Locus 4686

Sequence ID	3R_DroMel_CAF1
Location	12,337,625 – 12,337,736
Length	111
Max. P	0.865662

overview

Window 5

Location	12,337,625 – 12,337,736
Length	111
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	91.97
Mean single sequence MFE	-30.18
Consensus MFE	-23.76
Energy contribution	-24.00
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.88
Structure conservation index	0.79
SVM decision value	0.85
SVM RNA-class probability	0.865662
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12337625 111 + 27905053
UGUUUUGGUUGUUAAGCGCGUGAUUGCGCAAUGCCAACGCACAGAAAAUACGUAAUAUUAGAUGAUUAAAUAUGUAU--GUAUGUAUGUGCGAAAGACUGGCCUGUGUGGGUG
.((((((((......(((((....)))))...)))..((((((....((((((((((((.........))))).)))--))))...)))))).)))))..((((....)))). ( -31.60)
>DroSec_CAF1 6473 107 + 1
UGUUUGGGUUGUUAAGCGCAUGAUUGCGCAAUGCCAACGCACAGAAAAUACGUAAUAUUAGAUGAUUAAAUAUGUAU------GUAUGUGCGAAAGACUGGCCUGUGUGGGUG
.((((.(((......(((((....)))))...)))..((((((....(((((((..(((....)))....)))))))------...))))))..))))..((((....)))). ( -29.40)
>DroSim_CAF1 5640 107 + 1
UGUUUUGGUUGUUAAGCGCAUGAUUGCGCAAUGCCAACGCACAGAAAAUACGUAAUAUUAGAUGAUUAAAUAUGUAU------GUAUGUGCGAAAGACUGGCCUGUGUGGGUG
.((((((((......(((((....)))))...)))..((((((....(((((((..(((....)))....)))))))------...)))))).)))))..((((....)))). ( -30.30)
>DroEre_CAF1 5915 107 + 1
UGUUUUGGUUGUUAAGCGCAUGAUUGCGCAAUGCCAACGCACAGAAAAUACGUAAUAUUAGAUGAUUAAAUAUGUA------UGCAUGUGCGAAAGACUCUACUGUGUGGGUG
....(((((......(((((....)))))...)))))((((((....(((((((..(((....)))....))))))------)...))))))....((((........)))). ( -28.90)
>DroYak_CAF1 1951 113 + 1
UGUUUUGGUUGUUAGGCGCAUGAUUGCGCAAUGCCAACGCACAGCAAAUACGAAAUAUUAGAUGAUUAAAUAUGUACGAGUCUGCAUGUGCCAAAGACUCCACUGUGUGGGUG
....(((((......(((((....)))))...)))))(((((((..........(((((.........)))))....((((((((....))...))))))..))))))).... ( -30.70)
>consensus
UGUUUUGGUUGUUAAGCGCAUGAUUGCGCAAUGCCAACGCACAGAAAAUACGUAAUAUUAGAUGAUUAAAUAUGUAU_____UGUAUGUGCGAAAGACUGGCCUGUGUGGGUG
....(((((......(((((....)))))...)))))(((((((....((((((..(((....)))....))))))...........((.(....)))....))))))).... (-23.76 = -24.00 +   0.24)

alignment

secondary structure

dotplot

Window 6

Location	12,337,625 – 12,337,736
Length	111
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	91.97
Mean single sequence MFE	-23.26
Consensus MFE	-16.16
Energy contribution	-16.44
Covariance contribution	0.28
Combinations/Pair	1.05
Mean z-score	-2.65
Structure conservation index	0.69
SVM decision value	0.19
SVM RNA-class probability	0.625433
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12337625 111 - 27905053
CACCCACACAGGCCAGUCUUUCGCACAUACAUAC--AUACAUAUUUAAUCAUCUAAUAUUACGUAUUUUCUGUGCGUUGGCAUUGCGCAAUCACGCGCUUAACAACCAAAACA
...........(((((.....((((((...((((--.((.(((((.........))))))).))))....)))))))))))...((((......))))............... ( -21.90)
>DroSec_CAF1 6473 107 - 1
CACCCACACAGGCCAGUCUUUCGCACAUAC------AUACAUAUUUAAUCAUCUAAUAUUACGUAUUUUCUGUGCGUUGGCAUUGCGCAAUCAUGCGCUUAACAACCCAAACA
...........(((((.....((((((...------(((((((((.........)))))...))))....)))))))))))...(((((....)))))............... ( -21.60)
>DroSim_CAF1 5640 107 - 1
CACCCACACAGGCCAGUCUUUCGCACAUAC------AUACAUAUUUAAUCAUCUAAUAUUACGUAUUUUCUGUGCGUUGGCAUUGCGCAAUCAUGCGCUUAACAACCAAAACA
...........(((((.....((((((...------(((((((((.........)))))...))))....)))))))))))...(((((....)))))............... ( -21.60)
>DroEre_CAF1 5915 107 - 1
CACCCACACAGUAGAGUCUUUCGCACAUGCA------UACAUAUUUAAUCAUCUAAUAUUACGUAUUUUCUGUGCGUUGGCAUUGCGCAAUCAUGCGCUUAACAACCAAAACA
...............(((...((((((...(------((((((((.........)))))...))))....))))))..)))...(((((....)))))............... ( -20.00)
>DroYak_CAF1 1951 113 - 1
CACCCACACAGUGGAGUCUUUGGCACAUGCAGACUCGUACAUAUUUAAUCAUCUAAUAUUUCGUAUUUGCUGUGCGUUGGCAUUGCGCAAUCAUGCGCCUAACAACCAAAACA
...((((...)))).((.(((((((((.(((((..((...(((((.........)))))..))..))))))))))(((((....(((((....))))))))))...)))))). ( -31.20)
>consensus
CACCCACACAGGCCAGUCUUUCGCACAUACA_____AUACAUAUUUAAUCAUCUAAUAUUACGUAUUUUCUGUGCGUUGGCAUUGCGCAAUCAUGCGCUUAACAACCAAAACA
...............(((...((((((.........(((((((((.........)))))...))))....))))))..)))...((((......))))............... (-16.16 = -16.44 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:27 2006