Locus 3724

Sequence ID	X_DroMel_CAF1
Location	9,924,091 – 9,924,184
Length	93
Max. P	0.999665

overview

Window 4

Location	9,924,091 – 9,924,184
Length	93
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	77.24
Mean single sequence MFE	-39.34
Consensus MFE	-19.86
Energy contribution	-20.58
Covariance contribution	0.72
Combinations/Pair	1.11
Mean z-score	-3.12
Structure conservation index	0.50
SVM decision value	3.34
SVM RNA-class probability	0.999033
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9924091 93 + 22224390
UGAAGUGUGGUCCGAAAUUCGGACCCGGACCCGGUAACGGUCCAUUUGGUCUAAUGAACGGCCCGCCCGGACCUC------UAGGUCCAAAGUUGUGCC
......(.((((((.....)))))))(((((..(....(((((....((((........)))).....))))).)------..)))))........... ( -34.80)
>DroSec_CAF1 21273 78 + 1
UGAAGUGUGGUCCGAAAUUCGGACCCGGACCCG------GUCCAUUUGGUCUAAUAAACGGCC---------CUC------UAGGGCCAAAGUUGGGCC
......(.((((((.....)))))))((((...------))))....((((((((....((((---------(..------..)))))...)))))))) ( -34.20)
>DroSim_CAF1 21458 78 + 1
UGAAGUGUGGUCCGAAAUUCGGACCCGGACCCG------GUCCAUUUGGUCUAAUAAACGGCC---------CUC------UAGGGCCAAAGUUGGGCC
......(.((((((.....)))))))((((...------))))....((((((((....((((---------(..------..)))))...)))))))) ( -34.20)
>DroEre_CAF1 21703 93 + 1
UGAAGUUUGGUCCGAAAUUCGGACCUGGUCCCG------GCCCAUUUGGUCCAAAGAAUGGGCCCCCAGGACCGCCUGGGCCGUGGCCAAAGUUGGGCC
....((((((((((.....))))))(((((.((------(((((..((((((......(((....)))))))))..))))))).))))).....)))). ( -46.90)
>DroYak_CAF1 21501 93 + 1
UGAAGUUUGGUCCGAAAUGGGGACCUGGUCCCG------GUCCAUUUGGUCCAAAGAAUGGGCCACCCGGACCGCCUGGGCCAGGGCCAAAGUUGGGGC
.........((((.((....((.((((((((((------((((...(((((((.....)))))))...))))))...)))))))).))....)).)))) ( -46.60)
>consensus
UGAAGUGUGGUCCGAAAUUCGGACCCGGACCCG______GUCCAUUUGGUCUAAUGAACGGCCC_CC_GGACCUC______UAGGGCCAAAGUUGGGCC
........((((((.....))))))..............(((((((((((((...............................))))))))..))))). (-19.86 = -20.58 +   0.72)

alignment

secondary structure

dotplot

Window 5

Location	9,924,091 – 9,924,184
Length	93
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	77.24
Mean single sequence MFE	-38.82
Consensus MFE	-17.40
Energy contribution	-18.66
Covariance contribution	1.26
Combinations/Pair	1.06
Mean z-score	-3.53
Structure conservation index	0.45
SVM decision value	3.86
SVM RNA-class probability	0.999665
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9924091 93 - 22224390
GGCACAACUUUGGACCUA------GAGGUCCGGGCGGGCCGUUCAUUAGACCAAAUGGACCGUUACCGGGUCCGGGUCCGAAUUUCGGACCACACUUCA
........((((((((..------..))))))))(((((((((((((......)))))))((....))))))))((((((.....))))))........ ( -37.90)
>DroSec_CAF1 21273 78 - 1
GGCCCAACUUUGGCCCUA------GAG---------GGCCGUUUAUUAGACCAAAUGGAC------CGGGUCCGGGUCCGAAUUUCGGACCACACUUCA
(((((......(((((..------..)---------))))(((((((......)))))))------.)))))..((((((.....))))))........ ( -34.90)
>DroSim_CAF1 21458 78 - 1
GGCCCAACUUUGGCCCUA------GAG---------GGCCGUUUAUUAGACCAAAUGGAC------CGGGUCCGGGUCCGAAUUUCGGACCACACUUCA
(((((......(((((..------..)---------))))(((((((......)))))))------.)))))..((((((.....))))))........ ( -34.90)
>DroEre_CAF1 21703 93 - 1
GGCCCAACUUUGGCCACGGCCCAGGCGGUCCUGGGGGCCCAUUCUUUGGACCAAAUGGGC------CGGGACCAGGUCCGAAUUUCGGACCAAACUUCA
((((.......)))).(((((((...(((((..((((....))))..)))))...)))))------))......((((((.....))))))........ ( -46.20)
>DroYak_CAF1 21501 93 - 1
GCCCCAACUUUGGCCCUGGCCCAGGCGGUCCGGGUGGCCCAUUCUUUGGACCAAAUGGAC------CGGGACCAGGUCCCCAUUUCGGACCAAACUUCA
..(((..(((.(((....))).))).((((((..(((.(((.....))).)))..)))))------))))....(((((.......)))))........ ( -40.20)
>consensus
GGCCCAACUUUGGCCCUA______GAGGUCC_GG_GGGCCGUUCAUUAGACCAAAUGGAC______CGGGUCCGGGUCCGAAUUUCGGACCACACUUCA
..........((((((..........((.((....)).))..........((....)).........))).)))((((((.....))))))........ (-17.40 = -18.66 +   1.26)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:40 2006