Locus 1892

Sequence ID	3R_DroMel_CAF1
Location	5,419,632 – 5,419,744
Length	112
Max. P	0.852204

overview

Window 3

Location	5,419,632 – 5,419,744
Length	112
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	84.32
Mean single sequence MFE	-31.77
Consensus MFE	-22.72
Energy contribution	-23.22
Covariance contribution	0.50
Combinations/Pair	1.13
Mean z-score	-3.33
Structure conservation index	0.72
SVM decision value	0.79
SVM RNA-class probability	0.852204
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5419632 112 + 27905053
CGUUGUUGCCUUAAUGGCAGCAAA----AGCAACAACAACAA---CAACAAGAUCGCUCUGCAAUUUUACGCCAAA-CUAAAAAGGCGAGCGAUCGAGCAGAAAUCGAAGCGAUCGAAAA
.(((((((((.....))).((...----.)))))))).....---......(((((((...(.(((((.((((...-.......)))).((......)).))))).).)))))))..... ( -32.40)
>DroPse_CAF1 6914 110 + 1
UGUUGUUGCCUUAAUGGUG-CACAUACAAGCAACAA---------CAACAAGAUCGGUCUGCAAUUUUACGCCAAAGCUAAAAAGUCGACCGAUCGAGCCGCAAUCGAAACGAUCAACAG
(((((((((....(((...-..)))....)))))))---------))....((((((((.((..(((((.((....))))))).)).))))))))........((((...))))...... ( -30.70)
>DroSim_CAF1 6589 116 + 1
CGUUGUUGCCUUAAUGGCAGCAAA----AGCAACAACAACAACAGCAACAAGAUCGCUCUGCAAUUUUACGCCAAAGCUAAAAAGGCGAGCGAUCGAGCAAAAAUCGAAGCGAUCGAAAG
.(((((((((.....))).((...----.)))))))).......((.....((((((((.((..(((((.((....)))))))..))))))))))..)).....((((.....))))... ( -35.70)
>DroEre_CAF1 6793 107 + 1
UGUUGUUGCCUUAAUGGCAGCAAU----AGCAACAACAAC---------AAGAUCGGUCUGCAAUUUUACGCCAAAACUAAAAAGGCGAGCGAUCGAGCAGAAAUCGAAGCGAUCGGAAA
((((((((((.....)))))))))----)...........---------....((((((..........((((...........)))).((..((((.......)))).))))))))... ( -32.20)
>DroYak_CAF1 7028 116 + 1
CGUUGUUGCCUUAAUGGCACCAAA----AGCAACAACAACAACAGCCACAAGAUCGCUCUGCAAUUUUACGCCAAAGCUAAAAAGGCGAGCGAUCGAGCAGAAAUCGAAGCGAUCGGAAA
.((((((((.((..((....))))----.)))))))).......((.....((((((((.((..(((((.((....)))))))..))))))))))..)).....((((.....))))... ( -33.80)
>DroPer_CAF1 7455 110 + 1
UGUUGUUGCCUUAAUGGUG-CACAUACAAGCAACAA---------CAACAAGAUCGCUCUGCAAUUUUACGCCAAAGCUAAAAAGUCGACCGAUCGAGCCGCAAUCGAAACGAUCAACAG
(((((((((....(((...-..)))....)))))))---------))....(((((.(((((..(((((.((....)))))))..((((....))))...)))...))..)))))..... ( -25.80)
>consensus
CGUUGUUGCCUUAAUGGCAGCAAA____AGCAACAACAAC_____CAACAAGAUCGCUCUGCAAUUUUACGCCAAAGCUAAAAAGGCGAGCGAUCGAGCAGAAAUCGAAGCGAUCGAAAA
.(((((((((.....))))..........))))).................((((((((.((..(((((.((....)))))))..)))))))))).........((((.....))))... (-22.72 = -23.22 +   0.50)

alignment

secondary structure

dotplot

Window 4

Location	5,419,632 – 5,419,744
Length	112
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	84.32
Mean single sequence MFE	-35.57
Consensus MFE	-25.79
Energy contribution	-26.68
Covariance contribution	0.89
Combinations/Pair	1.06
Mean z-score	-2.84
Structure conservation index	0.73
SVM decision value	0.55
SVM RNA-class probability	0.779529
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5419632 112 - 27905053
UUUUCGAUCGCUUCGAUUUCUGCUCGAUCGCUCGCCUUUUUAG-UUUGGCGUAAAAUUGCAGAGCGAUCUUGUUG---UUGUUGUUGUUGCU----UUUGCUGCCAUUAAGGCAACAACG
...((((.....)))).....((..(((((((((((.......-...)))(((....))).))))))))..))..---.....(((((((((----((..........))))))))))). ( -36.10)
>DroPse_CAF1 6914 110 - 1
CUGUUGAUCGUUUCGAUUGCGGCUCGAUCGGUCGACUUUUUAGCUUUGGCGUAAAAUUGCAGACCGAUCUUGUUG---------UUGUUGCUUGUAUGUG-CACCAUUAAGGCAACAACA
((((.(((((...)))))))))...((((((((..(.(((((((....)).)))))..)..))))))))....((---------(((((((((..(((..-...)))..))))))))))) ( -36.00)
>DroSim_CAF1 6589 116 - 1
CUUUCGAUCGCUUCGAUUUUUGCUCGAUCGCUCGCCUUUUUAGCUUUGGCGUAAAAUUGCAGAGCGAUCUUGUUGCUGUUGUUGUUGUUGCU----UUUGCUGCCAUUAAGGCAACAACG
...((((.....)))).....((..((((((((((..(((((((....)).)))))..)).))))))))..))..........(((((((((----((..........))))))))))). ( -37.30)
>DroEre_CAF1 6793 107 - 1
UUUCCGAUCGCUUCGAUUUCUGCUCGAUCGCUCGCCUUUUUAGUUUUGGCGUAAAAUUGCAGACCGAUCUU---------GUUGUUGUUGCU----AUUGCUGCCAUUAAGGCAACAACA
.....(((((........(((((.........((((...........)))).......))))).)))))..---------..((((((((((----..............)))))))))) ( -26.93)
>DroYak_CAF1 7028 116 - 1
UUUCCGAUCGCUUCGAUUUCUGCUCGAUCGCUCGCCUUUUUAGCUUUGGCGUAAAAUUGCAGAGCGAUCUUGUGGCUGUUGUUGUUGUUGCU----UUUGGUGCCAUUAAGGCAACAACG
.............((((..(..(..((((((((((..(((((((....)).)))))..)).))))))))..)..)..))))..(((((((((----((((....))..))))))))))). ( -41.40)
>DroPer_CAF1 7455 110 - 1
CUGUUGAUCGUUUCGAUUGCGGCUCGAUCGGUCGACUUUUUAGCUUUGGCGUAAAAUUGCAGAGCGAUCUUGUUG---------UUGUUGCUUGUAUGUG-CACCAUUAAGGCAACAACA
..((((((((..((((.......)))).))))))))......((((((.((......))))))))........((---------(((((((((..(((..-...)))..))))))))))) ( -35.70)
>consensus
CUUUCGAUCGCUUCGAUUUCUGCUCGAUCGCUCGCCUUUUUAGCUUUGGCGUAAAAUUGCAGAGCGAUCUUGUUG_____GUUGUUGUUGCU____UUUGCUGCCAUUAAGGCAACAACA
.....(((((...))))).......((((((((((..(((((((....)).)))))..)).))))))))..............(((((((((......((....))....))))))))). (-25.79 = -26.68 +   0.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:02 2006