Locus 4780

Sequence ID X_DroMel_CAF1
Location 12,420,800 – 12,420,898
Length 98
Max. P 0.870357
window7823 window7824

overview

Window 3

Location 12,420,800 – 12,420,898
Length 98
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 81.04
Mean single sequence MFE -42.95
Consensus MFE -26.40
Energy contribution -26.81
Covariance contribution 0.41
Combinations/Pair 1.23
Mean z-score -1.62
Structure conservation index 0.61
SVM decision value 0.00
SVM RNA-class probability 0.533715
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12420800 98 + 22224390
GGUGGUGGCGGUGGG-CAAUUG-----UUGCCACCAUUCAG------GGCUG---CAGCCUCGUGCUCCAGGCGCUGAAACAUCUUAAGGGCCACCGGUGGGGUUUUGAAAAA
(((((..(((((...-..))))-----)..))))).(((((------((((.---((.((..((((.....)))).............((....)))))).)))))))))... ( -39.00)
>DroSec_CAF1 14849 98 + 1
GGUGGUGGCGGUGGG-CAAUUG-----UUGCCACCAUUCAG------GGCUG---CAGCCUCGUGCUCCAGGCGCUGAAACAUCUUAAGGGCCACCGGUGGGGUUUUGAAGAA
(((((..(((((...-..))))-----)..))))).(((((------(.(((---.(((.....))).))).).)))))...((((.((((((.((...)))))))).)))). ( -40.40)
>DroEre_CAF1 15150 98 + 1
GGCGGUGGCGGUGGG-CAAUUG-----UUGCCACCAUUCAG------AACUG---CAGCUUCGUGCUCCAGACGCUGGAACAUCUUAAGGGCCACCGGUGGGGUUUUGAAGAA
...((((((((..(.-...)..-----)))))))).(((((------((((.---((.(...(((.(((((...))))).))).....((....))).)).)))))))))... ( -38.60)
>DroYak_CAF1 14806 98 + 1
GGUGGUGGCGGUGGG-CAAUUG-----UUGCCACCAUUUAG------GGCGG---CAGCCUCGUGCUCUAGGCGCUGGAACAUUUUCAGGGCCACCGGUGGCGUUUUGAAGAA
(((((..(((((...-..))))-----)..))))).(((((------((((.---((.((..(....)..(((.(((((.....))))).)))...)))).)))))))))... ( -40.60)
>DroAna_CAF1 15500 107 + 1
GGCGGCAGCGGUGGUGGUGUUGUGGUCUGGCCACCAUUCAG------AGCGGCGGCCGCCUCGUGCUCCAGCCGCUGGAACAUCUUCAGGGCCACCGGCGGGGUCUUGAAGAA
((((((.((.((..(((....((((.....))))...))).------.)).)).))))))...((.(((((...))))).))(((((((((((.((...))))))))))))). ( -51.10)
>DroPer_CAF1 18600 97 + 1
GGCGGCGGCGG-GGA-CAGUUG-----------CCGUUGAGGCCGGCGGCGG---CCGCCUCAUGCUCCAGCCUCUGGAACAUCUUCAGGGCCACCGGCGGUGUCUUGAAAAA
((((((((((.-...-).))))-----------)))))((.((((.(((.((---((.....(((.(((((...))))).)))......)))).))).)))).))........ ( -48.00)
>consensus
GGCGGUGGCGGUGGG_CAAUUG_____UUGCCACCAUUCAG______GGCGG___CAGCCUCGUGCUCCAGGCGCUGGAACAUCUUAAGGGCCACCGGUGGGGUUUUGAAGAA
(.((((((((((((................)))))............(((((...)))))..(((.(((((...))))).))).......))))))).).............. (-26.40 = -26.81 +   0.41)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,420,800 – 12,420,898
Length 98
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 81.04
Mean single sequence MFE -36.08
Consensus MFE -29.91
Energy contribution -29.21
Covariance contribution -0.71
Combinations/Pair 1.29
Mean z-score -1.84
Structure conservation index 0.83
SVM decision value 0.87
SVM RNA-class probability 0.870357
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12420800 98 - 22224390
UUUUUCAAAACCCCACCGGUGGCCCUUAAGAUGUUUCAGCGCCUGGAGCACGAGGCUG---CAGCC------CUGAAUGGUGGCAA-----CAAUUG-CCCACCGCCACCACC
.................((((((...........(((((.(.(((.(((.....))).---))).)------))))).(((((((.-----....))-.)))))))))))... ( -35.20)
>DroSec_CAF1 14849 98 - 1
UUCUUCAAAACCCCACCGGUGGCCCUUAAGAUGUUUCAGCGCCUGGAGCACGAGGCUG---CAGCC------CUGAAUGGUGGCAA-----CAAUUG-CCCACCGCCACCACC
.................((((((...........(((((.(.(((.(((.....))).---))).)------))))).(((((((.-----....))-.)))))))))))... ( -35.20)
>DroEre_CAF1 15150 98 - 1
UUCUUCAAAACCCCACCGGUGGCCCUUAAGAUGUUCCAGCGUCUGGAGCACGAAGCUG---CAGUU------CUGAAUGGUGGCAA-----CAAUUG-CCCACCGCCACCGCC
................(((((((.............(((...(((.(((.....))).---)))..------)))...(((((((.-----....))-.)))))))))))).. ( -33.50)
>DroYak_CAF1 14806 98 - 1
UUCUUCAAAACGCCACCGGUGGCCCUGAAAAUGUUCCAGCGCCUAGAGCACGAGGCUG---CCGCC------CUAAAUGGUGGCAA-----CAAUUG-CCCACCGCCACCACC
.................((((((..((....(((((.((...)).)))))...(((((---(((((------......))))))).-----.....)-))))..))))))... ( -30.70)
>DroAna_CAF1 15500 107 - 1
UUCUUCAAGACCCCGCCGGUGGCCCUGAAGAUGUUCCAGCGGCUGGAGCACGAGGCGGCCGCCGCU------CUGAAUGGUGGCCAGACCACAACACCACCACCGCUGCCGCC
.((((((.(.((((...)).)).).)))))).((..((((((.(((.((.....))((((((((..------.....))))))))..............)))))))))..)). ( -40.50)
>DroPer_CAF1 18600 97 - 1
UUUUUCAAGACACCGCCGGUGGCCCUGAAGAUGUUCCAGAGGCUGGAGCAUGAGGCGG---CCGCCGCCGGCCUCAACGG-----------CAACUG-UCC-CCGCCGCCGCC
........((..(((.((((((((((....(((((((((...)))))))))..)).))---)))))).)))..))..(((-----------(.....-...-..))))..... ( -41.40)
>consensus
UUCUUCAAAACCCCACCGGUGGCCCUGAAGAUGUUCCAGCGCCUGGAGCACGAGGCUG___CAGCC______CUGAAUGGUGGCAA_____CAAUUG_CCCACCGCCACCACC
.................((((((........((((((((...))))))))...(((((...)))))............(((((................)))))))))))... (-29.91 = -29.21 +  -0.71)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:58 2006