Locus 2329

Sequence ID 2L_DroMel_CAF1
Location 6,324,789 – 6,324,957
Length 168
Max. P 0.984711
window3752 window3753 window3754 window3755 window3756

overview

Window 2

Location 6,324,789 – 6,324,886
Length 97
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 83.90
Mean single sequence MFE -29.21
Consensus MFE -18.52
Energy contribution -19.32
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.73
Structure conservation index 0.63
SVM decision value 1.23
SVM RNA-class probability 0.933813
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6324789 97 + 22407834
GUGUGCAUCGCAAUCAAAGCUCCGCAGAUGCCACUACAUCCG--CG-------------------AUUUGGGCCACCCUUUCUUCAAAUUGGCCCAAA-CGCUAUACAAUGGCUAAUCU
(((.(((((((............)).)))))))).......(--((-------------------.(((((((((..............)))))))))-)))................. ( -29.14)
>DroSec_CAF1 15893 97 + 1
GUGUGCAUCGCAAUCAAAGCUUCGCAGAUGCCACUACAUCCG--CG-------------------AUUUGGGCCACCCUUUCUUCAAAUUGGCCCAAA-CGCAAUACAAUGGCUAAUCU
(((.(((((((............)).)))))))).......(--((-------------------.(((((((((..............)))))))))-)))................. ( -29.64)
>DroSim_CAF1 16094 97 + 1
GUGUGCAUCGCAAUCAAAGCUCCGCAGAUGCCACUACAUCCG--CG-------------------AUUUGGGCCACCCUUUCUUCAAAUUGGCCCAAA-CGCAAUACAAUGGCUAAUCU
(((.(((((((............)).)))))))).......(--((-------------------.(((((((((..............)))))))))-)))................. ( -29.64)
>DroEre_CAF1 16205 115 + 1
GUGUGCAUCGCAAUCAAAGCUCUGCAGAUGCCACUACAUCAG--CGAUUUCUAUGAGCC--GCCGAUUCGGGCCACCCUUUCUUCAAAUUGCCCCAAAACGCAAUACAAUGGCUAAUCU
(((.((((((((..........))).))))))))........--...........((((--(((......)))..............(((((........))))).....))))..... ( -25.90)
>DroYak_CAF1 16156 117 + 1
GUGUGCAUCGCAAUCAAAGCUCUGCAGAUGCCACUACAUCCGGGGGAUUUCCGGGAACCGAGCCAAUUUGGCCCACCCUUUCUUUAAAUUAGCCCAAAA--CAAUACAAUGGCUAAUCU
(((.((((((((..........))).)))))))).......(((((....))(((..(((((....)))))))).))).........(((((((.....--.........))))))).. ( -31.74)
>consensus
GUGUGCAUCGCAAUCAAAGCUCCGCAGAUGCCACUACAUCCG__CG___________________AUUUGGGCCACCCUUUCUUCAAAUUGGCCCAAA_CGCAAUACAAUGGCUAAUCU
(((.(((((((............)).))))))))................................(((((((((..............)))))))))..................... (-18.52 = -19.32 +   0.80)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,324,789 – 6,324,886
Length 97
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 83.90
Mean single sequence MFE -38.70
Consensus MFE -26.23
Energy contribution -26.27
Covariance contribution 0.04
Combinations/Pair 1.09
Mean z-score -3.08
Structure conservation index 0.68
SVM decision value 1.98
SVM RNA-class probability 0.984711
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6324789 97 - 22407834
AGAUUAGCCAUUGUAUAGCG-UUUGGGCCAAUUUGAAGAAAGGGUGGCCCAAAU-------------------CG--CGGAUGUAGUGGCAUCUGCGGAGCUUUGAUUGCGAUGCACAC
......((.((((((.((((-(((((((((.(((......))).))))))))))-------------------((--(((((((....)))))))))..))).....)))))))).... ( -39.50)
>DroSec_CAF1 15893 97 - 1
AGAUUAGCCAUUGUAUUGCG-UUUGGGCCAAUUUGAAGAAAGGGUGGCCCAAAU-------------------CG--CGGAUGUAGUGGCAUCUGCGAAGCUUUGAUUGCGAUGCACAC
...........(((((((((-(((((((((.(((......))).)))))))))(-------------------((--(((((((....)))))))))).........)))))))))... ( -40.50)
>DroSim_CAF1 16094 97 - 1
AGAUUAGCCAUUGUAUUGCG-UUUGGGCCAAUUUGAAGAAAGGGUGGCCCAAAU-------------------CG--CGGAUGUAGUGGCAUCUGCGGAGCUUUGAUUGCGAUGCACAC
...........(((((((((-(((((((((.(((......))).))))))))))-------------------((--(((((((....)))))))))...........))))))))... ( -39.90)
>DroEre_CAF1 16205 115 - 1
AGAUUAGCCAUUGUAUUGCGUUUUGGGGCAAUUUGAAGAAAGGGUGGCCCGAAUCGGC--GGCUCAUAGAAAUCG--CUGAUGUAGUGGCAUCUGCAGAGCUUUGAUUGCGAUGCACAC
...........(((((((((..(..((((............((((.(((......)))--.)))).........(--(.(((((....))))).))...))))..).)))))))))... ( -37.20)
>DroYak_CAF1 16156 117 - 1
AGAUUAGCCAUUGUAUUG--UUUUGGGCUAAUUUAAAGAAAGGGUGGGCCAAAUUGGCUCGGUUCCCGGAAAUCCCCCGGAUGUAGUGGCAUCUGCAGAGCUUUGAUUGCGAUGCACAC
((((..(((((((((((.--...((((..............(((((((((.....))))))...)))((....)))))))))))))))))))))(((..((.......))..))).... ( -36.40)
>consensus
AGAUUAGCCAUUGUAUUGCG_UUUGGGCCAAUUUGAAGAAAGGGUGGCCCAAAU___________________CG__CGGAUGUAGUGGCAUCUGCGGAGCUUUGAUUGCGAUGCACAC
((((..(((((((((((....(((((((((.(((......))).)))))))))..........................)))))))))))))))(((..((.......))..))).... (-26.23 = -26.27 +   0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,324,828 – 6,324,923
Length 95
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 82.33
Mean single sequence MFE -28.90
Consensus MFE -18.00
Energy contribution -19.04
Covariance contribution 1.04
Combinations/Pair 1.04
Mean z-score -2.79
Structure conservation index 0.62
SVM decision value 1.65
SVM RNA-class probability 0.970029
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6324828 95 + 22407834
CCG--CG-------------------AUUUGGGCCACCCUUUCUUCAAAUUGGCCCAAA-CGCUAUACAAUGGCUAAUCUCUCGGCCAAUUGUUUUCGGUUACAAAAGCAAACAAUG
..(--((-------------------.(((((((((..............)))))))))-))).......(((((........))))).(((((((.(....).)))))))...... ( -28.74)
>DroSec_CAF1 15932 95 + 1
CCG--CG-------------------AUUUGGGCCACCCUUUCUUCAAAUUGGCCCAAA-CGCAAUACAAUGGCUAAUCUCUCGGCCAAUUGUUUUCGGUUAGAAAGCCAAACAAUG
..(--((-------------------.(((((((((..............)))))))))-))).......(((((........)))))(((((((..((((....))))))))))). ( -31.64)
>DroSim_CAF1 16133 95 + 1
CCG--CG-------------------AUUUGGGCCACCCUUUCUUCAAAUUGGCCCAAA-CGCAAUACAAUGGCUAAUCUCUCGGCCAAUUGUUUUCGGUUAGAAAGCCAAACAAUG
..(--((-------------------.(((((((((..............)))))))))-))).......(((((........)))))(((((((..((((....))))))))))). ( -31.64)
>DroEre_CAF1 16244 113 + 1
CAG--CGAUUUCUAUGAGCC--GCCGAUUCGGGCCACCCUUUCUUCAAAUUGCCCCAAAACGCAAUACAAUGGCUAAUCUCUCGGCCAAUUGUUUUCGGUUAGAAAGCCAAACAAUG
..(--(...(((((......--(((((...(((...))).........(((((........)))))(((((((((........)))).)))))..)))))))))).))......... ( -22.90)
>DroYak_CAF1 16195 115 + 1
CCGGGGGAUUUCCGGGAACCGAGCCAAUUUGGCCCACCCUUUCUUUAAAUUAGCCCAAAA--CAAUACAAUGGCUAAUCUGUUGUCCAAUUGUUUUCGGUUAGAAAGCCAAACAAUG
..(((((....))(((..(((((....)))))))).)))..........((((((.((((--(((((((((((.....)))))))...)))))))).)))))).............. ( -29.60)
>consensus
CCG__CG___________________AUUUGGGCCACCCUUUCUUCAAAUUGGCCCAAA_CGCAAUACAAUGGCUAAUCUCUCGGCCAAUUGUUUUCGGUUAGAAAGCCAAACAAUG
...........................(((((((((..............)))))))))...........(((((........)))))(((((((..((((....))))))))))). (-18.00 = -19.04 +   1.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,324,828 – 6,324,923
Length 95
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 82.33
Mean single sequence MFE -31.26
Consensus MFE -19.62
Energy contribution -19.94
Covariance contribution 0.32
Combinations/Pair 1.11
Mean z-score -1.71
Structure conservation index 0.63
SVM decision value -0.05
SVM RNA-class probability 0.507181
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6324828 95 - 22407834
CAUUGUUUGCUUUUGUAACCGAAAACAAUUGGCCGAGAGAUUAGCCAUUGUAUAGCG-UUUGGGCCAAUUUGAAGAAAGGGUGGCCCAAAU-------------------CG--CGG
..(((.((((....)))).)))..(((((.(((..(....)..))))))))...(((-(((((((((.(((......))).))))))))).-------------------))--).. ( -32.00)
>DroSec_CAF1 15932 95 - 1
CAUUGUUUGGCUUUCUAACCGAAAACAAUUGGCCGAGAGAUUAGCCAUUGUAUUGCG-UUUGGGCCAAUUUGAAGAAAGGGUGGCCCAAAU-------------------CG--CGG
.......(((((((((..((((......))))...))))...)))))......((((-(((((((((.(((......))).))))))))).-------------------))--)). ( -31.90)
>DroSim_CAF1 16133 95 - 1
CAUUGUUUGGCUUUCUAACCGAAAACAAUUGGCCGAGAGAUUAGCCAUUGUAUUGCG-UUUGGGCCAAUUUGAAGAAAGGGUGGCCCAAAU-------------------CG--CGG
.......(((((((((..((((......))))...))))...)))))......((((-(((((((((.(((......))).))))))))).-------------------))--)). ( -31.90)
>DroEre_CAF1 16244 113 - 1
CAUUGUUUGGCUUUCUAACCGAAAACAAUUGGCCGAGAGAUUAGCCAUUGUAUUGCGUUUUGGGGCAAUUUGAAGAAAGGGUGGCCCGAAUCGGC--GGCUCAUAGAAAUCG--CUG
........(((((((((.((.(((((...((((..(....)..))))..(.....)))))).))..............((((.(((......)))--.)))).))))))..)--)). ( -29.60)
>DroYak_CAF1 16195 115 - 1
CAUUGUUUGGCUUUCUAACCGAAAACAAUUGGACAACAGAUUAGCCAUUGUAUUG--UUUUGGGCUAAUUUAAAGAAAGGGUGGGCCAAAUUGGCUCGGUUCCCGGAAAUCCCCCGG
..........((((((..((((......)))).....(((((((((...(.....--.)...)))))))))..))))))..((((((.....))))))....((((.......)))) ( -30.90)
>consensus
CAUUGUUUGGCUUUCUAACCGAAAACAAUUGGCCGAGAGAUUAGCCAUUGUAUUGCG_UUUGGGCCAAUUUGAAGAAAGGGUGGCCCAAAU___________________CG__CGG
.....(((((........))))).(((((.(((.((....)).)))))))).......(((((((((.(((......))).)))))))))........................... (-19.62 = -19.94 +   0.32)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,324,847 – 6,324,957
Length 110
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 89.70
Mean single sequence MFE -24.85
Consensus MFE -17.16
Energy contribution -17.72
Covariance contribution 0.56
Combinations/Pair 1.20
Mean z-score -2.11
Structure conservation index 0.69
SVM decision value 0.08
SVM RNA-class probability 0.571935
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6324847 110 + 22407834
UUCUUCAAAUUGGCCCAAA-CGCUAUACAAUGGCUAAUCUCUCGGCCAAUUGUUUUCGGUUACAAAAGCAAACAAUGAACAAAUGGCAAUUUUAAAAGUUGCCACUAUUGU
....(((((((((((....-.(((((...))))).........))))))))(((((.(....).)))))......)))((((.((((((((.....))))))))...)))) ( -24.74)
>DroSec_CAF1 15951 109 + 1
UUCUUCAAAUUGGCCCAAA-CGCAAUACAAUGGCUAAUCUCUCGGCCAAUUGUUUUCGGUUAGAAAGCCAAACAAUGUACAAAUGGCAAUUAA-AAAGUUGCCACUGUUGU
.........(((((.....-......(((((((((........)))).)))))((((.....))))))))).......((((.((((((((..-..))))))))...)))) ( -26.50)
>DroSim_CAF1 16152 110 + 1
UUCUUCAAAUUGGCCCAAA-CGCAAUACAAUGGCUAAUCUCUCGGCCAAUUGUUUUCGGUUAGAAAGCCAAACAAUGUACAAAUGGCAAUUAAAAAAGUUGCCACUAUUGU
.........(((((.....-......(((((((((........)))).)))))((((.....)))))))))((((((......((((((((.....)))))))).)))))) ( -25.60)
>DroEre_CAF1 16280 111 + 1
UUCUUCAAAUUGCCCCAAAACGCAAUACAAUGGCUAAUCUCUCGGCCAAUUGUUUUCGGUUAGAAAGCCAAACAAUGUACAAACGGCAAUUAAAAUGGUCGCUUCUGUUGU
.......(((((((................(((((........)))))(((((((..((((....)))))))))))........)))))))..(((((......))))).. ( -22.20)
>DroYak_CAF1 16235 109 + 1
UUCUUUAAAUUAGCCCAAAA--CAAUACAAUGGCUAAUCUGUUGUCCAAUUGUUUUCGGUUAGAAAGCCAAACAAUGUACAAAUGGCAGUUAAAAACGUCGCUGCUAUUGU
.........((((((.((((--(((((((((((.....)))))))...)))))))).))))))..................(((((((((..........))))))))).. ( -25.20)
>consensus
UUCUUCAAAUUGGCCCAAA_CGCAAUACAAUGGCUAAUCUCUCGGCCAAUUGUUUUCGGUUAGAAAGCCAAACAAUGUACAAAUGGCAAUUAAAAAAGUUGCCACUAUUGU
.....................((((((...(((((........)))))(((((((..((((....))))))))))).......((((((((.....)))))))).)))))) (-17.16 = -17.72 +   0.56)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:25 2006