Locus 4278

Sequence ID 2R_DroMel_CAF1
Location 14,083,056 – 14,083,193
Length 137
Max. P 0.953236
window6864 window6865 window6866

overview

Window 4

Location 14,083,056 – 14,083,153
Length 97
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.38
Mean single sequence MFE -37.20
Consensus MFE -27.90
Energy contribution -27.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.63
Structure conservation index 0.75
SVM decision value 0.00
SVM RNA-class probability 0.535627
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14083056 97 + 20766785
GUUCGGGCCAAGAUUGGCACAACGACCACCG---GCGUGGCAGCUG--------------------UUUUGUGGCAGCCAUAAUUGGCAUGUGGAAAACUGGCGGAUUGGCCAUAAAAAG
.....((((((...((.(((..((.....))---..))).))((((--------------------((((.(.(((((((....)))).))).)))))).)))...))))))........ ( -32.90)
>DroSim_CAF1 8034 97 + 1
CUUCGGGCCAAGAUUGGCACAACGACCACCG---GCGUGGCAGCUG--------------------UUUUGUGGCAGCCAUAAUUGGCAUGUGGAAAACUGGCGGAGUGGCCAUAAAAAG
.....(((((....((.(((..((.....))---..))).))((((--------------------((((.(.(((((((....)))).))).)))))).)))....)))))........ ( -31.90)
>DroYak_CAF1 8621 120 + 1
GUUCGGGCCAAGAUUGGCGCAACGACCACCGUGGUCGUGGCAGCUGUUUUCUGCUGUUUUAUGCUGUUUUGUGGCAGCCAUAAUUGGCAUGUGGAAAACUGGCGGCGUGGCCAUAAAAAG
.....(((((....((.(((.((((((.....)))))).)).(((((((((..(((((((((((((((....))))).)))))..)))).)..)))))).)))).)))))))........ ( -46.80)
>consensus
GUUCGGGCCAAGAUUGGCACAACGACCACCG___GCGUGGCAGCUG____________________UUUUGUGGCAGCCAUAAUUGGCAUGUGGAAAACUGGCGGAGUGGCCAUAAAAAG
..(((.((((....))))....)))((((.......))))..........................(((((((((.((((....)))).(((.(.....).))).....))))))))).. (-27.90 = -27.90 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,083,056 – 14,083,153
Length 97
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.38
Mean single sequence MFE -30.07
Consensus MFE -24.90
Energy contribution -24.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.52
Structure conservation index 0.83
SVM decision value 0.17
SVM RNA-class probability 0.615611
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14083056 97 - 20766785
CUUUUUAUGGCCAAUCCGCCAGUUUUCCACAUGCCAAUUAUGGCUGCCACAAAA--------------------CAGCUGCCACGC---CGGUGGUCGUUGUGCCAAUCUUGGCCCGAAC
.......((((......))))...........(((((...((((.........(--------------------((((.(((((..---..))))).)))))))))...)))))...... ( -27.90)
>DroSim_CAF1 8034 97 - 1
CUUUUUAUGGCCACUCCGCCAGUUUUCCACAUGCCAAUUAUGGCUGCCACAAAA--------------------CAGCUGCCACGC---CGGUGGUCGUUGUGCCAAUCUUGGCCCGAAG
.......((((......))))...........(((((...((((.........(--------------------((((.(((((..---..))))).)))))))))...)))))...... ( -27.90)
>DroYak_CAF1 8621 120 - 1
CUUUUUAUGGCCACGCCGCCAGUUUUCCACAUGCCAAUUAUGGCUGCCACAAAACAGCAUAAAACAGCAGAAAACAGCUGCCACGACCACGGUGGUCGUUGCGCCAAUCUUGGCCCGAAC
........(((...)))((((((((((....(((...(((((.(((........))))))))....))))))))).((.((.((((((.....)))))).))))......))))...... ( -34.40)
>consensus
CUUUUUAUGGCCACUCCGCCAGUUUUCCACAUGCCAAUUAUGGCUGCCACAAAA____________________CAGCUGCCACGC___CGGUGGUCGUUGUGCCAAUCUUGGCCCGAAC
.......((((......))))...........(((((...((((((...)).......................((((.(((((.......))))).)))).))))...)))))...... (-24.90 = -24.90 +   0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,083,093 – 14,083,193
Length 100
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.47
Mean single sequence MFE -36.69
Consensus MFE -30.25
Energy contribution -30.03
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -2.91
Structure conservation index 0.82
SVM decision value 1.43
SVM RNA-class probability 0.953236
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14083093 100 + 20766785
CAGCUG--------------------UUUUGUGGCAGCCAUAAUUGGCAUGUGGAAAACUGGCGGAUUGGCCAUAAAAAGCAGGUCAGGCCACUGCUAAGACAAUCAAAUAAUGGCCACU
..((((--------------------((((.(.(((((((....)))).))).)))))).)))....(((((((....(((((.........)))))..(.....).....))))))).. ( -31.00)
>DroSim_CAF1 8071 100 + 1
CAGCUG--------------------UUUUGUGGCAGCCAUAAUUGGCAUGUGGAAAACUGGCGGAGUGGCCAUAAAAAGCAGGUCAGGCCACUGCUAAGACAAUCAAAUAAUGGCCACU
..((((--------------------((((.(.(((((((....)))).))).)))))).)))..(((((((((....(((((.........)))))..(.....).....))))))))) ( -35.00)
>DroYak_CAF1 8661 120 + 1
CAGCUGUUUUCUGCUGUUUUAUGCUGUUUUGUGGCAGCCAUAAUUGGCAUGUGGAAAACUGGCGGCGUGGCCAUAAAAAGCAGGUCAGGCCACUGCCAAGACAAUCAAAUAAUGGCCACU
..(((((((((..(((((((((((((((....))))).)))))..)))).)..)))))).)))...((((((((.........(((.(((....)))..))).........)))))))). ( -44.07)
>consensus
CAGCUG____________________UUUUGUGGCAGCCAUAAUUGGCAUGUGGAAAACUGGCGGAGUGGCCAUAAAAAGCAGGUCAGGCCACUGCUAAGACAAUCAAAUAAUGGCCACU
..............................(((((.((((....))))...........((((((..(((((...............)))))))))))................))))). (-30.25 = -30.03 +  -0.22)

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 11:15:59 2006