Locus 1256

Sequence ID 3R_DroMel_CAF1
Location 3,770,391 – 3,770,511
Length 120
Max. P 0.843542
window2048 window2049

overview

Window 8

Location 3,770,391 – 3,770,511
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -39.43
Consensus MFE -34.39
Energy contribution -34.83
Covariance contribution 0.45
Combinations/Pair 1.02
Mean z-score -2.10
Structure conservation index 0.87
SVM decision value 0.29
SVM RNA-class probability 0.670619
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3770391 120 + 27905053
GCUGUGGACUGAGAAAUGCAACGGGAUGCAUCCCUGGCGAUAUAUUUUGGCAGCAAGUAUUCGGUGGGUGUAUUUUUAGCUGGCCAAAAAUGAAUUUGCAUCGAAUGCAUCCGUCAGCAC
((((((((........(((...((((....))))((.(((......))).))))).((((((((((.(..(((((((.(....).)))))))....).)))))))))).)))).)))).. ( -39.40)
>DroSim_CAF1 3595 120 + 1
GCUGUGGACUGAGAAAUGCCACGGGAUGCAUCCCUGGCGAUACAUUUUGGCAGCAAGAAUUCGGAGGGUGUAUUUUUAGCUGGCCAAAAAUGAAUUUGCAUCGAAUGCAUCCGUCAGCAC
((((((((........(((((.((((....)))))))))...((((((((((((((((((.((.....)).)))))).))).))).))))))....(((((...))))))))).)))).. ( -40.40)
>DroYak_CAF1 2074 120 + 1
GCUGUGGACUGAGAAAUGCCACGGGAUGCAUCCCUGGCGAAAUAUUUUGGCAGCAAGUAUUCGGAGGAUGUAUUUUUAGCUGGCCAAAAAUGAAUUUGAAUCGAAUGCAUCCGUCAGCAC
(((((((((((.(((((((((.((((....)))))))).....)))))..)))...((((((((.((((.(((((((.(....).))))))).))))...)))))))).)))).)))).. ( -38.50)
>consensus
GCUGUGGACUGAGAAAUGCCACGGGAUGCAUCCCUGGCGAUAUAUUUUGGCAGCAAGUAUUCGGAGGGUGUAUUUUUAGCUGGCCAAAAAUGAAUUUGCAUCGAAUGCAUCCGUCAGCAC
(((((((((((.(((((((((.((((....)))))))).....)))))..)))...((((((((.((((.(((((((.(....).))))))).))))...)))))))).)))).)))).. (-34.39 = -34.83 +   0.45)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,770,391 – 3,770,511
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -34.41
Consensus MFE -30.63
Energy contribution -30.96
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.36
Structure conservation index 0.89
SVM decision value 0.76
SVM RNA-class probability 0.843542
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3770391 120 - 27905053
GUGCUGACGGAUGCAUUCGAUGCAAAUUCAUUUUUGGCCAGCUAAAAAUACACCCACCGAAUACUUGCUGCCAAAAUAUAUCGCCAGGGAUGCAUCCCGUUGCAUUUCUCAGUCCACAGC
(..((((..((((((...((((((.....((((((((....))))))))...(((..((((((.((.......)).))).)))...))).))))))....))))))..))))..)..... ( -33.90)
>DroSim_CAF1 3595 120 - 1
GUGCUGACGGAUGCAUUCGAUGCAAAUUCAUUUUUGGCCAGCUAAAAAUACACCCUCCGAAUUCUUGCUGCCAAAAUGUAUCGCCAGGGAUGCAUCCCGUGGCAUUUCUCAGUCCACAGC
..((((..((((......((((((.......(((((((.(((........................))))))))))))))))((((((((....)))).))))........)))).)))) ( -36.57)
>DroYak_CAF1 2074 120 - 1
GUGCUGACGGAUGCAUUCGAUUCAAAUUCAUUUUUGGCCAGCUAAAAAUACAUCCUCCGAAUACUUGCUGCCAAAAUAUUUCGCCAGGGAUGCAUCCCGUGGCAUUUCUCAGUCCACAGC
..(((...((((((((((((.......))..(((((((.(((........................))))))))))...........)))))))))).(((((........).))))))) ( -32.76)
>consensus
GUGCUGACGGAUGCAUUCGAUGCAAAUUCAUUUUUGGCCAGCUAAAAAUACACCCUCCGAAUACUUGCUGCCAAAAUAUAUCGCCAGGGAUGCAUCCCGUGGCAUUUCUCAGUCCACAGC
..(((...((((((((((((.......))..(((((((.(((........................))))))))))...........)))))))))).(((((........).))))))) (-30.63 = -30.96 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:49 2006