Locus 213

Sequence ID	3R_DroMel_CAF1
Location	879,771 – 879,926
Length	155
Max. P	0.660067

overview

Window 9

Location	879,771 – 879,886
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.09
Mean single sequence MFE	-38.14
Consensus MFE	-29.79
Energy contribution	-29.85
Covariance contribution	0.06
Combinations/Pair	1.17
Mean z-score	-1.59
Structure conservation index	0.78
SVM decision value	0.27
SVM RNA-class probability	0.660067
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 879771 115 - 27905053
CUGGUCAAAGGAACCUGGAGGCGGCGUGCCCUUCGUGCGGAGCCAUUCGUUAAUGGCAGAUCCGCAGAUUGCAUGUUCCGAACCCAUAAUCCUCUUCACUUGGAAACAU-----AUGACG
...((((.((((...(((...((((((((...((.((((((((((((....))))))...))))))))..)))))..)))...)))...)))).......((....)).-----.)))). ( -40.10)
>DroSec_CAF1 47780 115 - 1
CUGGUCAAUGGGACCUGGAAGUGGCUUGCCCUUCGUGCGGAGCCAUUUGUUAAUGGCACAGCCGCAGAUUGCAUGUUCCGAACCCAUAAUCCUCUUCACUUGGAAACAU-----AUGACG
..((...(((((...((((....((.(((...((.(((((.((((((....))))))....)))))))..))).))))))..)))))...))...(((..((....)).-----.))).. ( -37.30)
>DroSim_CAF1 46980 115 - 1
CUGGUCAAUGGGACCUGCAAGUGGCUUGCCCUUCGUGCGGAGCCAUUCGCUAAUGGCACAGCCGCAGAUUGCAUGUUCCGAACCCAUAAUCCUCUUCACUUGGAAACAU-----AUGACG
..(((...((((((.(((((((((((((((......(((((....)))))....)))).))))))...))))).)))))).)))...........(((..((....)).-----.))).. ( -40.70)
>DroEre_CAF1 46884 116 - 1
CAGGUCAAUAGGACCUGGAAGUGG----ACCUUCGUGUGGAGUUAUCCGUUAAUGGCAGAGCCGCAGAUUGCAUGUUCCGAACCCAUAAUCCUCUCUACUUGGAAACAUGUAGUAUGACG
((((((.....))))))...((((----..((((((.((((....))))...)))).))..))))..((((((((((((((..................)))).))))))))))...... ( -34.47)
>consensus
CUGGUCAAUGGGACCUGGAAGUGGCUUGCCCUUCGUGCGGAGCCAUUCGUUAAUGGCACAGCCGCAGAUUGCAUGUUCCGAACCCAUAAUCCUCUUCACUUGGAAACAU_____AUGACG
...((((..(((((.((((((.((....)))))).(((((.((((((....))))))....))))).....)).))))).....................((....)).......)))). (-29.79 = -29.85 +   0.06)

alignment

secondary structure

dotplot

Window 0

Location	879,806 – 879,926
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.29
Mean single sequence MFE	-34.65
Consensus MFE	-22.84
Energy contribution	-24.40
Covariance contribution	1.56
Combinations/Pair	1.14
Mean z-score	-1.57
Structure conservation index	0.66
SVM decision value	-0.00
SVM RNA-class probability	0.531852
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 879806 120 + 27905053
CGGAACAUGCAAUCUGCGGAUCUGCCAUUAACGAAUGGCUCCGCACGAAGGGCACGCCGCCUCCAGGUUCCUUUGACCAGGUCAUCCUUGCCUCGACCCUUUACCUUAAUCAUUUUAAUC
.(((((.((...((((((((...((((((....)))))))))))).)).((((.....)))).)).)))))........((((...........))))...................... ( -32.80)
>DroSec_CAF1 47815 118 + 1
CGGAACAUGCAAUCUGCGGCUGUGCCAUUAACAAAUGGCUCCGCACGAAGGGCAAGCCACUUCCAGGUCCCAUUGACCAGGUCAUCCUUGCCUCGACCCUUUACCUUAAUCAUUGCGA--
.......((((((.(((((....((((((....)))))).)))))(((..((((((......((.((((.....)))).)).....)))))))))................)))))).-- ( -37.00)
>DroSim_CAF1 47015 118 + 1
CGGAACAUGCAAUCUGCGGCUGUGCCAUUAGCGAAUGGCUCCGCACGAAGGGCAAGCCACUUGCAGGUCCCAUUGACCAGGUCAUCCUUGCCUCGACCCUUUACCUUAAUCAUUGCGA--
.......((((((.(((((....((((((....)))))).)))))..(((((((((...))))).((((.....)))).((((...........)))).....))))....)))))).-- ( -36.30)
>DroEre_CAF1 46924 112 + 1
CGGAACAUGCAAUCUGCGGCUCUGCCAUUAACGGAUAACUCCACACGAAGGU----CCACUUCCAGGUCCUAUUGACCUGGUCAUCUUUGGUGCGACCCU-UACCUGAGUCAGUU-GA--
...(((..((.....))(((((..........(((....))).......(((----(((((.(((((((.....)))))))........)))).))))..-.....))))).)))-..-- ( -32.50)
>consensus
CGGAACAUGCAAUCUGCGGCUCUGCCAUUAACGAAUGGCUCCGCACGAAGGGCAAGCCACUUCCAGGUCCCAUUGACCAGGUCAUCCUUGCCUCGACCCUUUACCUUAAUCAUUGCGA__
.((.........(((((((....((((((....)))))).))))).)).(((((((......((.((((.....)))).)).....)))))))..........))............... (-22.84 = -24.40 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:43 2006