Locus 4189

Sequence ID	2L_DroMel_CAF1
Location	12,004,042 – 12,004,155
Length	113
Max. P	0.990517

overview

Window 2

Location	12,004,042 – 12,004,155
Length	113
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	86.30
Mean single sequence MFE	-35.44
Consensus MFE	-30.14
Energy contribution	-32.64
Covariance contribution	2.50
Combinations/Pair	1.06
Mean z-score	-2.40
Structure conservation index	0.85
SVM decision value	2.22
SVM RNA-class probability	0.990517
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12004042 113 + 22407834
AUUGACUGGUUCGGCGAGCGGCUAACAGAGGGCGCCACCUUGAUGGUGAGGGGUUCCAUACAUAUGAAUAUGUAUGUAAAAACCCAGGGCGAAAAAGUCAUGAAAACCCAUUG
..(((((..((((.(..(((.((......)).)))((((.....))))..(((((.((((((((....))))))))....)))))..).))))..)))))............. ( -37.90)
>DroSec_CAF1 4810 105 + 1
AUUGACUGGUUCGCCGAGCGGCUAACAGAGGGCGCCACCUUGCCGGUGAGGGGUUCCAUACAUA--------UAUGUAAAAACCCAGGGCGAAAAAGUCAUGAAAACCCAUUG
..(((((..((((((..(((.((......)).)))((((.....))))..(((((...((((..--------..))))..)))))..))))))..)))))............. ( -36.60)
>DroSim_CAF1 4010 105 + 1
AUUGACUGGUUCGCCGAGCGGCUAACAGAGGGCGCCACCUUGCCGGUGAGGGGUUCCAUACAUA--------UAUGUAAAAACCCAGGGCGAAAAAGUCAUGAAAACCCAUUG
..(((((..((((((..(((.((......)).)))((((.....))))..(((((...((((..--------..))))..)))))..))))))..)))))............. ( -36.60)
>DroEre_CAF1 4002 96 + 1
AUUGACUGGUUCGCCGAGCGGCCAACAGAGGGCGCCACCUACCUGGUGAGGGGUUC-----------------AUAUAAAAACCCAGGGCGAAAAUGUCAUGAAAACCCAUUG
..((((...((((((..(((.((......)).)))((((.....))))..(((((.-----------------.......)))))..))))))...))))............. ( -34.90)
>DroYak_CAF1 4133 96 + 1
AUAGACUGGUUCGCCGAGCGGCCAACAGAGGGCGCCACCGUCGUGGUGAGGGGUUC-----------------AUAUAAAAACCUAGGGCGAAAAUGUCAUGAAAACCCAGUG
...(((...((((((..(((.((......)).)))((((.....))))..(((((.-----------------.......)))))..))))))...))).............. ( -31.20)
>consensus
AUUGACUGGUUCGCCGAGCGGCUAACAGAGGGCGCCACCUUGCUGGUGAGGGGUUCCAUACAUA________UAUGUAAAAACCCAGGGCGAAAAAGUCAUGAAAACCCAUUG
...((((..((((((..(((.((......)).)))((((.....))))..(((((...(((((((......)))))))..)))))..))))))..)))).............. (-30.14 = -32.64 +   2.50)

alignment

secondary structure

dotplot

Window 3

Location	12,004,042 – 12,004,155
Length	113
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	86.30
Mean single sequence MFE	-32.18
Consensus MFE	-24.04
Energy contribution	-27.54
Covariance contribution	3.50
Combinations/Pair	1.00
Mean z-score	-1.90
Structure conservation index	0.75
SVM decision value	0.56
SVM RNA-class probability	0.782193
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12004042 113 - 22407834
CAAUGGGUUUUCAUGACUUUUUCGCCCUGGGUUUUUACAUACAUAUUCAUAUGUAUGGAACCCCUCACCAUCAAGGUGGCGCCCUCUGUUAGCCGCUCGCCGAACCAGUCAAU
.............(((((..(((.....((((((...((((((((....))))))))))))))...........(((((((.(........).))).)))))))..))))).. ( -31.00)
>DroSec_CAF1 4810 105 - 1
CAAUGGGUUUUCAUGACUUUUUCGCCCUGGGUUUUUACAUA--------UAUGUAUGGAACCCCUCACCGGCAAGGUGGCGCCCUCUGUUAGCCGCUCGGCGAACCAGUCAAU
.............(((((..((((((..(((((((((((..--------..)))).)))))))...........((((((...........)))))).))))))..))))).. ( -33.40)
>DroSim_CAF1 4010 105 - 1
CAAUGGGUUUUCAUGACUUUUUCGCCCUGGGUUUUUACAUA--------UAUGUAUGGAACCCCUCACCGGCAAGGUGGCGCCCUCUGUUAGCCGCUCGGCGAACCAGUCAAU
.............(((((..((((((..(((((((((((..--------..)))).)))))))...........((((((...........)))))).))))))..))))).. ( -33.40)
>DroEre_CAF1 4002 96 - 1
CAAUGGGUUUUCAUGACAUUUUCGCCCUGGGUUUUUAUAU-----------------GAACCCCUCACCAGGUAGGUGGCGCCCUCUGUUGGCCGCUCGGCGAACCAGUCAAU
.............((((...((((((..((((((......-----------------))))))..((((.....))))(((.((......)).)))..))))))...)))).. ( -31.70)
>DroYak_CAF1 4133 96 - 1
CACUGGGUUUUCAUGACAUUUUCGCCCUAGGUUUUUAUAU-----------------GAACCCCUCACCACGACGGUGGCGCCCUCUGUUGGCCGCUCGGCGAACCAGUCUAU
.((((((((.....)))...((((((...(((((......-----------------)))))...((((.....))))(((.((......)).)))..))))))))))).... ( -31.40)
>consensus
CAAUGGGUUUUCAUGACUUUUUCGCCCUGGGUUUUUACAUA________UAUGUAUGGAACCCCUCACCAGCAAGGUGGCGCCCUCUGUUAGCCGCUCGGCGAACCAGUCAAU
.............(((((..((((((..(((((((((((((........)))))).)))))))...........((((((...........)))))).))))))..))))).. (-24.04 = -27.54 +   3.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:00 2006