Locus 2068

Sequence ID 3L_DroMel_CAF1
Location 5,687,903 – 5,688,020
Length 117
Max. P 0.934996
window3223 window3224

overview

Window 3

Location 5,687,903 – 5,688,020
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.64
Mean single sequence MFE -36.84
Consensus MFE -29.44
Energy contribution -29.48
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -1.38
Structure conservation index 0.80
SVM decision value -0.04
SVM RNA-class probability 0.512247
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5687903 117 + 23771897
UUGGGCGGGUGGCAGACUGAAAAUGUGGGCGUGGUGGCACUCAGUGU--GCAAGUUGCCGAAGCGGAAGCAGCCUAAAACCAA-AAGGAGAUUGACUUUAAAUUGAGAACACAAACCGCU
...((((((((.(((.((.......(((((.((((.((((.....))--)).....))))..((....)).)))))...((..-..)))).))).(((......)))..)))...))))) ( -32.30)
>DroSec_CAF1 60537 117 + 1
UUGGGCGGGUGGCAGACUGAAAACCUGGGCGUGGUGGCACUCAGUGU--GCGAGUUGCCGAAGCGGAAGCAGCCUAAAACCAA-AAGGAGAUUGACUUUAAAUUCAGAACACAAACCGCU
...((((((((.....(((((....(((((....((((((((.....--..))).)))))..((....)).)))))......(-(((........))))...)))))..)))...))))) ( -35.90)
>DroSim_CAF1 60810 117 + 1
UUGGGCGGGUGGCAGACUGAAAACCUGGGCGUGGUGGCACUCAGUGU--GCGAGUUGCCGAGGCGGAAGCUGCCUAAAACCAA-AAGGAGAUUGACUUUAAAUUCAGAACACAAACCGCU
...(((((..(((((.((.....(((.((((.(.(.((((.....))--)).).))))).)))....)))))))........(-(((........))))................))))) ( -37.50)
>DroEre_CAF1 64005 117 + 1
UUGGGCGGUGGGAAGCCUCAAAAUCUGGGCGUGGUGGCACUCAGUGU--GGGAGUUGCCGAAGCGGAAGCAGCCCAAAACCAA-AAGGAGAUUGACUUUAAAUUAAGAACACAUACCGCU
...((((((((....))....(((((((((.(((..((.(((.....--))).))..)))..((....)).))))....((..-..))))))).....................)))))) ( -39.60)
>DroYak_CAF1 62603 120 + 1
UUGGGCGGUUGGCAGCCUCAAAAUCUGGGCGUGGUGGCACUCAGUGUGUGUGAGUUGCCGAAGCGGAAGCAGCCUAAAACCAAAAAGGAGAUUGACUUUAAAUUAAGAGCACAAACCGCU
...(((((((.((........(((((((((....(((((((((.......)))).)))))..((....)).))))....((.....)))))))..(((......))).))...))))))) ( -38.90)
>consensus
UUGGGCGGGUGGCAGACUGAAAAUCUGGGCGUGGUGGCACUCAGUGU__GCGAGUUGCCGAAGCGGAAGCAGCCUAAAACCAA_AAGGAGAUUGACUUUAAAUUAAGAACACAAACCGCU
...(((((.................(((((....((((((((.........))).)))))..((....)).)))))...((.....))...........................))))) (-29.44 = -29.48 +   0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,687,903 – 5,688,020
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.64
Mean single sequence MFE -32.24
Consensus MFE -27.86
Energy contribution -27.70
Covariance contribution -0.16
Combinations/Pair 1.12
Mean z-score -1.62
Structure conservation index 0.86
SVM decision value 1.24
SVM RNA-class probability 0.934996
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5687903 117 - 23771897
AGCGGUUUGUGUUCUCAAUUUAAAGUCAAUCUCCUU-UUGGUUUUAGGCUGCUUCCGCUUCGGCAACUUGC--ACACUGAGUGCCACCACGCCCACAUUUUCAGUCUGCCACCCGCCCAA
.((((...(((.........((((..(((.......-)))..))))(((((.....((....)).....((--((.....)))).................)))))...))))))).... ( -25.90)
>DroSec_CAF1 60537 117 - 1
AGCGGUUUGUGUUCUGAAUUUAAAGUCAAUCUCCUU-UUGGUUUUAGGCUGCUUCCGCUUCGGCAACUCGC--ACACUGAGUGCCACCACGCCCAGGUUUUCAGUCUGCCACCCGCCCAA
(((((...(((..(((((...((((........)))-)....)))))..)))..)))))..(((.....((--(.((((((.(((..........))).)))))).))).....)))... ( -31.50)
>DroSim_CAF1 60810 117 - 1
AGCGGUUUGUGUUCUGAAUUUAAAGUCAAUCUCCUU-UUGGUUUUAGGCAGCUUCCGCCUCGGCAACUCGC--ACACUGAGUGCCACCACGCCCAGGUUUUCAGUCUGCCACCCGCCCAA
.((((...............((((..(((.......-)))..))))(((((((...((((.(((.....((--((.....))))......))).))))....)).)))))..)))).... ( -34.70)
>DroEre_CAF1 64005 117 - 1
AGCGGUAUGUGUUCUUAAUUUAAAGUCAAUCUCCUU-UUGGUUUUGGGCUGCUUCCGCUUCGGCAACUCCC--ACACUGAGUGCCACCACGCCCAGAUUUUGAGGCUUCCCACCGCCCAA
.(((((.............((((((((.....((..-..))...(((((.((....))...((((.(((..--.....))))))).....)))))))))))))((....))))))).... ( -33.70)
>DroYak_CAF1 62603 120 - 1
AGCGGUUUGUGCUCUUAAUUUAAAGUCAAUCUCCUUUUUGGUUUUAGGCUGCUUCCGCUUCGGCAACUCACACACACUGAGUGCCACCACGCCCAGAUUUUGAGGCUGCCAACCGCCCAA
.((((((.((((.(((((..((((..(((........)))..))))(((.((....))...((((.((((.......)))))))).....)))......))))))).)).)))))).... ( -35.40)
>consensus
AGCGGUUUGUGUUCUGAAUUUAAAGUCAAUCUCCUU_UUGGUUUUAGGCUGCUUCCGCUUCGGCAACUCGC__ACACUGAGUGCCACCACGCCCAGAUUUUCAGUCUGCCACCCGCCCAA
.((((...(((..(((((..((((..(((........)))..))))(((.((....))...((((.((((.......)))))))).....)))......)))))..)))...)))).... (-27.86 = -27.70 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:38 2006