Locus 2994

Sequence ID	2L_DroMel_CAF1
Location	8,552,777 – 8,552,899
Length	122
Max. P	0.953885

overview

Window 1

Location	8,552,777 – 8,552,884
Length	107
Sequences	4
Columns	109
Reading direction	reverse
Mean pairwise identity	89.64
Mean single sequence MFE	-27.30
Consensus MFE	-19.31
Energy contribution	-20.88
Covariance contribution	1.56
Combinations/Pair	1.04
Mean z-score	-1.71
Structure conservation index	0.71
SVM decision value	0.05
SVM RNA-class probability	0.557669
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8552777 107 - 22407834
CAUUCAUUCCCAUC--CAUCCCCUUUGGCUAGGAACCUCGUGUCGCCAGCGGGAUUGUCAACGCCGUUGACCUCAUCUCCACCGUCCAACUGCAAUAAGCCUCGAAUGG
(((((.........--((..(((.(((((((.(.....).))..))))).)))..)).....((.((((((............)).)))).))..........))))). ( -22.80)
>DroSec_CAF1 62420 106 - 1
CAUUCAUUCCCGUC--CAACCCCU-UGGCCAGGAACCUCCUGUCGCCACCGGGAUUGUCAACGCCGUUGACCUCAUCUCCACCGUCCAACUGCAAUAAGCCUCGAAUGG
(((((.........--((((((..-((((((((.....))))..))))..))).))).....((.((((((............)).)))).))..........))))). ( -27.40)
>DroSim_CAF1 63342 106 - 1
CAUUCAUUCCCAUC--CAUCCCCU-UGGCCAGAAACCUCCUGUCGCCAGCGGGAUUGUCAACGCCGUUGACCUCAUCUCCACCGUCCAACUGCAAUAAGCCUCGAAUGG
(((((.........--.(((((.(-(((((((.......)))..))))).))))).......((.((((((............)).)))).))..........))))). ( -25.70)
>DroYak_CAF1 63593 109 - 1
CAUUCAUUCAUUCCCACAUCCCCUUUGGACAGAAACCUCCAGUCGCCAGUGGGGUUGUCAACGCCGUUGACCUCAUCUCCACUGUCCAAUGGCUUUAAGCCUCGAAUGG
....(((((...............((((((((.((((.(((.(....).)))))))((((((...))))))..........)))))))).(((.....)))..))))). ( -33.30)
>consensus
CAUUCAUUCCCAUC__CAUCCCCU_UGGCCAGAAACCUCCUGUCGCCAGCGGGAUUGUCAACGCCGUUGACCUCAUCUCCACCGUCCAACUGCAAUAAGCCUCGAAUGG
(((((...............(((.(((((((((.....))))..))))).)))...((((((...))))))................................))))). (-19.31 = -20.88 +   1.56)

alignment

secondary structure

dotplot

Window 2

Location	8,552,807 – 8,552,899
Length	92
Sequences	4
Columns	94
Reading direction	forward
Mean pairwise identity	89.05
Mean single sequence MFE	-31.44
Consensus MFE	-24.61
Energy contribution	-25.92
Covariance contribution	1.31
Combinations/Pair	1.08
Mean z-score	-1.91
Structure conservation index	0.78
SVM decision value	0.67
SVM RNA-class probability	0.818776
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8552807 92 + 22407834
GAGAUGAGGUCAACGGCGUUGACAAUCCCGCUGGCGACACGAGGUUCCUAGCCAAAGGGGAUG--GAUGGGAAUGAAUGGAUGGGGACAUCCAU
........(((..(((((..........)))))..))).....(((((((.(((.......))--).)))))))..(((((((....))))))) ( -32.10)
>DroSec_CAF1 62450 91 + 1
GAGAUGAGGUCAACGGCGUUGACAAUCCCGGUGGCGACAGGAGGUUCCUGGCCA-AGGGGUUG--GACGGGAAUGAAUGGAUGGGGACAUCCAU
.........(((....((((..(((((((..((((..((((.....))))))))-.)))))))--))))....)))(((((((....))))))) ( -37.60)
>DroSim_CAF1 63372 91 + 1
GAGAUGAGGUCAACGGCGUUGACAAUCCCGCUGGCGACAGGAGGUUUCUGGCCA-AGGGGAUG--GAUGGGAAUGAAUGGAUAGGGACAUCCAU
........((((((...)))))).(((((..((((..(((((...)))))))))-..)))))(--((((..................))))).. ( -27.47)
>DroYak_CAF1 63623 94 + 1
GAGAUGAGGUCAACGGCGUUGACAACCCCACUGGCGACUGGAGGUUUCUGUCCAAAGGGGAUGUGGGAAUGAAUGAAUGGAUGGGGACAUCCCC
........((((((...))))))...(((((.((.(((.....))).))((((.....)))))))))...........(((((....))))).. ( -28.60)
>consensus
GAGAUGAGGUCAACGGCGUUGACAAUCCCGCUGGCGACAGGAGGUUCCUGGCCA_AGGGGAUG__GAUGGGAAUGAAUGGAUGGGGACAUCCAU
........((((((...))))))..((((..((((..(((((...)))))))))..))))................(((((((....))))))) (-24.61 = -25.92 +   1.31)

alignment

secondary structure

dotplot

Window 3

Location	8,552,807 – 8,552,899
Length	92
Sequences	4
Columns	94
Reading direction	reverse
Mean pairwise identity	89.05
Mean single sequence MFE	-25.78
Consensus MFE	-20.09
Energy contribution	-21.52
Covariance contribution	1.44
Combinations/Pair	1.12
Mean z-score	-2.65
Structure conservation index	0.78
SVM decision value	1.44
SVM RNA-class probability	0.953885
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8552807 92 - 22407834
AUGGAUGUCCCCAUCCAUUCAUUCCCAUC--CAUCCCCUUUGGCUAGGAACCUCGUGUCGCCAGCGGGAUUGUCAACGCCGUUGACCUCAUCUC
(((((((....)))))))...........--.(((((..(((((((.(.....).))..))))).))))).((((((...))))))........ ( -23.60)
>DroSec_CAF1 62450 91 - 1
AUGGAUGUCCCCAUCCAUUCAUUCCCGUC--CAACCCCU-UGGCCAGGAACCUCCUGUCGCCACCGGGAUUGUCAACGCCGUUGACCUCAUCUC
(((((((....)))))))...........--...(((..-((((((((.....))))..))))..)))...((((((...))))))........ ( -28.30)
>DroSim_CAF1 63372 91 - 1
AUGGAUGUCCCUAUCCAUUCAUUCCCAUC--CAUCCCCU-UGGCCAGAAACCUCCUGUCGCCAGCGGGAUUGUCAACGCCGUUGACCUCAUCUC
(((((((....)))))))...........--.(((((.(-(((((((.......)))..))))).))))).((((((...))))))........ ( -25.50)
>DroYak_CAF1 63623 94 - 1
GGGGAUGUCCCCAUCCAUUCAUUCAUUCCCACAUCCCCUUUGGACAGAAACCUCCAGUCGCCAGUGGGGUUGUCAACGCCGUUGACCUCAUCUC
((((....))))...............(((((.......(((((........)))))......)))))(..((((((...))))))..)..... ( -25.72)
>consensus
AUGGAUGUCCCCAUCCAUUCAUUCCCAUC__CAUCCCCU_UGGCCAGAAACCUCCUGUCGCCAGCGGGAUUGUCAACGCCGUUGACCUCAUCUC
(((((((....))))))).................(((.(((((((((.....))))..))))).)))...((((((...))))))........ (-20.09 = -21.52 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:39 2006