Locus 8742

Sequence ID	3R_DroMel_CAF1
Location	23,329,564 – 23,329,723
Length	159
Max. P	0.761228

overview

Window 5

Location	23,329,564 – 23,329,683
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.23
Mean single sequence MFE	-30.14
Consensus MFE	-24.60
Energy contribution	-24.48
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-1.75
Structure conservation index	0.82
SVM decision value	0.50
SVM RNA-class probability	0.761228
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23329564 119 - 27905053
AGGUAAUCCACAUGCUGCACUCAGUUAAUUAGAUGGCAUAGGAAGUGCACAUAAAUAAACA-AUUAGGUGGCAGCAGAUAACCGACGCGUAUACAUGCAAUUGCUGCAUAUUAAUUGAAG
.(((.(((....((((((((..((((..(((.(((((((.....)))).)))...)))..)-)))..)).))))))))).)))...........(((((.....)))))........... ( -28.40)
>DroSec_CAF1 126844 119 - 1
AGGUAAUCCACAUGCUGCACUCAGUUAAUUAGAUGGCGUAGGAAGUGCACAUAAAUAAACA-AUUAGGUGGCAGCAGAUAACCCAAGCGUGUACAUGCAAUUGCUGCAUAUUAAUUGAAG
.((....))..(((.(((((((.((((......))))....).))))))))).......((-(((((...(((((((......)..((((....))))...))))))...)))))))... ( -30.20)
>DroSim_CAF1 131197 119 - 1
AGGUAAUCCACAUGCUGCACUCAGUUAAUUAGAUGGCAUAGGAAGUGCACAUAAAUAAACA-AUUAGGUGGCAGCAGAUAACCCAAGCGUGUACAUGCAAUUGCUGCAUAUUAAUUGAAG
.((....))..(((.(((((((.((((......))))....).))))))))).......((-(((((...(((((((......)..((((....))))...))))))...)))))))... ( -29.10)
>DroEre_CAF1 133212 119 - 1
AGGUAAUCCACAUGCUGCACUCAGUUAAUUAGAUGGCAUAGGAAGUGCACAUAAAUAAACA-AUUGGGUGGCAGCAGAUAGCCCAGUCGUGUACAUGCAAUUGCUGCAUAUUAAUUGAAG
.(((.(((....((((((((((((((..(((.(((((((.....)))).)))...)))..)-))))))).))))))))).)))((((..(((....)))...)))).............. ( -33.00)
>DroYak_CAF1 138810 120 - 1
AGGUAAUCCACAUGCUGCACUCAGUUAAUUAGACGGCAUAGGAAGUGCACAUAAAUAAACAAAUUGGGUGGCAGCAGAUAACCCAGCCGUGUACAUGCAAUUGCUGCAUAUUAAUUGAAG
.(((.(((....((((((((((((((..(((....((((.....)))).......)))...)))))))).))))))))).)))((((..(((....)))...)))).............. ( -30.00)
>consensus
AGGUAAUCCACAUGCUGCACUCAGUUAAUUAGAUGGCAUAGGAAGUGCACAUAAAUAAACA_AUUAGGUGGCAGCAGAUAACCCAAGCGUGUACAUGCAAUUGCUGCAUAUUAAUUGAAG
.(((.(((....(((((((((.(((...(((.(((((((.....)))).)))...)))....))).))).))))))))).)))...........(((((.....)))))........... (-24.60 = -24.48 +  -0.12)

alignment

secondary structure

dotplot

Window 6

Location	23,329,604 – 23,329,723
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.99
Mean single sequence MFE	-27.56
Consensus MFE	-23.20
Energy contribution	-23.24
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.58
Structure conservation index	0.84
SVM decision value	0.10
SVM RNA-class probability	0.582414
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23329604 119 - 27905053
GAUCAAUUGAAACUGGCGAUAAACAACGGGUGGAAAUGACAGGUAAUCCACAUGCUGCACUCAGUUAAUUAGAUGGCAUAGGAAGUGCACAUAAAUAAACA-AUUAGGUGGCAGCAGAUA
.(((........(((...........)))(((((............))))).((((((((..((((..(((.(((((((.....)))).)))...)))..)-)))..)).))))))))). ( -27.20)
>DroSec_CAF1 126884 119 - 1
GAUCAAUUGAAACUGGCGAUAAACAACGGGUGGAAAUGACAGGUAAUCCACAUGCUGCACUCAGUUAAUUAGAUGGCGUAGGAAGUGCACAUAAAUAAACA-AUUAGGUGGCAGCAGAUA
.(((........(((...........)))(((((............))))).((((((((..((((..(((.((((((.......))).)))...)))..)-)))..)).))))))))). ( -24.70)
>DroSim_CAF1 131237 119 - 1
GAUCAAUUGAAACUGGCGAUAAACAACGGGUGGAAAUGACAGGUAAUCCACAUGCUGCACUCAGUUAAUUAGAUGGCAUAGGAAGUGCACAUAAAUAAACA-AUUAGGUGGCAGCAGAUA
.(((........(((...........)))(((((............))))).((((((((..((((..(((.(((((((.....)))).)))...)))..)-)))..)).))))))))). ( -27.20)
>DroEre_CAF1 133252 119 - 1
GAUCAAUUGAAACAGGCGAUAAACAACGGGUGGAAAUGACAGGUAAUCCACAUGCUGCACUCAGUUAAUUAGAUGGCAUAGGAAGUGCACAUAAAUAAACA-AUUGGGUGGCAGCAGAUA
.(((.........................(((((............))))).((((((((((((((..(((.(((((((.....)))).)))...)))..)-))))))).))))))))). ( -31.50)
>DroYak_CAF1 138850 120 - 1
GAUCAAUUGAAACAGGCGAUAAACAACGGGUGGAAAUGACAGGUAAUCCACAUGCUGCACUCAGUUAAUUAGACGGCAUAGGAAGUGCACAUAAAUAAACAAAUUGGGUGGCAGCAGAUA
.(((.........................(((((............))))).((((((((((((((..(((....((((.....)))).......)))...)))))))).))))))))). ( -27.20)
>consensus
GAUCAAUUGAAACUGGCGAUAAACAACGGGUGGAAAUGACAGGUAAUCCACAUGCUGCACUCAGUUAAUUAGAUGGCAUAGGAAGUGCACAUAAAUAAACA_AUUAGGUGGCAGCAGAUA
.(((.........................(((((............))))).(((((((((.(((...(((.(((((((.....)))).)))...)))....))).))).))))))))). (-23.20 = -23.24 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:18:42 2006