Locus 3820

Sequence ID X_DroMel_CAF1
Location 10,146,580 – 10,146,750
Length 170
Max. P 0.969831
window6281 window6282 window6283

overview

Window 1

Location 10,146,580 – 10,146,694
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.30
Mean single sequence MFE -27.42
Consensus MFE -22.62
Energy contribution -23.06
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.92
Structure conservation index 0.82
SVM decision value 1.42
SVM RNA-class probability 0.951864
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10146580 114 + 22224390
ACCUGUGGC------UGGAUAAAUAGCAAAGUGUGCUAAAUAAUUGAAUAAGGACAAUUGAUUGAUAGCCAAAAGCUUUUUAUACCGGCGCAUAGUUAACGAAGCGUAACAGGUAAAGCU
((((((.((------((((((((.(((....((.((((..((((((........)))))).....))))))...))).))))).)))))((...(....)...))...))))))...... ( -30.00)
>DroSec_CAF1 35803 114 + 1
ACCUGUGGC------UGGAUAAAUAGCAAAGUCUGCUAAAUAAUUGAAUAAGGACAAUUGAUUGAUAGCCAAAAGCUUUUUAUACCGGCGCAUAGUUAACGAAGCGUAACAGGUAAAGCU
((((((.((------((((((((.(((...(.(((.(((.((((((........)))))).))).))).)....))).))))).)))))((...(....)...))...))))))...... ( -27.50)
>DroSim_CAF1 28211 114 + 1
ACCUGUGGC------UGGAUAAAUAGCAAAGUCUGCUAAAUAAUUGAAUAAGGACAAUUGAUUGAUAGCCAAAAGCUUUUUAUACCGGCGCAUAGUUAACGAAGCGUAACAGGUAAAGCU
((((((.((------((((((((.(((...(.(((.(((.((((((........)))))).))).))).)....))).))))).)))))((...(....)...))...))))))...... ( -27.50)
>DroYak_CAF1 28843 114 + 1
ACCUGUGGC------UGGAUAAAUAGCAAAGUGUGCUAAAUAAUUGAAUAAGUACAAUUGAUUGAUAGCCAAAAGCUCUUUAUACCGGCGCAUAGUUAACGAAGCGUAACAGGUAGAGCU
((((((.((------((((((((.(((....((.((((..((((((........)))))).....))))))...))).))))).)))))((...(....)...))...))))))...... ( -29.80)
>DroAna_CAF1 50243 118 + 1
AUCCGUAGCCAGGUGAGGAUAAAUAGCAAAGUGUGCUAAAUAAUUGAAUAAGGACAAUUGAUUGAUAGCCAAAAGCUUUUUAUACCAGCGCAUAGUUAACGAAGCGUAACAGGUAAGA--
.......(((......(((((((.(((....((.((((..((((((........)))))).....))))))...))).))))).)).((((...(....)...))))....)))....-- ( -22.30)
>consensus
ACCUGUGGC______UGGAUAAAUAGCAAAGUGUGCUAAAUAAUUGAAUAAGGACAAUUGAUUGAUAGCCAAAAGCUUUUUAUACCGGCGCAUAGUUAACGAAGCGUAACAGGUAAAGCU
((((((..........(((((((.(((....((.((((..((((((........)))))).....))))))...))).))))).)).((((...(....)...)))).))))))...... (-22.62 = -23.06 +   0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,146,580 – 10,146,694
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.30
Mean single sequence MFE -22.56
Consensus MFE -20.84
Energy contribution -20.88
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.43
Structure conservation index 0.92
SVM decision value 1.27
SVM RNA-class probability 0.938106
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10146580 114 - 22224390
AGCUUUACCUGUUACGCUUCGUUAACUAUGCGCCGGUAUAAAAAGCUUUUGGCUAUCAAUCAAUUGUCCUUAUUCAAUUAUUUAGCACACUUUGCUAUUUAUCCA------GCCACAGGU
......((((((...((............))((.((.(((((.(((...((((((..(((.(((((........)))))))))))).))....))).))))))).------)).)))))) ( -23.90)
>DroSec_CAF1 35803 114 - 1
AGCUUUACCUGUUACGCUUCGUUAACUAUGCGCCGGUAUAAAAAGCUUUUGGCUAUCAAUCAAUUGUCCUUAUUCAAUUAUUUAGCAGACUUUGCUAUUUAUCCA------GCCACAGGU
......((((((...((............))((.((.(((((.(((.....((((..(((.(((((........)))))))))))).......))).))))))).------)).)))))) ( -23.10)
>DroSim_CAF1 28211 114 - 1
AGCUUUACCUGUUACGCUUCGUUAACUAUGCGCCGGUAUAAAAAGCUUUUGGCUAUCAAUCAAUUGUCCUUAUUCAAUUAUUUAGCAGACUUUGCUAUUUAUCCA------GCCACAGGU
......((((((...((............))((.((.(((((.(((.....((((..(((.(((((........)))))))))))).......))).))))))).------)).)))))) ( -23.10)
>DroYak_CAF1 28843 114 - 1
AGCUCUACCUGUUACGCUUCGUUAACUAUGCGCCGGUAUAAAGAGCUUUUGGCUAUCAAUCAAUUGUACUUAUUCAAUUAUUUAGCACACUUUGCUAUUUAUCCA------GCCACAGGU
......((((((...((............))((.((.(((((.(((...((((((..(((.(((((........)))))))))))).))....))).))))))).------)).)))))) ( -23.90)
>DroAna_CAF1 50243 118 - 1
--UCUUACCUGUUACGCUUCGUUAACUAUGCGCUGGUAUAAAAAGCUUUUGGCUAUCAAUCAAUUGUCCUUAUUCAAUUAUUUAGCACACUUUGCUAUUUAUCCUCACCUGGCUACGGAU
--......((((...(((.(((.......)))..((.(((((.(((...((((((..(((.(((((........)))))))))))).))....))).)))))))......))).)))).. ( -18.80)
>consensus
AGCUUUACCUGUUACGCUUCGUUAACUAUGCGCCGGUAUAAAAAGCUUUUGGCUAUCAAUCAAUUGUCCUUAUUCAAUUAUUUAGCACACUUUGCUAUUUAUCCA______GCCACAGGU
......((((((..(((............)))..((.(((((.(((.....((((..(((.(((((........)))))))))))).......))).)))))))..........)))))) (-20.84 = -20.88 +   0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,146,654 – 10,146,750
Length 96
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 89.61
Mean single sequence MFE -20.96
Consensus MFE -19.51
Energy contribution -19.32
Covariance contribution -0.19
Combinations/Pair 1.07
Mean z-score -2.04
Structure conservation index 0.93
SVM decision value 1.65
SVM RNA-class probability 0.969831
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10146654 96 + 22224390
UAUACCGGCGCAUAGUUAACGAAGCGUAACAGGUAAAGCUGGGUGAAAAGAACCCAGUUCCGAAGCAAAAUAUAUAAGUAAAAUACAAGGAGACGA-------
..((((.((((...(....)...))))....)))).((((((((.......)))))))).............................(....)..------- ( -22.50)
>DroSec_CAF1 35877 96 + 1
UAUACCGGCGCAUAGUUAACGAAGCGUAACAGGUAAAGCUGGGAGAAAAGGACCCAGCUCCGAAGGAAAAUAUAUAAGUAAAAUACAAGGAAUCGA-------
..((((.((((...(....)...))))....))))..((((((.........))))))(((...........................))).....------- ( -20.33)
>DroSim_CAF1 28285 96 + 1
UAUACCGGCGCAUAGUUAACGAAGCGUAACAGGUAAAGCUGGGAGAAAAGGACCCAGCUCCAAAGGAAAAUAUAUAAGUAAAAUACAAGGAAUCGA-------
..((((.((((...(....)...))))....)))).(((((((.........))))))).....................................------- ( -20.20)
>DroYak_CAF1 28917 103 + 1
UAUACCGGCGCAUAGUUAACGAAGCGUAACAGGUAGAGCUGGGAGUAGAGGACCCAGCAUCGAAGAAAAAUAUAUAAGUAAAAUACAAGGAAUCGGAAUCAGA
..((((.((((...(....)...))))....))))((((((((.........)))))).)).......................................... ( -20.80)
>consensus
UAUACCGGCGCAUAGUUAACGAAGCGUAACAGGUAAAGCUGGGAGAAAAGGACCCAGCUCCGAAGGAAAAUAUAUAAGUAAAAUACAAGGAAUCGA_______
..((((.((((...(....)...))))....))))..((((((.........))))))............................................. (-19.51 = -19.32 +  -0.19)

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 11:09:29 2006