Locus 6940

Sequence ID	3L_DroMel_CAF1
Location	18,704,948 – 18,705,042
Length	94
Max. P	0.634495

overview

Window 9

Location	18,704,948 – 18,705,042
Length	94
Sequences	4
Columns	112
Reading direction	forward
Mean pairwise identity	76.96
Mean single sequence MFE	-29.35
Consensus MFE	-14.91
Energy contribution	-17.41
Covariance contribution	2.50
Combinations/Pair	1.21
Mean z-score	-2.14
Structure conservation index	0.51
SVM decision value	0.21
SVM RNA-class probability	0.634495
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18704948 94 + 23771897
AAGCUUCGCUG-----------UGCCGCUUCAAUAAAGCGCUUGUAC-------GGAAAAAACAAAACUUUCCCACGAGCCAAGCAUUUUAGAGCAGGGAUUCCGUGCGAAA
..((((.((((-----------((((((((.....)))))...))))-------(((((.........)))))....))).))))........(((.((...)).))).... ( -25.00)
>DroSec_CAF1 34370 105 + 1
AAGCUUCGCACAGCUCUUCGCCAGCCGCUUCAAUAAAGCGCUUGGAC-------GGAAAAAACAAAACUUUCCCACGAGCCAAGCAUUUUAGAGCGGGGAUUCCGUGCGAAA
....(((((((.(.((((((((....((((.....))))((((((..-------(((((.........)))))......))))))......).)))))))..).))))))). ( -34.70)
>DroAna_CAF1 33336 111 + 1
AAGCCUUCUUGAGCUCUACGCCACCAAGUUCAAUAAUAUUGUUUAACAAGUCGGGCAAAAAACAAAACUUUCACACGAGCCAACAAUUUUUGAGCGGGUAAUCCC-CCGAAA
..((((..(((((((...........))))))).....(((.....)))...)))).............(((......(((((......))).))(((......)-))))). ( -18.30)
>DroSim_CAF1 35630 105 + 1
AAGCUUCGCACAGCUCUUCGCCAGCCGCUUCAAUAAAGCGCUUGGAC-------GGGAAAAACAAAACUUUCCCACGAGCCAAGCAUUUUAGAGCGGGGAUUCCGUGCGAAA
....(((((((.(.((((((((....((((.....))))((((((..-------((((((........)))))).....))))))......).)))))))..).))))))). ( -39.40)
>consensus
AAGCUUCGCACAGCUCUUCGCCAGCCGCUUCAAUAAAGCGCUUGGAC_______GGAAAAAACAAAACUUUCCCACGAGCCAAGCAUUUUAGAGCGGGGAUUCCGUGCGAAA
....(((((((.((((..........((((.....))))((((((.........(((((.........)))))......))))))......)))).((....))))))))). (-14.91 = -17.41 +   2.50)

alignment

secondary structure

dotplot

Window 0

Location	18,704,948 – 18,705,042
Length	94
Sequences	4
Columns	112
Reading direction	reverse
Mean pairwise identity	76.96
Mean single sequence MFE	-33.40
Consensus MFE	-20.10
Energy contribution	-20.91
Covariance contribution	0.81
Combinations/Pair	1.29
Mean z-score	-1.75
Structure conservation index	0.60
SVM decision value	0.11
SVM RNA-class probability	0.590188
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18704948 94 - 23771897
UUUCGCACGGAAUCCCUGCUCUAAAAUGCUUGGCUCGUGGGAAAGUUUUGUUUUUUCC-------GUACAAGCGCUUUAUUGAAGCGGCA-----------CAGCGAAGCUU
....(((.((....)))))........((((.(((.(((((((((.......))))))-------.......((((((...)))))).))-----------)))).)))).. ( -28.50)
>DroSec_CAF1 34370 105 - 1
UUUCGCACGGAAUCCCCGCUCUAAAAUGCUUGGCUCGUGGGAAAGUUUUGUUUUUUCC-------GUCCAAGCGCUUUAUUGAAGCGGCUGGCGAAGAGCUGUGCGAAGCUU
((((((((((..((((.(((.......((((((....((((((((......)))))))-------).))))))(((((...)))))))).)).))....))))))))))... ( -39.10)
>DroAna_CAF1 33336 111 - 1
UUUCGG-GGGAUUACCCGCUCAAAAAUUGUUGGCUCGUGUGAAAGUUUUGUUUUUUGCCCGACUUGUUAAACAAUAUUAUUGAACUUGGUGGCGUAGAGCUCAAGAAGGCUU
....((-(......)))((((((..((((((((((((.(..((((......))))..).)))...))).))))))....)))).((((..(((.....)))))))...)).. ( -24.00)
>DroSim_CAF1 35630 105 - 1
UUUCGCACGGAAUCCCCGCUCUAAAAUGCUUGGCUCGUGGGAAAGUUUUGUUUUUCCC-------GUCCAAGCGCUUUAUUGAAGCGGCUGGCGAAGAGCUGUGCGAAGCUU
((((((((((..((((.(((.......((((((....((((((((......)))))))-------).))))))(((((...)))))))).)).))....))))))))))... ( -42.00)
>consensus
UUUCGCACGGAAUCCCCGCUCUAAAAUGCUUGGCUCGUGGGAAAGUUUUGUUUUUUCC_______GUCCAAGCGCUUUAUUGAAGCGGCUGGCGAAGAGCUCAGCGAAGCUU
((((((((.......((((((((((.(((((((.....(((((((......))))))).........))))))).))))..).)))))..(((.....)))))))))))... (-20.10 = -20.91 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:43 2006