Locus 4058

Sequence ID	2L_DroMel_CAF1
Location	11,739,156 – 11,739,279
Length	123
Max. P	0.865096

overview

Window 5

Location	11,739,156 – 11,739,250
Length	94
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	75.32
Mean single sequence MFE	-22.00
Consensus MFE	-12.02
Energy contribution	-14.02
Covariance contribution	2.00
Combinations/Pair	1.10
Mean z-score	-1.93
Structure conservation index	0.55
SVM decision value	0.85
SVM RNA-class probability	0.865096
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11739156 94 + 22407834
CCUCAUUACUCAUACGCCACGUUGGCAAACAUGCUGCUAAUGCGCGUGUUAGCCAUACUCC-UCGGCCAUUUCUUGGCAC--ACACUUAUUAUUAUC
..............((....((((((.(((((((.((....))))))))).)))).))...-.))((((.....))))..--............... ( -24.70)
>DroSec_CAF1 198119 96 + 1
UCACGUUACUCAUACGCCACGUUGGCAAGCAUGCCGCUAAUGCGCGUGUUAGCCACACUCC-UCGGCCAUUUCUUUGCACAGACACUUAUUGUUAUC
....((.........(((..((((((.(((((((.((....))))))))).)))).))...-..))).........))...((((.....))))... ( -21.87)
>DroSim_CAF1 198733 94 + 1
UCACGUUACUCAUACGCCACGUUGGCAAACAUGCUGCUAAUGCGCGUGUUAGCCACACUCC-UCGGCCAUUUCUUGGCAC--ACACUUAUUGUUAUC
...(((.......)))....((((((.(((((((.((....))))))))).)))).))...-...((((.....))))..--............... ( -24.70)
>DroWil_CAF1 120971 81 + 1
UUAGAUGAAUCAUACGCCACGUAGACCAUU----UGUUAAUCUGAAUUU----C-UAUUCGUUCGGC---UUAGUCGCAU---UAUCUAUAAUUAU-
.(((((((....((((...))))(((....----...(((.((((((..----.-.....)))))).---))))))...)---)))))).......- ( -11.51)
>DroYak_CAF1 192415 94 + 1
CUGCGUUACUCAUACGCCACGUUGGCAAUCAUGCUGCUAAUGCGCGUGUUAGCCGUAUUCC-UUGGCUAUUUGUUGGCAC--ACACUUAAUGCUAUC
..((((((...((((((..((((((((.......)))))))).))))))((((((......-.))))))...........--.....)))))).... ( -27.20)
>consensus
UCACGUUACUCAUACGCCACGUUGGCAAACAUGCUGCUAAUGCGCGUGUUAGCCAUACUCC_UCGGCCAUUUCUUGGCAC__ACACUUAUUGUUAUC
........((.((((((..((((((((.......)))))))).)))))).)).............((((.....))))................... (-12.02 = -14.02 +   2.00)

alignment

secondary structure

dotplot

Window 6

Location	11,739,179 – 11,739,279
Length	100
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	75.99
Mean single sequence MFE	-25.62
Consensus MFE	-13.38
Energy contribution	-16.82
Covariance contribution	3.44
Combinations/Pair	1.21
Mean z-score	-1.97
Structure conservation index	0.52
SVM decision value	0.78
SVM RNA-class probability	0.849710
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11739179 100 + 22407834
GGCAAACAUGCUGCUAAUGCGCGUGUUAGCCAUACUCC-UCGGCCAUUUCUUGGCAC--ACACUUAUUAUUAUCAGUUCCCUUAGGGUUAAUAAUAUGAGGUU
(((.(((((((.((....))))))))).))).....((-(((((((.....))))..--.....((((((((......(((...))).))))))))))))).. ( -34.10)
>DroSec_CAF1 198142 102 + 1
GGCAAGCAUGCCGCUAAUGCGCGUGUUAGCCACACUCC-UCGGCCAUUUCUUUGCACAGACACUUAUUGUUAUCAGUUCCCUUAGGGUUAAUAAUAUUAGGUU
(((.(((((((.((....))))))))).))).......-......................(((((.((((((.....(((...)))...)))))).))))). ( -25.30)
>DroSim_CAF1 198756 100 + 1
GGCAAACAUGCUGCUAAUGCGCGUGUUAGCCACACUCC-UCGGCCAUUUCUUGGCAC--ACACUUAUUGUUAUCAGUUCCCUUAGGGUUAAUAAUAUUAGGUU
(((.(((((((.((....))))))))).))).......-...((((.....))))..--..(((((.((((((.....(((...)))...)))))).))))). ( -31.30)
>DroWil_CAF1 120994 87 + 1
GACCAUU----UGUUAAUCUGAAUUU----C-UAUUCGUUCGGC---UUAGUCGCAU---UAUCUAUAAUUAU-AAUCACCUACGGGUUAACAUAAUAAGGUU
((((...----.(((((.((((((..----.-.....)))))).---)))).)....---........(((((-....(((....)))....)))))..)))) ( -13.80)
>DroYak_CAF1 192438 97 + 1
GGCAAUCAUGCUGCUAAUGCGCGUGUUAGCCGUAUUCC-UUGGCUAUUUGUUGGCAC--ACACUUAAUGCUAUCAGUUCCCUUAGGGUUAAUAAU---AGGUU
(((...(((((.((....)))))))...)))....(((-(.((....(((.(((((.--........))))).)))...))..))))........---..... ( -23.60)
>consensus
GGCAAACAUGCUGCUAAUGCGCGUGUUAGCCAUACUCC_UCGGCCAUUUCUUGGCAC__ACACUUAUUGUUAUCAGUUCCCUUAGGGUUAAUAAUAUUAGGUU
(((.(((((((.((....))))))))).)))...........((((.....))))......((((..((((((.....(((...)))...))))))..)))). (-13.38 = -16.82 +   3.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:17 2006