Locus 7184

Sequence ID X_DroMel_CAF1
Location 18,000,345 – 18,000,504
Length 159
Max. P 0.984386
window11735 window11736 window11737

overview

Window 5

Location 18,000,345 – 18,000,464
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 80.17
Mean single sequence MFE -38.43
Consensus MFE -28.41
Energy contribution -27.97
Covariance contribution -0.44
Combinations/Pair 1.09
Mean z-score -2.49
Structure conservation index 0.74
SVM decision value 1.97
SVM RNA-class probability 0.984386
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18000345 119 + 22224390
AUGCGAGGCGGGGGGGCGUGGCCCUCCCAAAGGGG-GUGAGCGGCGUUUAAACGUUUGGUAAACGGCCAUUAGGCCAACGGCAAUGGCAAUGGCCAAGCAAAAUGGGGGAAAAAGAAAGC
.(((.(((((...((((((.((((((((...))))-).).)).))))))...))))).)))...((((((...((((.......)))).))))))......................... ( -43.00)
>DroSec_CAF1 12292 95 + 1
-----------------------CUCCCAAAGGGG-CUGAGCGGCGUUUAAACGUUUGUUAAACGGCCAUUAGGCCAACGGCAAUGGCAAUGGCCAAGCAAAAUGGGGGAA-AAGAAAGC
-----------------------((((((.....(-((.((((((((....))).)))))....((((((...((((.......)))).)))))).)))....))))))..-........ ( -32.00)
>DroEre_CAF1 13098 117 + 1
AUGCGGAGCAGG-GUGCGUGGUCCUCCCAAAGGGGAGGGAGCAGCGUUUAAACGUUUGGUAAACGGCCAUUAGGCCAACGGCGAUGGCGAUGGCCAAGCAAAAUGGGGGAAAA--AAAGC
.(((.((((..(-.(((....(((((((....))))))).))).)((....)))))).)))...(((((((..((((.......)))))))))))..................--..... ( -40.30)
>consensus
AUGCG__GC_GG_G_GCGUGG_CCUCCCAAAGGGG_GUGAGCGGCGUUUAAACGUUUGGUAAACGGCCAUUAGGCCAACGGCAAUGGCAAUGGCCAAGCAAAAUGGGGGAAAAAGAAAGC
.......................((((((.............(((((....)))))........(((((((..((((.......)))))))))))........))))))........... (-28.41 = -27.97 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,000,345 – 18,000,464
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.17
Mean single sequence MFE -31.07
Consensus MFE -23.81
Energy contribution -24.70
Covariance contribution 0.89
Combinations/Pair 1.04
Mean z-score -2.17
Structure conservation index 0.77
SVM decision value 1.50
SVM RNA-class probability 0.959462
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18000345 119 - 22224390
GCUUUCUUUUUCCCCCAUUUUGCUUGGCCAUUGCCAUUGCCGUUGGCCUAAUGGCCGUUUACCAAACGUUUAAACGCCGCUCAC-CCCCUUUGGGAGGGCCACGCCCCCCCGCCUCGCAU
((...................((..(((((((((((.......))))..)))))))(((((.........)))))...))....-.......(((.((((...)))).))).....)).. ( -33.40)
>DroSec_CAF1 12292 95 - 1
GCUUUCUU-UUCCCCCAUUUUGCUUGGCCAUUGCCAUUGCCGUUGGCCUAAUGGCCGUUUAACAAACGUUUAAACGCCGCUCAG-CCCCUUUGGGAG-----------------------
........-....((((....(((.(((((((((((.......))))..)))))))((((((.......)))))).......))-).....))))..----------------------- ( -27.00)
>DroEre_CAF1 13098 117 - 1
GCUUU--UUUUCCCCCAUUUUGCUUGGCCAUCGCCAUCGCCGUUGGCCUAAUGGCCGUUUACCAAACGUUUAAACGCUGCUCCCUCCCCUUUGGGAGGACCACGCAC-CCUGCUCCGCAU
.....--..............((..((((((.((((.......))))...))))))(((((.........)))))))(((..((((((....)))))).....((..-...))...))). ( -32.80)
>consensus
GCUUUCUUUUUCCCCCAUUUUGCUUGGCCAUUGCCAUUGCCGUUGGCCUAAUGGCCGUUUACCAAACGUUUAAACGCCGCUCAC_CCCCUUUGGGAGG_CCACGC_C_CC_GC__CGCAU
..........(((((((........(((((((((((.......))))..)))))))(((((.........)))))................)))).)))..................... (-23.81 = -24.70 +   0.89)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,000,384 – 18,000,504
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -28.30
Consensus MFE -25.41
Energy contribution -24.74
Covariance contribution -0.66
Combinations/Pair 1.07
Mean z-score -1.72
Structure conservation index 0.90
SVM decision value -0.00
SVM RNA-class probability 0.531480
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18000384 120 + 22224390
GCGGCGUUUAAACGUUUGGUAAACGGCCAUUAGGCCAACGGCAAUGGCAAUGGCCAAGCAAAAUGGGGGAAAAAGAAAGCAAACAGUGAACAUUUUAUGCCAGCAAAACAAAGAACAUUU
(((((((......(((((((.....(((((...(((...))).)))))....)))))))((((((.........................))))))))))).))................ ( -30.81)
>DroSec_CAF1 12308 119 + 1
GCGGCGUUUAAACGUUUGUUAAACGGCCAUUAGGCCAACGGCAAUGGCAAUGGCCAAGCAAAAUGGGGGAA-AAGAAAGCAAACAGAGAACAUUUUAUGCCAGAAAAACAAAGAACAUUU
..(((((..((..(((((((....((((....))))....((..((((....)))).))............-.....))))))).(....).))..)))))................... ( -26.20)
>DroEre_CAF1 13137 118 + 1
GCAGCGUUUAAACGUUUGGUAAACGGCCAUUAGGCCAACGGCGAUGGCGAUGGCCAAGCAAAAUGGGGGAAAA--AAAGCAAACAGAGAACAUUUUAUGCCAGCAAAACAAAGAACAUUU
(((((((....)))))(((((...(((((((..((((.......)))))))))))....((((((........--...............)))))).)))))))................ ( -27.90)
>consensus
GCGGCGUUUAAACGUUUGGUAAACGGCCAUUAGGCCAACGGCAAUGGCAAUGGCCAAGCAAAAUGGGGGAAAAAGAAAGCAAACAGAGAACAUUUUAUGCCAGCAAAACAAAGAACAUUU
.....((((....((((.((....((((....))))...((((.((((....))))...((((((.........................)))))).)))).)).))))...)))).... (-25.41 = -24.74 +  -0.66)

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 12:32:14 2006