Locus 3308

Sequence ID	X_DroMel_CAF1
Location	8,839,543 – 8,839,645
Length	102
Max. P	0.688559

overview

Window 2

Location	8,839,543 – 8,839,645
Length	102
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	81.32
Mean single sequence MFE	-31.97
Consensus MFE	-21.67
Energy contribution	-23.15
Covariance contribution	1.48
Combinations/Pair	1.12
Mean z-score	-1.61
Structure conservation index	0.68
SVM decision value	0.25
SVM RNA-class probability	0.654923
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8839543 102 + 22224390
AAUGCCCUAAUUUCCCGGCCACUUUAU----------GUUGACUUU--GAGUGGGUCUGACGUUGCCUUAGCACCUCGGUGCGAUUUGGCCAGAGUCGGGCAUUAUAUCGCAAA
(((((((.........((((((((...----------(....)...--)))).)))).(((...(((...((((....)))).....)))....)))))))))).......... ( -33.80)
>DroSec_CAF1 79814 102 + 1
AAUGCCCUAAUUUCCCGGCCACUUUAU----------GUUGACUUU--GAGUGGGUCUGACGUUGCCUUAGCACCUCGGUGCGAUUUGGCCAGAGUCGGGCAUUAUAUCUCACC
(((((((.........((((((((...----------(....)...--)))).)))).(((...(((...((((....)))).....)))....)))))))))).......... ( -33.80)
>DroSim_CAF1 71613 102 + 1
AAUGCCCUAAUUUCCCGGCCACUUUAU----------GUUGACUUU--GAGUGGGUCUGACGUUGCCUUAGCACCUCGGUGCGAUUUGGCCAGAGUCGGGCAUUAUAUCUCACC
(((((((.........((((((((...----------(....)...--)))).)))).(((...(((...((((....)))).....)))....)))))))))).......... ( -33.80)
>DroEre_CAF1 74982 97 + 1
AAUGCCCUAAUUUCCCGGCCACUUUAU----------GUUGACUUU--GAGUGGCUCUGACGUUGCCUUAGCACCUCGGUGCGAUUUGGCCAGAGUCGGCCAAUUUC-----CC
................((((((((...----------(....)...--))))(((((((.....(((...((((....)))).....))))))))))))))......-----.. ( -31.10)
>DroYak_CAF1 76581 102 + 1
AAUGCCCUAAUUUCCCGGCCACUUUAU----------GUUGACUUU--GAGUGGGUCUGCCGUUGCCUUAGCACCUCGGUGCGAUUUGGCCAGAGUCGGGCAUAUUAUCGAAUC
.((((((....(((..(((((..((..----------((.(((((.--....))))).))..........((((....))))))..))))).)))..))))))........... ( -31.40)
>DroMoj_CAF1 121283 110 + 1
AAUGCCCUAAUUUCUCGACCACUUUGGCCCUGCGGCCGCUGACGUCGCGACUUCGUCAGCUGCUUCUUUAGCACCUCGGUGUGAUUUGUUCAGCUUG----UUUAUGCUACACU
...............(((.......((((....))))(((((((.........)))))))((((.....))))..)))((((((.....))(((...----.....))))))). ( -27.90)
>consensus
AAUGCCCUAAUUUCCCGGCCACUUUAU__________GUUGACUUU__GAGUGGGUCUGACGUUGCCUUAGCACCUCGGUGCGAUUUGGCCAGAGUCGGGCAUUAUAUCGCACC
(((((((....(((..(((((..((...............(((((.......))))).............((((....))))))..))))).)))..))))))).......... (-21.67 = -23.15 +   1.48)

alignment

secondary structure

dotplot

Window 3

Location	8,839,543 – 8,839,645
Length	102
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	81.32
Mean single sequence MFE	-30.96
Consensus MFE	-21.46
Energy contribution	-23.35
Covariance contribution	1.89
Combinations/Pair	1.05
Mean z-score	-1.62
Structure conservation index	0.69
SVM decision value	0.32
SVM RNA-class probability	0.688559
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8839543 102 - 22224390
UUUGCGAUAUAAUGCCCGACUCUGGCCAAAUCGCACCGAGGUGCUAAGGCAACGUCAGACCCACUC--AAAGUCAAC----------AUAAAGUGGCCGGGAAAUUAGGGCAUU
..........(((((((...((((((((....((((....))))...(....)....(((......--...)))...----------......))))))))......))))))) ( -31.70)
>DroSec_CAF1 79814 102 - 1
GGUGAGAUAUAAUGCCCGACUCUGGCCAAAUCGCACCGAGGUGCUAAGGCAACGUCAGACCCACUC--AAAGUCAAC----------AUAAAGUGGCCGGGAAAUUAGGGCAUU
..........(((((((...((((((((....((((....))))...(....)....(((......--...)))...----------......))))))))......))))))) ( -31.70)
>DroSim_CAF1 71613 102 - 1
GGUGAGAUAUAAUGCCCGACUCUGGCCAAAUCGCACCGAGGUGCUAAGGCAACGUCAGACCCACUC--AAAGUCAAC----------AUAAAGUGGCCGGGAAAUUAGGGCAUU
..........(((((((...((((((((....((((....))))...(....)....(((......--...)))...----------......))))))))......))))))) ( -31.70)
>DroEre_CAF1 74982 97 - 1
GG-----GAAAUUGGCCGACUCUGGCCAAAUCGCACCGAGGUGCUAAGGCAACGUCAGAGCCACUC--AAAGUCAAC----------AUAAAGUGGCCGGGAAAUUAGGGCAUU
..-----....(((((((....)))))))...((.((((.((((....)).)).)).(.((((((.--.........----------....))))))).........))))... ( -28.74)
>DroYak_CAF1 76581 102 - 1
GAUUCGAUAAUAUGCCCGACUCUGGCCAAAUCGCACCGAGGUGCUAAGGCAACGGCAGACCCACUC--AAAGUCAAC----------AUAAAGUGGCCGGGAAAUUAGGGCAUU
...........((((((...((((((((....((((....))))...(....)....(((......--...)))...----------......))))))))......)))))). ( -30.90)
>DroMoj_CAF1 121283 110 - 1
AGUGUAGCAUAAA----CAAGCUGAACAAAUCACACCGAGGUGCUAAAGAAGCAGCUGACGAAGUCGCGACGUCAGCGGCCGCAGGGCCAAAGUGGUCGAGAAAUUAGGGCAUU
.((.((((.....----...)))).))..(((((.......((((.....))))(((((((.........)))))))((((....))))...)))))................. ( -31.00)
>consensus
GGUGAGAUAUAAUGCCCGACUCUGGCCAAAUCGCACCGAGGUGCUAAGGCAACGUCAGACCCACUC__AAAGUCAAC__________AUAAAGUGGCCGGGAAAUUAGGGCAUU
..........(((((((...((((((((....((((....)))).............(((...........)))...................))))))))......))))))) (-21.46 = -23.35 +   1.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:05 2006