Locus 7857

Sequence ID X_DroMel_CAF1
Location 19,570,670 – 19,570,820
Length 150
Max. P 0.996007
window12886 window12887 window12888

overview

Window 6

Location 19,570,670 – 19,570,790
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 69.97
Mean single sequence MFE -34.42
Consensus MFE -18.48
Energy contribution -19.98
Covariance contribution 1.50
Combinations/Pair 1.19
Mean z-score -1.92
Structure conservation index 0.54
SVM decision value 1.19
SVM RNA-class probability 0.928548
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19570670 120 + 22224390
CGUGUUUUUAUGUGAGCCAAGUGGUUAUGCCUGCCACCGUGCAAUGCGUUGGCUAAGUGGCUGCAAAAUGGCCAAUUUGAAGCCACCUGAAGUAGGUUGAAGUGAGUUACUGCUCACUGC
.(.(((((....((.((((.(..(((((....((((.(((.....))).))))...)))))..)....))))))....))))))(((((...)))))...(((((((....))))))).. ( -38.60)
>DroSec_CAF1 746 100 + 1
CGUGUUUUUAUGUGAGCCAAGUGGAUAUGCCAGCCACCGUUGAGUGCGUUGGCAAAGUGGCUGCAAAUUGGCCAAUUUGGAGCCACCUAAAGUAGGUUGA--------------------
..............((((.........((((((((((......))).)))))))..((((((.((((((....)))))).))))))........))))..-------------------- ( -34.90)
>DroSim_CAF1 686 100 + 1
CCUGUUUUUAUGUUAGCCAAGUGGAUAUGCCAGCCACCGUUGAGUGCGUUGGCUAAGUGGCUGUAAAUUGGCCAAUUUGGAGCCACCCAAAGUAGGUUGA--------------------
............((((((...(((....(((((((((......))).))))))...((((((.((((((....)))))).))))))))).....))))))-------------------- ( -35.10)
>DroEre_CAF1 724 95 + 1
-GUCUUUCUAUGAG-------U------GAUAG---CCAUUAAGUGCGGUGGCUAAGUGGCUGUAAAUUGGCCAAUUUAGAGCGCCC-UAAGUGGGUUAAAGUGAGU-------CACUAC
-.............-------.------..(((---(((((......))))))))(((((((.((..((((((.((((((......)-))))).))))))..)))))-------)))).. ( -29.10)
>consensus
CGUGUUUUUAUGUGAGCCAAGUGGAUAUGCCAGCCACCGUUGAGUGCGUUGGCUAAGUGGCUGCAAAUUGGCCAAUUUGGAGCCACCUAAAGUAGGUUGA____________________
......(((((.................(((((((((......))).))))))...((((((.((((((....)))))).)))))).....)))))........................ (-18.48 = -19.98 +   1.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,570,670 – 19,570,790
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 69.97
Mean single sequence MFE -26.67
Consensus MFE -15.29
Energy contribution -16.73
Covariance contribution 1.44
Combinations/Pair 1.15
Mean z-score -1.77
Structure conservation index 0.57
SVM decision value 1.09
SVM RNA-class probability 0.914362
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19570670 120 - 22224390
GCAGUGAGCAGUAACUCACUUCAACCUACUUCAGGUGGCUUCAAAUUGGCCAUUUUGCAGCCACUUAGCCAACGCAUUGCACGGUGGCAGGCAUAACCACUUGGCUCACAUAAAAACACG
...((((((...............(((.....((((((((.((((........)))).)))))))).((((.((.......)).)))))))((........))))))))........... ( -34.30)
>DroSec_CAF1 746 100 - 1
--------------------UCAACCUACUUUAGGUGGCUCCAAAUUGGCCAAUUUGCAGCCACUUUGCCAACGCACUCAACGGUGGCUGGCAUAUCCACUUGGCUCACAUAAAAACACG
--------------------....((......((((((((.((((((....)))))).))))))))(((((.(.((((....))))).))))).........))................ ( -27.30)
>DroSim_CAF1 686 100 - 1
--------------------UCAACCUACUUUGGGUGGCUCCAAAUUGGCCAAUUUACAGCCACUUAGCCAACGCACUCAACGGUGGCUGGCAUAUCCACUUGGCUAACAUAAAAACAGG
--------------------....(((....(((((((((..(((((....)))))..)))))))))((((.(.((((....))))).)))).........................))) ( -25.60)
>DroEre_CAF1 724 95 - 1
GUAGUG-------ACUCACUUUAACCCACUUA-GGGCGCUCUAAAUUGGCCAAUUUACAGCCACUUAGCCACCGCACUUAAUGG---CUAUC------A-------CUCAUAGAAAGAC-
(.((((-------(..........(((.....-))).(((.((((((....)))))).)))....((((((..........)))---)))))------)-------)))..........- ( -19.50)
>consensus
____________________UCAACCUACUUUAGGUGGCUCCAAAUUGGCCAAUUUACAGCCACUUAGCCAACGCACUCAACGGUGGCUGGCAUAUCCACUUGGCUCACAUAAAAACACG
................................((((((((.((((((....)))))).)))))))).((((.((.......)).))))................................ (-15.29 = -16.73 +   1.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,570,710 – 19,570,820
Length 110
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 76.69
Mean single sequence MFE -26.46
Consensus MFE -15.85
Energy contribution -18.72
Covariance contribution 2.87
Combinations/Pair 1.09
Mean z-score -2.69
Structure conservation index 0.60
SVM decision value 2.64
SVM RNA-class probability 0.996007
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19570710 110 - 22224390
CACCCUGCUCACUUCUGGUCACUGGCCAGAGCAGUGAGCAGUAACUCACUUCAACCUACUUCAGGUGGCUUCAAAUUGGCCAUUUUGCAGCCACUUAGCCAACGCAUUGC
....(((((((((((((((.....))))))..))))))))).....................((((((((.((((........)))).)))))))).((....))..... ( -39.30)
>DroSec_CAF1 786 86 - 1
CGCCCUGCUCACUUCUGGUCACUGGC------------------------UCAACCUACUUUAGGUGGCUCCAAAUUGGCCAAUUUGCAGCCACUUUGCCAACGCACUCA
.((((...........))....((((------------------------............((((((((.((((((....)))))).)))))))).))))..))..... ( -21.82)
>DroSim_CAF1 726 86 - 1
CACCCUGCUCACUUCUGGUCACUGGC------------------------UCAACCUACUUUGGGUGGCUCCAAAUUGGCCAAUUUACAGCCACUUAGCCAACGCACUCA
.....((((((....)))....((((------------------------(...((......))((((((..(((((....)))))..))))))..)))))..))).... ( -20.00)
>DroEre_CAF1 747 102 - 1
CACCCUGCUCACUUCUGGUCACUGGCCAGAGUAGUG-------ACUCACUUUAACCCACUUA-GGGCGCUCUAAAUUGGCCAAUUUACAGCCACUUAGCCACCGCACUUA
.....((((((((((((((.....))))))..))))-------)..........(((.....-))).(((.((((((....)))))).)))............))).... ( -24.70)
>consensus
CACCCUGCUCACUUCUGGUCACUGGC________________________UCAACCUACUUUAGGUGGCUCCAAAUUGGCCAAUUUACAGCCACUUAGCCAACGCACUCA
.....(((.....((((((.....))))))................................((((((((.((((((....)))))).)))))))).......))).... (-15.85 = -18.72 +   2.87)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:49:14 2006