Locus 3345

Sequence ID	3L_DroMel_CAF1
Location	9,816,259 – 9,816,406
Length	147
Max. P	0.690583

overview

Window 0

Location	9,816,259 – 9,816,366
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.43
Mean single sequence MFE	-39.62
Consensus MFE	-31.31
Energy contribution	-32.31
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.60
Structure conservation index	0.79
SVM decision value	0.33
SVM RNA-class probability	0.690583
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9816259 107 + 23771897
GCCCGGAGGUGUGUGGGCUUUGGCUGCCUAUUUAUAGAUGUGGCGUGGAUCGCACGUUUCCGGCACACCACUGCUCUCGUGUGCAUUAUUCGUUGCAACA-------------CAUGCAA
(((.(((..(((((((((....)))(((((((....)))).)))......))))))..)))))).......(((....(((((((........))).)))-------------)..))). ( -37.00)
>DroSec_CAF1 110342 104 + 1
GCCCGGAGGUGUGUGGGCUUUGGCUGCCUAUUUAUAGAUGUGGCGUGUAUCGCACGUUUCCGGCACAC---UACUCUCGUGUGCAUUAUUCGUUGCAACA-------------CAUGCAA
...((((..(((((((((....)))(((((((....)))).)))......))))))..))))((((((---.......))))))........(((((...-------------..))))) ( -36.70)
>DroSim_CAF1 113677 104 + 1
GCCCGGAGGUGUGUGGGCUUUGGCUGCCUAUUUAUAGAUGUGGCGUGGAUCGCACGUUUCCGGCACAC---UACUCUCGUGUGCAUUAUUCGUUGCAACA-------------CAUGCAA
...((((..(((((((((....)))(((((((....)))).)))......))))))..))))((((((---.......))))))........(((((...-------------..))))) ( -36.70)
>DroEre_CAF1 113219 115 + 1
GCCCGGAGGUGUGUGGGCUUCGGCUGCCUAUUUAUAGAUGUGGCGUGGAUCGCACGUUUCCGGCACAC---UAC--UCGUGUGCAUUAUUCGUUGCAACACGUUGGAGCGGCACAUGCAA
(((((((..(((((((((....)))(((((((....)))).)))......))))))..))))((((((---...--..)))))).......(((.(((....))).))))))........ ( -46.60)
>DroYak_CAF1 123278 115 + 1
GCCCGAAGGUGUGUGGGCUUUAGCUGCCUAUUUAUAGUUGUGGCGUGGAUCGCACGUUUCCGGCACAC---UAC--UCGUGUGCAUUAUUUGUUGCAACACGCUGGAGCAGCACAUGCAA
........(((((((.((((((((.(((.............)))(((....(((((......((((((---...--..))))))......)).)))..)))))))))))..))))))).. ( -41.12)
>consensus
GCCCGGAGGUGUGUGGGCUUUGGCUGCCUAUUUAUAGAUGUGGCGUGGAUCGCACGUUUCCGGCACAC___UACUCUCGUGUGCAUUAUUCGUUGCAACA_____________CAUGCAA
...((((..(((((((((....)))(((((((....)))).)))......))))))..))))((((((..........))))))........(((((..................))))) (-31.31 = -32.31 +   1.00)

alignment

secondary structure

dotplot

Window 1

Location	9,816,259 – 9,816,366
Length	107
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.43
Mean single sequence MFE	-33.27
Consensus MFE	-26.06
Energy contribution	-26.06
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.50
Structure conservation index	0.78
SVM decision value	0.10
SVM RNA-class probability	0.585076
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9816259 107 - 23771897
UUGCAUG-------------UGUUGCAACGAAUAAUGCACACGAGAGCAGUGGUGUGCCGGAAACGUGCGAUCCACGCCACAUCUAUAAAUAGGCAGCCAAAGCCCACACACCUCCGGGC
((((.((-------------(((.(((........))))))))(((...(((((((((((....)).)).....))))))).)))........)))).....((((..........)))) ( -32.50)
>DroSec_CAF1 110342 104 - 1
UUGCAUG-------------UGUUGCAACGAAUAAUGCACACGAGAGUA---GUGUGCCGGAAACGUGCGAUACACGCCACAUCUAUAAAUAGGCAGCCAAAGCCCACACACCUCCGGGC
..((.((-------------(((((((.........((((((.......---))))))((....))))))))))).(((.............))).))....((((..........)))) ( -33.42)
>DroSim_CAF1 113677 104 - 1
UUGCAUG-------------UGUUGCAACGAAUAAUGCACACGAGAGUA---GUGUGCCGGAAACGUGCGAUCCACGCCACAUCUAUAAAUAGGCAGCCAAAGCCCACACACCUCCGGGC
..((.((-------------..(((((.........((((((.......---))))))((....)))))))..)).(((.............))).))....((((..........)))) ( -29.32)
>DroEre_CAF1 113219 115 - 1
UUGCAUGUGCCGCUCCAACGUGUUGCAACGAAUAAUGCACACGA--GUA---GUGUGCCGGAAACGUGCGAUCCACGCCACAUCUAUAAAUAGGCAGCCGAAGCCCACACACCUCCGGGC
((((((((.(((......(((......)))......((((((..--...---)))))))))..)))))))).....(((.............))).......((((..........)))) ( -32.82)
>DroYak_CAF1 123278 115 - 1
UUGCAUGUGCUGCUCCAGCGUGUUGCAACAAAUAAUGCACACGA--GUA---GUGUGCCGGAAACGUGCGAUCCACGCCACAACUAUAAAUAGGCAGCUAAAGCCCACACACCUUCGGGC
........(((((....((((((((((.........((((((..--...---))))))((....)))))))..))))).....(((....))))))))....((((..........)))) ( -38.30)
>consensus
UUGCAUG_____________UGUUGCAACGAAUAAUGCACACGAGAGUA___GUGUGCCGGAAACGUGCGAUCCACGCCACAUCUAUAAAUAGGCAGCCAAAGCCCACACACCUCCGGGC
..((.................((((((.........((((((..........))))))((....))))))))....(((.............))).))....((((..........)))) (-26.06 = -26.06 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	9,816,299 – 9,816,406
Length	107
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.16
Mean single sequence MFE	-35.03
Consensus MFE	-24.22
Energy contribution	-24.60
Covariance contribution	0.38
Combinations/Pair	1.03
Mean z-score	-1.43
Structure conservation index	0.69
SVM decision value	-0.05
SVM RNA-class probability	0.508738
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9816299 107 - 23771897
UCAUUCGAUGUGCUUCGAUUUCAAUUGGUUCGGCUGUGAUUUGCAUG-------------UGUUGCAACGAAUAAUGCACACGAGAGCAGUGGUGUGCCGGAAACGUGCGAUCCACGCCA
...((((.(((((..((((....))))(((((..((..((.......-------------.))..)).)))))...))))))))).((.((((..(((((....)).)))..)))))).. ( -35.00)
>DroSec_CAF1 110382 104 - 1
UCAUUCGAUGUGCUUCGAUUGCAAUUGGUUCGUCUGCGAUUUGCAUG-------------UGUUGCAACGAAUAAUGCACACGAGAGUA---GUGUGCCGGAAACGUGCGAUACACGCCA
...((((.(((((((((.(((((((..(((((....)))...))...-------------.)))))))))))....))))))))).((.---((((((((....)).)).)))))).... ( -33.20)
>DroSim_CAF1 113717 104 - 1
UCAUUCGAUGUGCUUCGAUUGCAAUUGGUUCGUCUGCGAUUUGCAUG-------------UGUUGCAACGAAUAAUGCACACGAGAGUA---GUGUGCCGGAAACGUGCGAUCCACGCCA
......(.((((....(((((((....((((((.((((((.......-------------.))))))))))))...((((((.......---))))))((....))))))))))))).). ( -34.20)
>DroEre_CAF1 113259 111 - 1
----UCGAUGUGCUUCGAUUUCGAUUGGAUGGGCUGUGAUUUGCAUGUGCCGCUCCAACGUGUUGCAACGAAUAAUGCACACGA--GUA---GUGUGCCGGAAACGUGCGAUCCACGCCA
----((((......)))).............(((.(((..((((((((.(((......(((......)))......((((((..--...---)))))))))..))))))))..)))))). ( -37.70)
>consensus
UCAUUCGAUGUGCUUCGAUUGCAAUUGGUUCGGCUGCGAUUUGCAUG_____________UGUUGCAACGAAUAAUGCACACGAGAGUA___GUGUGCCGGAAACGUGCGAUCCACGCCA
...((((.(((((((((((((((..(.....)..))))))(((((..................)))))))))....))))))))).......((((((((....)).)))...))).... (-24.22 = -24.60 +   0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:33 2006