Locus 1613

Sequence ID 2R_DroMel_CAF1
Location 6,046,998 – 6,047,092
Length 94
Max. P 0.997887
window2701 window2702

overview

Window 1

Location 6,046,998 – 6,047,092
Length 94
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 84.70
Mean single sequence MFE -37.94
Consensus MFE -28.86
Energy contribution -29.46
Covariance contribution 0.60
Combinations/Pair 1.12
Mean z-score -2.56
Structure conservation index 0.76
SVM decision value 1.75
SVM RNA-class probability 0.975629
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6046998 94 + 20766785
UGAGCGUCGAACUCUCUCGCUCUCUCUCGUUUGGGGGCACGUUAUGAAAUUGCCAAGUAGGCAAAAGGAGCGAGUGAGAG-------GGCAGGCAAGCAGA-----
...(((((...(((((((((((.(((((((.((......))..))))..(((((.....)))))...))).)))))))))-------))..)))..))...----- ( -34.90)
>DroSec_CAF1 65273 106 + 1
UGAGCGCCGAGCUCUCUCGCUCUCUCUCGUUUGGGGGCACGUUAUGAAAUUGCCAAGUAGGCAAAAGGAGCGAGCGAGAGAGGACAAGGCAGGCAAGCAGAGGCAG
.....(((...(((((((((((.(((((((.((......))..))))..(((((.....)))))...))).)))))))))))......((......))...))).. ( -41.10)
>DroSim_CAF1 68353 106 + 1
UGAGCGACAAGCUCUCUCGCUCUCUCUCGUUUGGGGGCACGUUAUGAAAUUGCCAAGUAGGCAAAAGGAGCGAGCGAGAGAGGACAAGGCAGGCAAGCAGAGGCAG
...((......(((((((((((.(((((((.((......))..))))..(((((.....)))))...))).)))))))))))......((......))....)).. ( -37.50)
>DroEre_CAF1 66078 95 + 1
UGAGCGUCGAGCUCACUCGCUCUCUCCCGUUUGGGGGCACGUUAUGAAAUUGCCAAGUAGGCAAAAGGAGCGAGCGAGAGAAGGCAAGGUAGCCA-----------
(((((.....)))))(((((((.((((.(((....)))...........(((((.....)))))..)))).)))))))....(((......))).----------- ( -38.10)
>DroYak_CAF1 64937 94 + 1
UGAGCGUCGAGCUCUCUCGCUCUCUCCUGUUUGGGGGCACGUUAUAAAAUUGCCAAGUAGGCAAAGGGAGCGAGGGAGA-AGGGCAAGGUAGGCA-----------
.....(((...((((((((((((((..((((((..((((.(((....)))))))...)))))).)))))))))))))).-..)))..........----------- ( -38.10)
>consensus
UGAGCGUCGAGCUCUCUCGCUCUCUCUCGUUUGGGGGCACGUUAUGAAAUUGCCAAGUAGGCAAAAGGAGCGAGCGAGAGAGGACAAGGCAGGCAAGCAGA_____
...((......(((((((((((.((((.(((....)))...........(((((.....)))))..)))).)))))))))))......))................ (-28.86 = -29.46 +   0.60)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,046,998 – 6,047,092
Length 94
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 84.70
Mean single sequence MFE -34.30
Consensus MFE -27.54
Energy contribution -28.18
Covariance contribution 0.64
Combinations/Pair 1.04
Mean z-score -3.20
Structure conservation index 0.80
SVM decision value 2.95
SVM RNA-class probability 0.997887
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6046998 94 - 20766785
-----UCUGCUUGCCUGCC-------CUCUCACUCGCUCCUUUUGCCUACUUGGCAAUUUCAUAACGUGCCCCCAAACGAGAGAGAGCGAGAGAGUUCGACGCUCA
-----...(((((...((.-------(((((.(((.(((...(((((.....)))))........(((........))).))).))).))))).)).))).))... ( -28.40)
>DroSec_CAF1 65273 106 - 1
CUGCCUCUGCUUGCCUGCCUUGUCCUCUCUCGCUCGCUCCUUUUGCCUACUUGGCAAUUUCAUAACGUGCCCCCAAACGAGAGAGAGCGAGAGAGCUCGGCGCUCA
..(((...((......))...(..(((((((((((.(((...(((((.....)))))........(((........))).))).)))))))))))..))))..... ( -40.80)
>DroSim_CAF1 68353 106 - 1
CUGCCUCUGCUUGCCUGCCUUGUCCUCUCUCGCUCGCUCCUUUUGCCUACUUGGCAAUUUCAUAACGUGCCCCCAAACGAGAGAGAGCGAGAGAGCUUGUCGCUCA
..((..(.((......))......(((((((((((.(((...(((((.....)))))........(((........))).))).)))))))))))...)..))... ( -36.00)
>DroEre_CAF1 66078 95 - 1
-----------UGGCUACCUUGCCUUCUCUCGCUCGCUCCUUUUGCCUACUUGGCAAUUUCAUAACGUGCCCCCAAACGGGAGAGAGCGAGUGAGCUCGACGCUCA
-----------.(((......)))....(((((((.((((..(((((.....)))))........(((........))))))).)))))))(((((.....))))) ( -38.60)
>DroYak_CAF1 64937 94 - 1
-----------UGCCUACCUUGCCCU-UCUCCCUCGCUCCCUUUGCCUACUUGGCAAUUUUAUAACGUGCCCCCAAACAGGAGAGAGCGAGAGAGCUCGACGCUCA
-----------...............-((((.(((.((((..(((((.....))))).........((........)).)))).))).))))((((.....)))). ( -27.70)
>consensus
_____UCUGCUUGCCUGCCUUGCCCUCUCUCGCUCGCUCCUUUUGCCUACUUGGCAAUUUCAUAACGUGCCCCCAAACGAGAGAGAGCGAGAGAGCUCGACGCUCA
...........................((((((((.(((...(((((.....)))))........(((........))).))).))))))))((((.....)))). (-27.54 = -28.18 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:52 2006