Locus 1736

Sequence ID	2L_DroMel_CAF1
Location	4,759,470 – 4,759,613
Length	143
Max. P	0.999916

overview

Window 0

Location	4,759,470 – 4,759,581
Length	111
Sequences	3
Columns	111
Reading direction	reverse
Mean pairwise identity	72.17
Mean single sequence MFE	-31.97
Consensus MFE	-19.60
Energy contribution	-19.93
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.78
Structure conservation index	0.61
SVM decision value	4.53
SVM RNA-class probability	0.999916
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4759470 111 - 22407834
UUUUUCUUGGUGAGCAUCGCUGCUUCCUAUUUUCCCAGACAAAUGGCGUCGCACUUUGGUGGCGCCACUUUUUGUUGCCCCUGUUGUUGUCGGCAACAACACCACCACCAC
.......(((((((((....)))).............(((((((((((((((......)))))))))...)))))).....((((((((....)))))))).))))).... ( -36.60)
>DroSec_CAF1 207781 105 - 1
UUUUUCUUGGUGAGCAUCGCUUCUUCCUAUUUUCCCAGACAAAUGGCGUCGCACUUUGGUGGCGCCACUUUUUGUUGCCCCCGUUGUUGUCGGCAACACCACAAC------
.......(((((.........................(((((((((((((((......)))))))))...))))))(((..((....))..)))..)))))....------ ( -30.70)
>DroAna_CAF1 206111 85 - 1
UUUUU-UGGGCGAGA---GUUGCUUCCUAUUUGGGCAGACAAAUGGCGUCGCAGUUUCGUGGCGCCACCAGUUGUUAUU---GUUGGUGUUG-------------------
.....-...((((((---.((((..((((((((......))))))).)..))))))))))(((((((.((((....)))---).))))))).------------------- ( -28.60)
>consensus
UUUUUCUUGGUGAGCAUCGCUGCUUCCUAUUUUCCCAGACAAAUGGCGUCGCACUUUGGUGGCGCCACUUUUUGUUGCCCC_GUUGUUGUCGGCAACA_CAC_AC______
........((.(((........)))))..........(((((((((((((((......)))))))))...))))))................................... (-19.60 = -19.93 +   0.33)

alignment

secondary structure

dotplot

Window 1

Location	4,759,501 – 4,759,613
Length	112
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.89
Mean single sequence MFE	-33.77
Consensus MFE	-20.15
Energy contribution	-20.27
Covariance contribution	0.11
Combinations/Pair	1.26
Mean z-score	-1.83
Structure conservation index	0.60
SVM decision value	0.71
SVM RNA-class probability	0.829675
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4759501 112 - 22407834
GGUCACGUCCACAGAGCG--------AUAUUUUUCCGCAUUUUUUCUUGGUGAGCAUCGCUGCUUCCUAUUUUCCCAGACAAAUGGCGUCGCACUUUGGUGGCGCCACUUUUUGUUGCCC
(((.(((((......(((--------.........))).........(((..((((....))))..)))........)))...(((((((((......)))))))))......)).))). ( -32.00)
>DroPse_CAF1 226431 108 - 1
GGUCACGCCCAGA---CG--------GUUUUCCUUCUCUUAUUUUCUGUGUAUGUG-UGUUGCUUCCUAUUUCGGCAGACAAAUGGCGUCGCAGUUUCGUGGCGCCACCAGUUGUUGCCA
((.(((((..(.(---((--------(..................)))).)..)))-))......))......(((((.(((.(((((((((......)))))))))....)))))))). ( -32.47)
>DroEre_CAF1 196394 112 - 1
GGUCACGUCCAGAGCGCG--------AUAUUUUUCCGCAUUUUUUCUUAGUGAGCUUCGUUGCUUCCUAUUUUCCCAGACAAAUGGCGUCGCACUUUGGUGGCGCCACUUUGUGUUGCCC
(((((((((....(((.(--------(......))))).........(((..(((......)))..)))........)))...(((((((((......)))))))))....)))..))). ( -35.10)
>DroYak_CAF1 194500 112 - 1
GGUCACGUCCAGCGAGCG--------AUAUUUUUCCGCAUUUUUUCUUGGUGAGCUUCGCUGCUUCCUAUUUUCCCAGACAAAUGGCGUCGCACUUUGGUGGCGCCACUUUUUGUUGCCC
(((.(((((..(.(((((--------.........))).........(((..(((......)))..)))...)))..)))...(((((((((......)))))))))......)).))). ( -32.10)
>DroAna_CAF1 206121 115 - 1
GGUCAUGCCCGCAGCUCGUUUUUCUAAUAUUUUUCUUCCUUUUUU-UGGGCGAGA---GUUGCUUCCUAUUUGGGCAGACAAAUGGCGUCGCAGUUUCGUGGCGCCACCAGUUGUUAUU-
.(((.(((((((((((((((.....))).....((.(((......-.))).))))---))))).........))))))))...(((((((((......)))))))))............- ( -38.50)
>DroPer_CAF1 234192 108 - 1
GGUCACGCCCAGA---CG--------GUUUUCCUUCUCUUAUUUUCUGUGUAUGUG-UGUUGCUUCCUAUUUCGGCAGACAAAUGGCGUCGCAGUUUCGUGGCGCCACCAGUUGUUGCCA
((.(((((..(.(---((--------(..................)))).)..)))-))......))......(((((.(((.(((((((((......)))))))))....)))))))). ( -32.47)
>consensus
GGUCACGCCCAGAG_GCG________AUAUUUUUCCGCAUUUUUUCUGGGUGAGCG_CGUUGCUUCCUAUUUUCCCAGACAAAUGGCGUCGCACUUUCGUGGCGCCACCAGUUGUUGCCC
(((.............................................((.((((......)))).)).........(((((.(((((((((......)))))))))....)))))))). (-20.15 = -20.27 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:53 2006