Locus 8072

Sequence ID X_DroMel_CAF1
Location 20,100,138 – 20,100,288
Length 150
Max. P 0.999859
window13248 window13249 window13250

overview

Window 8

Location 20,100,138 – 20,100,258
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 70.51
Mean single sequence MFE -44.10
Consensus MFE -27.26
Energy contribution -27.17
Covariance contribution -0.10
Combinations/Pair 1.27
Mean z-score -2.46
Structure conservation index 0.62
SVM decision value 4.28
SVM RNA-class probability 0.999859
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20100138 120 + 22224390
AAAAAUAGCCAAAAGCACUGCAUACUUUCGGGCGCUUUAAGCCCCGCUCGUUUCGUUGGGCUUCCCCCAUAUCCGCAAAAACCCAGCCCCCAGCCCGAGUGGGUGGUGUGGUGUAUGGGG
...........(((((.(((........)))..)))))((((((.((.......)).)))))).(((((((((((((...(((((((.....)).....)))))..))))).)))))))) ( -42.10)
>DroSec_CAF1 10386 116 + 1
AAAAAUAGCCCAAAGCCGUGCAUACUUUCGGGCGCUUUAAGCCCCGCUCUUUUCGUGGGGCUUCCCCCAAACCCCC----UCCCAACCCCCCUUUCAAGUGGUAGGAGUGCGGUAUGGGG
.......((((((((.........)))).)))).....(((((((((.......))))))))).(((((.((((.(----(((..(((.(........).))).)))).).))).))))) ( -44.70)
>DroEre_CAF1 7752 95 + 1
AAAAAGAGCC-AGAGCACUGCACACUUUUGGGCGCUUUAAGCCCCACCCGCUGCGUGGGGAUUCCCCCA------------------------CCUGAGUGGGUGGCGUGCUGCAUGGGG
........((-(.(((((.((........((((.......))))((((((((..((((((....)))))------------------------)...)))))))))))))))...))).. ( -45.50)
>consensus
AAAAAUAGCC_AAAGCACUGCAUACUUUCGGGCGCUUUAAGCCCCGCUCGUUUCGUGGGGCUUCCCCCA_A_CC_C_____CCCA_CCCCC__CCCGAGUGGGUGGAGUGCUGUAUGGGG
........((....(((((((........(((.(....(((((((((.......))))))))).))))........................((((....))))...)))))))...)). (-27.26 = -27.17 +  -0.10)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,100,138 – 20,100,258
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 70.51
Mean single sequence MFE -47.20
Consensus MFE -21.45
Energy contribution -20.90
Covariance contribution -0.55
Combinations/Pair 1.17
Mean z-score -2.64
Structure conservation index 0.45
SVM decision value 1.09
SVM RNA-class probability 0.914280
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20100138 120 - 22224390
CCCCAUACACCACACCACCCACUCGGGCUGGGGGCUGGGUUUUUGCGGAUAUGGGGGAAGCCCAACGAAACGAGCGGGGCUUAAAGCGCCCGAAAGUAUGCAGUGCUUUUGGCUAUUUUU
(((((((..((.((..((((((((.......))).)))))...)).)).))))))).((((((..(.......)..)))))).....(((.((((((((...)))))))))))....... ( -43.80)
>DroSec_CAF1 10386 116 - 1
CCCCAUACCGCACUCCUACCACUUGAAAGGGGGGUUGGGA----GGGGGUUUGGGGGAAGCCCCACGAAAAGAGCGGGGCUUAAAGCGCCCGAAAGUAUGCACGGCUUUGGGCUAUUUUU
(((((.(((.(.((((((((.(((....))).)).)))))----)).))).))))).(((((((.(.......).))))))).....((((.(((((.......)))))))))....... ( -55.00)
>DroEre_CAF1 7752 95 - 1
CCCCAUGCAGCACGCCACCCACUCAGG------------------------UGGGGGAAUCCCCACGCAGCGGGUGGGGCUUAAAGCGCCCAAAAGUGUGCAGUGCUCU-GGCUCUUUUU
..(((.((((((((((((((.((...(------------------------(((((....))))))..)).)))))((((.......))))....))))))..)))..)-))........ ( -42.80)
>consensus
CCCCAUACAGCACACCACCCACUCGGG__GGGGG_UGGG_____G_GG_U_UGGGGGAAGCCCCACGAAACGAGCGGGGCUUAAAGCGCCCGAAAGUAUGCAGUGCUUU_GGCUAUUUUU
...(((((...........................................(((((....))))).........((((((.....)).))))...)))))....((.....))....... (-21.45 = -20.90 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,100,178 – 20,100,288
Length 110
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 68.11
Mean single sequence MFE -45.27
Consensus MFE -22.69
Energy contribution -23.03
Covariance contribution 0.35
Combinations/Pair 1.24
Mean z-score -2.55
Structure conservation index 0.50
SVM decision value 2.74
SVM RNA-class probability 0.996722
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20100178 110 + 22224390
GCCCCGCUCGUUUCGUUGGGCUUCCCCCAUAUCCGCAAAAACCCAGCCCCCAGCCCGAGUGGGUGGUGUGGUGUAUGGGGGGGCAUUGUCGCCAGCGCUAAAUGUGGCAU
((((((((((......)))))....((((((((((((...(((((((.....)).....)))))..))))).))))))))))))......((((.((.....)))))).. ( -47.60)
>DroSec_CAF1 10426 103 + 1
GCCCCGCUCUUUUCGUGGGGCUUCCCCCAAACCCCC----UCCCAACCCCCCUUUCAAGUGGUAGGAGUGCGGUAUGGGGG---AUUGUCACCCGCGCUAAAUGUGGCAU
(((((((.......))))))).(((((((.((((.(----(((..(((.(........).))).)))).).))).))))))---).((((((...........)))))). ( -44.90)
>DroEre_CAF1 7791 83 + 1
GCCCCACCCGCUGCGUGGGGAUUCCCCCA------------------------CCUGAGUGGGUGGCGUGCUGCAUGGGGC---AUUGUCGCCGGCGCUAAAUGUGGCAU
...(((((((((..((((((....)))))------------------------)...))))))))).((((..(((..(((---.(((....))).)))..)))..)))) ( -43.30)
>consensus
GCCCCGCUCGUUUCGUGGGGCUUCCCCCA_A_CC_C_____CCCA_CCCCC__CCCGAGUGGGUGGAGUGCUGUAUGGGGG___AUUGUCGCCAGCGCUAAAUGUGGCAU
(((((((.......)))))))..(((((........................((((....))))...(((...)))))))).....((((((...........)))))). (-22.69 = -23.03 +   0.35)

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 12:54:46 2006