Locus 4903

Sequence ID	2L_DroMel_CAF1
Location	14,023,199 – 14,023,289
Length	90
Max. P	0.954566

overview

Window 5

Location	14,023,199 – 14,023,289
Length	90
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	74.07
Mean single sequence MFE	-29.62
Consensus MFE	-11.20
Energy contribution	-12.55
Covariance contribution	1.35
Combinations/Pair	1.21
Mean z-score	-2.25
Structure conservation index	0.38
SVM decision value	0.78
SVM RNA-class probability	0.849298
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14023199 90 + 22407834
GCCGCA--------UUCGAUGAUAGUGUCAGUAAUGAUGACUACACUACAUGGG--GUGCAUC--UAUGCA-----UGGCCCGGUGCCGUAGCACCGACUAUCUCCA
...(((--------(((.(((.((((((.(((.......)))))))))))).))--))))...--.....(-----(((..((((((....)))))).))))..... ( -31.10)
>DroSec_CAF1 110743 88 + 1
GCCGCA--------AUCGAUGAUAGUAACAGUAAUGAUGACUA--UUACAUGGG--GUGCAUC--UAUGCA-----UGGCCCGGUGCCGUAGCACCGACUAUCUCCA
......--------...((.((((((....((((((.....))--))))..(((--(((((..--..))))-----)..)))(((((....))))).)))))))).. ( -26.90)
>DroSim_CAF1 115126 88 + 1
GCCGCA--------AUCGAUGAUAGUGACAGUAAUGAUGACUA--UUACAUGGG--GUGCAUC--UAUGCA-----UGGCCCGGUGCUGUAGCACCAACUAUCUCCA
......--------...((.((((((....((((((.....))--))))..(((--(((((..--..))))-----)..)))(((((....))))).)))))))).. ( -27.50)
>DroEre_CAF1 113815 97 + 1
GCCAUCACAUCGCUAUCGAUAAUAGUCACAGUAAUGAUGACUA--UUUCACG-G--GUGCAUCCAUAUGCA-----AGGCCCGGUGCCGUAGCGCCGACUAUCUCCA
(((............(((..((((((((((....)).))))))--))...))-)--.(((((....)))))-----.))).((((((....)))))).......... ( -30.00)
>DroYak_CAF1 121161 95 + 1
GCUAUA--------AUCGAUGAUAGUGACAGUAAUGAUGACUA--UUACACGGG--GUGCAUCCAUAUGGAUGCAUAUGCCCGGUGCCGUUGCACCGACUAUCUCCA
......--------...((.((((((....((((((.....))--))))..(((--((((((((....))))))))...)))(((((....))))).)))))))).. ( -34.90)
>DroAna_CAF1 110130 84 + 1
GCUGUC--------ACCGAUGAUAGUGACAGUAAUGAUGACUA--UGAUGUCCGGAGAGGA------GGAC-----UAGC-CGAU-CGAUCAGAUCGAUCAGGUUCU
((((((--------((........))))))))...........--....((((........------))))-----.(((-((((-((((...))))))).)))).. ( -27.30)
>consensus
GCCGCA________AUCGAUGAUAGUGACAGUAAUGAUGACUA__UUACAUGGG__GUGCAUC__UAUGCA_____UGGCCCGGUGCCGUAGCACCGACUAUCUCCA
.................((.((((((...............................(((((....)))))..........((((((....)))))))))))))).. (-11.20 = -12.55 +   1.35)

alignment

secondary structure

dotplot

Window 6

Location	14,023,199 – 14,023,289
Length	90
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	74.07
Mean single sequence MFE	-28.83
Consensus MFE	-15.41
Energy contribution	-15.73
Covariance contribution	0.32
Combinations/Pair	1.37
Mean z-score	-2.09
Structure conservation index	0.53
SVM decision value	1.44
SVM RNA-class probability	0.954566
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14023199 90 - 22407834
UGGAGAUAGUCGGUGCUACGGCACCGGGCCA-----UGCAUA--GAUGCAC--CCCAUGUAGUGUAGUCAUCAUUACUGACACUAUCAUCGAA--------UGCGGC
.........(((((((....)))))))(((.-----.((((.--((((...--.....((((((((((.......))).)))))))))))..)--------)))))) ( -30.40)
>DroSec_CAF1 110743 88 - 1
UGGAGAUAGUCGGUGCUACGGCACCGGGCCA-----UGCAUA--GAUGCAC--CCCAUGUAA--UAGUCAUCAUUACUGUUACUAUCAUCGAU--------UGCGGC
.........(((((((....)))))))(((.-----.(((..--((((...--.....((((--((((.......))))))))...))))...--------)))))) ( -28.70)
>DroSim_CAF1 115126 88 - 1
UGGAGAUAGUUGGUGCUACAGCACCGGGCCA-----UGCAUA--GAUGCAC--CCCAUGUAA--UAGUCAUCAUUACUGUCACUAUCAUCGAU--------UGCGGC
..((((((((.(((((....)))))(((...-----((((..--..)))).--)))..((((--(.......)))))....)))))).))...--------...... ( -23.80)
>DroEre_CAF1 113815 97 - 1
UGGAGAUAGUCGGCGCUACGGCACCGGGCCU-----UGCAUAUGGAUGCAC--C-CGUGAAA--UAGUCAUCAUUACUGUGACUAUUAUCGAUAGCGAUGUGAUGGC
.........((((.((....)).))))((((-----..(((((((......--)-)))((((--(((((((.......))))))))).)).......)))..).))) ( -29.70)
>DroYak_CAF1 121161 95 - 1
UGGAGAUAGUCGGUGCAACGGCACCGGGCAUAUGCAUCCAUAUGGAUGCAC--CCCGUGUAA--UAGUCAUCAUUACUGUCACUAUCAUCGAU--------UAUAGC
..((((((((((((((....))))))((((..(((((((....))))))).--.....((((--(.......))))))))))))))).))...--------...... ( -32.80)
>DroAna_CAF1 110130 84 - 1
AGAACCUGAUCGAUCUGAUCG-AUCG-GCUA-----GUCC------UCCUCUCCGGACAUCA--UAGUCAUCAUUACUGUCACUAUCAUCGGU--------GACAGC
.((....(((((((...))))-)))(-((((-----((((------........))))....--))))).))....((((((((......)))--------))))). ( -27.60)
>consensus
UGGAGAUAGUCGGUGCUACGGCACCGGGCCA_____UGCAUA__GAUGCAC__CCCAUGUAA__UAGUCAUCAUUACUGUCACUAUCAUCGAU________UACGGC
.((.((((((((((((....))))))..........(((((....)))))...............................)))))).))................. (-15.41 = -15.73 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:35 2006