Locus 7282

Sequence ID	X_DroMel_CAF1
Location	18,123,948 – 18,124,119
Length	171
Max. P	0.987845

overview

Window 1

Location	18,123,948 – 18,124,045
Length	97
Sequences	4
Columns	97
Reading direction	forward
Mean pairwise identity	85.55
Mean single sequence MFE	-31.55
Consensus MFE	-26.22
Energy contribution	-26.04
Covariance contribution	-0.19
Combinations/Pair	1.04
Mean z-score	-2.67
Structure conservation index	0.83
SVM decision value	2.10
SVM RNA-class probability	0.987845
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18123948 97 + 22224390
GGAUCGACGGCGAUCGGUGAUCGAAGAUCGAAGAUCGAAGAUCGGAGAUGGCAGAUCGGAGAUCUUCGGAGUUCGAGAUCCGUGCUACACAUUAGCA
(((((..(..(((((...)))))..).(((((..(((((((((...(((.....)))...)))))))))..)))))))))).(((((.....))))) ( -36.70)
>DroSec_CAF1 6503 76 + 1
GGAUCGGCGGCGAUCGGUGAUCGAAGAUCG---------------------CAGAUCGGAGAUCUUCGGAGUUCGAGAUCCGUGCUACACAUUAGCA
(((((.....(((((.((((((...)))))---------------------).)))))(((.((....)).)))..))))).(((((.....))))) ( -29.50)
>DroSim_CAF1 7160 76 + 1
GGAUCGGCGGCGAUCGGUGAUCGAAGAUCG---------------------CAGAUCGGAGAUCUUCGGAGUUCGAGAUCCGUGCUACACAUUAGCA
(((((.....(((((.((((((...)))))---------------------).)))))(((.((....)).)))..))))).(((((.....))))) ( -29.50)
>DroEre_CAF1 6326 76 + 1
GGAUCGGCGGCGAUCGGUGAUCGCAGAUCG---------------------GAGAUCGGAGAUCUUCGGAGCUCGAGAUCCGUGCUACACAUUAGCA
((((((((.((((((...))))))...(((---------------------((((((...))))))))).)))...))))).(((((.....))))) ( -30.50)
>consensus
GGAUCGGCGGCGAUCGGUGAUCGAAGAUCG_____________________CAGAUCGGAGAUCUUCGGAGUUCGAGAUCCGUGCUACACAUUAGCA
(((((..((((..((((.((((...((((........................))))...)))).)))).)).)).))))).(((((.....))))) (-26.22 = -26.04 +  -0.19)

alignment

secondary structure

dotplot

Window 2

Location	18,123,948 – 18,124,045
Length	97
Sequences	4
Columns	97
Reading direction	reverse
Mean pairwise identity	85.55
Mean single sequence MFE	-23.40
Consensus MFE	-18.33
Energy contribution	-18.58
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.66
Structure conservation index	0.78
SVM decision value	0.37
SVM RNA-class probability	0.710558
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18123948 97 - 22224390
UGCUAAUGUGUAGCACGGAUCUCGAACUCCGAAGAUCUCCGAUCUGCCAUCUCCGAUCUUCGAUCUUCGAUCUUCGAUCACCGAUCGCCGUCGAUCC
(((((.....))))).((...(((((...((((((((...((((..........))))...))))))))...)))))...))(((((....))))). ( -28.40)
>DroSec_CAF1 6503 76 - 1
UGCUAAUGUGUAGCACGGAUCUCGAACUCCGAAGAUCUCCGAUCUG---------------------CGAUCUUCGAUCACCGAUCGCCGCCGAUCC
(((((.....))))).((((((((.....)).))))))..((((.(---------------------((.....(((((...))))).))).)))). ( -21.50)
>DroSim_CAF1 7160 76 - 1
UGCUAAUGUGUAGCACGGAUCUCGAACUCCGAAGAUCUCCGAUCUG---------------------CGAUCUUCGAUCACCGAUCGCCGCCGAUCC
(((((.....))))).((((((((.....)).))))))..((((.(---------------------((.....(((((...))))).))).)))). ( -21.50)
>DroEre_CAF1 6326 76 - 1
UGCUAAUGUGUAGCACGGAUCUCGAGCUCCGAAGAUCUCCGAUCUC---------------------CGAUCUGCGAUCACCGAUCGCCGCCGAUCC
(((((.....))))).(((..(((.((..((.(((((...))))).---------------------))....((((((...)))))).)))))))) ( -22.20)
>consensus
UGCUAAUGUGUAGCACGGAUCUCGAACUCCGAAGAUCUCCGAUCUG_____________________CGAUCUUCGAUCACCGAUCGCCGCCGAUCC
(((((.....))))).(((((.((......(((((((...............................)))))))((((...))))..))..))))) (-18.33 = -18.58 +   0.25)

alignment

secondary structure

dotplot

Window 3

Location	18,124,005 – 18,124,119
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.62
Mean single sequence MFE	-32.91
Consensus MFE	-27.97
Energy contribution	-27.97
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.85
SVM decision value	0.40
SVM RNA-class probability	0.719437
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18124005 114 + 22224390
GGAGAUCUUCGGAGUUCGAGAUCCGUGCUACACAUUAGCAAUUACGCUCAUUACACUUAAUUACAGAAAACUAGGAGUGCAUGAAGAUUUCCACUUGCGGACGGACGACUCC------GA
(((((((((((......(((.....(((((.....)))))......)))....(((((................)))))..))))))))))).....((((.(.....))))------). ( -30.69)
>DroSec_CAF1 6539 114 + 1
GGAGAUCUUCGGAGUUCGAGAUCCGUGCUACACAUUAGCAAUUACGCUCAUUACACUUAAUUACAGAAAACUAGGAGUGCAUGAAGAUUUCCACUUGCGGACGGACGACUCC------GA
(((((((((((......(((.....(((((.....)))))......)))....(((((................)))))..))))))))))).....((((.(.....))))------). ( -30.69)
>DroSim_CAF1 7196 114 + 1
GGAGAUCUUCGGAGUUCGAGAUCCGUGCUACACAUUAGCAAUUACGCUCAUUACACUUAAUUACAGAAAACUAGGAGUGCAUGAAGAUUUCCACUUGCGGACGGACGACUCC------GA
(((((((((((......(((.....(((((.....)))))......)))....(((((................)))))..))))))))))).....((((.(.....))))------). ( -30.69)
>DroEre_CAF1 6362 120 + 1
GGAGAUCUUCGGAGCUCGAGAUCCGUGCUACACAUUAGCAAUUACGCUCAUUACACUUAAUUACAGAAAACUAGGAGUGCAUGAAGAUUUCCACUUGCGGACGGACGACUCCGACUCCGA
(((((((((((..(((((((.....(((((.....)))))......)))...............((....))..))))...))))))))))).....((((((((....))))..)))). ( -37.50)
>DroYak_CAF1 6904 120 + 1
GGAGAUCUUCGGAGUUCGAGAUCCGUGCUACACAUUAGCAAUUACGCUCAUUACACUUAAUUACAGAAAACUAGGAGUGCAUGAAGAUUUCCACUUGCGGACGGACGACUCCGACUCCGA
(((((((((((......(((.....(((((.....)))))......)))....(((((................)))))..))))))))))).....((((((((....))))..)))). ( -34.99)
>consensus
GGAGAUCUUCGGAGUUCGAGAUCCGUGCUACACAUUAGCAAUUACGCUCAUUACACUUAAUUACAGAAAACUAGGAGUGCAUGAAGAUUUCCACUUGCGGACGGACGACUCC______GA
(((((((((((......(((.....(((((.....)))))......)))....(((((................)))))..)))))))))))......(((.(.....))))........ (-27.97 = -27.97 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:35:06 2006