Locus 1253

Sequence ID 2L_DroMel_CAF1
Location 3,311,324 – 3,311,524
Length 200
Max. P 0.899367
window2049 window2050

overview

Window 9

Location 3,311,324 – 3,311,444
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 90.67
Mean single sequence MFE -47.80
Consensus MFE -41.43
Energy contribution -42.07
Covariance contribution 0.64
Combinations/Pair 1.16
Mean z-score -1.98
Structure conservation index 0.87
SVM decision value 1.01
SVM RNA-class probability 0.899367
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3311324 120 + 22407834
CAGAAGGUGGACCUAUCGGCCUUCUCCGCCUGGCUGCCCGUCACCCUAAUGGCCUUCAUCAUCUUCAUUGCCAACGUGGGCGUUAUCUCGGUGACGAUGGUGGUUUUGGUGGAGAUCCUG
(((.((((.((....)).))))((((((((.(((..(((((((((.....(((................)))((((....)))).....)))))))..))..)))..))))))))..))) ( -46.19)
>DroSec_CAF1 20245 120 + 1
CAGAAGGCGGACCUGUCGGCCUUCUCCGCCUGGCUGCCCGUCACCCUGAUGGCCUUCAUCAUCUUCAUUGCCAACGUGGGCGUUAUCUCGGUGUCGAUGGUGGUUUUGGUGGAGAUCCUG
(((.((((.((....)).))))((((((((.(((..((((.((((.(((((.....)))))........(((......)))........)))).))..))..)))..))))))))..))) ( -48.10)
>DroSim_CAF1 20219 120 + 1
CAGAAGGUGGACCUGUCGGCCUUCUCCGCCUGGCUGCCCGUCACCCUGAUGGCCUUCAUCAUCUUCAUUGCCAACGUGGGCGUUAUCUCGGUGACGAUGGUGGUAUUGGUGGAGAUCCUG
(((.((((.((....)).))))((((((((..((..(((((((((.(((((.....)))))........(((......)))........)))))))..))..))...))))))))..))) ( -51.00)
>DroEre_CAF1 28463 120 + 1
CAGAAGGUGGACCUGUCGGCCUUCUCCGCCUGGCUGCCCGUCACCCUGAUGGCCUUCAUCAUCUUCAUUGCCAACGUGGGCGUCAUCUCGGUGACGAUGGUGGUUUUGGUGGAGAUCCUG
(((.((((.((....)).))))((((((((.(((..(((((((((..((((((.(((((................))))).))))))..)))))))..))..)))..))))))))..))) ( -52.79)
>DroYak_CAF1 20504 120 + 1
GAGAAGGCGGACCUAUCGGCCUUUUCCGCCUGGCUACCCGUCACCCUGAUGGCCUUUAUCAUCUUCAUUGCCAACGUGGGCGUCAUCUCGGUGACAAUGGUGGUUUUGGUGGAGAUCCUG
..((((((.((....)).))))))((((((.(((((((.((((((..((((((................(((......)))))))))..))))))...)))))))..))))))....... ( -47.99)
>DroAna_CAF1 30184 120 + 1
CUGGAAGCAGACAUGUCUGCCUACUCCGCGUGGCUGCCCGUGUGCCUCAUGUCCUUCAUUAUAUUCAUUGCCAACGUGGGAGUCAUUUCGGUCACCAUGGUGGUCCUGGUGGAGAUCCUG
..(((.(((((....)))))...((((((((((((.(((((..((...(((..............))).))..))).)).))))))...(..(((....)))..)...)))))).))).. ( -40.74)
>consensus
CAGAAGGCGGACCUGUCGGCCUUCUCCGCCUGGCUGCCCGUCACCCUGAUGGCCUUCAUCAUCUUCAUUGCCAACGUGGGCGUCAUCUCGGUGACGAUGGUGGUUUUGGUGGAGAUCCUG
..((((((.((....)).))))))((((((..(((((((((((((..((((((.(((((................))))).))))))..)))))))..))))))...))))))....... (-41.43 = -42.07 +   0.64)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,311,404 – 3,311,524
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 90.89
Mean single sequence MFE -47.82
Consensus MFE -40.74
Energy contribution -40.27
Covariance contribution -0.47
Combinations/Pair 1.22
Mean z-score -1.72
Structure conservation index 0.85
SVM decision value 0.33
SVM RNA-class probability 0.693462
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3311404 120 + 22407834
CGUUAUCUCGGUGACGAUGGUGGUUUUGGUGGAGAUCCUGCCGCAGAAGAUCCGCGCGGUGGCCACCAGCUUCUGCCUGGGCUGCCUCAGUUUCUUCGCCUUCGCCUCGCUGAAGACUUU
.....(((((((((....(((((....((((((((..(((..((((....((((.((((.(((.....))).)))).))))))))..)))..)))))))).))))))))))).))).... ( -48.00)
>DroSec_CAF1 20325 120 + 1
CGUUAUCUCGGUGUCGAUGGUGGUUUUGGUGGAGAUCCUGCCGCAGAAAAUCCGCGCGGUGGCCACCAGCUUCUGUCUGGGCUGCCUUAGUUUCUUCGCCUUCGCCUCGCUGAAGACCUU
.....((((((((.....(((((....((((((((..(((((((.(......)..)))))(((..(((((....).))))...)))..))..)))))))).))))).))))).))).... ( -44.60)
>DroSim_CAF1 20299 120 + 1
CGUUAUCUCGGUGACGAUGGUGGUAUUGGUGGAGAUCCUGCCGCAGAAGAUCCGCGCGGUGGCCACCAGCUUCUGUCUGGGCUGCCUCAGUUUCUUUGCCUUCGCCUCGCUGAAGACCUU
.....(((((((((....(((((....((..((((..(((..((((....((((.((((.(((.....))).)))).))))))))..)))..))))..)).))))))))))).))).... ( -45.00)
>DroEre_CAF1 28543 120 + 1
CGUCAUCUCGGUGACGAUGGUGGUUUUGGUGGAGAUCCUGCCGCAGAAGAUCCGGGCGGUGGCCACCAGCUUCUGCCUGGGCUCCCUCAGCUUCUUUGCCUUCGUCUCGCUGAAGACCUU
.(((...(((((((.(((((.(((...((..(.....)..))...(((((.((((((((.(((.....))).))))))))(((.....))).)))))))).)))))))))))).)))... ( -47.00)
>DroYak_CAF1 20584 120 + 1
CGUCAUCUCGGUGACAAUGGUGGUUUUGGUGGAGAUCCUGCCGCAGAAGAUCCGGGCGGUGGCCACCAGCUUCUGCCUGGGCUGCCUUAGUUUCUUCGCCUUCACCUCGCUGAAGACCUU
.(((...(((((((....(((((....((((((((..(((..((((....(((((((((.(((.....))).)))))))))))))..)))..)))))))).)))))))))))).)))... ( -54.60)
>DroAna_CAF1 30264 120 + 1
AGUCAUUUCGGUCACCAUGGUGGUCCUGGUGGAGAUCCUGCCGCAGAGAAUCCGAGCAGUGGCCACCAGCUUCUGCCUGGGCAGUCUGAGCUUCUUCGCGUUCACUUCGGUGAAGACCUU
.........((((....(((((((((((.((((..(((((...))).)).))))..))).))))))))((((((((....))))...)))).........(((((....))))))))).. ( -47.70)
>consensus
CGUCAUCUCGGUGACGAUGGUGGUUUUGGUGGAGAUCCUGCCGCAGAAGAUCCGCGCGGUGGCCACCAGCUUCUGCCUGGGCUGCCUCAGUUUCUUCGCCUUCGCCUCGCUGAAGACCUU
.(((...(((((((....(((((....((((((((..(((..((((....((((.((((.(((.....))).)))).))))))))..)))..)))))))).)))))))))))).)))... (-40.74 = -40.27 +  -0.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:49 2006