Locus 3306

Sequence ID	X_DroMel_CAF1
Location	8,827,461 – 8,827,561
Length	100
Max. P	0.955332

overview

Window 9

Location	8,827,461 – 8,827,561
Length	100
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.87
Mean single sequence MFE	-33.39
Consensus MFE	-22.61
Energy contribution	-21.67
Covariance contribution	-0.94
Combinations/Pair	1.24
Mean z-score	-2.62
Structure conservation index	0.68
SVM decision value	1.15
SVM RNA-class probability	0.923251
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8827461 100 + 22224390
-----------GGU--UA--GGUCGCC-AUGGCUUUGCGGCUUGCAUGCAAAUU-UUAUGUUUUAAUAAUAAGU-CUCUGGCAUGCAAGCGCCGCAUAUUUUAUGC-CAAUUGAU-GGAG
-----------(((--..--....)))-.((((..((((((((((((((....(-((((.........))))).-.....))))))))..))))))........))-))......-.... ( -29.70)
>DroVir_CAF1 106081 111 + 1
CUUUGGCGUCUGCU--UG--AGUCGC--UUAGCUUUGCGGCUUGCAUGCAAAUU-UUAUGUUUUAAUAACAAGUUCUCUGGCAUGCAAGCGGCGCAUAUUUUAUGC-CAAUUGCC-GUGC
....((((.(((((--((--((((((--........)))))))((((((.....-...((((.....)))).........)))))))))))))(((((...)))))-.....)))-.... ( -36.73)
>DroWil_CAF1 13655 105 + 1
-----------GGU--UGUUGUGCGCCUUUAGGUUUGCGGCUUGCAUGCAAAUUUUUAUGUUUUAAUAAUAAGU-CUGAGGCAUGCAAGCAGCGUAUAUUUUAUGC-CAAUUGCCUGGUA
-----------(((--.((((.(((((....)))..((.((((((((((.....(((((.........))))).-.....)))))))))).))...........))-)))).)))..... ( -33.70)
>DroMoj_CAF1 109110 110 + 1
UUUUGGCGUCUGCU--UG--AGUCGC--UUAGCUUUGUGGCUUGCAUGCAAAUU-UUAUGUUUUAAUAACAAGU-CUCUGGCAUGCAAGCGGCGCAUAUUUUAUGC-CAAUUGCC-GUGC
....((((.(((((--((--((((((--........)))))))((((((.....-...((((.....))))...-.....)))))))))))))(((((...)))))-.....)))-.... ( -35.39)
>DroAna_CAF1 56662 98 + 1
-----------GGU--UG--GGUCGCC---GGCUCUGCGGCUUGCAUGCAAAUU-UUAUGUUUUAAUAAUAAGU-CUCUGGCAUGCAAGCGUCGCAUAUUUUAUGC-CGAUUGCU-GCUG
-----------(((--..--....)))---(((...(((((((((((((....(-((((.........))))).-.....))))))))))((((((((...)))).-))))))).-))). ( -30.40)
>DroPer_CAF1 69762 104 + 1
-----------GGUUUUG--GGUCGCCUCUGGCUUUGCGGCUUGCAUGCAAAUU-UUAUGUUUUAAUAAUAAGU-CUGUGGCAUGCAAGCAUCGCAUAUUUUAUGCCCAAUUGCU-GGGA
-----------(((.(((--(((.(((...)))..((((((((((((((....(-((((.........))))).-.....))))))))))..))))........))))))..)))-.... ( -34.40)
>consensus
___________GGU__UG__GGUCGCC_UUAGCUUUGCGGCUUGCAUGCAAAUU_UUAUGUUUUAAUAAUAAGU_CUCUGGCAUGCAAGCGGCGCAUAUUUUAUGC_CAAUUGCC_GGGA
...........(((.........(((..........)))((((((((((.........((((.....)))).........)))))))))))))(((((...))))).............. (-22.61 = -21.67 +  -0.94)

alignment

secondary structure

dotplot

Window 0

Location	8,827,461 – 8,827,561
Length	100
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.87
Mean single sequence MFE	-28.46
Consensus MFE	-18.75
Energy contribution	-19.36
Covariance contribution	0.61
Combinations/Pair	1.04
Mean z-score	-3.22
Structure conservation index	0.66
SVM decision value	1.45
SVM RNA-class probability	0.955332
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8827461 100 - 22224390
CUCC-AUCAAUUG-GCAUAAAAUAUGCGGCGCUUGCAUGCCAGAG-ACUUAUUAUUAAAACAUAA-AAUUUGCAUGCAAGCCGCAAAGCCAU-GGCGACC--UA--ACC-----------
(.((-((......-(((((...)))))(((((((((((((.(((.-..((((.........))))-..)))))))))))))......)))))-)).)...--..--...----------- ( -25.80)
>DroVir_CAF1 106081 111 - 1
GCAC-GGCAAUUG-GCAUAAAAUAUGCGCCGCUUGCAUGCCAGAGAACUUGUUAUUAAAACAUAA-AAUUUGCAUGCAAGCCGCAAAGCUAA--GCGACU--CA--AGCAGACGCCAAAG
....-(((.....-(((((...)))))((.((((((((((.(((.....((((.....))))...-..))))))))))))).))........--((....--..--.))....))).... ( -34.50)
>DroWil_CAF1 13655 105 - 1
UACCAGGCAAUUG-GCAUAAAAUAUACGCUGCUUGCAUGCCUCAG-ACUUAUUAUUAAAACAUAAAAAUUUGCAUGCAAGCCGCAAACCUAAAGGCGCACAACA--ACC-----------
.....((...(((-((...........((.((((((((((.....-.........................)))))))))).))...((....)).)).)))..--.))----------- ( -23.11)
>DroMoj_CAF1 109110 110 - 1
GCAC-GGCAAUUG-GCAUAAAAUAUGCGCCGCUUGCAUGCCAGAG-ACUUGUUAUUAAAACAUAA-AAUUUGCAUGCAAGCCACAAAGCUAA--GCGACU--CA--AGCAGACGCCAAAA
....-(((..(((-(((((...)))))...((((((((((.(((.-...((((.....))))...-..)))))))))))))..)))......--((....--..--.))....))).... ( -31.40)
>DroAna_CAF1 56662 98 - 1
CAGC-AGCAAUCG-GCAUAAAAUAUGCGACGCUUGCAUGCCAGAG-ACUUAUUAUUAAAACAUAA-AAUUUGCAUGCAAGCCGCAGAGCC---GGCGACC--CA--ACC-----------
....-.((...((-((........((((..((((((((((.(((.-..((((.........))))-..)))))))))))))))))..)))---)))....--..--...----------- ( -26.40)
>DroPer_CAF1 69762 104 - 1
UCCC-AGCAAUUGGGCAUAAAAUAUGCGAUGCUUGCAUGCCACAG-ACUUAUUAUUAAAACAUAA-AAUUUGCAUGCAAGCCGCAAAGCCAGAGGCGACC--CAAAACC-----------
....-.....((((((........((((..((((((((((.....-...................-.....))))))))))))))..(((...)))).))--)))....----------- ( -29.55)
>consensus
CCCC_AGCAAUUG_GCAUAAAAUAUGCGCCGCUUGCAUGCCAGAG_ACUUAUUAUUAAAACAUAA_AAUUUGCAUGCAAGCCGCAAAGCCAA_GGCGACC__CA__ACC___________
..............((........((((..((((((((((.(((....((((.........))))...))))))))))))))))).........))........................ (-18.75 = -19.36 +   0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:02 2006