Locus 568

Sequence ID	3R_DroMel_CAF1
Location	2,122,875 – 2,123,028
Length	153
Max. P	0.992177

overview

Window 3

Location	2,122,875 – 2,122,970
Length	95
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	86.24
Mean single sequence MFE	-30.35
Consensus MFE	-23.70
Energy contribution	-23.65
Covariance contribution	-0.05
Combinations/Pair	1.12
Mean z-score	-2.32
Structure conservation index	0.78
SVM decision value	0.30
SVM RNA-class probability	0.677796
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2122875 95 + 27905053
UUUAUUUUGGCC--------------GCUUUUGGCCGUUUUACGCGGCUAAAACAAUAACCGAAAAUAAAGGCGCGUCACUCAUACGCAUCGUGUGACAAGCCGACGCC
((((((((((..--------------..((((((((((.....))))))))))......)).))))))))((((((.(..(((((((...)))))))...).)).)))) ( -30.20)
>DroSec_CAF1 265959 93 + 1
--UUUUUGGGCC--------------ACUUUUGGCCGUUUUACGCGGCUAAAACAAUAACCGAAAAUAAAGGCGCGUCACUCAUACGCAGCGUGUGACAAGCCGCCGCC
--(((((((...--------------..((((((((((.....))))))))))......)))))))....((((.((...(((((((...)))))))...))))))... ( -33.40)
>DroSim_CAF1 284582 95 + 1
UUUUUUUGGGCC--------------GCUUUUGGCCGUUUUACGCGGCUAAAACAAUAACCGAAAAUAAAGGCGCGUCACUCAUACGCAGCGUGUGACAAGCCGCCGCC
..(((((((...--------------..((((((((((.....))))))))))......)))))))....((((.((...(((((((...)))))))...))))))... ( -33.60)
>DroEre_CAF1 268973 92 + 1
U---CUCGGACU--------------GCUUUUGGCCGUUUUACGCGGCUAAAACAAUAACCGAAAAUAAAGGCGCGUCACUCAUACGCAGCGUGUGACAAGCCGACGCC
.---.((((..(--------------(.((((((((((.....))))))))))))....)))).......((((((.(..(((((((...)))))))...).)).)))) ( -30.90)
>DroWil_CAF1 267483 109 + 1
UUCUUUCCCUCCGCAACUCCUCCCUUGCUUUGCUUUGUUUUACGCAGCUAAAACAAUAACCGAAAAUAAAGGCGCGUCACUCAUACGCAGCGUGUGACAAGCCGACGCC
...((((.....((((........))))......((((((((......)))))))).....)))).....((((((.(..(((((((...)))))))...).)).)))) ( -21.60)
>DroYak_CAF1 270153 91 + 1
U----UCGGGCC--------------GCUUUUGGCCGUUUUACGCGGCUAAAACAAUAACCGAAAAUAAAGGCGUGUCACUCAUACGCAGCGUGUGACAAGCCGACGCC
(----((((...--------------..((((((((((.....))))))))))......)))))......(((.((((((.(.........).)))))).)))...... ( -32.40)
>consensus
U_UUUUCGGGCC______________GCUUUUGGCCGUUUUACGCGGCUAAAACAAUAACCGAAAAUAAAGGCGCGUCACUCAUACGCAGCGUGUGACAAGCCGACGCC
............................((((((((((.....)))))))))).................((((((.(..(((((((...)))))))...).)).)))) (-23.70 = -23.65 +  -0.05)

alignment

secondary structure

dotplot

Window 4

Location	2,122,930 – 2,123,028
Length	98
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	70.96
Mean single sequence MFE	-31.90
Consensus MFE	-16.94
Energy contribution	-17.89
Covariance contribution	0.95
Combinations/Pair	1.14
Mean z-score	-2.36
Structure conservation index	0.53
SVM decision value	2.31
SVM RNA-class probability	0.992177
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2122930 98 + 27905053
AGGCGCGUCACUCAUACGCAUCGUGUGACAAGCCGACGCCCGCGGCUGG-----------UAUGCCCAGCAACAAUC-----AGCCGGCAA-UAACAAUAACAAUAAGCAAGACA
.((.(((((..(((((((...)))))))......)))))))((((((((-----------(.(((...)))...)))-----)))).))..-....................... ( -29.40)
>DroSec_CAF1 266012 98 + 1
AGGCGCGUCACUCAUACGCAGCGUGUGACAAGCCGCCGCCCGCGGCUGG-----------UUUGCCCAGCAACAAUC-----AGCCGGCAA-UAACAAUAACAAUAAGCAAGACA
.((((.((...(((((((...)))))))...))))))(((...((((((-----------(((((...)))..))))-----)))))))..-....................... ( -31.60)
>DroEre_CAF1 269025 92 + 1
AGGCGCGUCACUCAUACGCAGCGUGUGACAAGCCGACGCCCGCGGCUGG-----------UUUGUCGAGCAACAAUC-----AGCCGGCAA-UAA------CAAUAAGCAAGACC
.((.(((((..(((((((...)))))))......)))))))((((((((-----------((.((......))))))-----)))).))..-...------.............. ( -29.90)
>DroMoj_CAF1 279818 84 + 1
AGGCGCGUCACUCAUACGCAGCGUGUGACAUGGCGACGCCCGUAGGCG-----------------UCAGCCAAAUUC-----ACAGAGCAG-AAAC--CAAAAGCAA------CA
..((((((.......)))).((.(((((..((((((((((....))))-----------------)).))))...))-----)))..))..-....--.....))..------.. ( -31.80)
>DroAna_CAF1 238900 99 + 1
AGGCGCGUCACUCAUACGCAGCGUGUGACACGCCGACGCCCGCGGCUGAAUUUUUUUUUUUUUGGCCAGCAACAAUC-----AGUUGGCUAAAAACGACAACAU-----------
.((((.(((((.(.........).))))).))))...(((...)))............((((((((((((.......-----.)))))))))))).........----------- ( -32.90)
>DroPer_CAF1 241113 90 + 1
AGGCGCGUCACUCAUACGCAGCGUGUGACAAGCCGACGCCCGCGGCCG--------------UGGCC-GCAACAGGCCUGCCGCCCGGCAA-CAACAGCAAUAACA---------
.(((..(((((.(.........).)))))..)))...(((.(((((..--------------.((((-......)))).)))))..)))..-..............--------- ( -35.80)
>consensus
AGGCGCGUCACUCAUACGCAGCGUGUGACAAGCCGACGCCCGCGGCUGG___________UUUGCCCAGCAACAAUC_____AGCCGGCAA_UAACAACAACAAUAA______CA
.((.(((((..(((((((...)))))))......)))))))...(((((.............((.....)).............))))).......................... (-16.94 = -17.89 +   0.95)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:17 2006