Locus 4655

Sequence ID	3R_DroMel_CAF1
Location	12,257,644 – 12,257,776
Length	132
Max. P	0.706923

overview

Window 5

Location	12,257,644 – 12,257,753
Length	109
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.18
Mean single sequence MFE	-28.46
Consensus MFE	-23.82
Energy contribution	-23.85
Covariance contribution	0.03
Combinations/Pair	1.04
Mean z-score	-0.92
Structure conservation index	0.84
SVM decision value	0.37
SVM RNA-class probability	0.706923
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12257644 109 - 27905053
----CUCAAA-UCGU----GUUCC--AAUAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCACGGCGCCAUAUUCACGCAUGUGGC
----......-.(((----((...--(((((((.((((((((((.((......)))))))(((((.....)))))))((((.........))))..))).))).))))...))))).... ( -29.60)
>DroVir_CAF1 89204 113 - 1
UACAAUU-AA-UUGUACGCGUCCC---AUAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCACGGCGCCAUUUGCG--CAUGACCG
(((((..-..-))))).((((...---...(((.((((((((((.((......)))))))(((((.....)))))))((((.........))))..))).)))....)))--)....... ( -30.60)
>DroPse_CAF1 80919 109 - 1
----UACCAAUAUUU----CUUGUA-GAAAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCACGGCGCCAUGUGGC--CAUGUUGU
----...((((((((----(.....-))))((((.(((.(((((.((......))))))))))........(((((((((.................)))))).))))))--).))))). ( -30.53)
>DroGri_CAF1 101295 113 - 1
UU-UAUC-AA-UUG--CGGUUUCCACAAUAGGCCCCGACGAGAUUCGAACUCAUGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCACGGCGCCACUGGCA--CAUUGCUG
..-....-.(-(((--.((...)).)))).(((.(((..((((((.........))))))(((((.....)))))(.((((.........))))).))).)))...(((.--....))). ( -25.40)
>DroMoj_CAF1 98968 103 - 1
-AUAUUC-AA-CUGU------------GUAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCACGGCGCCGUUACUC--CACAACCA
-......-..-.(((------------(..(((.((((((((((.((......)))))))(((((.....)))))))((((.........))))..))).))).......--)))).... ( -26.30)
>DroAna_CAF1 71300 106 - 1
----UUACAA-UU------GCUCC---AUAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCACGGCGCCAUGCAGACUGCUAGGGU
----......-..------..(((---...(((.((((((((((.((......)))))))(((((.....)))))))((((.........))))..))).)))..((.....))..))). ( -28.30)
>consensus
____UUC_AA_UUGU____GUUCC___AUAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCACGGCGCCAUUUGCA__CAUGACGG
..............................(((.((((((((((.((......)))))))(((((.....)))))))((((.........))))..))).)))................. (-23.82 = -23.85 +   0.03)

alignment

secondary structure

dotplot

Window 6

Location	12,257,684 – 12,257,776
Length	92
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	81.82
Mean single sequence MFE	-23.57
Consensus MFE	-16.55
Energy contribution	-17.38
Covariance contribution	0.83
Combinations/Pair	1.13
Mean z-score	-1.40
Structure conservation index	0.70
SVM decision value	0.05
SVM RNA-class probability	0.558803
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12257684 92 - 27905053
AUAGAAAAAAUAUUACUGGCACACUCAAA-UCGUGUUCC-AAUAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCU
............(((.(((.((((.....-..)))).))-).))).....((((((((.((......))))))((((((.....)))))))))) ( -20.30)
>DroPse_CAF1 80957 89 - 1
GUUGGCAAAAAG-----GAAAUAUACCAAUAUUUCUUGUAGAAAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCU
...(((....((-----(((((((....)))))))))........)))..((((((((.((......))))))((((((.....)))))))))) ( -22.80)
>DroSim_CAF1 71903 92 - 1
AUAGAAAAAAUAUUACUGGCACACUCAAA-UCGUGUUCC-AAUAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCU
............(((.(((.((((.....-..)))).))-).))).....((((((((.((......))))))((((((.....)))))))))) ( -20.30)
>DroEre_CAF1 75279 90 - 1
--GGAAAAAAGGUUAGUGAAACACUCUAA-UUGUGUUCC-AGUAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCU
--........(((((.((.(((((.....-..))))).)-).)).)))..((((((((.((......))))))((((((.....)))))))))) ( -23.00)
>DroYak_CAF1 73539 91 - 1
--AGCAAAAAAGUUUAUGGGACACUCAAAGUUGUGUUCC-AGUAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCU
--(((......(((((((((((((........)))))))-).)))))....(((((((.((......)))))))(((((.....)))))))))) ( -29.00)
>DroAna_CAF1 71340 89 - 1
AUAAAAAAAAAGUAAAUGGAGCGUUACAA-UU--GCUCC--AUAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCU
...........((..((((((((......-.)--)))))--))..))...((((((((.((......))))))((((((.....)))))))))) ( -26.00)
>consensus
AUAGAAAAAAAGUUAAUGGAACACUCAAA_UUGUGUUCC_AAUAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCU
.................(((((((........)))))))...........((((((((.((......))))))((((((.....)))))))))) (-16.55 = -17.38 +   0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:39 2006