Locus 5962

Sequence ID	3R_DroMel_CAF1
Location	15,739,291 – 15,739,412
Length	121
Max. P	0.800089

overview

Window 5

Location	15,739,291 – 15,739,382
Length	91
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	75.64
Mean single sequence MFE	-16.05
Consensus MFE	-7.47
Energy contribution	-7.37
Covariance contribution	-0.11
Combinations/Pair	1.38
Mean z-score	-1.81
Structure conservation index	0.47
SVM decision value	-0.05
SVM RNA-class probability	0.508446
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15739291 91 + 27905053
UACAGAAAUUACAGAAAAUUCCAAUGUAUUAUUCAACU-CACGAAGUACA---UUUUCAUUGAAUUAUCA----UUUCGCUGCGCGAUGUACUUUACUU
....(((..((((...........))))...)))....-...((((((((---((..((.((((......----.)))).))...)))))))))).... ( -14.60)
>DroVir_CAF1 10816 91 + 1
-AAAGAAGUAAAGCAAAACUCGAGCGUAUUUUCUAUGUACAUAUAGUAUAUAGUUUUAAUUGAGGUCUUAUCAAUUUUAAUU--UGAUGUA-----CUC
-.....((((........(((((...((....((((((((.....))))))))...)).)))))....((((((.......)--)))))))-----)). ( -17.10)
>DroSec_CAF1 7852 86 + 1
UACAGAUGU-----AGAAUUCCAAUGUAUUAUUCAACU-CACUAAGUACA---UUUUCAUUGAAUUAACA----UUUCGAUGCGCGAUGUACUUUACCU
....((.((-----.((((...........)))).)))-)...(((((((---((..(((((((......----.)))))))...)))))))))..... ( -16.70)
>DroSim_CAF1 7939 86 + 1
UACAGAAGU-----AGAAUUCCAAUGUAUUAUUCAACU-CACUAAGUACA---UUUUCAUUGAAUUAUAA----UUUCGAUGCGCGAUGUACUUUACCU
....((.((-----.((((...........)))).)))-)...(((((((---((..(((((((......----.)))))))...)))))))))..... ( -16.70)
>DroEre_CAF1 7823 86 + 1
UACAGAAGU-----AGAAUUCCAAUGUAUUAUUCAACU-CACCAAGUACA---UUUUGAUUGAAUUAUUA----UUUCGAUGUGCGAUGUACUACUCUU
....((.((-----.((((...........)))).)))-)....((((((---((...((((((......----.))))))....))))))))...... ( -13.30)
>DroYak_CAF1 8001 86 + 1
UACAGCAGU-----AGAAUUCCAAUGUAUUAUUCAACU-CAUGAAGUACA---UUAUCAUUGAAUUAUUA----UUUCGAUGUACGAUGUACUAUACUU
..((..(((-----.((((...........)))).)))-..)).((((((---((..(((((((......----.)))))))...))))))))...... ( -17.90)
>consensus
UACAGAAGU_____AGAAUUCCAAUGUAUUAUUCAACU_CACGAAGUACA___UUUUCAUUGAAUUAUUA____UUUCGAUGCGCGAUGUACUUUACUU
............................................((((((.......(((((((...........))))))).....))))))...... ( -7.47 =  -7.37 +  -0.11)

alignment

secondary structure

dotplot

Window 6

Location	15,739,316 – 15,739,412
Length	96
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	83.26
Mean single sequence MFE	-17.66
Consensus MFE	-13.69
Energy contribution	-14.42
Covariance contribution	0.72
Combinations/Pair	1.09
Mean z-score	-2.17
Structure conservation index	0.78
SVM decision value	0.61
SVM RNA-class probability	0.800089
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15739316 96 + 27905053
GUAUUAUUCAACUCACGAAGUACAUUUUCAUUGAAUUAUCAUUUCGCUGCGCGAUGUACUUUACUUUGUAUCUUUGCUUUAUUAAUUUGUAAUGCA
(((((((.........((((((((((..((.((((.......)))).))...)))))))))).....(((....)))...........))))))). ( -17.60)
>DroSec_CAF1 7872 96 + 1
GUAUUAUUCAACUCACUAAGUACAUUUUCAUUGAAUUAACAUUUCGAUGCGCGAUGUACUUUACCUUGUAUCUUUGCUUUAUUAAUUUGUAAUGCA
(((((((..........(((((((((..(((((((.......)))))))...)))))))))......(((....)))...........))))))). ( -19.70)
>DroSim_CAF1 7959 96 + 1
GUAUUAUUCAACUCACUAAGUACAUUUUCAUUGAAUUAUAAUUUCGAUGCGCGAUGUACUUUACCUUGUAUCUUUGCUUUAUUAAUUUGUAAUGCA
(((((((..........(((((((((..(((((((.......)))))))...)))))))))......(((....)))...........))))))). ( -19.70)
>DroEre_CAF1 7843 96 + 1
GUAUUAUUCAACUCACCAAGUACAUUUUGAUUGAAUUAUUAUUUCGAUGUGCGAUGUACUACUCUUUGUAUCUUUGCUUUAUUAAUUUGUAAUGCA
(((((((...........((((((((...((((((.......))))))....)))))))).......(((....)))...........))))))). ( -16.30)
>DroYak_CAF1 8021 96 + 1
GUAUUAUUCAACUCAUGAAGUACAUUAUCAUUGAAUUAUUAUUUCGAUGUACGAUGUACUAUACUUUGUAUCUUUGCUUUAUUAAUUUGUAAUGCA
(((((((.......((((((((((((..(((((((.......)))))))...)))))))).......(((....))).))))......))))))). ( -20.32)
>DroAna_CAF1 8008 75 + 1
G-----------------AUUACAUCUUCUGUGAGUUA---CUUGGAUGCAUGAUGUAUUAUGCUUUGUAU-UUUGCUUUAUUAAUAUGUAAUGCA
.-----------------(((((((.......((((..---..((.(.((((((....))))))..).)).-...)))).......)))))))... ( -12.34)
>consensus
GUAUUAUUCAACUCACGAAGUACAUUUUCAUUGAAUUAUCAUUUCGAUGCGCGAUGUACUAUACUUUGUAUCUUUGCUUUAUUAAUUUGUAAUGCA
..................((((((((..(((((((.......)))))))...))))))))..............(((.((((......)))).))) (-13.69 = -14.42 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:09:03 2006