Locus 4688

Sequence ID X_DroMel_CAF1
Location 12,214,196 – 12,214,287
Length 91
Max. P 0.998810
window7693 window7694

overview

Window 3

Location 12,214,196 – 12,214,287
Length 91
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 72.67
Mean single sequence MFE -30.72
Consensus MFE -17.32
Energy contribution -19.10
Covariance contribution 1.78
Combinations/Pair 1.26
Mean z-score -3.65
Structure conservation index 0.56
SVM decision value 3.23
SVM RNA-class probability 0.998810
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12214196 91 + 22224390
CAUUUG-CUGGCACUUGUUAGGCACUCGGUACGACAAGCCAC-AAUCUGCCUU----------------------CACAAUAUGCACCUGCAUAUUGU-UGGCAUUCUGCCGG-CUA
.....(-((((((((((((..((.....))..))))))....-....((((..----------------------.(((((((((....)))))))))-.))))...))))))-).. ( -35.20)
>DroSec_CAF1 40918 91 + 1
CAUUUG-CUGGCACUUGUUAGGCACUCGGAACGACAAGCCAC-AAUCUGCCUU----------------------CACAAUAUGCACCUGCAUAUUGU-UGGCAUUCUGCCGG-CUA
.....(-((((((.((((..(((..(((...)))...)))))-))..((((..----------------------.(((((((((....)))))))))-.))))...))))))-).. ( -34.00)
>DroEre_CAF1 38413 91 + 1
CAUUUG-CUGGCACUUGUUAGGCACUCGGAACGACAAGCCAC-AAUCUGCCUU----------------------CACAAUAUGCACCUGCAUAUUGU-UGGCAUUCUGCCGG-CUA
.....(-((((((.((((..(((..(((...)))...)))))-))..((((..----------------------.(((((((((....)))))))))-.))))...))))))-).. ( -34.00)
>DroWil_CAF1 5041 77 + 1
CAUUUGGCUGGCAGCCCUCAAUCCCU-------GCCACCCGUACACCUGCCAC-------------------------------CACCUGGACAU-GU-UGGCAUGCUGCCUGUCUA
.....(((.((((((..........(-------((((.......((.(((((.-------------------------------....))).)).-))-))))).)))))).))).. ( -20.91)
>DroYak_CAF1 25813 91 + 1
CAUUUG-CUGGCACUUGUUAGGCACUCGGAACGACAAGCCGC-AAUCUGCCUU----------------------CACAAUAUGCACCUGCAUAUUGU-UGGCAUUCUGCCGG-CUA
.....(-((((((.((((..(((..(((...)))...)))))-))..((((..----------------------.(((((((((....)))))))))-.))))...))))))-).. ( -34.30)
>DroAna_CAF1 53086 110 + 1
CAUUUG-CCAGCGCUUGUAAGGA-C---AAAAUACAGGCCAC-AAUCUGCUUGCCACAAACACACAUACACCCCCCAGUAUAUGCACCUGCACAUUGUUUGGCAUUUUGCCGG-CUA
.....(-((.(((((((((....-.---....)))))))...-........(((((..((((...((((........)))).(((....)))...)))))))))....)).))-).. ( -25.90)
>consensus
CAUUUG_CUGGCACUUGUUAGGCACUCGGAACGACAAGCCAC_AAUCUGCCUU______________________CACAAUAUGCACCUGCAUAUUGU_UGGCAUUCUGCCGG_CUA
.....((((((((((((((.............)))))).........((((.........................(((((((((....)))))))))..))))...)))))))).. (-17.32 = -19.10 +   1.78)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,214,196 – 12,214,287
Length 91
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 72.67
Mean single sequence MFE -32.69
Consensus MFE -16.63
Energy contribution -18.31
Covariance contribution 1.68
Combinations/Pair 1.16
Mean z-score -2.55
Structure conservation index 0.51
SVM decision value 2.44
SVM RNA-class probability 0.993951
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12214196 91 - 22224390
UAG-CCGGCAGAAUGCCA-ACAAUAUGCAGGUGCAUAUUGUG----------------------AAGGCAGAUU-GUGGCUUGUCGUACCGAGUGCCUAACAAGUGCCAG-CAAAUG
..(-(.(((....((((.-(((((((((....))))))))).----------------------..))))....-...((((((.((((...))))...))))))))).)-)..... ( -33.20)
>DroSec_CAF1 40918 91 - 1
UAG-CCGGCAGAAUGCCA-ACAAUAUGCAGGUGCAUAUUGUG----------------------AAGGCAGAUU-GUGGCUUGUCGUUCCGAGUGCCUAACAAGUGCCAG-CAAAUG
..(-(.((((...((((.-(((((((((....))))))))).----------------------..))))..((-(((((...(((...)))..)))..)))).)))).)-)..... ( -33.10)
>DroEre_CAF1 38413 91 - 1
UAG-CCGGCAGAAUGCCA-ACAAUAUGCAGGUGCAUAUUGUG----------------------AAGGCAGAUU-GUGGCUUGUCGUUCCGAGUGCCUAACAAGUGCCAG-CAAAUG
..(-(.((((...((((.-(((((((((....))))))))).----------------------..))))..((-(((((...(((...)))..)))..)))).)))).)-)..... ( -33.10)
>DroWil_CAF1 5041 77 - 1
UAGACAGGCAGCAUGCCA-AC-AUGUCCAGGUG-------------------------------GUGGCAGGUGUACGGGUGGC-------AGGGAUUGAGGGCUGCCAGCCAAAUG
.......(((.(.(((((-.(-((......)))-------------------------------.)))))).)))..((.((((-------((..........)))))).))..... ( -26.90)
>DroYak_CAF1 25813 91 - 1
UAG-CCGGCAGAAUGCCA-ACAAUAUGCAGGUGCAUAUUGUG----------------------AAGGCAGAUU-GCGGCUUGUCGUUCCGAGUGCCUAACAAGUGCCAG-CAAAUG
..(-(.((((...((((.-(((((((((....))))))))).----------------------..))))....-..(((...(((...)))..))).......)))).)-)..... ( -32.10)
>DroAna_CAF1 53086 110 - 1
UAG-CCGGCAAAAUGCCAAACAAUGUGCAGGUGCAUAUACUGGGGGGUGUAUGUGUGUUUGUGGCAAGCAGAUU-GUGGCCUGUAUUUU---G-UCCUUACAAGCGCUGG-CAAAUG
..(-(((((..........((((.(((((((((((((((((....))))))))).((((((...))))))....-...)))))))).))---)-)..........)))))-)..... ( -37.75)
>consensus
UAG_CCGGCAGAAUGCCA_ACAAUAUGCAGGUGCAUAUUGUG______________________AAGGCAGAUU_GUGGCUUGUCGUUCCGAGUGCCUAACAAGUGCCAG_CAAAUG
......(((.....)))..(((((((((....))))))))).........................((((.......(((..............))).......))))......... (-16.63 = -18.31 +   1.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:03 2006