Locus 7098

Sequence ID	2L_DroMel_CAF1
Location	19,867,376 – 19,867,469
Length	93
Max. P	0.993323

overview

Window 5

Location	19,867,376 – 19,867,469
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	78.28
Mean single sequence MFE	-21.30
Consensus MFE	-18.11
Energy contribution	-19.16
Covariance contribution	1.05
Combinations/Pair	1.00
Mean z-score	-1.66
Structure conservation index	0.85
SVM decision value	1.15
SVM RNA-class probability	0.922731
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19867376 93 + 22407834
AGCCACCCACAUGAGCAACCGCCUCCGGUUACAUUGCAUGGCAUGGCCAUUUCCCAUCCAUCUGCAUCUGCAUCUGACUCUGAAUCCGAAUCC
.........((.(((((((((....)))))....(((((((.((((.......)))))))..))))...)).))))................. ( -17.00)
>DroSec_CAF1 44121 87 + 1
AGCCACCCACAUGUGCAACCGCCUCCGGUUGCAUGGUAUGGCAUGGCCAGUUCACAUCCAUCUGCAUCUGCAUC------UGAAUCCGAAUCC
.((((.(((..((((((((((....))))))))))...)))..))))..((((..((.((..(((....)))..------)).))..)))).. ( -26.00)
>DroSim_CAF1 53737 81 + 1
AGCCACCCACAUGUGCAACCGCCUCCGGCUGCAUGGCAUGGCAUGGCCAUUUCACAUCCAUCUG------CAUC------CGAAUCCGAAUCC
.((((.(((..((((((.(((....))).))))))...)))..)))).................------....------............. ( -18.00)
>DroEre_CAF1 51380 87 + 1
AGCCACCCACAUGUGCAACCGCCUCCGGUUGCA-----UGGCCUGGCCACUUUCCAUCCAUCUGCAUCUGCAUCUGCAUCUGACUCUGAG-UC
.((((.(((....((((((((....))))))))-----)))..)))).((((......((..((((........))))..)).....)))-). ( -23.40)
>DroYak_CAF1 49588 76 + 1
AGCCACCCACAUGUGCAACCGCCUCCGGUUGCA-----UGGCUUGGCCAUUUCCCAUCCAUCUGCAUCUGCAUCUGAGU------------UC
.((((.(((....((((((((....))))))))-----)))..))))...........((..(((....)))..))...------------.. ( -22.10)
>consensus
AGCCACCCACAUGUGCAACCGCCUCCGGUUGCAU_G_AUGGCAUGGCCAUUUCCCAUCCAUCUGCAUCUGCAUCUG__U_UGAAUCCGAAUCC
.((((.(((...(((((((((....)))))))))....)))..))))...............(((....)))..................... (-18.11 = -19.16 +   1.05)

alignment

secondary structure

dotplot

Window 6

Location	19,867,376 – 19,867,469
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	78.28
Mean single sequence MFE	-32.00
Consensus MFE	-22.91
Energy contribution	-23.96
Covariance contribution	1.05
Combinations/Pair	1.14
Mean z-score	-2.53
Structure conservation index	0.72
SVM decision value	2.39
SVM RNA-class probability	0.993323
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19867376 93 - 22407834
GGAUUCGGAUUCAGAGUCAGAUGCAGAUGCAGAUGGAUGGGAAAUGGCCAUGCCAUGCAAUGUAACCGGAGGCGGUUGCUCAUGUGGGUGGCU
.........(((....(((..(((....)))..)))....)))..((((((.(((((....(((((((....))))))).)))).).)))))) ( -31.40)
>DroSec_CAF1 44121 87 - 1
GGAUUCGGAUUCA------GAUGCAGAUGCAGAUGGAUGUGAACUGGCCAUGCCAUACCAUGCAACCGGAGGCGGUUGCACAUGUGGGUGGCU
((.((((.(((((------..(((....)))..))))).))))))((((((.(((((...((((((((....))))))))..))))))))))) ( -39.20)
>DroSim_CAF1 53737 81 - 1
GGAUUCGGAUUCG------GAUG------CAGAUGGAUGUGAAAUGGCCAUGCCAUGCCAUGCAGCCGGAGGCGGUUGCACAUGUGGGUGGCU
...((((.(((((------....------....))))).))))..((((((.(((((...((((((((....)))))))))))).).)))))) ( -32.60)
>DroEre_CAF1 51380 87 - 1
GA-CUCAGAGUCAGAUGCAGAUGCAGAUGCAGAUGGAUGGAAAGUGGCCAGGCCA-----UGCAACCGGAGGCGGUUGCACAUGUGGGUGGCU
((-(.....)))..((.((..(((....)))..)).))....(((.(((..((..-----((((((((....))))))))...)).))).))) ( -29.30)
>DroYak_CAF1 49588 76 - 1
GA------------ACUCAGAUGCAGAUGCAGAUGGAUGGGAAAUGGCCAAGCCA-----UGCAACCGGAGGCGGUUGCACAUGUGGGUGGCU
..------------.((((..(((....)))......))))....(((((..(((-----((((((((....))))))))....))).))))) ( -27.50)
>consensus
GGAUUCGGAUUCA_A__CAGAUGCAGAUGCAGAUGGAUGGGAAAUGGCCAUGCCAU_C_AUGCAACCGGAGGCGGUUGCACAUGUGGGUGGCU
.....................(((....)))..............((((((.(((((...((((((((....))))))))..))))))))))) (-22.91 = -23.96 +   1.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:29 2006