Locus 4839

Sequence ID X_DroMel_CAF1
Location 12,569,716 – 12,569,848
Length 132
Max. P 0.949021
window7907 window7908 window7909

overview

Window 7

Location 12,569,716 – 12,569,825
Length 109
Sequences 3
Columns 109
Reading direction forward
Mean pairwise identity 76.11
Mean single sequence MFE -25.17
Consensus MFE -15.96
Energy contribution -15.93
Covariance contribution -0.02
Combinations/Pair 1.10
Mean z-score -1.67
Structure conservation index 0.63
SVM decision value 0.54
SVM RNA-class probability 0.773810
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12569716 109 + 22224390
AUUGGGGCAAUUUGAUCAAAAUGAAAUAACGGCAAUUACGCAGGUGCUAUUAUUGCGCACACCGCUGUGCAUGCAUACAUGUGUAGCGUCUAUAUGUAUGCGUGUGCUA
...((.((.((((.((....)).))))....(((((...((....))....)))))))...))...(..((((((((((((((.......))))))))))))))..).. ( -33.00)
>DroEre_CAF1 37113 86 + 1
----------UUUGAUCAAAAUGAAAUUACUGCAAUUACACAGGUGCUAUUAUUGCGCACACCGCUGUGCAUACAUGCAUG-------------UGUAUGCGUGUGCUA
----------.....................(((((..((....)).....)))))((((((......((((((((....)-------------))))))))))))).. ( -21.30)
>DroYak_CAF1 25802 92 + 1
AAUAAGGCAAUUUGAUCAAAAUAAAAUAACAGCAAUUACACAGGUGCUAUUAUUGCGCACACCGCUGUGCA----UGCGUA-------------UGUAUGUGUGUGCUA
.....(((.((((.....))))...............(((((.(((((((...((((((......))))))----...)))-------------.)))).)))))))). ( -21.20)
>consensus
A_U__GGCAAUUUGAUCAAAAUGAAAUAACAGCAAUUACACAGGUGCUAUUAUUGCGCACACCGCUGUGCAU_CAUGCAUG_____________UGUAUGCGUGUGCUA
...............................(((((..((....)).....)))))((((((.((.((((((.....................)))))))))))))).. (-15.96 = -15.93 +  -0.02)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,569,716 – 12,569,825
Length 109
Sequences 3
Columns 109
Reading direction reverse
Mean pairwise identity 76.11
Mean single sequence MFE -22.47
Consensus MFE -15.29
Energy contribution -14.63
Covariance contribution -0.66
Combinations/Pair 1.19
Mean z-score -1.63
Structure conservation index 0.68
SVM decision value 0.82
SVM RNA-class probability 0.858498
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12569716 109 - 22224390
UAGCACACGCAUACAUAUAGACGCUACACAUGUAUGCAUGCACAGCGGUGUGCGCAAUAAUAGCACCUGCGUAAUUGCCGUUAUUUCAUUUUGAUCAAAUUGCCCCAAU
..(((...((((((((.(((...)))...)))))))).)))...((((.((((.........))))))))((((((...((((........))))..))))))...... ( -26.80)
>DroEre_CAF1 37113 86 - 1
UAGCACACGCAUACA-------------CAUGCAUGUAUGCACAGCGGUGUGCGCAAUAAUAGCACCUGUGUAAUUGCAGUAAUUUCAUUUUGAUCAAA----------
..(((((((((((((-------------......)))))))......))))))(((((.((((...))))...))))).....................---------- ( -21.70)
>DroYak_CAF1 25802 92 - 1
UAGCACACACAUACA-------------UACGCA----UGCACAGCGGUGUGCGCAAUAAUAGCACCUGUGUAAUUGCUGUUAUUUUAUUUUGAUCAAAUUGCCUUAUU
..((.(((((.....-------------..(((.----......)))))))).))((((((((((..........))))))))))........................ ( -18.91)
>consensus
UAGCACACGCAUACA_____________CAUGCAUG_AUGCACAGCGGUGUGCGCAAUAAUAGCACCUGUGUAAUUGCAGUUAUUUCAUUUUGAUCAAAUUGCC__A_U
..(((...((.....................(((....)))...((((.((((.........))))))))))...)))............................... (-15.29 = -14.63 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,569,756 – 12,569,848
Length 92
Sequences 3
Columns 92
Reading direction forward
Mean pairwise identity 81.37
Mean single sequence MFE -29.03
Consensus MFE -20.60
Energy contribution -21.49
Covariance contribution 0.89
Combinations/Pair 1.09
Mean z-score -2.40
Structure conservation index 0.71
SVM decision value 1.39
SVM RNA-class probability 0.949021
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12569756 92 + 22224390
CAGGUGCUAUUAUUGCGCACACCGCUGUGCAUGCAUACAUGUGUAGCGUCUAUAUGUAUGCGUGUGCUAUGCCAAUACAAACAGUAGGCGGC
...((((.......))))...((((((..((((((((((((((.......))))))))))))))..)........(((.....)))))))). ( -35.20)
>DroEre_CAF1 37143 78 + 1
CAGGUGCUAUUAUUGCGCACACCGCUGUGCAUACAUGCAUG-------------UGUAUGCGUGUGCUAUGCCAAAGCAAACAGUAGGCGG-
...((((.......))))...(((((..((((((((....)-------------)))))))((.((((.......)))).))....)))))- ( -27.80)
>DroYak_CAF1 25842 75 + 1
CAGGUGCUAUUAUUGCGCACACCGCUGUGCA----UGCGUA-------------UGUAUGUGUGUGCUAUGCCAAAGCAAACAGUAGGCGGC
...((((.......))))...((((((..((----(((((.-------------...)))))))..)..(((....))).......))))). ( -24.10)
>consensus
CAGGUGCUAUUAUUGCGCACACCGCUGUGCAU_CAUGCAUG_____________UGUAUGCGUGUGCUAUGCCAAAGCAAACAGUAGGCGGC
...((((.......))))...((((((..(((.((((((...............)))))).)))..)..(((....))).......))))). (-20.60 = -21.49 +   0.89)

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 11:34:18 2006