Locus 5007

Sequence ID 3L_DroMel_CAF1
Location 13,761,865 – 13,762,035
Length 170
Max. P 0.997064
window7923 window7924

overview

Window 3

Location 13,761,865 – 13,761,955
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -31.36
Consensus MFE -29.98
Energy contribution -30.18
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.18
Structure conservation index 0.96
SVM decision value 2.79
SVM RNA-class probability 0.997064
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13761865 90 - 23771897
AGCUAGCUGGAAAGCUCAUUGUUUUUUGGUUGAGGACAAAAAAGGAGCAGCUCCACACUGGCCCACGUGUGUGCUGUCCUGUUGUUAGGG
...((((..((((((.....))))))..))))..(((((...((((.((((..(((((........))))).)))))))).))))).... ( -32.30)
>DroSec_CAF1 8418 90 - 1
AGCUAGCUGGAAAGCUCAUUGUUUUUUGGUCGAGGACAAAAAAGGAGCAGCUCCACACUGGCCCACGUGUGUGCUGUCCUGUUGUUAGGG
..((.((..((((((.....))))))..))..))(((((...((((.((((..(((((........))))).)))))))).))))).... ( -30.80)
>DroSim_CAF1 4986 90 - 1
AGCUAGCUGGAAAGCUCAUUGUUUUUUGGUUGAGGACAAAAAAGGAGCAGCUCCACACUGGCCCACGUGUGUGCUGUCCUGUUGUUAGGG
...((((..((((((.....))))))..))))..(((((...((((.((((..(((((........))))).)))))))).))))).... ( -32.30)
>DroEre_CAF1 7671 90 - 1
AGCUAGCUGGAAAGCUCAUUGUUUUUUGGUUGAGGACAAAAAAGGAGCAGCUCAACACUGGCCCACGUGUGUGCUGUCCUGUUGUUAGGG
...((((..((((((.....))))))..))))..(((((...((((.((((...((((........))))..)))))))).))))).... ( -30.70)
>DroYak_CAF1 5674 90 - 1
AGCUAGCUGGAAAGCUCAUUGUUUUUUGGUUGAGGACAAAAAAGGAGCAGCUCAACACUGGCCCACGUGUGUGCUGUCCUGUUGUUAGGG
...((((..((((((.....))))))..))))..(((((...((((.((((...((((........))))..)))))))).))))).... ( -30.70)
>consensus
AGCUAGCUGGAAAGCUCAUUGUUUUUUGGUUGAGGACAAAAAAGGAGCAGCUCCACACUGGCCCACGUGUGUGCUGUCCUGUUGUUAGGG
...((((..((((((.....))))))..))))..(((((...((((.((((.(.((((........))))).)))))))).))))).... (-29.98 = -30.18 +   0.20)

alignment

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secondary structure

Postscript

dotplot

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Window 4

Location 13,761,915 – 13,762,035
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.08
Mean single sequence MFE -29.14
Consensus MFE -27.43
Energy contribution -27.83
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.40
Structure conservation index 0.94
SVM decision value 0.76
SVM RNA-class probability 0.843490
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13761915 120 - 23771897
AAUGGUCAGAAAAGUUGCAGACAACACAAACACAGCCUGGCCAACAGAAGGAAGGAGCAAGAGGAACUGUGGGCAAAAGAAGCUAGCUGGAAAGCUCAUUGUUUUUUGGUUGAGGACAAA
....(((......((((....)))).......(((((..(((.((((...................)))).)))..(((((((.((((....))))....))))))))))))..)))... ( -29.21)
>DroSec_CAF1 8468 120 - 1
AAUGGUCAGAAAAGUUGCAGACAACACAAACACAGCCUGGCCAACAGAAGGAAGGAGCGAGAGGAACUGUGGGCAAAAGAAGCUAGCUGGAAAGCUCAUUGUUUUUUGGUCGAGGACAAA
..((..((((((.((((....))))((((.((((((((..((.......)).)))..(....)...)))))(((.......)))((((....))))..))))))))))..))........ ( -28.60)
>DroSim_CAF1 5036 120 - 1
AAUGGUCAGAAAAGUUGCAGACAACACAAACACAGCCUGGCCAACAGAAGGAAGGAGCGAGAGGAACUGUGGGCAAAAGAAGCUAGCUGGAAAGCUCAUUGUUUUUUGGUUGAGGACAAA
....(((......((((....)))).......(((((..(((.((((...................)))).)))..(((((((.((((....))))....))))))))))))..)))... ( -29.21)
>DroEre_CAF1 7721 120 - 1
AAUGGUCAGAAAAGUUGCAGACAACACAAACACAGCCUGGCCAACAGAAGGAAGGAGCGAGAGGAACUAUGGGCAGAAGAAGCUAGCUGGAAAGCUCAUUGUUUUUUGGUUGAGGACAAA
....(((......((((....)))).......(((((((.(((.(....)..((...(....)...)).))).)).(((((((.((((....))))....))))))))))))..)))... ( -25.70)
>DroYak_CAF1 5724 120 - 1
AAUGGUCAGAAAAGUUGCAGACAACACAAACACAGCCUGGCCAACAGAAGGCAGGAGCCAGAGGAACUGUGGGCAAAAGAAGCUAGCUGGAAAGCUCAUUGUUUUUUGGUUGAGGACAAA
....(((......((((....)))).......(((((..(((.((((..(((....))).......)))).)))..(((((((.((((....))))....))))))))))))..)))... ( -33.00)
>consensus
AAUGGUCAGAAAAGUUGCAGACAACACAAACACAGCCUGGCCAACAGAAGGAAGGAGCGAGAGGAACUGUGGGCAAAAGAAGCUAGCUGGAAAGCUCAUUGUUUUUUGGUUGAGGACAAA
....(((......((((....)))).......(((((..(((.((((...................)))).)))..(((((((.((((....))))....))))))))))))..)))... (-27.43 = -27.83 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:29 2006