Locus 1784

Sequence ID 3R_DroMel_CAF1
Location 5,113,857 – 5,114,171
Length 314
Max. P 0.949863
window2937 window2938 window2939 window2940 window2941

overview

Window 7

Location 5,113,857 – 5,113,976
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.13
Mean single sequence MFE -31.38
Consensus MFE -24.62
Energy contribution -25.46
Covariance contribution 0.84
Combinations/Pair 1.10
Mean z-score -1.74
Structure conservation index 0.78
SVM decision value 0.46
SVM RNA-class probability 0.744869
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5113857 119 - 27905053
CAGACUUACAAUACCAUUUAAUUACAAUCGAUUGC-AAUGAAAACAACAGCAAAAUGUUUCAUUUUGAUUGCAUGUGGCUGGCCGCAAACGUUGCCGGCACUUCGAGGUAGUAAACAGAU
....................(((((..((((.(((-(((.((((.((((......))))...)))).))))))....((((((.((....)).))))))...)))).)))))........ ( -28.80)
>DroSec_CAF1 15487 119 - 1
CAGACUUACAAUGCCAUUUAAUUACAAGCGAUUGC-AUUGAAAACAGCAGCAAAAUGUUUCAUUUUGAUUGCAUGUGGCAUGCCGCAAACGUUGCCGGCACUUCGAGGUGGUAAACAGAU
.....((((.(((((((.......(((((....))-.)))......(((((((((((...))))))).))))..)))))))((((((.....)).))))...........))))...... ( -29.00)
>DroSim_CAF1 16019 119 - 1
CAGACUUACAAUGCCAUUUAAUUACAAGCGAUUGC-AAUGAAAACAGCAGCAAAAUGUUUCAUUUUGAUUGCAUGUGGCACGCCGCAAACGUUGCCGGCACUUCGAGGUGGCAAACAGAU
...........((((((((......(((.(...((-((((......(((((((((((...))))))).)))).(((((....)))))..))))))...).)))..))))))))....... ( -33.80)
>DroEre_CAF1 16849 117 - 1
CGGACUUACAAUGCCAUUUAAUUACAAGCGAUUGC-AAUGAAAACAACG--AAAAUGUUUCAUUUUGAUUGCAUGUGGCUGGCCACACACGUUGCCGGCCCUUUGAGGUAGUAAACAGAU
.....((((..((((........(((.(((((((.-(((((((.((...--....))))))))).))))))).)))(((((((.((....)).)))))))......))))))))...... ( -33.60)
>DroYak_CAF1 16789 120 - 1
CAGACUUACAAUGCCAUUUAAUUACAAGCGAUUGCCACUGAAAACAGCAGCAAAAUGUUUCAUUUUGAUUGCAUGUGGCUGGCCGCAAACGUUGCCGGCACUUUGAGGUAGUAAACAGAU
.....((((..((((.......((((.((((((((..(((....)))..))((((((...)))))))))))).))))((((((.((....)).)))))).......))))))))...... ( -31.70)
>consensus
CAGACUUACAAUGCCAUUUAAUUACAAGCGAUUGC_AAUGAAAACAGCAGCAAAAUGUUUCAUUUUGAUUGCAUGUGGCUGGCCGCAAACGUUGCCGGCACUUCGAGGUAGUAAACAGAU
...........((((.......((((.((((((...(((((((.((.........)))))))))..)))))).))))((((((.((....)).)))))).......)))).......... (-24.62 = -25.46 +   0.84)

alignment

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secondary structure

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Window 8

Location 5,113,897 – 5,114,016
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.04
Mean single sequence MFE -26.44
Consensus MFE -19.64
Energy contribution -19.44
Covariance contribution -0.20
Combinations/Pair 1.11
Mean z-score -2.05
Structure conservation index 0.74
SVM decision value 0.44
SVM RNA-class probability 0.735483
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5113897 119 + 27905053
AGCCACAUGCAAUCAAAAUGAAACAUUUUGCUGUUGUUUUCAUU-GCAAUCGAUUGUAAUUAAAUGGUAUUGUAAGUCUGCUCAUUAAAACAACACUCGCACAUGCCAUAUUAAAGGUGA
.(((...(((((((((((((...))))))...(((((.......-))))).))))))).(((((((((((((..(((.................)))..)).))))))).)))).))).. ( -23.83)
>DroSec_CAF1 15527 119 + 1
UGCCACAUGCAAUCAAAAUGAAACAUUUUGCUGCUGUUUUCAAU-GCAAUCGCUUGUAAUUAAAUGGCAUUGUAAGUCUGCUCAUUAAAACAACAAUCGCACAUGCCAUAUUAAAGGUUU
.((((((.(((..(((((((...))))))).))))))......(-((((....))))).(((((((((((.((..(..((.............))..)..))))))))).)))).))).. ( -20.42)
>DroSim_CAF1 16059 119 + 1
UGCCACAUGCAAUCAAAAUGAAACAUUUUGCUGCUGUUUUCAUU-GCAAUCGCUUGUAAUUAAAUGGCAUUGUAAGUCUGCUCAUUAAAACAACACUUGCACAUGCCAUAUUAAAGGUUU
.((((((.(((..(((((((...))))))).))))))....(((-((((....)))))))...((((((((((((((.................))))))).)))))))......))).. ( -27.43)
>DroEre_CAF1 16889 117 + 1
AGCCACAUGCAAUCAAAAUGAAACAUUUU--CGUUGUUUUCAUU-GCAAUCGCUUGUAAUUAAAUGGCAUUGUAAGUCCGCUCAUUUAAUCGACACUCGCACAUGCCAUGUUAAAGGCAU
.((((((.((.((...(((((((((....--...)).)))))))-...)).)).)))..(((((((((((((..(((....((........)).)))..)).))))))).)))).))).. ( -27.20)
>DroYak_CAF1 16829 120 + 1
AGCCACAUGCAAUCAAAAUGAAACAUUUUGCUGCUGUUUUCAGUGGCAAUCGCUUGUAAUUAAAUGGCAUUGUAAGUCUGCUCAUUUAAUCGACACUCGCACAUGCCAUAUUAAAGGCAU
.((((((.((..((.....))......((((..(((....)))..))))..)).)))..(((((((((((((..(((....((........)).)))..)).))))))).)))).))).. ( -33.30)
>consensus
AGCCACAUGCAAUCAAAAUGAAACAUUUUGCUGCUGUUUUCAUU_GCAAUCGCUUGUAAUUAAAUGGCAUUGUAAGUCUGCUCAUUAAAACAACACUCGCACAUGCCAUAUUAAAGGUAU
.((((((.((...(((((((...)))))))....(((........)))...)).)))..((((((((((((((.(((.((..........))..))).))).))))))).)))).))).. (-19.64 = -19.44 +  -0.20)

alignment

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secondary structure

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Window 9

Location 5,113,897 – 5,114,016
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.04
Mean single sequence MFE -32.14
Consensus MFE -24.18
Energy contribution -25.54
Covariance contribution 1.36
Combinations/Pair 1.02
Mean z-score -2.76
Structure conservation index 0.75
SVM decision value 1.40
SVM RNA-class probability 0.949863
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5113897 119 - 27905053
UCACCUUUAAUAUGGCAUGUGCGAGUGUUGUUUUAAUGAGCAGACUUACAAUACCAUUUAAUUACAAUCGAUUGC-AAUGAAAACAACAGCAAAAUGUUUCAUUUUGAUUGCAUGUGGCU
.............(.(((((((((.(((((((((..((((....))))......(((((((((......))))).-))))))))))))).(((((((...))))))).))))))))).). ( -26.80)
>DroSec_CAF1 15527 119 - 1
AAACCUUUAAUAUGGCAUGUGCGAUUGUUGUUUUAAUGAGCAGACUUACAAUGCCAUUUAAUUACAAGCGAUUGC-AUUGAAAACAGCAGCAAAAUGUUUCAUUUUGAUUGCAUGUGGCA
............((.(((((((((((((((((((..((((....))))((((((.(((...........))).))-))))))))))))).(((((((...))))))))))))))))).)) ( -31.80)
>DroSim_CAF1 16059 119 - 1
AAACCUUUAAUAUGGCAUGUGCAAGUGUUGUUUUAAUGAGCAGACUUACAAUGCCAUUUAAUUACAAGCGAUUGC-AAUGAAAACAGCAGCAAAAUGUUUCAUUUUGAUUGCAUGUGGCA
......((((.(((((((.((.((((.((((((....)))))))))).)))))))))))))(((((.(((((((.-(((((((.((.........))))))))).))))))).))))).. ( -31.70)
>DroEre_CAF1 16889 117 - 1
AUGCCUUUAACAUGGCAUGUGCGAGUGUCGAUUAAAUGAGCGGACUUACAAUGCCAUUUAAUUACAAGCGAUUGC-AAUGAAAACAACG--AAAAUGUUUCAUUUUGAUUGCAUGUGGCU
..(((.((((.(((((((.((..(((.(((.((....)).))))))..)))))))))))))..(((.(((((((.-(((((((.((...--....))))))))).))))))).)))))). ( -32.30)
>DroYak_CAF1 16829 120 - 1
AUGCCUUUAAUAUGGCAUGUGCGAGUGUCGAUUAAAUGAGCAGACUUACAAUGCCAUUUAAUUACAAGCGAUUGCCACUGAAAACAGCAGCAAAAUGUUUCAUUUUGAUUGCAUGUGGCU
..(((.......(((((..(((...(((.(((((((((.(((.........))))))))))))))).)))..)))))......((((((((((((((...))))))).)))).)))))). ( -38.10)
>consensus
AAACCUUUAAUAUGGCAUGUGCGAGUGUUGUUUUAAUGAGCAGACUUACAAUGCCAUUUAAUUACAAGCGAUUGC_AAUGAAAACAGCAGCAAAAUGUUUCAUUUUGAUUGCAUGUGGCU
......((((.(((((((.((..(((.((((((....)))))))))..)))))))))))))(((((.((((((...(((((((.((.........)))))))))..)))))).))))).. (-24.18 = -25.54 +   1.36)

alignment

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secondary structure

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Window 0

Location 5,113,937 – 5,114,056
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.94
Mean single sequence MFE -23.90
Consensus MFE -17.64
Energy contribution -18.08
Covariance contribution 0.44
Combinations/Pair 1.11
Mean z-score -1.55
Structure conservation index 0.74
SVM decision value -0.03
SVM RNA-class probability 0.516924
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5113937 119 + 27905053
CAUU-GCAAUCGAUUGUAAUUAAAUGGUAUUGUAAGUCUGCUCAUUAAAACAACACUCGCACAUGCCAUAUUAAAGGUGAUCAUUGGCCAACAUGCAUACACAAUUUUAGUCCCACUAGC
...(-(((...(((..(..(((((((((((((..(((.................)))..)).))))))).))))..)..)))..((.....)))))).........((((.....)))). ( -19.23)
>DroSec_CAF1 15567 119 + 1
CAAU-GCAAUCGCUUGUAAUUAAAUGGCAUUGUAAGUCUGCUCAUUAAAACAACAAUCGCACAUGCCAUAUUAAAGGUUUUCAUUGGCCAACAAGCAUACACAAUUACUGACCCACUGGC
....-......((((((..(((((((((((.((..(..((.............))..)..))))))))).)))).((((......)))).))))))........................ ( -21.02)
>DroSim_CAF1 16099 119 + 1
CAUU-GCAAUCGCUUGUAAUUAAAUGGCAUUGUAAGUCUGCUCAUUAAAACAACACUUGCACAUGCCAUAUUAAAGGUUUUCAUUGGCCAACAAGCAUACACAAUUACUGACCCACUGGC
....-......((((((..((((((((((((((((((.................))))))).))))))).)))).((((......)))).))))))........................ ( -27.03)
>DroEre_CAF1 16927 118 + 1
CAUU-GCAAUCGCUUGUAAUUAAAUGGCAUUGUAAGUCCGCUCAUUUAAUCGACACUCGCACAUGCCAUGUUAAAGGCAUUAUUCGCCC-ACAAGCAUACCCAAUUACCAUCCCAAUAGC
....-......((((((..(((((((((((((..(((....((........)).)))..)).))))))).)))).(((.......))).-))))))........................ ( -24.40)
>DroYak_CAF1 16869 120 + 1
CAGUGGCAAUCGCUUGUAAUUAAAUGGCAUUGUAAGUCUGCUCAUUUAAUCGACACUCGCACAUGCCAUAUUAAAGGCAUUAUUUGCCCAACAAGCAUACACAAUUACGGUCCCAAUGGC
..(((......((((((..(((((((((((((..(((....((........)).)))..)).))))))).)))).((((.....))))..))))))...))).................. ( -27.80)
>consensus
CAUU_GCAAUCGCUUGUAAUUAAAUGGCAUUGUAAGUCUGCUCAUUAAAACAACACUCGCACAUGCCAUAUUAAAGGUAUUCAUUGGCCAACAAGCAUACACAAUUACUGUCCCACUGGC
...........((((((..((((((((((((((.(((.((..........))..))).))).))))))).)))).(((........))).))))))........................ (-17.64 = -18.08 +   0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,114,056 – 5,114,171
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.01
Mean single sequence MFE -30.84
Consensus MFE -23.54
Energy contribution -24.42
Covariance contribution 0.88
Combinations/Pair 1.06
Mean z-score -1.79
Structure conservation index 0.76
SVM decision value 0.48
SVM RNA-class probability 0.751984
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5114056 115 - 27905053
G--CUACUAACUCAAUCUUGACCGUUUGAUUGAUAGAUUGAUUGAUGCAGGGCAGCCGAA-AUUGAAUUUUUGCUCUACGA--AACAAUUGGUUAUGCAUUAAUUGAUUGAAUCAUGGUC
.--................(((((..(((((....(((..(((((((((....((((((.-.(((...(((((.....)))--))))))))))).)))))))))..))).)))))))))) ( -27.70)
>DroSec_CAF1 15686 118 - 1
U--CUAGUAACUCAAUCUUGACCGUUUGAUUAAUAGAUUGAUUGAUGCAGGUCAGCCGAAAAUUGGAUUUUUGCCCUGCGAGAAGCAAUUGGUUAUGCAUUAAUUGAUUGAAUCAUGGUC
.--................(((((..(((((....(((..(((((((((....((((((...(((..(((((((...))))))).))))))))).)))))))))..))).)))))))))) ( -33.70)
>DroSim_CAF1 16218 120 - 1
UCGCUACUAACUCAAUCUUGAACGUUUGAUUGAUAGAUUGAUUGAUGCAGGUCAGCCGAAAAUUGGAUUUUUGCUCUGCGAGAAGCAAUUGGUUAUGCAUUAAUUGAUUGAAUCAUGGUC
..((((.....((((((..........))))))..(((..(((((((((....((((((...(((..(((((((...))))))).))))))))).)))))))))..)))......)))). ( -30.50)
>DroEre_CAF1 17045 114 - 1
G--CUACUAACUCAAUCUUGAGCGAUUGAUUGCCAGAUUGAUUGAUGCAGGUCAGCCGAA-AUUGAAUUUUUGCCC-UCG--AAGCAAUUGGUUGUGCAUUAAUUGAUUGAAUCAUGCUC
.--................(((((..(((((....(((..(((((((((...(((((((.-.........((((..-...--..))))))))))))))))))))..))).)))))))))) ( -29.80)
>DroYak_CAF1 16989 115 - 1
G--CUACUAACUCAAUCUUGAGCGAUUGAUUGAUAGAUUGAUUGAUGCAGGGCAGCCAAA-AUUGAAUUUUUGCUCUUCG--AAGCAAUUGGUUGGGCAUUAAUUGAUUGAAUCAUGGUC
.--..((((..((((((......)))))).((((.(((..((((((((....(((((((.-.........(((((.....--.)))))))))))).))))))))..)))..)))))))). ( -32.50)
>consensus
G__CUACUAACUCAAUCUUGACCGUUUGAUUGAUAGAUUGAUUGAUGCAGGUCAGCCGAA_AUUGAAUUUUUGCUCUGCGA_AAGCAAUUGGUUAUGCAUUAAUUGAUUGAAUCAUGGUC
...................(((((..(((((....(((..(((((((((....((((((...........(((((........))))))))))).)))))))))..))).)))))))))) (-23.54 = -24.42 +   0.88)

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 10:19:27 2006