Locus 2925

Sequence ID X_DroMel_CAF1
Location 7,833,832 – 7,833,965
Length 133
Max. P 0.741316
window4789 window4790 window4791

overview

Window 9

Location 7,833,832 – 7,833,928
Length 96
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 78.73
Mean single sequence MFE -27.03
Consensus MFE -17.98
Energy contribution -18.37
Covariance contribution 0.39
Combinations/Pair 1.18
Mean z-score -1.22
Structure conservation index 0.66
SVM decision value 0.05
SVM RNA-class probability 0.556266
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7833832 96 - 22224390
UGCCAGUG----UGUAAAAACUGCUGUUGCCACUUUGAUGUUGGCAACUUUGUUGCAAAAUGUGCAGCAAGUAAGUGGGA--------------GAAAAUCCGGCGGCGAAAGU
.(((....----.........((((((((((((......).)))))))..(((((((.....))))))))))).((.(((--------------.....))).)))))...... ( -32.50)
>DroSec_CAF1 9725 96 - 1
UCCCACUG----UGUAAAAACUGCUGCUGCUACUUUGAUGUUGCCAACUUUGUUGCAAAAUGUGCAGCAAGUAAGAGGGA--------------GAAAAUCCGGCGGCGAAAGU
........----..........((....)).(((((..(((((((.((((.((((((.....)))))))))).....(((--------------.....))))))))))))))) ( -25.20)
>DroSim_CAF1 15109 96 - 1
UCCCACUG----UGUAAAAACUGCUGUUGCUACUUUGAUGUUGGCAACUUUGUUGCGAAAUGUGCAGCAAGUAAGAGGGA--------------GAAAAUCCGGCGGCGAAAGU
((((.(((----(......))((((((((((((......).)))))))..(((((((.....))))))))))))).))))--------------............((....)) ( -25.40)
>DroEre_CAF1 17479 107 - 1
UCCCACUG----UGUAC-AACUGCUGUUGCUACUUUGAUGUUGCCAACUUUGUUGCGAAAUGUGCAGCAAGUAGGGGGAACGAAAAACAAC--AAAAAAUGCGGCGGAGAAAGU
((((.(((----(((((-(((....)))).)))((((.((((.((.((((.((((((.....)))))))))).))(....)....)))).)--)))....)))).)).)).... ( -28.60)
>DroYak_CAF1 14038 95 - 1
UCUUGCUG----UGUAA-AACUGCUGUUGCUACUUUGUUGUUGGCAACUUUGUUGCGAAAUGUGCAGCAAGUGAGAGGAA--------------AAAAUGGCGGCGGAGAAAGU
((((((((----(....-.......((((((((......).)))))))(((((((((.....))))))))).........--------------......))))).)))).... ( -25.50)
>DroAna_CAF1 6532 110 - 1
UUCUACUGACACUGCCACUGCUGCUUCUGCUGCUGUGCUUCUGGCAACUUUGUUGCGAAAUGUGCAGCAAAUAAGACUAA----AAAAAAUUGCAAAAAUCCGCCGGAGAAAGU
.............((.((.((.((....)).)).))))(((((((...(((((((((.....))))))))).........----.....(((.....)))..)))))))..... ( -25.00)
>consensus
UCCCACUG____UGUAAAAACUGCUGUUGCUACUUUGAUGUUGGCAACUUUGUUGCGAAAUGUGCAGCAAGUAAGAGGAA______________AAAAAUCCGGCGGAGAAAGU
....................(((((((((((((......)).))))))(((((((((.....)))))))))...............................)))))....... (-17.98 = -18.37 +   0.39)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,833,852 – 7,833,965
Length 113
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 78.75
Mean single sequence MFE -24.95
Consensus MFE -10.52
Energy contribution -10.75
Covariance contribution 0.23
Combinations/Pair 1.40
Mean z-score -2.31
Structure conservation index 0.42
SVM decision value 0.04
SVM RNA-class probability 0.555968
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7833852 113 + 22224390
UCCCACUUACUUGCUGCACAUUUUGCAACAAAGUUGCCAACAUCAAAGUGGCAACAGCAGUUUUUACA----CACUGGCAAAAUUGCAG--UUCUCAAAAGCAAGAACAUUAAUAAAUU
.....(((.(((((((((.(((((((......(((((((.(......))))))))..((((.......----.))))))))))))))))--)......))).))).............. ( -29.60)
>DroSec_CAF1 9745 113 + 1
UCCCUCUUACUUGCUGCACAUUUUGCAACAAAGUUGGCAACAUCAAAGUAGCAGCAGCAGUUUUUACA----CAGUGGGAAAAUUUUAG--UUCUCAAGAGCAAGAACUUUAAUUAAUU
((((.((....((((((......(((.((.....((....)).....)).)))))))))((....)).----.)).)))).((((..((--((((........))))))..)))).... ( -27.10)
>DroSim_CAF1 15129 113 + 1
UCCCUCUUACUUGCUGCACAUUUCGCAACAAAGUUGCCAACAUCAAAGUAGCAACAGCAGUUUUUACA----CAGUGGGAAAAUUUCAG--UUCUCAAAAGCAAGAAUUUCAAUUAAUU
((((.((.....(((((...(((......)))(((((..((......)).))))).))))).......----.)).)))).((((..((--((((........))))))..)))).... ( -19.72)
>DroEre_CAF1 17511 109 + 1
UUCCCCCUACUUGCUGCACAUUUCGCAACAAAGUUGGCAACAUCAAAGUAGCAACAGCAGUU-GUACA----CAGUGGGAAAAUGGCAU--UCCUC---AGCAAGAACUUGAAUAACUU
.........((((((((((.....(((((...(.((....)).)......((....)).)))-))...----..)))((((.......)--))).)---)))))).............. ( -23.50)
>DroYak_CAF1 14058 110 + 1
UUCCUCUCACUUGCUGCACAUUUCGCAACAAAGUUGCCAACAACAAAGUAGCAACAGCAGUU-UUACA----CAGCAAGAAAACUGUAG--UUCUCA--AGCAAGAAGUUAAUUAAAAA
.........((((((((.......))(((...(((((..((......)).))))).((((((-((.(.----......))))))))).)--))....--)))))).............. ( -21.30)
>DroAna_CAF1 6562 116 + 1
UUAGUCUUAUUUGCUGCACAUUUCGCAACAAAGUUGCCAGAAGCACAGCAGCAGAAGCAGCAGUGGCAGUGUCAGUAGAAAAAGUGGAAGCAUCUCUACAAAAAGAAAU---AUUAAUU
....((((.((((((((((.(((.(((((...))))).)))..(((.((.((....)).)).)))...))).)))))))....(((((......)))))...))))...---....... ( -28.50)
>consensus
UCCCUCUUACUUGCUGCACAUUUCGCAACAAAGUUGCCAACAUCAAAGUAGCAACAGCAGUUUUUACA____CAGUGGGAAAAUUGCAG__UUCUCAA_AGCAAGAACUUUAAUAAAUU
....(((((((((((((.......(((((...)))))..........))))))).....((....)).......))))))....................................... (-10.52 = -10.75 +   0.23)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,833,852 – 7,833,965
Length 113
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 78.75
Mean single sequence MFE -28.78
Consensus MFE -17.57
Energy contribution -17.77
Covariance contribution 0.20
Combinations/Pair 1.30
Mean z-score -1.70
Structure conservation index 0.61
SVM decision value 0.45
SVM RNA-class probability 0.741316
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7833852 113 - 22224390
AAUUUAUUAAUGUUCUUGCUUUUGAGAA--CUGCAAUUUUGCCAGUG----UGUAAAAACUGCUGUUGCCACUUUGAUGUUGGCAACUUUGUUGCAAAAUGUGCAGCAAGUAAGUGGGA
.............(((..(((.......--((((((((((((((((.----.......))))..((((((((......).)))))))......))))))).))))).....)))..))) ( -32.80)
>DroSec_CAF1 9745 113 - 1
AAUUAAUUAAAGUUCUUGCUCUUGAGAA--CUAAAAUUUUCCCACUG----UGUAAAAACUGCUGCUGCUACUUUGAUGUUGCCAACUUUGUUGCAAAAUGUGCAGCAAGUAAGAGGGA
..........(((((((......)))))--)).......((((.(((----(......))(((((((((.((.......((((.(((...)))))))...))))))).)))))).)))) ( -27.00)
>DroSim_CAF1 15129 113 - 1
AAUUAAUUGAAAUUCUUGCUUUUGAGAA--CUGAAAUUUUCCCACUG----UGUAAAAACUGCUGUUGCUACUUUGAUGUUGGCAACUUUGUUGCGAAAUGUGCAGCAAGUAAGAGGGA
............(((((......)))))--.........((((.(((----(......))((((((((((((......).)))))))..(((((((.....))))))))))))).)))) ( -25.10)
>DroEre_CAF1 17511 109 - 1
AAGUUAUUCAAGUUCUUGCU---GAGGA--AUGCCAUUUUCCCACUG----UGUAC-AACUGCUGUUGCUACUUUGAUGUUGCCAACUUUGUUGCGAAAUGUGCAGCAAGUAGGGGGAA
..(.(((((.(((....)))---...))--))).)...(((((....----.((((-(((....)))).)))..........((.((((.((((((.....)))))))))).))))))) ( -28.10)
>DroYak_CAF1 14058 110 - 1
UUUUUAAUUAACUUCUUGCU--UGAGAA--CUACAGUUUUCUUGCUG----UGUAA-AACUGCUGUUGCUACUUUGUUGUUGGCAACUUUGUUGCGAAAUGUGCAGCAAGUGAGAGGAA
...........(((((..((--((....--.((((((......))))----))...-..((((..((((.((...((((....))))...)).)))).....))))))))..))))).. ( -34.30)
>DroAna_CAF1 6562 116 - 1
AAUUAAU---AUUUCUUUUUGUAGAGAUGCUUCCACUUUUUCUACUGACACUGCCACUGCUGCUUCUGCUGCUGUGCUUCUGGCAACUUUGUUGCGAAAUGUGCAGCAAAUAAGACUAA
.......---...((((...(((((((...........)))))))......(((((..((.((.......))...))...)))))..(((((((((.....))))))))).)))).... ( -25.40)
>consensus
AAUUAAUUAAAGUUCUUGCU_UUGAGAA__CUGCAAUUUUCCCACUG____UGUAAAAACUGCUGUUGCUACUUUGAUGUUGGCAACUUUGUUGCGAAAUGUGCAGCAAGUAAGAGGAA
............(((((((.............................................((((((((......)).)))))).((((((((.....)))))))))))))))... (-17.57 = -17.77 +   0.20)

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 10:46:47 2006