Locus 5498

Sequence ID 2R_DroMel_CAF1
Location 17,652,856 – 17,653,148
Length 292
Max. P 0.999784
window8778 window8779 window8780 window8781

overview

Window 8

Location 17,652,856 – 17,652,976
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.61
Mean single sequence MFE -37.42
Consensus MFE -34.50
Energy contribution -34.06
Covariance contribution -0.44
Combinations/Pair 1.12
Mean z-score -2.46
Structure conservation index 0.92
SVM decision value 4.07
SVM RNA-class probability 0.999784
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17652856 120 + 20766785
UUGCUGGCCACGUUAAUGUGGCCAUCAUAAAAAGCGUGUGAACCCAGUGUUAACGUGUCGAAGCCUAGACAAUAAGCCACACUUGGCGACACUUUUCCCUGGCCUUCGCUUUUCCCAGCU
..((((((((((....)))))))......(((((((.......((((.(..((.(((((...(......).....((((....))))))))).))..)))))....)))))))...))). ( -37.80)
>DroSec_CAF1 6470 118 + 1
UUGCUGGCCACGUUAAUGUGGCCACCAUAAAAAGCGUGUGAACCCAGUGCUAACGUGUCGAA--CCAGACAAUAAGCCACACUUGGCGACACUUUUCCCUGGCCUUCGCUUUUCCCAGCU
..((((((((((....)))))))......(((((((.......((((.(..((.((((((..--.....).....((((....))))))))).))..)))))....)))))))...))). ( -36.40)
>DroSim_CAF1 12368 118 + 1
UUGCUGGCCACGUUAAUGUGGCCACCAUAAAAAGCGUGUGAACCCAGUGUUAACGUGUCGAA--CCAGACAAUAAGCCACACUUGGCGACACUUUUCCCUGGCCUUCGCUUUUCCCAGCU
..((((((((((....)))))))......(((((((.......((((.(..((.((((((..--.....).....((((....))))))))).))..)))))....)))))))...))). ( -37.40)
>DroEre_CAF1 6591 118 + 1
UUGUUGGCCACGUUAAUGUGGCCACCAUAAAAAGCGUGUGAACCAAGUGUUAACGUGUCGAA--CCAGACAAUAAGUCGCACUUGGCGACACUUUUCCCUGGCCAUCGCUUUUCCUCGCU
.((.((((((((....)))))))).))..((((((((((...((((((((..((.((((...--...))))....)).))))))))..))))....(....).....))))))....... ( -37.20)
>DroYak_CAF1 17947 118 + 1
UUGUUGGCCACGUUAAUGUGGCCACCAUAAAAAGCGUGUGAACCCAGUGUUAACGUGUCGAA--CCAGACAAUAAGCCACACUUGGCGACACUUUUCUCUGGCCAUCGCUUUUCCUCGCC
.((.((((((((....)))))))).))..(((((((.(((...((((.(..((.((((((..--.....).....((((....)))))))))))..).)))).))))))))))....... ( -38.30)
>consensus
UUGCUGGCCACGUUAAUGUGGCCACCAUAAAAAGCGUGUGAACCCAGUGUUAACGUGUCGAA__CCAGACAAUAAGCCACACUUGGCGACACUUUUCCCUGGCCUUCGCUUUUCCCAGCU
.((.((((((((....)))))))).))..(((((((.......((((.(..((.((((((.....).........((((....))))))))).))..)))))....)))))))....... (-34.50 = -34.06 +  -0.44)

alignment

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secondary structure

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Window 9

Location 17,652,856 – 17,652,976
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.61
Mean single sequence MFE -42.60
Consensus MFE -38.34
Energy contribution -38.78
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -2.41
Structure conservation index 0.90
SVM decision value 3.62
SVM RNA-class probability 0.999460
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17652856 120 - 20766785
AGCUGGGAAAAGCGAAGGCCAGGGAAAAGUGUCGCCAAGUGUGGCUUAUUGUCUAGGCUUCGACACGUUAACACUGGGUUCACACGCUUUUUAUGAUGGCCACAUUAACGUGGCCAGCAA
.(((..((((((((.((.(((((..((.((((((..((((.((((.....).))).)))))))))).))..).)))).))....)))))))).....((((((......))))))))).. ( -45.20)
>DroSec_CAF1 6470 118 - 1
AGCUGGGAAAAGCGAAGGCCAGGGAAAAGUGUCGCCAAGUGUGGCUUAUUGUCUGG--UUCGACACGUUAGCACUGGGUUCACACGCUUUUUAUGGUGGCCACAUUAACGUGGCCAGCAA
......((((((((.((.((((......(((((((((.....(((.....))))))--..)))))).......)))).))....)))))))).((.(((((((......))))))).)). ( -42.52)
>DroSim_CAF1 12368 118 - 1
AGCUGGGAAAAGCGAAGGCCAGGGAAAAGUGUCGCCAAGUGUGGCUUAUUGUCUGG--UUCGACACGUUAACACUGGGUUCACACGCUUUUUAUGGUGGCCACAUUAACGUGGCCAGCAA
......((((((((.((.(((((..((.(((((((((.....(((.....))))))--..)))))).))..).)))).))....)))))))).((.(((((((......))))))).)). ( -42.80)
>DroEre_CAF1 6591 118 - 1
AGCGAGGAAAAGCGAUGGCCAGGGAAAAGUGUCGCCAAGUGCGACUUAUUGUCUGG--UUCGACACGUUAACACUUGGUUCACACGCUUUUUAUGGUGGCCACAUUAACGUGGCCAACAA
......((((((((.((((((((.....(((((((((.....(((.....))))))--..)))))).......))))).)))..)))))))).((.(((((((......))))))).)). ( -43.00)
>DroYak_CAF1 17947 118 - 1
GGCGAGGAAAAGCGAUGGCCAGAGAAAAGUGUCGCCAAGUGUGGCUUAUUGUCUGG--UUCGACACGUUAACACUGGGUUCACACGCUUUUUAUGGUGGCCACAUUAACGUGGCCAACAA
.((........))....((((..(((((((((.(((.((((((((....((((...--...)))).))).))))).)))....))))))))).))))((((((......))))))..... ( -39.50)
>consensus
AGCUGGGAAAAGCGAAGGCCAGGGAAAAGUGUCGCCAAGUGUGGCUUAUUGUCUGG__UUCGACACGUUAACACUGGGUUCACACGCUUUUUAUGGUGGCCACAUUAACGUGGCCAGCAA
......((((((((.((.((((......((((((........(((.....))).......)))))).......)))).))....)))))))).((.(((((((......))))))).)). (-38.34 = -38.78 +   0.44)

alignment

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secondary structure

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Window 0

Location 17,652,936 – 17,653,055
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.50
Mean single sequence MFE -30.21
Consensus MFE -19.99
Energy contribution -20.82
Covariance contribution 0.83
Combinations/Pair 1.12
Mean z-score -1.59
Structure conservation index 0.66
SVM decision value -0.05
SVM RNA-class probability 0.507892
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17652936 119 - 20766785
GAAAUCAUUAGGGGAAAUGGAAAUGGCGAAGAAAAACCGCCUUCAACUUUG-GCCGGUAAAAACGGCUCAUUGGACUUGCAGCUGGGAAAAGCGAAGGCCAGGGAAAAGUGUCGCCAAGU
....(((((......)))))...((((((.......((((((((..(..((-((((.......)))).))..)........(((......)))))))))..))........))))))... ( -35.86)
>DroSec_CAF1 6548 107 - 1
GAAAUCAUUAGGGGAAAUGGAAAUGGCGGAGAAAAAUCGCCUUCAACUUUAGG-------------CCCAAUCGAAUUGCAGCUGGGAAAAGCGAAGGCCAGGGAAAAGUGUCGCCAAGU
....(((((......)))))...(((((((......))((((((..((((...-------------((((.............)))).)))).)))))).............)))))... ( -24.62)
>DroSim_CAF1 12446 120 - 1
GAAAUCAUUAGGGGAAAUGGAAAUGGCGGAGAAAAACCGCCUUCAACUUUAGGCCGGUAAAAACGGCCCAAUCGACUUGCAGCUGGGAAAAGCGAAGGCCAGGGAAAAGUGUCGCCAAGU
....(((((......)))))...((((((.......((((((((.......(((((.......))))).............(((......)))))))))..))........))))))... ( -35.96)
>DroEre_CAF1 6669 96 - 1
GAAAUCAUUAGGGAAAAUGGAAAUGGCGAUGAAAA-CCGCCUUCAACUUU-----------------------GACUUACAGCGAGGAAAAGCGAUGGCCAGGGAAAAGUGUCGCCAAGU
....(((((......)))))...((((((((....-(((((.((..((((-----------------------..(((.....)))..)))).)).)))..))......))))))))... ( -23.70)
>DroYak_CAF1 18025 119 - 1
GAAAUCAUUAGGGCGAAUGGAAAUGGUGAAGAAAAGCCGCAUUCACUUUUG-GCCGGUAAAAACGACCCAAUCGACUUACGGCGAGGAAAAGCGAUGGCCAGAGAAAAGUGUCGCCAAGU
...........(((((.((((..((((........))))..)))).(((((-((((((.......)))..((((.(((.(.....)...))))))))))))))).......))))).... ( -30.90)
>consensus
GAAAUCAUUAGGGGAAAUGGAAAUGGCGAAGAAAAACCGCCUUCAACUUUA_GCCGGUAAAAACG_CCCAAUCGACUUGCAGCUGGGAAAAGCGAAGGCCAGGGAAAAGUGUCGCCAAGU
....(((((......)))))...((((((.......((((((((........((((.......))))..............((........))))))))..))........))))))... (-19.99 = -20.82 +   0.83)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,653,055 – 17,653,148
Length 93
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.52
Mean single sequence MFE -25.53
Consensus MFE -19.88
Energy contribution -20.72
Covariance contribution 0.84
Combinations/Pair 1.22
Mean z-score -1.27
Structure conservation index 0.78
SVM decision value 0.33
SVM RNA-class probability 0.689979
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17653055 93 - 20766785
-------------------------AGUUUACUACGAAGUAGGGAAAGAAAUUCGGAAACAGCAGAGUAAGUGCGGAAAAGUAUAUUUUUUCCUGCUCU--GUGGGCGAAAAUCUCAACG
-------------------------......(((((.((((((((((((.....(....)..........((((......)))).)))))))))))).)--))))............... ( -24.30)
>DroSec_CAF1 6655 106 - 1
-----------UAAUGGGUCUAAA-AGUUUACUACGAAGUAGGGAAAGAAAUUCGGAAACAGCAGAGUAAGUGCGGAAAAGUAUAUUUUUUCCUGCUCU--GUGAGCGAAAAUUUCAACG
-----------...((((......-.((((((...((.(((((((((((.....(....)..........((((......)))).))))))))))))).--))))))......))))... ( -24.22)
>DroSim_CAF1 12566 106 - 1
-----------UCAUGGGUCUAAA-AGUUUACUACGAAGUAGGGAAAGAAAUUCGGAAACAGCAGAGUAAGUGCGGAAAAGUAUAUUUUUUCCUGCUCU--GUGAGCGAAAAUCUCAACG
-----------...((((......-.((((((...((.(((((((((((.....(....)..........((((......)))).))))))))))))).--))))))......))))... ( -26.52)
>DroEre_CAF1 6765 120 - 1
UCUCUGUACUCCCAUGGGUCAACAAAGUUGUUAACAAAGUAGGGAACGAAAUUCGGAAACAGCGCAGUAAGUGCGGAAAAGUAUAUUUUUUCCUGCUCUGUGUGGGCCAAAAACCCAACG
...((((..((((((..((.((((....)))).))...)).)))).((.....))...))))(((((.....(((((((((.....))))))).)).)))))((((.......))))... ( -29.40)
>DroYak_CAF1 18144 117 - 1
UCUCUGAUUUUCCGUGGGUAAAAAUUGUGUAUAGCAAAGUAGGAAAAGAAAUU-GGAAGCAGCAAAGUAAGUGCGGAAAAGUAUAUUUUUUCCUGCUUU--AAGGGCUAAAAUCUCAACG
.....(((((..((..(.......)..))..((((((((((((((((((..((-(....)))........((((......)))).))))))))))))))--....)))))))))...... ( -23.20)
>consensus
___________CCAUGGGUCAAAA_AGUUUACUACGAAGUAGGGAAAGAAAUUCGGAAACAGCAGAGUAAGUGCGGAAAAGUAUAUUUUUUCCUGCUCU__GUGGGCGAAAAUCUCAACG
..............((((........((((((.....((((((((((((.....(....)..........((((......)))).))))))))))))....))))))......))))... (-19.88 = -20.72 +   0.84)

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 11:46:32 2006