Locus 724

Sequence ID 3L_DroMel_CAF1
Location 2,200,428 – 2,200,525
Length 97
Max. P 0.595131
window1111 window1112

overview

Window 1

Location 2,200,428 – 2,200,525
Length 97
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 85.15
Mean single sequence MFE -31.02
Consensus MFE -23.42
Energy contribution -23.38
Covariance contribution -0.04
Combinations/Pair 1.05
Mean z-score -1.61
Structure conservation index 0.75
SVM decision value 0.12
SVM RNA-class probability 0.595131
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2200428 97 + 23771897
UUGCAAGGUUGCGAGGCCACAGGAGAGAGCAGCAGAAGCUGUCAUCCGUUGAAAGGUGGCAAGUACCCUGUAUGGUCCGCGAUUUUGUUUAACAUGA
..(((((((((((.(((((((((.((..(((((....)))))..)).(((.......)))......)))))..)))))))))))))))......... ( -34.40)
>DroSec_CAF1 252424 97 + 1
UUGCAAGGUUGCGAGGCCACAGGAGAGAGCAGCAGAAGCUGUCAUCCGUUGAAAGGUGGCAAGUACCCUGUAUAGUCUGGGAUUUUGUUCAACAUGA
..((((((((((...(((((.(((....(((((....)))))..)))........)))))..)))(((.(......).))))))))))......... ( -26.90)
>DroSim_CAF1 252935 97 + 1
UUGCAAGGUUGCGAGGCCACAGGAGAGAGCAGCAGAAGCUGUCAUCCGUUGAAAGGUGGCAAGUACCCUGUAUAGUCCGGGAUUUUGUUUAACAUGA
..((((((((.((.(((.(((((.((..(((((....)))))..)).(((.......)))......)))))...))))).))))))))......... ( -27.20)
>DroEre_CAF1 257778 90 + 1
UUGG-AGGUUGCGAGGCCACAGGAAUGAACAGCAGAAGCUGUCAUCCGUUGGCAGGUGGCAAGUACCCUGU----UGCGGGUUUCGGUUUAA--UGA
((((-((.((((((.((((..(((.(((.((((....))))))))))..)))).((((.....))))...)----))))).)))))).....--... ( -30.10)
>DroYak_CAF1 251472 85 + 1
------GGUUGCGAGGCCACAGGAGAGAACAGCAGAAGCUGUCAUCCGUCGGCAGGUGGCAAGUACCCUGC----UGCGGAUUCCUGUUUAA--UGA
------((((....))))(((((((.((.((((....)))))).((((.(((((((.(.......))))))----)))))))))))))....--... ( -36.50)
>consensus
UUGCAAGGUUGCGAGGCCACAGGAGAGAGCAGCAGAAGCUGUCAUCCGUUGAAAGGUGGCAAGUACCCUGUAU_GUCCGGGAUUUUGUUUAACAUGA
.....(((.(((...(((((.(((....(((((....)))))..)))........)))))..))).)))............................ (-23.42 = -23.38 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,200,428 – 2,200,525
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 85.15
Mean single sequence MFE -24.40
Consensus MFE -17.08
Energy contribution -18.08
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.71
Structure conservation index 0.70
SVM decision value 0.09
SVM RNA-class probability 0.579654
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2200428 97 - 23771897
UCAUGUUAAACAAAAUCGCGGACCAUACAGGGUACUUGCCACCUUUCAACGGAUGACAGCUUCUGCUGCUCUCUCCUGUGGCCUCGCAACCUUGCAA
.................(.((.(((((.(((((.......))))).....(((.((((((....)))).))..)))))))))).)(((....))).. ( -22.40)
>DroSec_CAF1 252424 97 - 1
UCAUGUUGAACAAAAUCCCAGACUAUACAGGGUACUUGCCACCUUUCAACGGAUGACAGCUUCUGCUGCUCUCUCCUGUGGCCUCGCAACCUUGCAA
...........................((((((....(((((........(((.((((((....)))).))..))).)))))......))))))... ( -20.60)
>DroSim_CAF1 252935 97 - 1
UCAUGUUAAACAAAAUCCCGGACUAUACAGGGUACUUGCCACCUUUCAACGGAUGACAGCUUCUGCUGCUCUCUCCUGUGGCCUCGCAACCUUGCAA
...........................((((((....(((((........(((.((((((....)))).))..))).)))))......))))))... ( -20.60)
>DroEre_CAF1 257778 90 - 1
UCA--UUAAACCGAAACCCGCA----ACAGGGUACUUGCCACCUGCCAACGGAUGACAGCUUCUGCUGUUCAUUCCUGUGGCCUCGCAACCU-CCAA
...--..........((((...----...))))..((((.....((((..((((((((((....)))).))))))...))))...))))...-.... ( -27.00)
>DroYak_CAF1 251472 85 - 1
UCA--UUAAACAGGAAUCCGCA----GCAGGGUACUUGCCACCUGCCGACGGAUGACAGCUUCUGCUGUUCUCUCCUGUGGCCUCGCAACC------
...--....((((((((((((.----(((((..........))))).).)))))((((((....))))))...))))))............------ ( -31.40)
>consensus
UCAUGUUAAACAAAAUCCCGGAC_AUACAGGGUACUUGCCACCUUUCAACGGAUGACAGCUUCUGCUGCUCUCUCCUGUGGCCUCGCAACCUUGCAA
...........................((((((....(((((........(((.((((((....)))).))..))).)))))......))))))... (-17.08 = -18.08 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:32 2006