Locus 4826

Sequence ID 3R_DroMel_CAF1
Location 12,621,506 – 12,621,606
Length 100
Max. P 0.995296
window7911 window7912

overview

Window 1

Location 12,621,506 – 12,621,606
Length 100
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 86.94
Mean single sequence MFE -31.95
Consensus MFE -23.85
Energy contribution -24.48
Covariance contribution 0.62
Combinations/Pair 1.04
Mean z-score -2.06
Structure conservation index 0.75
SVM decision value 0.82
SVM RNA-class probability 0.859246
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12621506 100 + 27905053
AAAG---A---AAGAAGGAAGCGAAAUGCCUGAGAUUCCUGCCCUUUUUGGGAAGGUGGAGUCGGAGCA-----------AGGCAUUCAUAUUUAUGCCUGGCCAGGACAUCGGAUG
....---.---..........(((..((((((.((((((..(((.....))).....))))))...((.-----------((((((........)))))).)))))).))))).... ( -32.10)
>DroSec_CAF1 103975 100 + 1
AAAG---A---AAGAAAGAAGCGAAAUGCCUGAGAUUCCUGCCCUUUUUGGGAAGGUGGAGUCGGAGCA-----------AGGCAUUCAUAUUUAUGCCUGGCCAGGACAUCGGAUG
....---.---..........(((..((((((.((((((..(((.....))).....))))))...((.-----------((((((........)))))).)))))).))))).... ( -32.10)
>DroSim_CAF1 104684 100 + 1
AAAG---A---AAGAAAGGAGCGAAAUGCCUGAGAUUCCUGCCCUUUUUGGGAAGGUGGAGUCGGGGCA-----------AGGCAUUCAUAUUUAUGCCUGGCCAGGACAUCGGAUG
....---.---..........(((..(((((..((((((..(((.....))).....))))))..(((.-----------((((((........)))))).)))))).))))).... ( -33.10)
>DroYak_CAF1 104176 116 + 1
AAAGGAGAAAGAAGAAAGGGGAGAAAUGCCUGAGAUUCCUGCCCUU-UUGGGAAGGUGUAGCAGGAGCAGGAGCAGGAGCAGACAUUCAUAUUUAUGUCUGGCCAGGACAUCGGAUG
.................(((.(....).)))(((.((((((((((.-(((.(....).))).))).)))))))).((..(((((((........))))))).))......))..... ( -30.50)
>consensus
AAAG___A___AAGAAAGAAGCGAAAUGCCUGAGAUUCCUGCCCUUUUUGGGAAGGUGGAGUCGGAGCA___________AGGCAUUCAUAUUUAUGCCUGGCCAGGACAUCGGAUG
.....................(((..((((((.((((((..(((.....))).....)))))).................((((((........))))))...)))).))))).... (-23.85 = -24.48 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 12,621,506 – 12,621,606
Length 100
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 86.94
Mean single sequence MFE -27.92
Consensus MFE -23.62
Energy contribution -23.25
Covariance contribution -0.38
Combinations/Pair 1.05
Mean z-score -3.17
Structure conservation index 0.85
SVM decision value 2.56
SVM RNA-class probability 0.995296
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12621506 100 - 27905053
CAUCCGAUGUCCUGGCCAGGCAUAAAUAUGAAUGCCU-----------UGCUCCGACUCCACCUUCCCAAAAAGGGCAGGAAUCUCAGGCAUUUCGCUUCCUUCUU---U---CUUU
.....((((.((((((.((((((........))))))-----------.))..........(((.(((.....))).))).....)))))))).............---.---.... ( -27.10)
>DroSec_CAF1 103975 100 - 1
CAUCCGAUGUCCUGGCCAGGCAUAAAUAUGAAUGCCU-----------UGCUCCGACUCCACCUUCCCAAAAAGGGCAGGAAUCUCAGGCAUUUCGCUUCUUUCUU---U---CUUU
.....((((.((((((.((((((........))))))-----------.))..........(((.(((.....))).))).....)))))))).............---.---.... ( -27.10)
>DroSim_CAF1 104684 100 - 1
CAUCCGAUGUCCUGGCCAGGCAUAAAUAUGAAUGCCU-----------UGCCCCGACUCCACCUUCCCAAAAAGGGCAGGAAUCUCAGGCAUUUCGCUCCUUUCUU---U---CUUU
.....((((((..(((.((((((........))))))-----------.)))..)))....(((.(((.....))).))).)))...(((.....)))........---.---.... ( -27.40)
>DroYak_CAF1 104176 116 - 1
CAUCCGAUGUCCUGGCCAGACAUAAAUAUGAAUGUCUGCUCCUGCUCCUGCUCCUGCUACACCUUCCCAA-AAGGGCAGGAAUCUCAGGCAUUUCUCCCCUUUCUUCUUUCUCCUUU
.....((((.(((((.(((((((........))))))).((((((....((....))....((((.....-))))))))))...)))))))))........................ ( -30.10)
>consensus
CAUCCGAUGUCCUGGCCAGGCAUAAAUAUGAAUGCCU___________UGCUCCGACUCCACCUUCCCAAAAAGGGCAGGAAUCUCAGGCAUUUCGCUCCUUUCUU___U___CUUU
.....((((.(((((..((((((........))))))........................(((.(((.....))).)))....)))))))))........................ (-23.62 = -23.25 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:49 2006