Locus 4060

Sequence ID 2L_DroMel_CAF1
Location 11,744,343 – 11,744,475
Length 132
Max. P 0.998159
window6398 window6399

overview

Window 8

Location 11,744,343 – 11,744,450
Length 107
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 79.17
Mean single sequence MFE -28.42
Consensus MFE -14.82
Energy contribution -16.42
Covariance contribution 1.60
Combinations/Pair 1.12
Mean z-score -1.94
Structure conservation index 0.52
SVM decision value 0.23
SVM RNA-class probability 0.643353
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11744343 107 + 22407834
--CAGCCGACGACAAAUGUUUGUCAUAUGCUUUUUGACAGUUUUGCUUUGGGCACGCAAGUGACAACUGCAAAGCACACUCUAGAAAACACAUCUUGUGUGUAAACACA--
--.(((....(((((....)))))....)))........(((((((.(((..(((....))).)))..)))))))((((.(.(((.......))).).)))).......-- ( -27.20)
>DroSec_CAF1 2797 107 + 1
--CAGCCGACGACAAAUGUUUGUCAUAUGCUUUUUGACAGUUUUGCUUUGGUCACGCAAGUGACAACUGCAAAGCACACUCUAGAAAACACAUCUUGUGUCUGAGCACA--
--..((((((.((((((((.(((((.........)))))(((((((....(((((....)))))....)))))))..............)))).))))))).).))...-- ( -33.60)
>DroEre_CAF1 9852 106 + 1
--AUGCCGACGACAAAUGUUUGGCAUAUGCUUUUUGACAGUUUUGCUUUGGGCACGCAAGUGACAACUGCAAAGCACACUCA-GAAAACACAUUUUGUGUC--AGCACACG
--(((((((..((....))))))))).((((((((((..(((((((.(((..(((....))).)))..)))))))....)))-))))((((.....)))).--.))).... ( -32.30)
>DroYak_CAF1 2781 109 + 1
GUCUGCCGACGACAAAUGUUUGGCAUAUGCUUUUUGACAGCUAUGCUUUGGGCACGCAAGUGGCAACUGCAAAGCUUACUCUGGAAAACACAUCUUGUCUG--GGCACACG
((.((((.(.(((((.((((.(((....)))....))))(((.(((....(.(((....))).)....))).)))...................)))))).--)))).)). ( -34.50)
>DroAna_CAF1 4840 90 + 1
--CGGCUGACGACAAAUGUUUGUCAUAUGCUUUCUGACAAUCUCUCUAUGGUCACCCAAGUGACAUCUGCAGA---CACUGA-CU--AUAUAUAUU---------CA----
--(((.((..(((((....)))))........((((.((....(.....)(((((....)))))...))))))---))))).-..--.........---------..---- ( -14.50)
>consensus
__CAGCCGACGACAAAUGUUUGUCAUAUGCUUUUUGACAGUUUUGCUUUGGGCACGCAAGUGACAACUGCAAAGCACACUCU_GAAAACACAUCUUGUGUC__AGCACA__
...........((((((((.(((((.........)))))(((((((....(.(((....))).)....)))))))..............)))).))))............. (-14.82 = -16.42 +   1.60)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,744,379 – 11,744,475
Length 96
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 68.32
Mean single sequence MFE -22.81
Consensus MFE -11.50
Energy contribution -13.24
Covariance contribution 1.74
Combinations/Pair 1.19
Mean z-score -2.59
Structure conservation index 0.50
SVM decision value 3.02
SVM RNA-class probability 0.998159
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11744379 96 + 22407834
AGUUUUGCUUUGGGCACGCAAGUGACAACUGCAAAGCACACUCUAGAAAACACAUCUUGUGUGUAAACACA--CA----CACA--CCCACAUUCCCAAAC----GGAC
.(((((((.(((..(((....))).)))..)))))))....................(((((((......)--))----))))--.......(((.....----))). ( -25.90)
>DroSec_CAF1 2833 100 + 1
AGUUUUGCUUUGGUCACGCAAGUGACAACUGCAAAGCACACUCUAGAAAACACAUCUUGUGUCUGAGCACA--CACACUCACA--CACACAUUCCCAAAC----GGAC
.(((((((....(((((....)))))....)))))))....................(((((.((((....--....)))).)--))))...(((.....----))). ( -30.70)
>DroEre_CAF1 9888 101 + 1
AGUUUUGCUUUGGGCACGCAAGUGACAACUGCAAAGCACACUCA-GAAAACACAUUUUGUGUC--AGCACACGCACACGCACACAUUCCCAUUCCCAAAC----GGAC
.(((((((.(((..(((....))).)))..))))))).......-............(((((.--.((....))..)))))...........(((.....----))). ( -23.00)
>DroYak_CAF1 2819 90 + 1
AGCUAUGCUUUGGGCACGCAAGUGGCAACUGCAAAGCUUACUCUGGAAAACACAUCUUGUCUG--GGCACACGCACA------------CAUUCCCAAAC----GGAA
((((.(((....(.(((....))).)....))).))))................(((.((.((--((..........------------....)))).))----))). ( -22.04)
>DroAna_CAF1 4876 87 + 1
AAUCUCUCUAUGGUCACCCAAGUGACAUCUGCAGA---CACUGA-CU--AUAUAUAUU---------CA----UAUAUCCAUA--CAAGUGAUCCCAUACACUAGUAG
....((((....(((((....)))))....).)))---...((.-.(--((((.....---------.)----))))..))((--(.((((........)))).))). ( -12.40)
>consensus
AGUUUUGCUUUGGGCACGCAAGUGACAACUGCAAAGCACACUCU_GAAAACACAUCUUGUGUC__AGCACA__CACA__CACA__CACACAUUCCCAAAC____GGAC
.(((((((....(.(((....))).)....)))))))....................(((((....)))))..................................... (-11.50 = -13.24 +   1.74)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:20 2006