Locus 3670

Sequence ID	3R_DroMel_CAF1
Location	9,946,733 – 9,946,844
Length	111
Max. P	0.907466

overview

Window 2

Location	9,946,733 – 9,946,844
Length	111
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	78.64
Mean single sequence MFE	-43.00
Consensus MFE	-17.77
Energy contribution	-18.33
Covariance contribution	0.56
Combinations/Pair	1.46
Mean z-score	-2.38
Structure conservation index	0.41
SVM decision value	0.14
SVM RNA-class probability	0.605207
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9946733 111 + 27905053
UGGUGGUGGUAGUCAUCGUUGAAGAAGCCGUCGACAUU---CGCUUUGGAUGCCCAAUAGGAUAGUUGGGAGCGUAGUGCGAUGGCACCUGUGGUGGAUUGACCACAGGCGGAG
(..(((((.....)))))..).....(((((((.((((---((((((.(((.((.....))...))).)))))).))))))))))).((((((((......))))))))..... ( -45.80)
>DroVir_CAF1 42019 105 + 1
UGGUAGUGGUUGU------GGACGAGGCCGUGGACAUG---CGCUUGGGAUGUCCGAUUGGAUAGUUGGGCGCAUAAUGCGAAGGUACCUGCGGUGGAUUGACCACAGGCGGCG
.....((.(((((------((.(((.((((..(..(((---((((..(..(((((....))))).)..)))))))..(((....))).)..))))...))).))))).)).)). ( -44.20)
>DroGri_CAF1 35116 108 + 1
UGGUAUUGGUGGU---GGUGGACGAGGCCGUCGACAUA---CGCUUGGGAUGCCCAAUGGGAUAGUUGGGCGCAUAGUGCGACGGCACCUGGGGCGGAUUAACCACCGGUGGUG
.(.((((((((((---.((.((((....)))).))...---(((((.((..(((((((......))))))).....((((....)))))).))))).....)))))))))).). ( -47.60)
>DroWil_CAF1 31957 108 + 1
UUGUGGUGGUGGU------AGACGAAGCCGUCGACAUGGGACGUUUGGGAUGUCCCAUGGGAUAAUUUGGAGCAUAAUGCGAAGGCACCUGAGGCGGAUUGACCACCGGUGGCG
....(.(((((((------.((((....))))..(((((((((((...)))))))))))...(((((((...((...(((....)))..))...)))))))))))))).).... ( -40.20)
>DroMoj_CAF1 38175 108 + 1
UGGUGGUGGUUGU---GGUGGACGAGGCCGUUGACAUG---CGCUUGGGAUGUCCAAUUGGAUAGUUGGGAGCAUAGUGUGAGGGCACUUGCGGUGGAUUUACCACUGGAGGCG
.((((((((...(---..(.(.(((((((.((((((((---(.((..(..(((((....))))).)..)).)))).)).))).))).))))).)..)..))))))))....... ( -36.50)
>DroAna_CAF1 35440 108 + 1
UUCCGGCCACUGUGCC---CGACGAAGCUGUGGACAUA---CGCUUGGGAUGCCCAAUUGGAUAGUUUGGUGCAUAAUGCGAGGGCACCUGCGGUGGAUUGACCACCGGCGGAG
.((((.((...(((((---(..(.((((.(((....))---))))).).((((((((.........)))).)))).......))))))....(((((.....))))))))))). ( -43.70)
>consensus
UGGUGGUGGUUGU______GGACGAAGCCGUCGACAUG___CGCUUGGGAUGCCCAAUUGGAUAGUUGGGAGCAUAAUGCGAAGGCACCUGCGGUGGAUUGACCACCGGCGGCG
..........................((((((..............((((((((((((......)))))..))))..(((....))))))..(((((.....))))))))))). (-17.77 = -18.33 +   0.56)

alignment

secondary structure

dotplot

Window 3

Location	9,946,733 – 9,946,844
Length	111
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	78.64
Mean single sequence MFE	-31.85
Consensus MFE	-12.82
Energy contribution	-13.27
Covariance contribution	0.44
Combinations/Pair	1.22
Mean z-score	-2.92
Structure conservation index	0.40
SVM decision value	1.05
SVM RNA-class probability	0.907466
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9946733 111 - 27905053
CUCCGCCUGUGGUCAAUCCACCACAGGUGCCAUCGCACUACGCUCCCAACUAUCCUAUUGGGCAUCCAAAGCG---AAUGUCGACGGCUUCUUCAACGAUGACUACCACCACCA
....(((((((((......)))))))))(((.(((.((..(((((((((........))))).......))))---...))))).))).......................... ( -32.71)
>DroVir_CAF1 42019 105 - 1
CGCCGCCUGUGGUCAAUCCACCGCAGGUACCUUCGCAUUAUGCGCCCAACUAUCCAAUCGGACAUCCCAAGCG---CAUGUCCACGGCCUCGUCC------ACAACCACUACCA
.((((((((((((......)))))))))..........(((((((.......(((....)))........)))---)))).....))).......------............. ( -30.96)
>DroGri_CAF1 35116 108 - 1
CACCACCGGUGGUUAAUCCGCCCCAGGUGCCGUCGCACUAUGCGCCCAACUAUCCCAUUGGGCAUCCCAAGCG---UAUGUCGACGGCCUCGUCCACC---ACCACCAAUACCA
.......((((((....((......)).(((((((.(((((((((((((........)))))).......)))---)).))))))))).......)))---))).......... ( -37.61)
>DroWil_CAF1 31957 108 - 1
CGCCACCGGUGGUCAAUCCGCCUCAGGUGCCUUCGCAUUAUGCUCCAAAUUAUCCCAUGGGACAUCCCAAACGUCCCAUGUCGACGGCUUCGUCU------ACCACCACCACAA
.......((((((..((..(((((.(((((....)))))................((((((((.........))))))))..)).)))...))..------))))))....... ( -32.00)
>DroMoj_CAF1 38175 108 - 1
CGCCUCCAGUGGUAAAUCCACCGCAAGUGCCCUCACACUAUGCUCCCAACUAUCCAAUUGGACAUCCCAAGCG---CAUGUCAACGGCCUCGUCCACC---ACAACCACCACCA
........(((((.........(((((((......)))).)))................((((......((.(---(.((....)))))).)))))))---))........... ( -19.00)
>DroAna_CAF1 35440 108 - 1
CUCCGCCGGUGGUCAAUCCACCGCAGGUGCCCUCGCAUUAUGCACCAAACUAUCCAAUUGGGCAUCCCAAGCG---UAUGUCCACAGCUUCGUCG---GGCACAGUGGCCGGAA
.(((((((((((.....)))))....((((((..((.....))...............(((((((.(.....)---.)))))))..........)---)))))...)).)))). ( -38.80)
>consensus
CGCCGCCGGUGGUCAAUCCACCGCAGGUGCCCUCGCACUAUGCUCCCAACUAUCCAAUUGGACAUCCCAAGCG___CAUGUCGACGGCCUCGUCC______ACAACCACCACCA
....(((.(((((......))))).)))(((...((.....)).................(((((............)))))...))).......................... (-12.82 = -13.27 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:00 2006