Locus 2398

Sequence ID 3L_DroMel_CAF1
Location 6,748,776 – 6,748,888
Length 112
Max. P 0.997231
window3698 window3699

overview

Window 8

Location 6,748,776 – 6,748,888
Length 112
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 91.89
Mean single sequence MFE -26.42
Consensus MFE -23.04
Energy contribution -22.77
Covariance contribution -0.28
Combinations/Pair 1.07
Mean z-score -2.85
Structure conservation index 0.87
SVM decision value 2.50
SVM RNA-class probability 0.994632
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6748776 112 + 23771897
UAACCUCGGCAAAAAUCGCGUUUUGAAUUUGAAAUGCGAUUUUUGUGGUUGCGUUUUAGUUGGGUUUUGUGUGUUUAUUUUUAUAUUUUGGUGUUUCGCUUCAAA--AAUUUAU
(((((...((((((((((((((((......))))))))))))))))))))).........((((((((..(((..((((..........))))...)))....))--)))))). ( -26.40)
>DroSec_CAF1 11794 112 + 1
UAACCUCGGCAAAAAUCGCGUUUUGAAUUUGAAAUGCGAUUUUUGUGGUUGCGUUUUAGUUUGGUCUUGUGUGUUUUUUUUUAUAUUUUGGUGUUUCGCUUCAAA--AAUUUAU
.((((...((((((((((((((((......))))))))))))))))))))(((.......(..(....(((((........))))).)..).....)))......--....... ( -25.70)
>DroSim_CAF1 11893 112 + 1
UAACCUCGGCAAAAAUCGCGUUUUGAAUUUGAAAUGCGAUUUUUGUGGUUGCGUUUUAGUUUGGUCUUGUGUGUUUAUUUUUAUAUUUUGGUGUUUCGCUUCAAA--AAUUUAU
.((((...((((((((((((((((......))))))))))))))))))))(((.......(..(....(((((........))))).)..).....)))......--....... ( -25.70)
>DroEre_CAF1 24407 112 + 1
UAACCUCGGCAAAAAUCGCGUUUUGAAUUUGAAAUGCGAUUUUUGUGGUUGCGUUUUAGUUUGGACUCGUGUGUUUAUUUUUAUAUUUUGGUGUUUCGCUUCAAA--AAUUUAU
(((((...((((((((((((((((......)))))))))))))))))))))..........(((((......)))))........((((((.(.....).)))))--)...... ( -26.70)
>DroYak_CAF1 14323 114 + 1
UAACCUCGGCAAAAAUCGCGUUUUGAAUUUGAAAUGCGAUUUUUGUGGUUGCGUUUUAGUUUGGUCUUGUGUGUUUAUUUUUAUAUUUUGGUGUUUCGCUUCAAAAAAAUUUAU
.((((...((((((((((((((((......))))))))))))))))))))(((.......(..(....(((((........))))).)..).....)))............... ( -25.70)
>DroAna_CAF1 20274 100 + 1
UAACCUCGGCAAGAAUCGCGUUUUGAAUUUGAAAUGCGAUUUUUGUGGUUGUGUUUUAUUUU-------UUUGACUACGU-----UUUUGGUGUUUCGUUUCAAA--AAUUUAU
(((((...((((((((((((((((......))))))))))))))))))))).....((..((-------(((((..(((.-----...........))).)))))--))..)). ( -28.30)
>consensus
UAACCUCGGCAAAAAUCGCGUUUUGAAUUUGAAAUGCGAUUUUUGUGGUUGCGUUUUAGUUUGGUCUUGUGUGUUUAUUUUUAUAUUUUGGUGUUUCGCUUCAAA__AAUUUAU
(((((...((((((((((((((((......)))))))))))))))))))))...................................(((((.(.....).)))))......... (-23.04 = -22.77 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,748,776 – 6,748,888
Length 112
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 91.89
Mean single sequence MFE -14.98
Consensus MFE -13.43
Energy contribution -13.60
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.65
Structure conservation index 0.90
SVM decision value 2.82
SVM RNA-class probability 0.997231
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6748776 112 - 23771897
AUAAAUU--UUUGAAGCGAAACACCAAAAUAUAAAAAUAAACACACAAAACCCAACUAAAACGCAACCACAAAAAUCGCAUUUCAAAUUCAAAACGCGAUUUUUGCCGAGGUUA
.......--......(((...........................................)))((((.((((((((((.(((........))).))))))))))....)))). ( -14.63)
>DroSec_CAF1 11794 112 - 1
AUAAAUU--UUUGAAGCGAAACACCAAAAUAUAAAAAAAAACACACAAGACCAAACUAAAACGCAACCACAAAAAUCGCAUUUCAAAUUCAAAACGCGAUUUUUGCCGAGGUUA
.......--......(((...........................................)))((((.((((((((((.(((........))).))))))))))....)))). ( -14.63)
>DroSim_CAF1 11893 112 - 1
AUAAAUU--UUUGAAGCGAAACACCAAAAUAUAAAAAUAAACACACAAGACCAAACUAAAACGCAACCACAAAAAUCGCAUUUCAAAUUCAAAACGCGAUUUUUGCCGAGGUUA
.......--......(((...........(((....)))........((......))....)))((((.((((((((((.(((........))).))))))))))....)))). ( -14.80)
>DroEre_CAF1 24407 112 - 1
AUAAAUU--UUUGAAGCGAAACACCAAAAUAUAAAAAUAAACACACGAGUCCAAACUAAAACGCAACCACAAAAAUCGCAUUUCAAAUUCAAAACGCGAUUUUUGCCGAGGUUA
.......--......(((...........(((....)))........(((....)))....)))((((.((((((((((.(((........))).))))))))))....)))). ( -16.00)
>DroYak_CAF1 14323 114 - 1
AUAAAUUUUUUUGAAGCGAAACACCAAAAUAUAAAAAUAAACACACAAGACCAAACUAAAACGCAACCACAAAAAUCGCAUUUCAAAUUCAAAACGCGAUUUUUGCCGAGGUUA
...............(((...........(((....)))........((......))....)))((((.((((((((((.(((........))).))))))))))....)))). ( -14.80)
>DroAna_CAF1 20274 100 - 1
AUAAAUU--UUUGAAACGAAACACCAAAA-----ACGUAGUCAAA-------AAAAUAAAACACAACCACAAAAAUCGCAUUUCAAAUUCAAAACGCGAUUCUUGCCGAGGUUA
.....((--(((((.(((...........-----.)))..)))))-------))..........((((.(((.((((((.(((........))).)))))).)))....)))). ( -15.00)
>consensus
AUAAAUU__UUUGAAGCGAAACACCAAAAUAUAAAAAUAAACACACAAGACCAAACUAAAACGCAACCACAAAAAUCGCAUUUCAAAUUCAAAACGCGAUUUUUGCCGAGGUUA
................................................................((((.((((((((((.(((........))).))))))))))....)))). (-13.43 = -13.60 +   0.17)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:20 2006