Locus 5560

Sequence ID	3R_DroMel_CAF1
Location	14,703,612 – 14,703,717
Length	105
Max. P	0.993390

overview

Window 3

Location	14,703,612 – 14,703,717
Length	105
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	75.07
Mean single sequence MFE	-22.97
Consensus MFE	-13.69
Energy contribution	-13.58
Covariance contribution	-0.11
Combinations/Pair	1.21
Mean z-score	-2.57
Structure conservation index	0.60
SVM decision value	2.32
SVM RNA-class probability	0.992332
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14703612 105 + 27905053
UGUGCACAAACAAAUGCCAAUCAAAUGCAUAAUGGCAUCGACGAACAAAACGAGACG----------AGACGAGACGCGCUCAACAUGACAUGUCGCUGAUGGCAGCACAUUAAU
(((((........((((.........))))..((.(((((.(((.((...((.(..(----------((.((.....)))))..).))...))))).))))).)))))))..... ( -23.90)
>DroPse_CAF1 113590 89 + 1
UGUGCACAAACAAAUGCCAAUCAAAUGCAUAAUAGCAUCGAAG---------CGACG----------CGUC-------AUGGAACAUGACAUGCCAUUGAUGGCAGCACAUUAAU
(((((.........(((((.((((..((((....((.(((...---------))).)----------)(((-------(((...))))))))))..))))))))))))))..... ( -27.50)
>DroWil_CAF1 138752 87 + 1
UGCGCACAAACAAAUGCCAAUCAAAUGCAUAACAGCAUCGACGAGAGCCAUGA----------------------------GAACAUGACACGUCGUUGACGGCAGCACAUUAAU
((((......)...((((.......(((......)))((((((((.(.((((.----------------------------...)))).).).))))))).)))))))....... ( -20.00)
>DroYak_CAF1 123326 108 + 1
UGUGCACAAACAAAUGCCAAUCAAAUGCAUAAUGGCAUCGACGAACAAAACGAUACGAAACGAAACAAGAC-------GCCCAACAUGACAUGCCGCUGAUGGCAGCACAUUAAU
(((((.........(((((.(((.((((((...(((((((..........)))).((...)).........-------)))....))).))).....)))))))))))))..... ( -19.00)
>DroAna_CAF1 123503 84 + 1
UGUGCGCAAACAAAUGCCAAUCAAAUGCAUAAUAGCACCGACG------------------------ACAU-------GCACAACAUGACAUGCCAUUGAUGGCAGCACAUUAAU
((((((....)...(((((.((((.(((......))).....(------------------------.(((-------(((.....)).)))).).))))))))))))))..... ( -19.90)
>DroPer_CAF1 116044 89 + 1
UGUGCACAAACAAAUGCCAAUCAAAUGCAUAAUAGCAUCGAAG---------CGACG----------CGUC-------AUGGAACAUGACAUGCCAUUGAUGGCAGCACAUUAAU
(((((.........(((((.((((..((((....((.(((...---------))).)----------)(((-------(((...))))))))))..))))))))))))))..... ( -27.50)
>consensus
UGUGCACAAACAAAUGCCAAUCAAAUGCAUAAUAGCAUCGACG_________AGACG__________AGAC_______GCGCAACAUGACAUGCCAUUGAUGGCAGCACAUUAAU
(((((...................((((......)))).....................................................(((((....))))))))))..... (-13.69 = -13.58 +  -0.11)

alignment

secondary structure

dotplot

Window 4

Location	14,703,612 – 14,703,717
Length	105
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	75.07
Mean single sequence MFE	-28.65
Consensus MFE	-17.71
Energy contribution	-16.93
Covariance contribution	-0.78
Combinations/Pair	1.22
Mean z-score	-2.62
Structure conservation index	0.62
SVM decision value	2.39
SVM RNA-class probability	0.993390
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14703612 105 - 27905053
AUUAAUGUGCUGCCAUCAGCGACAUGUCAUGUUGAGCGCGUCUCGUCU----------CGUCUCGUUUUGUUCGUCGAUGCCAUUAUGCAUUUGAUUGGCAUUUGUUUGUGCACA
.....((((((((((((((((((....((...((((.(((........----------)))))))...))...))))((((......)))))))).))))).........))))) ( -26.00)
>DroPse_CAF1 113590 89 - 1
AUUAAUGUGCUGCCAUCAAUGGCAUGUCAUGUUCCAU-------GACG----------CGUCG---------CUUCGAUGCUAUUAUGCAUUUGAUUGGCAUUUGUUUGUGCACA
.....((((((((((((((..((((((((((...)))-------)))(----------(((((---------...))))))....))))..)))).))))).........))))) ( -31.20)
>DroWil_CAF1 138752 87 - 1
AUUAAUGUGCUGCCGUCAACGACGUGUCAUGUUC----------------------------UCAUGGCUCUCGUCGAUGCUGUUAUGCAUUUGAUUGGCAUUUGUUUGUGCGCA
.....(((((((((((((((((((.((((((...----------------------------.))))))...)))))((((......)))))))).))))).........))))) ( -30.80)
>DroYak_CAF1 123326 108 - 1
AUUAAUGUGCUGCCAUCAGCGGCAUGUCAUGUUGGGC-------GUCUUGUUUCGUUUCGUAUCGUUUUGUUCGUCGAUGCCAUUAUGCAUUUGAUUGGCAUUUGUUUGUGCACA
.....((((((((((((((..(((((..(((..((((-------(........))))).((((((..........))))))))))))))..)))).))))).........))))) ( -26.30)
>DroAna_CAF1 123503 84 - 1
AUUAAUGUGCUGCCAUCAAUGGCAUGUCAUGUUGUGC-------AUGU------------------------CGUCGGUGCUAUUAUGCAUUUGAUUGGCAUUUGUUUGCGCACA
.....((((((((((((((((((((((........))-------))))------------------------))).(((((......)))))))).)))))...(....)))))) ( -26.40)
>DroPer_CAF1 116044 89 - 1
AUUAAUGUGCUGCCAUCAAUGGCAUGUCAUGUUCCAU-------GACG----------CGUCG---------CUUCGAUGCUAUUAUGCAUUUGAUUGGCAUUUGUUUGUGCACA
.....((((((((((((((..((((((((((...)))-------)))(----------(((((---------...))))))....))))..)))).))))).........))))) ( -31.20)
>consensus
AUUAAUGUGCUGCCAUCAACGGCAUGUCAUGUUCCGC_______GUCU__________CGUCU_________CGUCGAUGCUAUUAUGCAUUUGAUUGGCAUUUGUUUGUGCACA
.....(((((((((((((..(((((...)))))...........................................(((((......)))))))).))))).........))))) (-17.71 = -16.93 +  -0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:06 2006