Locus 2002

Sequence ID 2L_DroMel_CAF1
Location 5,425,862 – 5,425,957
Length 95
Max. P 0.971586
window3224 window3225

overview

Window 4

Location 5,425,862 – 5,425,957
Length 95
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 81.78
Mean single sequence MFE -26.05
Consensus MFE -15.46
Energy contribution -16.35
Covariance contribution 0.89
Combinations/Pair 1.09
Mean z-score -2.68
Structure conservation index 0.59
SVM decision value 0.70
SVM RNA-class probability 0.825423
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5425862 95 + 22407834
GCCACCAGCCGCCAUUGUUUUUCAACAUUUUUAUGGUAAAAUGUUAAAUGAGCUGGGCGGCACUCGCACUCGCUGUUGGAUGAUGGGGAUUUUAU
.((.(((((((((...((((...((((((((......))))))))....))))..)))))).((.(((.....))).))....)))))....... ( -29.30)
>DroSec_CAF1 45569 72 + 1
GCCACCAGCCGCCAUUGUUUUUCAACAUUUUUAUGGUAAAAUGUUAAAUGAGCUGGG-----------------------UGGUGGGGAUUUUAU
.((.(((.(((((...((((...((((((((......))))))))....))))..))-----------------------))))))))....... ( -23.30)
>DroSim_CAF1 56603 72 + 1
GCCACCAGCCGCCAUUGUUUUUCAACAUUUUUAUGGUAAAAUGUUAAAUGAGCUGGG-----------------------UGGUGGGGAUUUUAU
.((.(((.(((((...((((...((((((((......))))))))....))))..))-----------------------))))))))....... ( -23.30)
>DroEre_CAF1 44435 85 + 1
GCCACCCGCCGCCAUUGUUUUUCAACAUUUUUAUGGUAAAAUGUUAAAUGAGCUGGGCGGCAAUU------GCUGU----UGGUGGGGAUUUUAU
.(((((.((((((...((((...((((((((......))))))))....))))..))))))(((.------...))----))))))......... ( -29.30)
>DroYak_CAF1 52071 85 + 1
GCCACCAGCCGCCAUUGUUUUUCAACAUUUUUAUGGUAAAAUGUUAAAUGAGCUGGGCGGCAAUC------GCUGG----UGGUGGGGAUUUUAU
(((((((((((((...((((...((((((((......))))))))....))))..))))))....------..)))----))))........... ( -31.50)
>DroAna_CAF1 48205 82 + 1
UCAUAGCGACGCCAUUGUUUUUCAACAUUUUUAUGGUAAAAUGUUAAAUGAGCUGGGCGGCG---------GCCGA----CAAGGGGGUUUUUAU
..((((.(((.((.(((((....((((((((......))))))))..........(((....---------)))))----))).)).))).)))) ( -19.60)
>consensus
GCCACCAGCCGCCAUUGUUUUUCAACAUUUUUAUGGUAAAAUGUUAAAUGAGCUGGGCGGCA_________GCUG_____UGGUGGGGAUUUUAU
.(((((....(((...((((...((((((((......))))))))....))))..)))(((..........))).......)))))......... (-15.46 = -16.35 +   0.89)

alignment

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secondary structure

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dotplot

Postscript

Window 5

Location 5,425,862 – 5,425,957
Length 95
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 81.78
Mean single sequence MFE -24.04
Consensus MFE -13.10
Energy contribution -14.66
Covariance contribution 1.56
Combinations/Pair 1.05
Mean z-score -4.33
Structure conservation index 0.54
SVM decision value 1.68
SVM RNA-class probability 0.971586
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5425862 95 - 22407834
AUAAAAUCCCCAUCAUCCAACAGCGAGUGCGAGUGCCGCCCAGCUCAUUUAACAUUUUACCAUAAAAAUGUUGAAAAACAAUGGCGGCUGGUGGC
.........((((((.......((....))....((((((.......(((((((((((......))))))))))).......)))))))))))). ( -28.24)
>DroSec_CAF1 45569 72 - 1
AUAAAAUCCCCACCA-----------------------CCCAGCUCAUUUAACAUUUUACCAUAAAAAUGUUGAAAAACAAUGGCGGCUGGUGGC
.........((((((-----------------------.((.((.(((((((((((((......))))))))))......))))))).)))))). ( -21.60)
>DroSim_CAF1 56603 72 - 1
AUAAAAUCCCCACCA-----------------------CCCAGCUCAUUUAACAUUUUACCAUAAAAAUGUUGAAAAACAAUGGCGGCUGGUGGC
.........((((((-----------------------.((.((.(((((((((((((......))))))))))......))))))).)))))). ( -21.60)
>DroEre_CAF1 44435 85 - 1
AUAAAAUCCCCACCA----ACAGC------AAUUGCCGCCCAGCUCAUUUAACAUUUUACCAUAAAAAUGUUGAAAAACAAUGGCGGCGGGUGGC
.........(((((.----.....------...(((((((.......(((((((((((......))))))))))).......)))))))))))). ( -27.24)
>DroYak_CAF1 52071 85 - 1
AUAAAAUCCCCACCA----CCAGC------GAUUGCCGCCCAGCUCAUUUAACAUUUUACCAUAAAAAUGUUGAAAAACAAUGGCGGCUGGUGGC
............(((----(((..------....((((((.......(((((((((((......))))))))))).......)))))))))))). ( -28.54)
>DroAna_CAF1 48205 82 - 1
AUAAAAACCCCCUUG----UCGGC---------CGCCGCCCAGCUCAUUUAACAUUUUACCAUAAAAAUGUUGAAAAACAAUGGCGUCGCUAUGA
...............----..(((---------.(.((((.......(((((((((((......))))))))))).......)))).)))).... ( -17.04)
>consensus
AUAAAAUCCCCACCA_____CAGC_________UGCCGCCCAGCUCAUUUAACAUUUUACCAUAAAAAUGUUGAAAAACAAUGGCGGCUGGUGGC
.........((((((.....................((((.......(((((((((((......))))))))))).......))))..)))))). (-13.10 = -14.66 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:53 2006