Locus 5607

Sequence ID 3R_DroMel_CAF1
Location 14,791,629 – 14,791,802
Length 173
Max. P 0.982492
window9134 window9135 window9136

overview

Window 4

Location 14,791,629 – 14,791,726
Length 97
Sequences 3
Columns 101
Reading direction forward
Mean pairwise identity 85.95
Mean single sequence MFE -22.90
Consensus MFE -17.60
Energy contribution -17.17
Covariance contribution -0.43
Combinations/Pair 1.21
Mean z-score -2.04
Structure conservation index 0.77
SVM decision value 0.30
SVM RNA-class probability 0.678147
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14791629 97 + 27905053
CACCUGUUCGCAA-ACGGUAAAUAUAUUUAGCAGACAACUUGUUUGC-CCAAUGAAAUUGCUGCCAUUUAGCAGCU-UUUCAUUGCUU-CAGUUAGUUUUC
.(((.(((....)-)))))...........((((((.....))))))-.((((((((..(((((......))))).-))))))))...-............ ( -24.80)
>DroSim_CAF1 51788 97 + 1
CACCUGUUCGCAA-ACGGUAAAUAUAUUUAGCAGACAACUUGUUUGC-CCAAUGGAAUUGCUGCCAUUUAGCAGCU-UUUCAUUGCUU-CAGUUAGUUUUC
...(((...((((-..........((((..((((((.....))))))-..))))(((..(((((......))))).-.))).))))..-)))......... ( -24.90)
>DroAna_CAF1 52404 101 + 1
CACCUGUUCGCAGAGCGGUAAAUACGUUUAGCAGGCAACUUGUUUCCCCCAAUGGAAAUUCUGUUAUUUAGCAGCCAUUUUAUUGCAUCCAUUUUGUUUUU
....(((..((.(((((.......))))).))..)))............((((((((...(((((....)))))...))))))))................ ( -19.00)
>consensus
CACCUGUUCGCAA_ACGGUAAAUAUAUUUAGCAGACAACUUGUUUGC_CCAAUGGAAUUGCUGCCAUUUAGCAGCU_UUUCAUUGCUU_CAGUUAGUUUUC
.(((.((.......)))))...........((((((.....))))))..((((((((..(((((......)))))..))))))))................ (-17.60 = -17.17 +  -0.43)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,791,666 – 14,791,764
Length 98
Sequences 3
Columns 102
Reading direction forward
Mean pairwise identity 80.79
Mean single sequence MFE -31.34
Consensus MFE -14.77
Energy contribution -13.89
Covariance contribution -0.88
Combinations/Pair 1.22
Mean z-score -3.81
Structure conservation index 0.47
SVM decision value 0.28
SVM RNA-class probability 0.665971
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14791666 98 + 27905053
CUUGUUUGC-CCAAUGAAAUUGCUGCCAUUUAGCAGCU-UUUCAUUGCUU-CAGUUAGUUUUCACGGC-ACGCAAUUAAAAGCUGCAGCAUUGUGCUGCGCU
.((((.(((-(((((((((..(((((......))))).-))))))))...-......((....)))))-).)))).....(((.(((((.....)))))))) ( -34.70)
>DroSim_CAF1 51825 97 + 1
CUUGUUUGC-CCAAUGGAAUUGCUGCCAUUUAGCAGCU-UUUCAUUGCUU-CAGUUAGUUUUCACGGC-ACGCAAUUAAAAGCUGCAGCAUUGUGCAG-GCU
...((((((-.(((((((((.......)))).((((((-(((.(((((..-..((........))...-..))))).)))))))))..))))).))))-)). ( -29.40)
>DroAna_CAF1 52442 102 + 1
CUUGUUUCCCCCAAUGGAAAUUCUGUUAUUUAGCAGCCAUUUUAUUGCAUCCAUUUUGUUUUUACGGAUCCGCAAUUAAAAUGUGCUGCAUUUUUGGAGGCA
..(((((((...(((((.....))))).....((((((((((((((((((((.............))))..)))).))))))).)))))......))))))) ( -29.92)
>consensus
CUUGUUUGC_CCAAUGGAAUUGCUGCCAUUUAGCAGCU_UUUCAUUGCUU_CAGUUAGUUUUCACGGC_ACGCAAUUAAAAGCUGCAGCAUUGUGCAG_GCU
...........((((((((..(((((......)))))..))))))))....(((((........((....))........))))).(((..........))) (-14.77 = -13.89 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,791,695 – 14,791,802
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 69.56
Mean single sequence MFE -28.38
Consensus MFE -10.92
Energy contribution -11.12
Covariance contribution 0.20
Combinations/Pair 1.31
Mean z-score -2.28
Structure conservation index 0.38
SVM decision value 1.92
SVM RNA-class probability 0.982492
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14791695 107 - 27905053
GCUGCGCCUCGAUUUCAAUGCCAUC-GCAGCU-GGAACAAAGCGCAGCACAAUGCUG-CAGCUUUUAAUUGCGU-GCCGUGAAAA-------CUAACUG-AAGCAAUGAAA-AGCUGCUA
(((((((...(.(((((.(((....-)))..)-)))))...)))))))........(-((((((((.(((((..-.(.((.....-------...)).)-..))))).)))-)))))).. ( -39.70)
>DroPse_CAF1 48145 107 - 1
GCACCGACUCGGUUUCAAUGCCACCAGCCGCU-UGAACAAUGCAU-AAAAAAUGCAACCAGCUUUUAAUUGCGU-AUUGUAAAAAUGAAAAACUAACU---------GAGA-AGCUGCCA
(((.(..(((((((((((.((........)))-)))(((((((.(-((((((.((.....))))))..))).))-)))))..............))))---------))).-.).))).. ( -22.20)
>DroSim_CAF1 51854 106 - 1
GCUGCGCCUCGGAUUCAAUGCCAUC-GCAGCU-GGAACAAAGC-CUGCACAAUGCUG-CAGCUUUUAAUUGCGU-GCCGUGAAAA-------CUAACUG-AAGCAAUGAAA-AGCUGCUA
((((((....((........))..)-))))).-..........-..((.....)).(-((((((((.(((((..-.(.((.....-------...)).)-..))))).)))-)))))).. ( -31.70)
>DroAna_CAF1 52472 100 - 1
-----------UUUUCAAUGCCAAG-GGAGCUCGGAACAAUGCCUCCAAAAAUGCAG-CACAUUUUAAUUGCGGAUCCGUAAAAA-------CAAAAUGGAUGCAAUAAAAUGGCUGCUA
-----------.............(-(..((..........))..))......((((-(.(((((((.((((..((((((.....-------....)))))))))))))))))))))).. ( -28.60)
>DroPer_CAF1 48288 107 - 1
GCACCGACUCGGUUUCAAUGCCACCAGCCGCU-UGAACAAUGCAU-AAAAAAUGCAACCAGCUUUUAAUUGCGU-AUUGUAAAAAUGAAAAACUAACU---------GAGA-AGCCGCCA
((..(..(((((((((((.((........)))-)))(((((((.(-((((((.((.....))))))..))).))-)))))..............))))---------))).-.)..)).. ( -19.70)
>consensus
GCACCGACUCGGUUUCAAUGCCACC_GCAGCU_GGAACAAUGCAU_AAAAAAUGCAG_CAGCUUUUAAUUGCGU_ACCGUAAAAA_______CUAACUG_A_GCAAUGAAA_AGCUGCUA
..........................((((((........(((((......)))))............(((((....)))))..............................)))))).. (-10.92 = -11.12 +   0.20)

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 11:59:14 2006