Locus 1879

Sequence ID 3L_DroMel_CAF1
Location 5,247,902 – 5,248,035
Length 133
Max. P 0.999580
window2928 window2929 window2930

overview

Window 8

Location 5,247,902 – 5,248,012
Length 110
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 95.40
Mean single sequence MFE -27.84
Consensus MFE -24.50
Energy contribution -24.42
Covariance contribution -0.08
Combinations/Pair 1.10
Mean z-score -2.84
Structure conservation index 0.88
SVM decision value 3.75
SVM RNA-class probability 0.999580
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5247902 110 + 23771897
AGUGUAAAUGAUAUUUCCUUUUGGACUCUGCAGGAAAGUAUUUAAUUUCCUAAUUACUGAAGUGGGAAAUAAGAACUUAGACUGACAAGUCGGAGAAUGCCGAAGGGAAA
.............(((((((((((..(((.(....((((.(((.((((((((.((....)).)))))))).))))))).((((....))))).)))...))))))))))) ( -31.20)
>DroSec_CAF1 2594 108 + 1
AGUGUAAAUGAUAUUUCCUUUUGGAC--UGCAGGAAAGUAUUUAAUUUCCUAAUUACUGAAGUGGGAAAUAAGAACUUAGACUGACAAGUCGGAGAACGCCGAAGGGAAA
.............(((((((((((.(--(.(....((((.(((.((((((((.((....)).)))))))).))))))).((((....))))).))....))))))))))) ( -28.50)
>DroSim_CAF1 704 108 + 1
AGUGUAAAUGAUAUUUCCUUUUGGAC--UGCAGGAAAGUAUUUAAUUUCCUAAUUACUGAAGUGGGAAAUAAGAACUUAGACUGACAAGUUGGAGAACGCCGAAGGGAAA
.............(((((((((((..--(((((..((((.(((.((((((((.((....)).)))))))).)))))))...))).)).(((....))).))))))))))) ( -26.50)
>DroEre_CAF1 721 107 + 1
AGUGUAAAUGAUAUUUCCUUUUGGAC--AGCAGGAAAGUAUUUAAUUUCCUAAUUACUGAAAUGGGAAAUAAGAACUUAGACUGACAAGUCAGAGAACGCCGAAG-GAAA
.((((......((((((((((..(..--...((((((........)))))).....)..))..))))))))....(((.((((....)))).))).)))).....-.... ( -24.50)
>DroYak_CAF1 2694 108 + 1
AGUGUAAAUGAUAUUUCCUUUCGGAC--UGCAGGAUAGUAUUUAAUUUCCUAAUUACUGAAAUGGGAAAUAAGAAGUUAGACUGACAAGUCGGAGAACGCUGAAGGGAAA
.............(((((((((((((--(.(((..(((..(((.((((((((.((....)).)))))))).)))..)))..)))...))))(.....)..)))))))))) ( -28.50)
>consensus
AGUGUAAAUGAUAUUUCCUUUUGGAC__UGCAGGAAAGUAUUUAAUUUCCUAAUUACUGAAGUGGGAAAUAAGAACUUAGACUGACAAGUCGGAGAACGCCGAAGGGAAA
.............(((((((((((................(((.((((((((.((....)).)))))))).))).(((.((((....)))).)))....))))))))))) (-24.50 = -24.42 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,247,902 – 5,248,012
Length 110
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 95.40
Mean single sequence MFE -17.22
Consensus MFE -14.79
Energy contribution -15.23
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -1.38
Structure conservation index 0.86
SVM decision value 0.34
SVM RNA-class probability 0.695819
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5247902 110 - 23771897
UUUCCCUUCGGCAUUCUCCGACUUGUCAGUCUAAGUUCUUAUUUCCCACUUCAGUAAUUAGGAAAUUAAAUACUUUCCUGCAGAGUCCAAAAGGAAAUAUCAUUUACACU
(((((....((......))(((((..(((...((((....((((((..............)))))).....))))..)))..))))).....)))))............. ( -18.54)
>DroSec_CAF1 2594 108 - 1
UUUCCCUUCGGCGUUCUCCGACUUGUCAGUCUAAGUUCUUAUUUCCCACUUCAGUAAUUAGGAAAUUAAAUACUUUCCUGCA--GUCCAAAAGGAAAUAUCAUUUACACU
.......((((......))))......(((.(((((...(((((((.((....))...(((((((........)))))))..--........)))))))..))))).))) ( -17.60)
>DroSim_CAF1 704 108 - 1
UUUCCCUUCGGCGUUCUCCAACUUGUCAGUCUAAGUUCUUAUUUCCCACUUCAGUAAUUAGGAAAUUAAAUACUUUCCUGCA--GUCCAAAAGGAAAUAUCAUUUACACU
.........((((..........))))(((.(((((...(((((((.((....))...(((((((........)))))))..--........)))))))..))))).))) ( -16.20)
>DroEre_CAF1 721 107 - 1
UUUC-CUUCGGCGUUCUCUGACUUGUCAGUCUAAGUUCUUAUUUCCCAUUUCAGUAAUUAGGAAAUUAAAUACUUUCCUGCU--GUCCAAAAGGAAAUAUCAUUUACACU
((((-((((((((..((..((((....))))..))..).....................((((((........)))))))))--).....)))))))............. ( -19.40)
>DroYak_CAF1 2694 108 - 1
UUUCCCUUCAGCGUUCUCCGACUUGUCAGUCUAACUUCUUAUUUCCCAUUUCAGUAAUUAGGAAAUUAAAUACUAUCCUGCA--GUCCGAAAGGAAAUAUCAUUUACACU
(((((.(((...(.....)((((.(.(((..((.......((((((..............)))))).......))..)))))--))).))).)))))............. ( -14.38)
>consensus
UUUCCCUUCGGCGUUCUCCGACUUGUCAGUCUAAGUUCUUAUUUCCCACUUCAGUAAUUAGGAAAUUAAAUACUUUCCUGCA__GUCCAAAAGGAAAUAUCAUUUACACU
.........((((..........))))(((.(((((...(((((((............(((((((........)))))))............)))))))..))))).))) (-14.79 = -15.23 +   0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,247,933 – 5,248,035
Length 102
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 95.59
Mean single sequence MFE -24.00
Consensus MFE -19.70
Energy contribution -19.14
Covariance contribution -0.56
Combinations/Pair 1.15
Mean z-score -1.90
Structure conservation index 0.82
SVM decision value 1.03
SVM RNA-class probability 0.902804
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5247933 102 + 23771897
AGGAAAGUAUUUAAUUUCCUAAUUACUGAAGUGGGAAAUAAGAACUUAGACUGACAAGUCGGAGAAUGCCGAAGGGAAAUAUUUCGUUUUCUGUAGCUUCUA
((((((........)))))).......(((((.(((((...((((((.((((....)))).)))....((....))......)))..)))))...))))).. ( -24.90)
>DroSec_CAF1 2623 102 + 1
AGGAAAGUAUUUAAUUUCCUAAUUACUGAAGUGGGAAAUAAGAACUUAGACUGACAAGUCGGAGAACGCCGAAGGGAAAUAUUUCGUUUUCUGUAGCUUCUA
((((((........)))))).......(((((.(((((...((((((.((((....)))).)))....((....))......)))..)))))...))))).. ( -24.90)
>DroSim_CAF1 733 102 + 1
AGGAAAGUAUUUAAUUUCCUAAUUACUGAAGUGGGAAAUAAGAACUUAGACUGACAAGUUGGAGAACGCCGAAGGGAAAUAUUUCGUUUUCUGUAGCUUCUA
((((((........)))))).......(((((.(((((...((((((.((((....)))).)))....((....))......)))..)))))...))))).. ( -23.20)
>DroEre_CAF1 750 101 + 1
AGGAAAGUAUUUAAUUUCCUAAUUACUGAAAUGGGAAAUAAGAACUUAGACUGACAAGUCAGAGAACGCCGAAG-GAAAUAUUUUGUUUUCUGAAGCUUCUA
....((((.(((.((((((((.((....)).)))))))).))))))).((((....))))..((((.((...((-(((((.....)))))))...)))))). ( -22.40)
>DroYak_CAF1 2723 102 + 1
AGGAUAGUAUUUAAUUUCCUAAUUACUGAAAUGGGAAAUAAGAAGUUAGACUGACAAGUCGGAGAACGCUGAAGGGAAAUAUUUCGUUUUCUGCAGCUUCUA
.............((((((((.((....)).)))))))).(((((((.((((....))))((((((((..(((........)))))))))))..))))))). ( -24.60)
>consensus
AGGAAAGUAUUUAAUUUCCUAAUUACUGAAGUGGGAAAUAAGAACUUAGACUGACAAGUCGGAGAACGCCGAAGGGAAAUAUUUCGUUUUCUGUAGCUUCUA
.(((.(((.(((.((((((((.((....)).)))))))).))).....((((....))))((((((((((....))........))))))))...)))))). (-19.70 = -19.14 +  -0.56)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:59 2006