAGUGACAUUUUGGCCAGAAGCUAUUGGCAUAAACACAGUCGAGAAAA-AAGUCAACAAGCGUCUGCGAUAAGCGUUGGGGGCGGGUCAAAAUCAAAUCAC
.....................((((.(((((((((....(((.(((((...................-..)))))..)))((((.((((....)))).)))).)))))))))....)))) ( -25.40)
>consensus
UCAUAAAAAGACCAUAAAAAAGUGACAUUUUGGCCAGAAGCUAUUGGCAUAAACUCAGUCGAGAAAA_AAGUCAACAAGCGUCUGCGAUAAGCGUUGGGGGCGGGUCAAAAUCAAAUCAC
.....................((((.(((((((((....(((.(((((.....(((....))).......)))))..)))((((.((((....)))).)))).)))))))))....)))) (-26.74 = -26.98 +   0.24) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:28:31 2006