Locus 3339

Sequence ID	3R_DroMel_CAF1
Location	8,990,512 – 8,990,603
Length	91
Max. P	0.950030

overview

Window 7

Location	8,990,512 – 8,990,603
Length	91
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	88.14
Mean single sequence MFE	-29.08
Consensus MFE	-23.38
Energy contribution	-25.18
Covariance contribution	1.80
Combinations/Pair	1.00
Mean z-score	-2.11
Structure conservation index	0.80
SVM decision value	1.40
SVM RNA-class probability	0.950030
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8990512 91 + 27905053
UCGCUUUGGAAGUUUUUCAGGUGUACUA------CUUGCGACUGCAUGCAAAUGCUCCGCAUGAGCAUUGUGCAACGGCAGUUGCAAUUCACACACA
.....(((((.....)))))((((....------.((((((((((.(((((((((((.....))))))).))))...)))))))))).....)))). ( -33.50)
>DroSec_CAF1 104583 97 + 1
UCGCUAUGGAAGUUUUUCAGGUGUAUUAGCAACCGUUGCGACUGCAUGCAAAUGCUCCGCAUGAGCAUUGUGCAACGGCAGUUGCAAUUCACACACA
......((((.....))))(((((....)).)))(((((((((((.(((((((((((.....))))))).))))...)))))))))))......... ( -33.10)
>DroSim_CAF1 107693 97 + 1
UCGCUAUGAAAGUUUUUCAGGUGUAUUAGCAACGGUUGCGACUGCAUGCAAAUGCACCGCAUGAGCAUUGUGCAACGGCAGUUGCAAUUCACACACA
......((((.((((....((((((((.(((.((((....))))..))).))))))))....))))....((((((....)))))).))))...... ( -29.80)
>DroEre_CAF1 109891 97 + 1
UCCCUAUGGUUAUUUUUCAGGUGUAUAAGCAACGUAAGCGACUGGAUGCAAAUGCUCCGCAUGAGCAUUGUGCAGCGGCAGUUGCAAUUCACACACA
....................((((....((...))..(((((((..(((((((((((.....))))))).))))....))))))).....))))... ( -25.10)
>DroYak_CAF1 111228 97 + 1
UCCUUAUGGUUAUUUUUCAGGUGUAUUAGCAACGUAAACGACUGCAUGCAAAUGCUCCGCAUGAGCUCUGUGCAACGGCAGUUGCAAUUCACACACA
.((....))...........(((.(((.(((.((....))(((((.((((...((((.....))))....))))...))))))))))).)))..... ( -23.90)
>consensus
UCGCUAUGGAAGUUUUUCAGGUGUAUUAGCAACGGUUGCGACUGCAUGCAAAUGCUCCGCAUGAGCAUUGUGCAACGGCAGUUGCAAUUCACACACA
....................((((...........((((((((((.(((((((((((.....))))))).))))...))))))))))...))))... (-23.38 = -25.18 +   1.80)

alignment

secondary structure

dotplot

Window 8

Location	8,990,512 – 8,990,603
Length	91
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	88.14
Mean single sequence MFE	-28.40
Consensus MFE	-23.08
Energy contribution	-24.00
Covariance contribution	0.92
Combinations/Pair	1.12
Mean z-score	-1.85
Structure conservation index	0.81
SVM decision value	0.96
SVM RNA-class probability	0.890074
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8990512 91 - 27905053
UGUGUGUGAAUUGCAACUGCCGUUGCACAAUGCUCAUGCGGAGCAUUUGCAUGCAGUCGCAAG------UAGUACACCUGAAAAACUUCCAAAGCGA
...(((((..((((.(((((...((((.(((((((.....))))))))))).))))).)))).------...))))).................... ( -31.00)
>DroSec_CAF1 104583 97 - 1
UGUGUGUGAAUUGCAACUGCCGUUGCACAAUGCUCAUGCGGAGCAUUUGCAUGCAGUCGCAACGGUUGCUAAUACACCUGAAAAACUUCCAUAGCGA
..((((.(((((((.(((((...((((.(((((((.....))))))))))).))))).))))(((.((......)).)))......))))))).... ( -30.40)
>DroSim_CAF1 107693 97 - 1
UGUGUGUGAAUUGCAACUGCCGUUGCACAAUGCUCAUGCGGUGCAUUUGCAUGCAGUCGCAACCGUUGCUAAUACACCUGAAAAACUUUCAUAGCGA
.(..(((((.(((((..(((...(((((...((....)).)))))...)))))))))))))..).((((((.......((((.....)))))))))) ( -26.61)
>DroEre_CAF1 109891 97 - 1
UGUGUGUGAAUUGCAACUGCCGCUGCACAAUGCUCAUGCGGAGCAUUUGCAUCCAGUCGCUUACGUUGCUUAUACACCUGAAAAAUAACCAUAGGGA
.((((((((...(((((.((.((((((.(((((((.....))))))))))....))).))....)))))))))))))...........((....)). ( -28.20)
>DroYak_CAF1 111228 97 - 1
UGUGUGUGAAUUGCAACUGCCGUUGCACAGAGCUCAUGCGGAGCAUUUGCAUGCAGUCGUUUACGUUGCUAAUACACCUGAAAAAUAACCAUAAGGA
.((((((.....(((((.((..(((((((((((((.....)))).))))..)))))..))....)))))..))))))...........((....)). ( -25.80)
>consensus
UGUGUGUGAAUUGCAACUGCCGUUGCACAAUGCUCAUGCGGAGCAUUUGCAUGCAGUCGCAAACGUUGCUAAUACACCUGAAAAACUUCCAUAGCGA
.((((((...((((.(((((...((((.(((((((.....))))))))))).))))).)))).........)))))).................... (-23.08 = -24.00 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:44 2006