Locus 5097

Sequence ID	3R_DroMel_CAF1
Location	13,435,742 – 13,435,943
Length	201
Max. P	0.712298

overview

Window 6

Location	13,435,742 – 13,435,838
Length	96
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	80.42
Mean single sequence MFE	-32.42
Consensus MFE	-21.48
Energy contribution	-21.48
Covariance contribution	0.00
Combinations/Pair	1.29
Mean z-score	-1.32
Structure conservation index	0.66
SVM decision value	0.01
SVM RNA-class probability	0.539160
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13435742 96 - 27905053
GAUCCACUUCAGGAUCGCUCUGCGCAUCUCCAGCAGGACGAACUGGAUCUCUUAGAGGAUCUCUGACUGGAACACCAGGCACCACGGCCGAGUUAA
(((((..(((((..(((..((((.........))))..))).)))))((.....)))))))..(((((((....)).(((......))).))))). ( -30.00)
>DroPse_CAF1 15975 93 - 1
GAUCCACGGCAGGAUCGCUCUGUAAGUCCCC-GCCGGCCGAA--GGAGGGCGGAUAGGAUCCGACAGGGGAACACCCGGCACAGUCGCGGCUCCAA
(((((......))))).((((((..((((((-(((..((...--))..)))))...))))...)))))).....((((((...)))).))...... ( -34.40)
>DroSec_CAF1 5356 93 - 1
GAUCCACUUCGGGAUCGCUCUGCGCAUCAC---CAGGACGAACUGGAUCUCUCAGAGGAUCUCUGACUGGAACACCAGGCACCACGGCCGAGUUCA
..((((.((.((((((.(((((.(.....(---(((......))))....).))))))))))).)).))))......(((......)))....... ( -30.80)
>DroSim_CAF1 5150 93 - 1
GAUCCACUUCGGGAUCGCUCUGCGCAUCAC---CAGGACGAACUGGAUCUCUCAGAGGAUCUCUGACUGGAACACCAGGCACCACGGCCGAGUUCA
..((((.((.((((((.(((((.(.....(---(((......))))....).))))))))))).)).))))......(((......)))....... ( -30.80)
>DroEre_CAF1 5445 96 - 1
GAUCCACUUCAGGAUCGCUCUGCGCAUCGCCAGCAGGACGAACUGGAUCUCUCAGAGGAUCCCUAACUGGAACUCCAGGAACCACAGCGGAAUUCA
(((((......)))))..(((((...(((((....)).)))...((((((......))))))....((((....))))........)))))..... ( -30.50)
>DroYak_CAF1 3421 96 - 1
GAUCCACUUCAGGGUCGCUCUGCGCAUCUCCAGCCGGGCGAACUGGAUCUCUAAGGGGAUCCCUGACAGGAACACCUGGCACCACUGCAGAGUUCA
(((((......)))))(((((((((.......)).((((.....(((((((....)))))))....((((....)))))).))...)))))))... ( -38.00)
>consensus
GAUCCACUUCAGGAUCGCUCUGCGCAUCACC_GCAGGACGAACUGGAUCUCUCAGAGGAUCCCUGACUGGAACACCAGGCACCACGGCCGAGUUCA
(((((......)))))((((.((.....................((((((......))))))....((((....))))........)).))))... (-21.48 = -21.48 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	13,435,838 – 13,435,943
Length	105
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	77.54
Mean single sequence MFE	-28.58
Consensus MFE	-21.73
Energy contribution	-21.73
Covariance contribution	0.00
Combinations/Pair	1.16
Mean z-score	-1.05
Structure conservation index	0.76
SVM decision value	0.38
SVM RNA-class probability	0.712298
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13435838 105 + 27905053
CCAACUAUGCGGCACCUCCGCCAGUAAGGCGACCUGUUCCGAAUCGUGUGUACUACGAUUCUGCGGGAGCGGUAAGUUCAUU---AACUUUAAUAUAUUGCGAAUUUU
..((((.(((.((.....((((.....)))).(((((...((((((((.....)))))))).))))).)).)))))))....---....................... ( -29.50)
>DroSec_CAF1 5449 105 + 1
CCAACUAUGCGGCACCACCGCCAGUGAGGCGGCCUGUUCCAAAUCGUGUGUACUAUGACUCUGCGGGAGCGGUAAGUUCAUU---UACCUUAAUAUAUUGCGAGUCUU
.......((..(((...(((((.....)))))..)))..))...............(((((.((....))((((((....))---))))............))))).. ( -27.40)
>DroSim_CAF1 5243 99 + 1
CCAACUAUGCGGCACCACCGCCAGUGAGGCGACCUGUUCCGAAUCGUGUGUACUAUGAUUCUGCGGGAGCGGUAAGUUCAU---------UAAUAUAUUGCAAGUCUU
...(((..((((.....)))).)))(((((..(((((...((((((((.....)))))))).))))).((((((.(((...---------.))).))))))..))))) ( -29.20)
>DroEre_CAF1 5541 97 + 1
CCAACUAUGCGGCACCUCCGCCAGUGAGGCGACCUGUUCCCAAUCGUGUGUACUACGAUUCCGUGGGAGCGGUAAGUUUAAUCAAAUCUUUUAU-----------UUU
..((((.((((((.(((((....).)))).).))((((((((((((((.....))))))....)))))))))))))))................-----------... ( -26.70)
>DroYak_CAF1 3517 91 + 1
CCAACUAUGCGGCACCUCCGCCAGUGAGGCGACCUGUUCCGAAUCGUGUGUACUACGAUUCGGCGGGAGCGGUAAGUUUAAU---AUCUUAAAU--------------
..((((.(((.((.....((((.....)))).((((..((((((((((.....)))))))))))))).)).)))))))....---.........-------------- ( -32.60)
>DroAna_CAF1 4595 100 + 1
CAAGCUAUGCUGCACCGCCACCAGUUCGAAGACCUGUUCCCAAUCGGGUCUAUUAUGAUUCUGCAGGAGCGGUAAGUUUU-----CUUUUAAAGAAAGUGC---UCUU
..(((...(((..((((((..(((.(((.(((((((........)))))))....)))..)))...).))))).)))(((-----((.....)))))..))---)... ( -26.10)
>consensus
CCAACUAUGCGGCACCUCCGCCAGUGAGGCGACCUGUUCCGAAUCGUGUGUACUACGAUUCUGCGGGAGCGGUAAGUUCAUU___AUCUUUAAUAUAUUGC___UCUU
..((((.(((.((.....((((.....)))).(((((....(((((((.....)))))))..))))).)).))))))).............................. (-21.73 = -21.73 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:04 2006