Locus 4053

Sequence ID	2L_DroMel_CAF1
Location	11,732,801 – 11,732,931
Length	130
Max. P	0.929349

overview

Window 6

Location	11,732,801 – 11,732,896
Length	95
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.61
Mean single sequence MFE	-28.93
Consensus MFE	-11.84
Energy contribution	-11.95
Covariance contribution	0.11
Combinations/Pair	1.06
Mean z-score	-2.32
Structure conservation index	0.41
SVM decision value	-0.01
SVM RNA-class probability	0.528392
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11732801 95 - 22407834
-----------AGGCAGUUUUUAGCUUUUGUCAAGGUGGG--CAGACGACUACCUUUGUGCA-------AAGCUGGCUGA-----AGAUAAUCUACAAUAAUAAAUUUAUUGGCAACAAU
-----------..((.(((((((((((((((((((((((.--.......))))).))).)))-------))...))))))-----))))......((((((.....))))))))...... ( -27.00)
>DroPse_CAF1 187417 93 - 1
-----------UGUCAGUUUUUACCUUUUGUCAAGGUGGCUCCA---GCCCACCUCUGUUUG-------GGGGU-GUGGC-----AGAUAAUCUACAAUAAUAAAUUUAUUGGCAACAAU
-----------((((.....(((((((.....))))))).....---((((((((((....)-------)))))-).)))-----.)))).....((((((.....))))))........ ( -27.20)
>DroEre_CAF1 210695 95 - 1
-----------AGGCAGUUUUUAGCUUUUGUCAAGGUGGG--CAGACGACUACCUUUGUGCG-------AAGGUGGCUGC-----AGAUAAUCUACAAUAAUAAAUUUAUUGGCAACAAU
-----------..((((((....((((((((((((((((.--.......))))).))).)))-------)))))))))))-----..........((((((.....))))))........ ( -27.00)
>DroYak_CAF1 185101 95 - 1
-----------AGGCAGUUUUUAGCUUUUGUCAAGGUGGG--CAGACGACUACCUUUGUGCG-------AAGGUGGCUGA-----AGAUAAUCUACAAUAAUAAAUUUAUUGGCAACAAU
-----------..((.(((((((((((((((((((((((.--.......))))).))).)))-------))...))))))-----))))......((((((.....))))))))...... ( -26.70)
>DroAna_CAF1 190373 111 - 1
GGCCAGCCAGCAGGAGGUUCUUAGCUUUUGUCAAGGUGGG--CAGAUGCCUACCUUUGUGCC-------AAGUCGAGGGAUUCCUAGAUAAUCUACAAUAAUAAAUUUAUUGGCAACAAU
((....)).(((((((.((((..((((....(((((((((--(....))))))).)))....-------))))..)))).)))))..........((((((.....))))))))...... ( -35.60)
>DroPer_CAF1 184022 103 - 1
-----------UGUCAGUUUUUAGCUUUUGUCAAGGUGGCUCCUGUGGCCCACCUGUGUUUGUGGGGGUGGGGG-GUGGC-----AGAUAAUCUACAAUAAUAAAUUUAUUGGCAACAAU
-----------(((((((.((((....((((..((((.....((((.((((.((..(.((....)).)..))))-)).))-----))...))))))))...))))...)))))))..... ( -30.10)
>consensus
___________AGGCAGUUUUUAGCUUUUGUCAAGGUGGG__CAGACGACUACCUUUGUGCG_______AAGGUGGCGGA_____AGAUAAUCUACAAUAAUAAAUUUAUUGGCAACAAU
...........................((((.(((((((..........))))))).......................................((((((.....)))))))))).... (-11.84 = -11.95 +   0.11)

alignment

secondary structure

dotplot

Window 7

Location	11,732,836 – 11,732,931
Length	95
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	82.31
Mean single sequence MFE	-31.23
Consensus MFE	-15.15
Energy contribution	-14.82
Covariance contribution	-0.33
Combinations/Pair	1.19
Mean z-score	-3.12
Structure conservation index	0.49
SVM decision value	0.39
SVM RNA-class probability	0.717909
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11732836 95 + 22407834
UCAGCCAGCUUUGCACAAAGGUAGUCGUCUG--CCCACCUUGACAAAAGCUAAAAACUGCCU--------------GCCGGAUGCCGAGUUAACCCUUGGCAU--CCAACAAU
......((((((...(((.(((((....)))--))....)))...))))))...........--------------...((((((((((......))))))))--))...... ( -30.10)
>DroPse_CAF1 187452 95 + 1
GCCAC-ACCCCCAAACAGAGGUGGGC---UGGAGCCACCUUGACAAAAGGUAAAAACUGACA--------------ACCGGAUGCCGGGUUAAACCCUGGCCUGGCCAACAAU
(((.(-(((.(......).)))))))---(((....(((((.....)))))...........--------------.((((..((((((......)))))))))))))..... ( -31.60)
>DroSim_CAF1 185014 95 + 1
UCAGCCACCUUCGCACAAAGGUAGUCGUCUG--CCCACCUUGACAAAAGCUAAAAACUGCCU--------------GCCGGAUGCCGAGUUAACCCUUGGCAU--CCAACAAU
...((.......)).....(((((..(((..--........)))....((........))))--------------)))((((((((((......))))))))--))...... ( -28.30)
>DroEre_CAF1 210730 95 + 1
GCAGCCACCUUCGCACAAAGGUAGUCGUCUG--CCCACCUUGACAAAAGCUAAAAACUGCCU--------------GCCGGAUGCCGAGUUAACCCUUGGCAU--CCAACAAU
((((.((((((......))))).((((....--.......))))..............).))--------------)).((((((((((......))))))))--))...... ( -29.30)
>DroYak_CAF1 185136 95 + 1
UCAGCCACCUUCGCACAAAGGUAGUCGUCUG--CCCACCUUGACAAAAGCUAAAAACUGCCU--------------GCCGGAUGCCGAGUUAACCCUUGGCAU--CCAACAAU
...((.......)).....(((((..(((..--........)))....((........))))--------------)))((((((((((......))))))))--))...... ( -28.30)
>DroAna_CAF1 190413 109 + 1
UCCCUCGACUUGGCACAAAGGUAGGCAUCUG--CCCACCUUGACAAAAGCUAAGAACCUCCUGCUGGCUGGCCGAUGCCGGAUGCCGGGUUAACCCUUGGCAU--CCAACAAU
........((((((...(((((.(((....)--)).))))).......))))))...........(((........)))((((((((((....)))..)))))--))...... ( -39.80)
>consensus
UCAGCCACCUUCGCACAAAGGUAGUCGUCUG__CCCACCUUGACAAAAGCUAAAAACUGCCU______________GCCGGAUGCCGAGUUAACCCUUGGCAU__CCAACAAU
.................(((((.(..........).)))))......................................((((((((((......))))))))..))...... (-15.15 = -14.82 +  -0.33)

alignment

secondary structure

dotplot

Window 8

Location	11,732,836 – 11,732,931
Length	95
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	82.31
Mean single sequence MFE	-41.77
Consensus MFE	-23.33
Energy contribution	-23.37
Covariance contribution	0.03
Combinations/Pair	1.29
Mean z-score	-3.75
Structure conservation index	0.56
SVM decision value	1.20
SVM RNA-class probability	0.929349
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11732836 95 - 22407834
AUUGUUGG--AUGCCAAGGGUUAACUCGGCAUCCGGC--------------AGGCAGUUUUUAGCUUUUGUCAAGGUGGG--CAGACGACUACCUUUGUGCAAAGCUGGCUGA
.(((((((--(((((.((......)).))))))))))--------------)).((((...(((((((.((((((((((.--.......))))).))).))))))))))))). ( -40.70)
>DroPse_CAF1 187452 95 - 1
AUUGUUGGCCAGGCCAGGGUUUAACCCGGCAUCCGGU--------------UGUCAGUUUUUACCUUUUGUCAAGGUGGCUCCA---GCCCACCUCUGUUUGGGGGU-GUGGC
.......((((.(((.(((.....))))))....(((--------------((..(((...((((((.....))))))))).))---)))(((((((....))))))-))))) ( -34.80)
>DroSim_CAF1 185014 95 - 1
AUUGUUGG--AUGCCAAGGGUUAACUCGGCAUCCGGC--------------AGGCAGUUUUUAGCUUUUGUCAAGGUGGG--CAGACGACUACCUUUGUGCGAAGGUGGCUGA
.(((((((--(((((.((......)).))))))))))--------------)).(((((....((((((((((((((((.--.......))))).))).))))))))))))). ( -40.90)
>DroEre_CAF1 210730 95 - 1
AUUGUUGG--AUGCCAAGGGUUAACUCGGCAUCCGGC--------------AGGCAGUUUUUAGCUUUUGUCAAGGUGGG--CAGACGACUACCUUUGUGCGAAGGUGGCUGC
.(((((((--(((((.((......)).))))))))))--------------))((((((....((((((((((((((((.--.......))))).))).)))))))))))))) ( -43.00)
>DroYak_CAF1 185136 95 - 1
AUUGUUGG--AUGCCAAGGGUUAACUCGGCAUCCGGC--------------AGGCAGUUUUUAGCUUUUGUCAAGGUGGG--CAGACGACUACCUUUGUGCGAAGGUGGCUGA
.(((((((--(((((.((......)).))))))))))--------------)).(((((....((((((((((((((((.--.......))))).))).))))))))))))). ( -40.90)
>DroAna_CAF1 190413 109 - 1
AUUGUUGG--AUGCCAAGGGUUAACCCGGCAUCCGGCAUCGGCCAGCCAGCAGGAGGUUCUUAGCUUUUGUCAAGGUGGG--CAGAUGCCUACCUUUGUGCCAAGUCGAGGGA
......((--(((((..(((....))))))))))((((((.(((.(((.(((((((.(....).)))))))...))).))--).))))))..((((((........)))))). ( -50.30)
>consensus
AUUGUUGG__AUGCCAAGGGUUAACUCGGCAUCCGGC______________AGGCAGUUUUUAGCUUUUGUCAAGGUGGG__CAGACGACUACCUUUGUGCGAAGGUGGCUGA
...(((((..(((((.((......)).))))))))))..........................((((((((((((((((..........)))))).)).))))))))...... (-23.33 = -23.37 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:09 2006