Locus 846

Sequence ID 3L_DroMel_CAF1
Location 2,560,572 – 2,560,720
Length 148
Max. P 0.687844
window1303 window1304

overview

Window 3

Location 2,560,572 – 2,560,685
Length 113
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 72.28
Mean single sequence MFE -23.32
Consensus MFE -7.44
Energy contribution -7.88
Covariance contribution 0.45
Combinations/Pair 1.28
Mean z-score -2.12
Structure conservation index 0.32
SVM decision value 0.32
SVM RNA-class probability 0.687844
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2560572 113 + 23771897
AAAAAAGAAAAGAAAAAAAAACACCCUGGCCAAAUUGAAAUUAUGAUUAAG---GCAAGCGGCAGCAGGCCACCAAAUGGCAAAAAUUGGUCAACACAAU--UCUGUGACGUUUGAUA
..................((((....(((((((.................(---((..((....))..))).((....))......))))))).((((..--..))))..)))).... ( -22.30)
>DroSec_CAF1 22451 102 + 1
AAAA----------GAAAAAACACCCAGGCCAAAUUGAAAUUAUGAUUAAG---GCAAGCGGCAGCAGGC---CAAAUGUCAAAAAUUGGUCAAAACAUUGGUCUGUGACGUUUGAUA
....----------....((((..(((((((((.((((.....((((...(---((..((....))..))---)....))))........))))....)))))))).)..)))).... ( -23.12)
>DroSim_CAF1 19428 102 + 1
AAAA----------GAAAAAACACCCAGGCCAAAUUGAAAUUAUGAUUAAG---GCAAGCGGCAGCGGGC---CAAAUGGCAAAAAUUGGUCAACACAUUGGUCUGUGACGUUUGAUA
....----------....((((..(((((((((..((.............(---((..((....))..))---)...((((........)))).))..)))))))).)..)))).... ( -25.20)
>DroEre_CAF1 36687 91 + 1
AAAG----------AAA-AAACACCCAGACCAAAAUGAAAUUAUGAUUAAGC-----------AGCAGGC---CAAAUGGCAAAAAUUGGUCAACACG--GCUCUGUGACGUUUGAUA
....----------...-((((.....((((((..((...(((....))).)-----------)....((---(....))).....))))))..((((--....))))..)))).... ( -17.30)
>DroYak_CAF1 21093 103 + 1
AAAG----------AAAAAAACACCCAGACCAAAAUGAAAUUAUGAUUAAGCAGGCAGCAGGCAGCAGGC---CAAAUGGCAAAAAUUGGUCAACACG--GCUCUGUGACGUUUGAUA
....----------....((((.....((((((.................((..((.....)).))..((---(....))).....))))))..((((--....))))..)))).... ( -21.00)
>DroAna_CAF1 20513 91 + 1
AAUCGAGAAAA---AUAAACAGAGCCAGGCCGGAGCC-------------GGAGACACCAGGC--CAGGC---CAGGUUGCAAAAUUUGGCCAGCA------GCUGUGACGUUUGAUA
.((((((....---....((((.((..((((((....-------------(....).)).)))--).(((---((((((....))))))))).)).------.))))....)))))). ( -31.00)
>consensus
AAAA__________AAAAAAACACCCAGGCCAAAUUGAAAUUAUGAUUAAG___GCAAGCGGCAGCAGGC___CAAAUGGCAAAAAUUGGUCAACACA__G_UCUGUGACGUUUGAUA
..................((((.....((((((.....................((.....)).....((.........)).....))))))..((((......))))..)))).... ( -7.44 =  -7.88 +   0.45)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,560,612 – 2,560,720
Length 108
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 84.47
Mean single sequence MFE -32.90
Consensus MFE -20.22
Energy contribution -20.26
Covariance contribution 0.04
Combinations/Pair 1.12
Mean z-score -1.97
Structure conservation index 0.61
SVM decision value 0.03
SVM RNA-class probability 0.550847
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2560612 108 + 23771897
UUAUGAUUAAG---GCAAGCGGCAGCAGGCCACCAAAUGGCAAAAAUUGGUCAACACAAU--UCUGUGACGUUUGAUAAGCUGUUGGGGCCAAAAAGGUGACUCUCGCCCCGA
...........---.((((((...((((((((.....))))...(((((.......))))--)))))..))))))........(((((((.....((....))...))))))) ( -32.50)
>DroSec_CAF1 22481 100 + 1
UUAUGAUUAAG---GCAAGCGGCAGCAGGC---CAAAUGUCAAAAAUUGGUCAAAACAUUGGUCUGUGACGUUUGAUAAGCUGCUGGGGCCAAAAAGGUGGCUCUC-------
...........---.....(((((((..(.---(((((((((......(..(((....)))..)..))))))))).)..)))))))((((((......))))))..------- ( -34.40)
>DroSim_CAF1 19458 100 + 1
UUAUGAUUAAG---GCAAGCGGCAGCGGGC---CAAAUGGCAAAAAUUGGUCAACACAUUGGUCUGUGACGUUUGAUAAGCUGCUGGGGCCAAAAAGGUGGCUCUC-------
...........---.....(((((((..((---(....)))........(((((((((......))))....)))))..)))))))((((((......))))))..------- ( -31.00)
>DroEre_CAF1 36716 97 + 1
UUAUGAUUAAGC-----------AGCAGGC---CAAAUGGCAAAAAUUGGUCAACACG--GCUCUGUGACGUUUGAUAAGCUGCUGGGGCCAAAAAGGUGGCUCUCGUCUCGA
....(((..(((-----------(((..((---(....)))........(((((.(((--.........))))))))..))))))(((((((......))))))).))).... ( -30.10)
>DroYak_CAF1 21123 108 + 1
UUAUGAUUAAGCAGGCAGCAGGCAGCAGGC---CAAAUGGCAAAAAUUGGUCAACACG--GCUCUGUGACGUUUGAUAAGCUGCUGGGGCCAAAAAGGUGGCUCUCGCCUCGA
..........(.((((....((((((..((---(....)))........(((((.(((--.........))))))))..))))))(((((((......))))))).))))).. ( -36.50)
>consensus
UUAUGAUUAAG___GCAAGCGGCAGCAGGC___CAAAUGGCAAAAAUUGGUCAACACA_UGCUCUGUGACGUUUGAUAAGCUGCUGGGGCCAAAAAGGUGGCUCUCG_C_CGA
......................((((((.....((((((.((.....)).....((((......)))).)))))).....))))))((((((......))))))......... (-20.22 = -20.26 +   0.04)

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 09:52:39 2006