Locus 1576

Sequence ID 3L_DroMel_CAF1
Location 4,595,484 – 4,595,583
Length 99
Max. P 0.986486
window2442 window2443

overview

Window 2

Location 4,595,484 – 4,595,583
Length 99
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 80.00
Mean single sequence MFE -23.96
Consensus MFE -13.69
Energy contribution -15.09
Covariance contribution 1.40
Combinations/Pair 1.08
Mean z-score -2.54
Structure conservation index 0.57
SVM decision value 1.60
SVM RNA-class probability 0.966832
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4595484 99 + 23771897
ACGGCGAAUCACCUUAUGAACC---UUAUGAUUAAGGGCACAAAUAAAUUCUUG------AAGACUAUUCGUCACGGAUUUGACGUCAAUGAA-AUAAACUGACGUCAA-
..(((((((...(((.....((---(((....)))))...(((........)))------)))...)))))))......(((((((((.....-......)))))))))- ( -23.80)
>DroSec_CAF1 172121 101 + 1
ACGGAGAAUUACUUUAUAAAGUUAUUU--ACUUAAGGGCAUAAAUAAAUUCUUG------AAGACUAUUCGUCAUGAAGUUGACGUCAAUGAA-AUUAAGUGACGUCAAA
..(..((((..(((((..((.((((((--(((....))..))))))).))..))------)))...))))..)......(((((((((.(...-....).))))))))). ( -19.90)
>DroSim_CAF1 172530 103 + 1
ACGGCGAAUAACUUUAUGAAGGUAUUUAUACUUUAGGGCACAAAUAAAUUCUUG------AAGACAAUUCGUCAUGAAGUUGACGUCAAUGAA-AUAAACUGACGUCAAA
..(((((((..(((((.(((..(((((...((....))...)))))..))).))------)))...)))))))......(((((((((.....-......))))))))). ( -26.70)
>DroEre_CAF1 180762 106 + 1
ACGGCGAAUAACUUCAUGACGGUAUUU--AAUUACGGACA-AAAUAAAUUCUGGGAACACAAGGCAAUUCGUCAUGAAUUUGACGUCAAAGUAAAUAUACUUACGUCAA-
............((((((((((((...--...))).....-..........((....))..........))))))))).(((((((..(((((....))))))))))))- ( -23.30)
>DroYak_CAF1 177808 103 + 1
ACGGCGAAUAACUUUAUGAAGGUAUUU--ACUUACGAGCA-AAAUAAAUUCUCAGAA--CAAGGCUAUUCGUCAUGAAUUUGACGUCAAAGUA-AUACGCUGACGUCAA-
..((((((((.((((......(((...--...)))(((.(-(......)))))....--.)))).))))))))......(((((((((..(..-...)..)))))))))- ( -26.10)
>consensus
ACGGCGAAUAACUUUAUGAAGGUAUUU__ACUUAAGGGCA_AAAUAAAUUCUUG______AAGACUAUUCGUCAUGAAUUUGACGUCAAUGAA_AUAAACUGACGUCAA_
..(((((((..(((((................)))))............((((.......))))..)))))))......(((((((((............))))))))). (-13.69 = -15.09 +   1.40)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,595,484 – 4,595,583
Length 99
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 80.00
Mean single sequence MFE -24.84
Consensus MFE -13.96
Energy contribution -15.04
Covariance contribution 1.08
Combinations/Pair 1.25
Mean z-score -2.78
Structure conservation index 0.56
SVM decision value 2.04
SVM RNA-class probability 0.986486
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4595484 99 - 23771897
-UUGACGUCAGUUUAU-UUCAUUGACGUCAAAUCCGUGACGAAUAGUCUU------CAAGAAUUUAUUUGUGCCCUUAAUCAUAA---GGUUCAUAAGGUGAUUCGCCGU
-(((((((((((....-...)))))))))))......(((.....)))..------...(((((..((((((.(((((....)))---))..))))))..)))))..... ( -26.80)
>DroSec_CAF1 172121 101 - 1
UUUGACGUCACUUAAU-UUCAUUGACGUCAACUUCAUGACGAAUAGUCUU------CAAGAAUUUAUUUAUGCCCUUAAGU--AAAUAACUUUAUAAAGUAAUUCUCCGU
.(((((((((......-.....)))))))))(((...(((.....)))..------.))).(((((((((......)))))--)))).((((....)))).......... ( -19.30)
>DroSim_CAF1 172530 103 - 1
UUUGACGUCAGUUUAU-UUCAUUGACGUCAACUUCAUGACGAAUUGUCUU------CAAGAAUUUAUUUGUGCCCUAAAGUAUAAAUACCUUCAUAAAGUUAUUCGCCGU
.(((((((((((....-...)))))))))))....(((.(((((...(((------...(((..(((((((((......)))))))))..)))...)))..))))).))) ( -27.60)
>DroEre_CAF1 180762 106 - 1
-UUGACGUAAGUAUAUUUACUUUGACGUCAAAUUCAUGACGAAUUGCCUUGUGUUCCCAGAAUUUAUUU-UGUCCGUAAUU--AAAUACCGUCAUGAAGUUAUUCGCCGU
-((((((((((((....)))))..))))))).(((((((((................(((((....)))-))...(((...--...))))))))))))............ ( -23.70)
>DroYak_CAF1 177808 103 - 1
-UUGACGUCAGCGUAU-UACUUUGACGUCAAAUUCAUGACGAAUAGCCUUG--UUCUGAGAAUUUAUUU-UGCUCGUAAGU--AAAUACCUUCAUAAAGUUAUUCGCCGU
-((((((((((.(...-..).))))))))))....(((.((((((((.(((--(...(.(.((((((((-.......))))--)))).))...)))).)))))))).))) ( -26.80)
>consensus
_UUGACGUCAGUUUAU_UUCAUUGACGUCAAAUUCAUGACGAAUAGUCUU______CAAGAAUUUAUUU_UGCCCUUAAGU__AAAUACCUUCAUAAAGUUAUUCGCCGU
.(((((((((((........)))))))))))............................((((...((((((...(((........)))...))))))...))))..... (-13.96 = -15.04 +   1.08)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:02 2006