Locus 1717

Sequence ID 2L_DroMel_CAF1
Location 4,720,135 – 4,720,245
Length 110
Max. P 0.878407
window2752 window2753

overview

Window 2

Location 4,720,135 – 4,720,245
Length 110
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 83.83
Mean single sequence MFE -31.53
Consensus MFE -22.92
Energy contribution -25.03
Covariance contribution 2.11
Combinations/Pair 1.03
Mean z-score -2.39
Structure conservation index 0.73
SVM decision value 0.90
SVM RNA-class probability 0.878407
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4720135 110 + 22407834
GCACAAAAUAUGGACAGGCUAUUUGGGCUGCAGAGGUUUUGUAGCCUGGCUUCUGGACCACUGAGUACUGUCAGCCAAUAAAGUGUUUUUCU------UGUUUUUGCUGAAAUAUC
(((.((((((.(((.((((.((((.(((((((((((((....))))).((((..(.....).)))).))).)))))....)))))))).)))------)))))))))......... ( -28.70)
>DroSec_CAF1 148488 102 + 1
GCACAAAAUAUGGACAGGCUAUUAGAGCUGCAGAGGUUUA--------------UGGCCACUGAGUACUGUCAGCCAAUAAAGAGUUUUUCUUUCCAUUGUUUGUGCUGAAAUAUC
(((((((..(((((..((((..(((.(((.(((.(((...--------------..))).)))))).)))..))))....(((((...))))))))))..)))))))......... ( -33.30)
>DroSim_CAF1 144540 102 + 1
GCACAAAAUAUGGACAGGCUAUUAGGGCUGCAGAGGUUUA--------------UGGCCACUGAGUACUGUCAGCCAAUAAAGUGUUUUUCUUUCCAUUGUUUGUGCUGAAAUAUC
(((((((..(((((..((((..(((..((.(((.(((...--------------..))).)))))..)))..))))....(((.......))))))))..)))))))......... ( -32.60)
>consensus
GCACAAAAUAUGGACAGGCUAUUAGGGCUGCAGAGGUUUA______________UGGCCACUGAGUACUGUCAGCCAAUAAAGUGUUUUUCUUUCCAUUGUUUGUGCUGAAAUAUC
(((((((...((((..((((..(((..((.(((.((((.................)))).)))))..)))..))))....(((.......)))))))...)))))))......... (-22.92 = -25.03 +   2.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 4,720,135 – 4,720,245
Length 110
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 83.83
Mean single sequence MFE -24.97
Consensus MFE -16.03
Energy contribution -18.37
Covariance contribution 2.33
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 0.64
SVM decision value 0.07
SVM RNA-class probability 0.568311
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4720135 110 - 22407834
GAUAUUUCAGCAAAAACA------AGAAAAACACUUUAUUGGCUGACAGUACUCAGUGGUCCAGAAGCCAGGCUACAAAACCUCUGCAGCCCAAAUAGCCUGUCCAUAUUUUGUGC
...............(((------(((...(((..((((((((((.(((......((((.((........)))))).......))))))))..)))))..))).....)))))).. ( -21.82)
>DroSec_CAF1 148488 102 - 1
GAUAUUUCAGCACAAACAAUGGAAAGAAAAACUCUUUAUUGGCUGACAGUACUCAGUGGCCA--------------UAAACCUCUGCAGCUCUAAUAGCCUGUCCAUAUUUUGUGC
.........(((((((..(((((((((.....))))....(((((..((..(((((.((...--------------....)).))).))..))..)))))..)))))..))))))) ( -27.50)
>DroSim_CAF1 144540 102 - 1
GAUAUUUCAGCACAAACAAUGGAAAGAAAAACACUUUAUUGGCUGACAGUACUCAGUGGCCA--------------UAAACCUCUGCAGCCCUAAUAGCCUGUCCAUAUUUUGUGC
.........(((((((..((((((((.......)))....(((((..((..(((((.((...--------------....)).))).))..))..)))))..)))))..))))))) ( -25.60)
>consensus
GAUAUUUCAGCACAAACAAUGGAAAGAAAAACACUUUAUUGGCUGACAGUACUCAGUGGCCA______________UAAACCUCUGCAGCCCUAAUAGCCUGUCCAUAUUUUGUGC
.........(((((((..(((((..(((......)))...(((((..((..(((((.((.....................)).))).))..))..)))))..)))))..))))))) (-16.03 = -18.37 +   2.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:18 2006