Locus 1160

Sequence ID X_DroMel_CAF1
Location 3,452,208 – 3,452,363
Length 155
Max. P 0.982398
window1863 window1864 window1865

overview

Window 3

Location 3,452,208 – 3,452,302
Length 94
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 77.57
Mean single sequence MFE -26.20
Consensus MFE -16.93
Energy contribution -16.52
Covariance contribution -0.42
Combinations/Pair 1.16
Mean z-score -2.27
Structure conservation index 0.65
SVM decision value 1.62
SVM RNA-class probability 0.968046
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3452208 94 - 22224390
CAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCCAGCAGAGAGCAAAGACUUUUGCGAAAAAAAAGGGGGGGUCGGU---GUUGGAAAUGG---------------
....((((((((((((((....)))))))))).))))(((((((..((.(.....(((((.......)))))....).))..)---)))))).....--------------- ( -29.80)
>DroSec_CAF1 24291 74 - 1
CAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCCAGCAGAGAGCAAAGACUUU--------------------CGGU---GUUGGAAAUGG---------------
....((((((((((((((....)))))))))).))))((((((((((((......))))--------------------)..)---)))))).....--------------- ( -25.90)
>DroSim_CAF1 23985 74 - 1
CAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCCAGCAGAGAGCAAAGACUUU--------------------CGGU---GUUGGAAAUGG---------------
....((((((((((((((....)))))))))).))))((((((((((((......))))--------------------)..)---)))))).....--------------- ( -25.90)
>DroEre_CAF1 27560 87 - 1
CAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCCAGCAGAGAGCAAAGACUUUGG-----GAAAA--UGGGGGCGGG---GUUGGAAAAUG---------------
....((((((((((((((....)))))))))).))))((((((.....((.....((..(.-----.....--)..))))...---)))))).....--------------- ( -22.50)
>DroYak_CAF1 25609 83 - 1
CAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCCAGCAGAGAGCAAAGACUUUGG-----AAAAA------GGCGGU---GUUAGAAAUAG---------------
((((((((((((((((((....))))))))))...(((((....).))))...........-----....)------))))))---)..........--------------- ( -23.40)
>DroAna_CAF1 46114 105 - 1
CAUCGUCUAGUCAAAUUGCAAGUGAUUUGGUUCAGGCUCCAGCAGAGAGCAAGGACUUUCG-----AAAAA--GGGGCUAGGGAGACAUGGCAAGGGCCUGGGGGAAAGCGG
...(((....((((((((....))))))))(((((((.((....(((((......))))).-----.....--...((((.(....).))))..))))))))).....))). ( -29.70)
>consensus
CAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCCAGCAGAGAGCAAAGACUUU_G_____AAAAA______G_CGGU___GUUGGAAAUGG_______________
....((((((((((((((....))))))))))...(((((....).))))..))))........................................................ (-16.93 = -16.52 +  -0.42) 

alignment

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secondary structure

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dotplot

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Window 4

Location 3,452,230 – 3,452,333
Length 103
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 90.92
Mean single sequence MFE -22.44
Consensus MFE -19.80
Energy contribution -19.56
Covariance contribution -0.24
Combinations/Pair 1.05
Mean z-score -1.84
Structure conservation index 0.88
SVM decision value 1.91
SVM RNA-class probability 0.982398
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3452230 103 - 22224390
GCGCUGAAAGAACAAAAAAAAAAUGUCGCGACAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCCAGCAGAGAGCAAAGACUUUUGCGAAAAAAAAG
((((((................((((....)))).((((((((((((((....)))))))))).))))..)))).(((((......))))))).......... ( -24.70)
>DroSec_CAF1 24306 87 - 1
GCGUUGAAAGAACAAA---AAAAUGUCGCGACAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCCAGCAGAGAGCAAAGACUUU-------------
..((((...((.((..---....)))).))))...((((((((((((((....))))))))))...(((((....).))))..))))...------------- ( -21.70)
>DroSim_CAF1 24000 87 - 1
GCGUUGAAAGAACAAA---AAAAUGUCGCGACAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCCAGCAGAGAGCAAAGACUUU-------------
..((((...((.((..---....)))).))))...((((((((((((((....))))))))))...(((((....).))))..))))...------------- ( -21.70)
>DroEre_CAF1 27581 94 - 1
GCGUUGAAAGAACAAA---AAAAUGUCGCGACAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCCAGCAGAGAGCAAAGACUUUGG-----GAAAA-
..((((...((.((..---....)))).))))...((((((((((((((....)))))))))).))))(((..(((((........))))))-----))...- ( -22.80)
>DroYak_CAF1 25626 94 - 1
GCGCUGAAAGAACAAA---AAAAUGUCGCGACAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCCAGCAGAGAGCAAAGACUUUGG-----AAAAA-
..((((..........---...((((....)))).((((((((((((((....)))))))))).))))..))))..((((......))))..-----.....- ( -21.30)
>consensus
GCGUUGAAAGAACAAA___AAAAUGUCGCGACAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCCAGCAGAGAGCAAAGACUUU_G______AAAA_
..((((................((((....)))).((((((((((((((....)))))))))).))))..))))............................. (-19.80 = -19.56 +  -0.24) 

alignment

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secondary structure

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dotplot

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Window 5

Location 3,452,262 – 3,452,363
Length 101
Sequences 4
Columns 101
Reading direction reverse
Mean pairwise identity 96.98
Mean single sequence MFE -18.07
Consensus MFE -17.09
Energy contribution -17.34
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.04
Structure conservation index 0.95
SVM decision value 0.96
SVM RNA-class probability 0.890473
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3452262 101 - 22224390
UACAAAAACCAAGUCGAAAAUAAAAACAAAGCGCUGAAAGAACAAAAAAAAAAUGUCGCGACAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCC
............((((..........((......))...((.((.........)))).))))...((((((((((((((....)))))))))).))))... ( -16.80)
>DroSec_CAF1 24325 98 - 1
UACAAAAACCAAGUCGAAAAUAAAAACAAAGCGUUGAAAGAACAAA---AAAAUGUCGCGACAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCC
............((((........(((.....)))....((.((..---....)))).))))...((((((((((((((....)))))))))).))))... ( -18.50)
>DroSim_CAF1 24019 98 - 1
UACAAAAACCAAGUCGAAAAUAAAAACAAAGCGUUGAAAGAACAAA---AAAAUGUCGCGACAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCC
............((((........(((.....)))....((.((..---....)))).))))...((((((((((((((....)))))))))).))))... ( -18.50)
>DroEre_CAF1 27607 97 - 1
UACAAAAACA-AGUCGAAAAUAAAAACAAAGCGUUGAAAGAACAAA---AAAAUGUCGCGACAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCC
..........-.((((........(((.....)))....((.((..---....)))).))))...((((((((((((((....)))))))))).))))... ( -18.50)
>consensus
UACAAAAACCAAGUCGAAAAUAAAAACAAAGCGUUGAAAGAACAAA___AAAAUGUCGCGACAUCGUCUAGUCAAAUUGCAAGUGAUUUGACUCAGGCUCC
............((((..(..............((....))..............)..))))...((((((((((((((....)))))))))).))))... (-17.09 = -17.34 +   0.25) 

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 10:02:47 2006