Locus 1928

Sequence ID 3L_DroMel_CAF1
Location 5,384,849 – 5,384,984
Length 135
Max. P 0.939465
window3005 window3006

overview

Window 5

Location 5,384,849 – 5,384,962
Length 113
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 88.95
Mean single sequence MFE -21.22
Consensus MFE -19.52
Energy contribution -19.55
Covariance contribution 0.03
Combinations/Pair 1.03
Mean z-score -1.29
Structure conservation index 0.92
SVM decision value 0.33
SVM RNA-class probability 0.690513
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5384849 113 + 23771897
UGGUCG---CCCCCACCAUCACCCUUAAGUUUUGUGCUUGAACUUAUUUGCCGGCUUUUACCUGCAAUUAGACGCAAUUAAAAUCGCAAAAUGUAAUUUAUUUUAAUUGCUGUUUG
((((..---.....)))).......(((((((.......))))))).((((.((......)).)))).((((((((((((((((.((.....)).....))))))))))).))))) ( -21.30)
>DroSec_CAF1 33999 111 + 1
UGG-----CCCCCCACCGCCACCCUUAAGUUUUGUGCUUGAACUUAUUUGCCGGCUUUUACCUGCAAUUAGACGCAAUUAAAAUUGCAAAAUGUAAUUUAUUUUAAUUGCUGUUUG
(((-----(........))))....(((((((.......))))))).((((.((......)).)))).(((((((((((((((((((.....)))....))))))))))).))))) ( -25.30)
>DroSim_CAF1 32236 116 + 1
UGGUCGCACCCCCCACCACCACCCUUAAGUUUUGUGCUUGAACUUAUUUGCCGGCUUUUACCUGCAAUUAGACGCAAUUAAAAUCGCAAAAUGUAAUUUAUUUUAAUUGCUGUUUG
((((.(......).)))).......(((((((.......))))))).((((.((......)).)))).((((((((((((((((.((.....)).....))))))))))).))))) ( -21.20)
>DroEre_CAF1 33970 98 + 1
------------------CCACCCUUAAGUUUUGUGCUUGAACUUAUUUGCCGGCUUUUACCUGCAAUUAGACGCAAUUAAAAUCGCAAAAUGUAAUUUAUUUUAAUUGCUGUUUG
------------------.......(((((((.......))))))).((((.((......)).)))).((((((((((((((((.((.....)).....))))))))))).))))) ( -19.40)
>DroYak_CAF1 32667 112 + 1
UGUUUU---CCAUC-GCACCACCCUUAAGUUUUGUGCUUGAACUUAUUUGCCGGCUUUUACCUGCAAUUAGACGCAAUUAAAAUCGCAAAAUGUAAUUUAUUUUAAUUGCUGUUUG
......---.....-((((.(..(....)..).))))..(((((((.((((.((......)).)))).)))..(((((((((((.((.....)).....))))))))))).)))). ( -19.40)
>DroAna_CAF1 32093 99 + 1
-----------------UCCACCCUGAAGUUCUGUGCUUGAACUUAUUUGCUGGCUUUUACCUGCAAUUAGACGCAAUUAAAAUCGCAAAAUGUAAUUUAUUUUAAUUGCUGUUUG
-----------------.........((((((.......))))))..((((.((......)).)))).((((((((((((((((.((.....)).....))))))))))).))))) ( -20.70)
>consensus
UGG______CCCCC_CCACCACCCUUAAGUUUUGUGCUUGAACUUAUUUGCCGGCUUUUACCUGCAAUUAGACGCAAUUAAAAUCGCAAAAUGUAAUUUAUUUUAAUUGCUGUUUG
.........................(((((((.......))))))).((((.((......)).)))).((((((((((((((((.((.....)).....))))))))))).))))) (-19.52 = -19.55 +   0.03)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,384,884 – 5,384,984
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 88.56
Mean single sequence MFE -23.75
Consensus MFE -20.33
Energy contribution -20.42
Covariance contribution 0.08
Combinations/Pair 1.13
Mean z-score -2.41
Structure conservation index 0.86
SVM decision value 1.30
SVM RNA-class probability 0.939465
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5384884 100 - 23771897
GGCUUUGGCCAAAAAGUUGUUU--------------------CAAACAGCAAUUAAAAUAAAUUACAUUUUGCGAUUUUAAUUGCGUCUAAUUGCAGGUAAAAGCCGGCAAAUAAGUUCA
((((((.(((.....(((....--------------------..))).(((((((((((.((.......))...)))))))))))...........))).)))))).............. ( -24.30)
>DroSec_CAF1 34032 100 - 1
GGCUUUGGCCAAAAAGUUGUUU--------------------CAAACAGCAAUUAAAAUAAAUUACAUUUUGCAAUUUUAAUUGCGUCUAAUUGCAGGUAAAAGCCGGCAAAUAAGUUCA
((((((.(((.....(((....--------------------..))).(((((((....(((......)))(((((....)))))...))))))).))).)))))).............. ( -23.90)
>DroEre_CAF1 33990 100 - 1
GGCUUUGGCCAAAAAGUUGUUU--------------------CAAACAGCAAUUAAAAUAAAUUACAUUUUGCGAUUUUAAUUGCGUCUAAUUGCAGGUAAAAGCCGGCAAAUAAGUUCA
((((((.(((.....(((....--------------------..))).(((((((((((.((.......))...)))))))))))...........))).)))))).............. ( -24.30)
>DroWil_CAF1 24880 117 - 1
GGUUU-GUUGUUAUUGUUGUUUUUUGUUUUUCGUUGUCUUCACAAACAGCAAUUAAAAUAAAUUACAUUUUGCGAUUUUAAUUGCGUCUAAUUGCAGGUAAAAGCCAGAAAA--ACUUUA
(((((-(((((......(((..((((((((..(((((........)))))....))))))))..)))....))))).(((.(((((......))))).))))))))......--...... ( -21.40)
>DroYak_CAF1 32701 100 - 1
GGCUUUGGCCAAAAAGUUGUUU--------------------CAAACAGCAAUUAAAAUAAAUUACAUUUUGCGAUUUUAAUUGCGUCUAAUUGCAGGUAAAAGCCGGCAAAUAAGUUCA
((((((.(((.....(((....--------------------..))).(((((((((((.((.......))...)))))))))))...........))).)))))).............. ( -24.30)
>DroAna_CAF1 32114 100 - 1
GGCUUUGGCCAAAAAGUUGUUU--------------------CAAACAGCAAUUAAAAUAAAUUACAUUUUGCGAUUUUAAUUGCGUCUAAUUGCAGGUAAAAGCCAGCAAAUAAGUUCA
((((((.(((.....(((....--------------------..))).(((((((((((.((.......))...)))))))))))...........))).)))))).............. ( -24.30)
>consensus
GGCUUUGGCCAAAAAGUUGUUU____________________CAAACAGCAAUUAAAAUAAAUUACAUUUUGCGAUUUUAAUUGCGUCUAAUUGCAGGUAAAAGCCGGCAAAUAAGUUCA
((((((.(((.....(((((((.....................)))))))....................(((((((............)))))))))).)))))).............. (-20.33 = -20.42 +   0.08)

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 10:20:10 2006