Locus 956

Sequence ID X_DroMel_CAF1
Location 2,720,461 – 2,720,566
Length 105
Max. P 0.998272
window1552 window1553

overview

Window 2

Location 2,720,461 – 2,720,566
Length 105
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 91.86
Mean single sequence MFE -14.18
Consensus MFE -11.40
Energy contribution -11.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.25
Structure conservation index 0.80
SVM decision value 1.74
SVM RNA-class probability 0.974865
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2720461 105 + 22224390
AUAUAAAGCAAAUAUCAAUUACAGUUCUCUUUGUUUCGUCUUUUGCUGCCUUUUAUUCCUCUGGUUUUUUGCCCCUCCGGAAUUU----CCC---AUUUUUUCACUUGCUCC
......((((((........((((......)))).......)))))).......(((((...(((.....))).....)))))..----...---................. ( -12.26)
>DroSec_CAF1 109136 102 + 1
ACAUAAAGCAAAUAUCAAUUACAGUUCUCUUUGUUUCGUCUUUUGCUGCCUUUUAUUCCUCUGGGUUUU---CCCUCCGGAAUUU----CCC---AUUUUUUCACUUGCUCC
......((((((........((((......)))).......))))))..............((((..((---((....))))...----)))---)................ ( -16.26)
>DroSim_CAF1 97182 102 + 1
ACAUAAAGCAAAUAUCAAUUACAGUUCUCUUUGUUUCGUCUUUUGCUGCCUUUUAUUCCUCUGGUUUUU---CCCUCCGGAAUUU----CCC---AUUUUUUCACUUGCUCC
......((((((........((((......)))).......)))))).......(((((...((.....---.))...)))))..----...---................. ( -12.16)
>DroEre_CAF1 123558 109 + 1
ACAUAAAGCAAAUAUCAAUUACAGUUCUCUUUGUUUCGUCUUUUGCUGCCUUUUAUUCCUCUGGUUUUU---CCCACCGGAAUUUCAAUCCGGCCUUUUUUUCACUUACUCC
......((((((........((((......)))).......))))))(((....(((((..(((.....---.)))..)))))........))).................. ( -16.76)
>DroYak_CAF1 118153 105 + 1
ACAUAAAGCAAAUAUCAAUUACAGUUCUCUUUGUUUCGUCUUUUGCUGCCUUUUAUUCCUCUGGCUUUU---CCCACCGGAAUUC----CCCACUUUUUUCUCACUUGCUCC
......((((((........((((......)))).......)))))).......(((((..(((.....---.)))..)))))..----....................... ( -13.46)
>consensus
ACAUAAAGCAAAUAUCAAUUACAGUUCUCUUUGUUUCGUCUUUUGCUGCCUUUUAUUCCUCUGGUUUUU___CCCUCCGGAAUUU____CCC___AUUUUUUCACUUGCUCC
......((((((........((((......)))).......))))))............(((((............)))))............................... (-11.40 = -11.40 +   0.00) 

alignment

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secondary structure

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dotplot

Postscript

Window 3

Location 2,720,461 – 2,720,566
Length 105
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 91.86
Mean single sequence MFE -19.52
Consensus MFE -16.86
Energy contribution -16.70
Covariance contribution -0.16
Combinations/Pair 1.05
Mean z-score -2.41
Structure conservation index 0.86
SVM decision value 3.05
SVM RNA-class probability 0.998272
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2720461 105 - 22224390
GGAGCAAGUGAAAAAAU---GGG----AAAUUCCGGAGGGGCAAAAAACCAGAGGAAUAAAAGGCAGCAAAAGACGAAACAAAGAGAACUGUAAUUGAUAUUUGCUUUAUAU
((((((((((.......---...----..(((((....((........))...))))).....((((.....................))))......)))))))))).... ( -18.40)
>DroSec_CAF1 109136 102 - 1
GGAGCAAGUGAAAAAAU---GGG----AAAUUCCGGAGGG---AAAACCCAGAGGAAUAAAAGGCAGCAAAAGACGAAACAAAGAGAACUGUAAUUGAUAUUUGCUUUAUGU
((((((((((.......---...----..(((((...(((---....)))...))))).....((((.....................))))......)))))))))).... ( -20.00)
>DroSim_CAF1 97182 102 - 1
GGAGCAAGUGAAAAAAU---GGG----AAAUUCCGGAGGG---AAAAACCAGAGGAAUAAAAGGCAGCAAAAGACGAAACAAAGAGAACUGUAAUUGAUAUUUGCUUUAUGU
((((((((((.......---...----..(((((...((.---.....))...))))).....((((.....................))))......)))))))))).... ( -18.20)
>DroEre_CAF1 123558 109 - 1
GGAGUAAGUGAAAAAAAGGCCGGAUUGAAAUUCCGGUGGG---AAAAACCAGAGGAAUAAAAGGCAGCAAAAGACGAAACAAAGAGAACUGUAAUUGAUAUUUGCUUUAUGU
((((((((((........(((........(((((..(((.---.....)))..)))))....))).............(((........)))......)))))))))).... ( -21.10)
>DroYak_CAF1 118153 105 - 1
GGAGCAAGUGAGAAAAAAGUGGG----GAAUUCCGGUGGG---AAAAGCCAGAGGAAUAAAAGGCAGCAAAAGACGAAACAAAGAGAACUGUAAUUGAUAUUUGCUUUAUGU
((((((((((.............----..(((((..(((.---.....)))..))))).....((((.....................))))......)))))))))).... ( -19.90)
>consensus
GGAGCAAGUGAAAAAAU___GGG____AAAUUCCGGAGGG___AAAAACCAGAGGAAUAAAAGGCAGCAAAAGACGAAACAAAGAGAACUGUAAUUGAUAUUUGCUUUAUGU
((((((((((...................(((((...((.........))...))))).....((((.....................))))......)))))))))).... (-16.86 = -16.70 +  -0.16) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:03 2006