Locus 689

Sequence ID 3L_DroMel_CAF1
Location 2,067,543 – 2,067,728
Length 185
Max. P 0.994846
window1053 window1054 window1055

overview

Window 3

Location 2,067,543 – 2,067,649
Length 106
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 79.56
Mean single sequence MFE -23.73
Consensus MFE -16.30
Energy contribution -17.97
Covariance contribution 1.67
Combinations/Pair 1.00
Mean z-score -2.82
Structure conservation index 0.69
SVM decision value 2.52
SVM RNA-class probability 0.994846
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2067543 106 + 23771897
CUGUUCCUCGAUGAGCUCUUCUUCUGGAGCCACGUCUUCUGGAACUUCCUCUACUGGAACUUCCUCUACUGGAACUUCCUCUCCUGGCAAUUCCUCAACAUCAGUC
..(((((..((((.(((((......)))))..))))....)))))..((......((((.((((......)))).))))......))................... ( -26.80)
>DroSec_CAF1 124290 92 + 1
NNNNNNNNNNNUGGGCUCUUCUUCUGGAGCCACGUCUUCUGGAACUUC--------------UCUCUAGUGGAACUUCCUCUGCUGGCAAUUCCUCAACAUCAGUC
.............((((((......)))))).........((((....--------------...((((..((......))..))))...))))............ ( -20.10)
>DroSim_CAF1 127187 106 + 1
CUGUUCCUCGAUGGGCUCUUCUUCUGGAGCCACCUCUUCUGGAACUUCCUCAACUAUAACUUCCUCUGCUGGAACUUCCUCUGCUGGCAAUUCCUCAACAUCAGUC
.........((((((((((......)))))).((......((((.((((.....................)))).))))......))...........)))).... ( -24.30)
>consensus
CUGUUCCUCGAUGGGCUCUUCUUCUGGAGCCACGUCUUCUGGAACUUCCUC_ACU__AACUUCCUCUACUGGAACUUCCUCUGCUGGCAAUUCCUCAACAUCAGUC
.........((((((((((......))))))..(((....((((.((((.....................)))).))))......)))..........)))).... (-16.30 = -17.97 +   1.67) 

alignment

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secondary structure

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dotplot

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Window 4

Location 2,067,543 – 2,067,649
Length 106
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 79.56
Mean single sequence MFE -25.87
Consensus MFE -16.95
Energy contribution -17.40
Covariance contribution 0.45
Combinations/Pair 1.05
Mean z-score -1.57
Structure conservation index 0.66
SVM decision value -0.02
SVM RNA-class probability 0.524554
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2067543 106 - 23771897
GACUGAUGUUGAGGAAUUGCCAGGAGAGGAAGUUCCAGUAGAGGAAGUUCCAGUAGAGGAAGUUCCAGAAGACGUGGCUCCAGAAGAAGAGCUCAUCGAGGAACAG
..((((((((..((((((.((......)).))))))......((((.((((......)))).))))....)))))(((((........)))))..........))) ( -30.10)
>DroSec_CAF1 124290 92 - 1
GACUGAUGUUGAGGAAUUGCCAGCAGAGGAAGUUCCACUAGAGA--------------GAAGUUCCAGAAGACGUGGCUCCAGAAGAAGAGCCCANNNNNNNNNNN
.....(((((..((((((.((......)).)))))).((.(((.--------------....))).))..)))))(((((........)))))............. ( -19.30)
>DroSim_CAF1 127187 106 - 1
GACUGAUGUUGAGGAAUUGCCAGCAGAGGAAGUUCCAGCAGAGGAAGUUAUAGUUGAGGAAGUUCCAGAAGAGGUGGCUCCAGAAGAAGAGCCCAUCGAGGAACAG
..((..((((..((((((.((......)).))))))))))..)).................(((((....((.(.(((((........)))))).))..))))).. ( -28.20)
>consensus
GACUGAUGUUGAGGAAUUGCCAGCAGAGGAAGUUCCAGUAGAGGAAGUU__AGU_GAGGAAGUUCCAGAAGACGUGGCUCCAGAAGAAGAGCCCAUCGAGGAACAG
..(((.((..((....))..)).))).((((.((((.....................)))).)))).......(.(((((........))))))............ (-16.95 = -17.40 +   0.45) 

alignment

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secondary structure

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dotplot

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Window 5

Location 2,067,609 – 2,067,728
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 85.38
Mean single sequence MFE -26.82
Consensus MFE -17.32
Energy contribution -18.60
Covariance contribution 1.28
Combinations/Pair 1.24
Mean z-score -1.82
Structure conservation index 0.65
SVM decision value -0.05
SVM RNA-class probability 0.510032
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2067609 119 - 23771897
CUGCUGAGGACCAGCAACUAGUCGUUGAAGAGAGCAAAAAGGUUAAAAAAGUAAAGAAACCAACUGGGACAGUUGAAAAGACUGAUGUUGAGGAAUUGCCAGGAGAGGAAGUUCCAGUA
.(((((.....))))).(((((.(((......))).....((((.............)))).)))))..(((((.....))))).......((((((.((......)).)))))).... ( -26.22)
>DroSec_CAF1 124342 119 - 1
CUGCUGAGGACCAGCAACUAGUCGUUGAAGAGAGCAAAAAGGUUAAAAAAGUAAAGAAACCAACUCGGAAAGUUGAAAAGACUGAUGUUGAGGAAUUGCCAGCAGAGGAAGUUCCACUA
((((((.....((((........))))......((((...((((.............))))..(((((..((((.....))))....)))))...)))))))))).((.....)).... ( -26.12)
>DroSim_CAF1 127253 119 - 1
CUGCUGAGGACCAGCAACUAGUCGUUGAAGAGAGCAAAAAGGUUAAAAAAGUAAAGAAACCAACUCGGAAAGUUGAAAAGACUGAUGUUGAGGAAUUGCCAGCAGAGGAAGUUCCAGCA
((((((.....((((........))))......((((...((((.............))))..(((((..((((.....))))....)))))...)))))))))).((.....)).... ( -26.12)
>DroEre_CAF1 128538 119 - 1
CUGUUGAGAAGCAGCAAUCAGUUGUUGAAGAAAGCGAAAAGGUUAAAAAAGUAAAGAAACCAACACGAACGGUUGAAAAGCUUGAUGUCCAGGAACUGCCAGAAGAGGAUGUUCCGGAA
..((..((......(((((..(((((......)))))...((((.............)))).........))))).....))..)).(((.(((((..((......))..)))))))). ( -25.12)
>DroYak_CAF1 122697 109 - 1
CUGCUGACG---------UUGUUGUCGAAGAGAGCAAACAGGUUAAAAAGGUAAAGAAACCAACUCGAACAGUUGAAAAGACUGAUGUUGAGGAUCUGCCAGUAGAGGAAGUUCCAAA-
((((((...---------(((((.((...)).))))).((((((.....(((......)))..(((((.(((((.....)))))...))))))))))).)))))).((.....))...- ( -30.50)
>consensus
CUGCUGAGGACCAGCAACUAGUCGUUGAAGAGAGCAAAAAGGUUAAAAAAGUAAAGAAACCAACUCGGACAGUUGAAAAGACUGAUGUUGAGGAAUUGCCAGCAGAGGAAGUUCCAGAA
((((((.....((((........))))......(((....((((.............))))..(((((.(((((.....)))))...)))))....))))))))).((.....)).... (-17.32 = -18.60 +   1.28) 

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 09:48:36 2006