Locus 5599

Sequence ID X_DroMel_CAF1
Location 14,454,987 – 14,455,107
Length 120
Max. P 0.940604
window9092 window9093

overview

Window 2

Location 14,454,987 – 14,455,107
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 78.81
Mean single sequence MFE -37.27
Consensus MFE -25.17
Energy contribution -27.43
Covariance contribution 2.26
Combinations/Pair 1.17
Mean z-score -2.10
Structure conservation index 0.68
SVM decision value 1.31
SVM RNA-class probability 0.940604
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14454987 120 + 22224390
AAUGGGCCAAGAUUUCGAUAUAGAAUGCUGCAAAUUGGGUUGGGGCAAUGGAACCCAGAUUGGCAGUGGAUCUGCUAGAUGGGAGUGCUAUUUGUCUAGCGGGACAUUGGCUUAGGCUGG
..((((((((..(..((...((((.((((.(((......))).))))((((..((((..(((((((.....))))))).))))....))))...)))).))..)..))))))))...... ( -41.70)
>DroSim_CAF1 762 113 + 1
AAUGGGCCAAGAUUUCGAUCUAGAAUGGUGCGACUUGGGUUGGGCCAA-------CAGAUUGGCAGUGGAUCUGCUGGAUGGGAGUGCUAUUUGUCUAGCGGGAUAUUGGCUUAGGCUGG
....((((...(((((.((((((..((((.((((....)))).)))).-------((((((.......)))))))))))).)))))((((..(((((....))))).))))...)))).. ( -40.30)
>DroEre_CAF1 350 95 + 1
AACGUGCCAAGAUU-GGAUACAGAAUGCUGC-----------------------CCAGAUUGGCAGUGGAUCCG-CGGAUGGGAGUGCUAUUUGUCUAGCGGGACAUUGGCUUAGGCUGG
..((.(((......-((((......((((((-----------------------(......))))))).))))(-(.((((....(((((......)))))...)))).))...))))). ( -29.80)
>consensus
AAUGGGCCAAGAUUUCGAUAUAGAAUGCUGC_A_UUGGGUUGGG_CAA______CCAGAUUGGCAGUGGAUCUGCUGGAUGGGAGUGCUAUUUGUCUAGCGGGACAUUGGCUUAGGCUGG
....((((.................((((.((((....)))).))))..............(.(((((..((((((((((..(.......)..)))))))))).))))).)...)))).. (-25.17 = -27.43 +   2.26)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 3

Location 14,454,987 – 14,455,107
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.81
Mean single sequence MFE -24.60
Consensus MFE -13.59
Energy contribution -13.37
Covariance contribution -0.22
Combinations/Pair 1.07
Mean z-score -2.38
Structure conservation index 0.55
SVM decision value 0.46
SVM RNA-class probability 0.746273
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14454987 120 - 22224390
CCAGCCUAAGCCAAUGUCCCGCUAGACAAAUAGCACUCCCAUCUAGCAGAUCCACUGCCAAUCUGGGUUCCAUUGCCCCAACCCAAUUUGCAGCAUUCUAUAUCGAAAUCUUGGCCCAUU
.........(((((.((..(((((((...............))))))(((....((((.(((.((((((..........))))))))).))))...))).....)..)).)))))..... ( -26.16)
>DroSim_CAF1 762 113 - 1
CCAGCCUAAGCCAAUAUCCCGCUAGACAAAUAGCACUCCCAUCCAGCAGAUCCACUGCCAAUCUG-------UUGGCCCAACCCAAGUCGCACCAUUCUAGAUCGAAAUCUUGGCCCAUU
.........(((((.((..(((((((......(((((.....(((((((((.........)))))-------)))).........))).)).....)))))..))..)).)))))..... ( -22.84)
>DroEre_CAF1 350 95 - 1
CCAGCCUAAGCCAAUGUCCCGCUAGACAAAUAGCACUCCCAUCCG-CGGAUCCACUGCCAAUCUGG-----------------------GCAGCAUUCUGUAUCC-AAUCUUGGCACGUU
.........(((((......((((......))))..........(-((((....(((((......)-----------------------))))...)))))....-....)))))..... ( -24.80)
>consensus
CCAGCCUAAGCCAAUGUCCCGCUAGACAAAUAGCACUCCCAUCCAGCAGAUCCACUGCCAAUCUGG______UUG_CCCAACCCAA_U_GCAGCAUUCUAUAUCGAAAUCUUGGCCCAUU
.........(((((......((((......))))............(((((.........))))).............................................)))))..... (-13.59 = -13.37 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:57 2006