Locus 3957

Sequence ID 3R_DroMel_CAF1
Location 10,705,097 – 10,705,270
Length 173
Max. P 0.958461
window6342 window6343 window6344

overview

Window 2

Location 10,705,097 – 10,705,196
Length 99
Sequences 3
Columns 100
Reading direction reverse
Mean pairwise identity 73.58
Mean single sequence MFE -25.57
Consensus MFE -15.30
Energy contribution -14.87
Covariance contribution -0.43
Combinations/Pair 1.25
Mean z-score -1.91
Structure conservation index 0.60
SVM decision value 1.36
SVM RNA-class probability 0.945974
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10705097 99 - 27905053
CAACAAAAGGGAA-AUCGUGAUGUAAACAAAAAGCAGCUGACUUCAGCUGUUGCAGCCCUCGUUGGCCUGCGUGAAACGAUCUGGCAACGUCAUGCAUAA
.............-..((((((((...((...((((((((....))))))))((((.((.....)).))))...........))...))))))))..... ( -29.60)
>DroSim_CAF1 146 79 - 1
CAACAAAAGGGAU-A-CGCGAUGUAAACAAAAGACAGCUGACUUCAGCUGUUGCAGCCCU-------------------AUCUGGCAACGCCGGGCAUAA
.......((((..-.-.((..((....))...((((((((....))))))))))..))))-------------------.((((((...))))))..... ( -25.40)
>DroYak_CAF1 146 100 - 1
CAACAAGAGAGAGGAACGCGAUGUAAACAAAAAACAGCUGACUUAAGCUGUUGCAGCCCUAUUGGAAGUGUGUGAGUAGAUCUGGCAACGCCGAGAAUAC
...(((...((.((...((..((....))...(((((((......)))))))))..)))).)))...((((((.((.....)).)).))))......... ( -21.70)
>consensus
CAACAAAAGGGAA_A_CGCGAUGUAAACAAAAAACAGCUGACUUCAGCUGUUGCAGCCCU__U_G___UG_GUGA___GAUCUGGCAACGCCGAGCAUAA
.......((((......((..((....))...((((((((....))))))))))..))))......................((((...))))....... (-15.30 = -14.87 +  -0.43)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,705,117 – 10,705,235
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 79.89
Mean single sequence MFE -33.07
Consensus MFE -23.51
Energy contribution -22.97
Covariance contribution -0.55
Combinations/Pair 1.16
Mean z-score -2.24
Structure conservation index 0.71
SVM decision value 1.49
SVM RNA-class probability 0.958461
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10705117 118 - 27905053
UG-GGAAAAACGUGCGUUUUUCACCGGCGCAGGAAAAUGACAACAAAAGGGAA-AUCGUGAUGUAAACAAAAAGCAGCUGACUUCAGCUGUUGCAGCCCUCGUUGGCCUGCGUGAAACGA
.(-((((((((....))))))).)).(((((((..(((((........(((..-...((.......))....((((((((....))))))))....))))))))..)))))))....... ( -41.60)
>DroSim_CAF1 166 99 - 1
UGAGGAAAAACGUGCGUUUUUCACCGGCGCAGGAAAAUGACAACAAAAGGGAU-A-CGCGAUGUAAACAAAAGACAGCUGACUUCAGCUGUUGCAGCCCU-------------------A
.(..(((((((....)))))))..)(((((...................(..(-(-(.....)))..)....((((((((....)))))))))).)))..-------------------. ( -27.10)
>DroYak_CAF1 166 119 - 1
UG-GGGAAAACGUGCGUUUUUCACCGGCGCAGGAAAAUGACAACAAGAGAGAGGAACGCGAUGUAAACAAAAAACAGCUGACUUAAGCUGUUGCAGCCCUAUUGGAAGUGUGUGAGUAGA
((-(((...(((((((((((((.((......))....((....)).....))))))))).))))........(((((((......)))))))....)))))................... ( -30.50)
>consensus
UG_GGAAAAACGUGCGUUUUUCACCGGCGCAGGAAAAUGACAACAAAAGGGAA_A_CGCGAUGUAAACAAAAAACAGCUGACUUCAGCUGUUGCAGCCCU__U_G___UG_GUGA___GA
....(((((((....)))))))...(((((............(((...(.(.....).)..)))........((((((((....)))))))))).)))...................... (-23.51 = -22.97 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,705,157 – 10,705,270
Length 113
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 93.00
Mean single sequence MFE -27.73
Consensus MFE -24.81
Energy contribution -24.37
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -1.79
Structure conservation index 0.89
SVM decision value 0.16
SVM RNA-class probability 0.610874
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10705157 113 - 27905053
CGUGUAUAAAUAGCUUUUGUUUAUGUCGGUGAAAAUG-GGAAAAACGUGCGUUUUUCACCGGCGCAGGAAAAUGACAACAAAAGGGAA-AUCGUGAUGUAAACAAAAAGCAGCUG
............(((((((((((((((.(((....((-((((((((....))))))).))).)))......((((...(.....)...-.))))))))))))).))))))..... ( -27.50)
>DroSim_CAF1 187 113 - 1
CGUUUAUAAAUAGCUUUUGUUUAUGUCGGUGAAAAUGAGGAAAAACGUGCGUUUUUCACCGGCGCAGGAAAAUGACAACAAAAGGGAU-A-CGCGAUGUAAACAAAAGACAGCUG
............(((((((((((((((((((........(((((((....))))))).((......))...................)-)-).))))))))))))))).)..... ( -27.70)
>DroYak_CAF1 206 114 - 1
CGUGUAUAAAUAGCUUUUGUUUAUGUCGGUGAAAAUG-GGGAAAACGUGCGUUUUUCACCGGCGCAGGAAAAUGACAACAAGAGAGAGGAACGCGAUGUAAACAAAAAACAGCUG
..........(((((((((((((((((((((....((-((((((((....))))))).))).))).(........).................)))))))))))))....))))) ( -28.00)
>consensus
CGUGUAUAAAUAGCUUUUGUUUAUGUCGGUGAAAAUG_GGAAAAACGUGCGUUUUUCACCGGCGCAGGAAAAUGACAACAAAAGGGAA_A_CGCGAUGUAAACAAAAAACAGCUG
..........((((((((((((((((((...........(((((((....))))))).((......)).........................)))))))))))))....))))) (-24.81 = -24.37 +  -0.44)

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 11:14:27 2006