Locus 2790

Sequence ID	X_DroMel_CAF1
Location	7,479,410 – 7,479,589
Length	179
Max. P	0.986614

overview

Window 4

Location	7,479,410 – 7,479,512
Length	102
Sequences	3
Columns	102
Reading direction	forward
Mean pairwise identity	98.04
Mean single sequence MFE	-24.60
Consensus MFE	-23.83
Energy contribution	-23.17
Covariance contribution	-0.66
Combinations/Pair	1.11
Mean z-score	-1.49
Structure conservation index	0.97
SVM decision value	0.05
SVM RNA-class probability	0.557629
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7479410 102 + 22224390
UAAGCGUUCGCCUCGUUUCGUUUCGGUUUUGUCGUAUCUUUUCUUUGUUGGAAAGAUCAUCAUUAAGCAUUCAUCCAUUGAAUGCGUGGGAGCAUUCGAUUU
.....((((.((.(...............((..(.((((((((......)))))))))..))....(((((((.....)))))))).))))))......... ( -25.20)
>DroSec_CAF1 12573 102 + 1
UAAGCGUUCGCCUCGCUUCGUUUCGGUUUUGUCGUAUUUUUUCUUUGUUGGAAAGAUCAUCAUUAAGCAUUCAUCCAUUGAAUGCGUGGGAGCAUUCGAUUU
....((...(((((((.............((..(.((((((((......)))))))))..))....(((((((.....)))))))))))).))...)).... ( -24.30)
>DroSim_CAF1 12600 102 + 1
UAAGCGUUCGCCUCGCUUCGUUUUGGUUUUGUCGUAUUUUUUCUUUGUUGGAAAGAUCAUCAUUAAGCAUUCAUCCAUUGAAUGCGUGGGAGCAUUCGAUUU
....((...(((((((.............((..(.((((((((......)))))))))..))....(((((((.....)))))))))))).))...)).... ( -24.30)
>consensus
UAAGCGUUCGCCUCGCUUCGUUUCGGUUUUGUCGUAUUUUUUCUUUGUUGGAAAGAUCAUCAUUAAGCAUUCAUCCAUUGAAUGCGUGGGAGCAUUCGAUUU
.(((((.......))))).(((((.....((..(.((((((((......)))))))))..))....(((((((.....)))))))...)))))......... (-23.83 = -23.17 +  -0.66)

alignment

secondary structure

dotplot

Window 5

Location	7,479,447 – 7,479,552
Length	105
Sequences	3
Columns	105
Reading direction	forward
Mean pairwise identity	98.73
Mean single sequence MFE	-27.20
Consensus MFE	-27.20
Energy contribution	-27.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.79
Structure conservation index	1.00
SVM decision value	2.05
SVM RNA-class probability	0.986614
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7479447 105 + 22224390
CUUUUCUUUGUUGGAAAGAUCAUCAUUAAGCAUUCAUCCAUUGAAUGCGUGGGAGCAUUCGAUUUUAAUUUUGAUUUUGAUUUCACAUUGAAGGUCAUGCCACUC
...........(((...((((.(((....(((((((.....)))))))(((..(.((.((((........))))...)).)..)))..))).))))...)))... ( -27.20)
>DroSec_CAF1 12610 105 + 1
UUUUUCUUUGUUGGAAAGAUCAUCAUUAAGCAUUCAUCCAUUGAAUGCGUGGGAGCAUUCGAUUUUAAUUUUGAUUUUGAUUUCACAUUGAAGGUCACGCCACUC
...........(((...((((.(((....(((((((.....)))))))(((..(.((.((((........))))...)).)..)))..))).))))...)))... ( -27.20)
>DroSim_CAF1 12637 105 + 1
UUUUUCUUUGUUGGAAAGAUCAUCAUUAAGCAUUCAUCCAUUGAAUGCGUGGGAGCAUUCGAUUUUAAUUUUGAUUUUGAUUUCACAUUGAAGGUCACGCCACUC
...........(((...((((.(((....(((((((.....)))))))(((..(.((.((((........))))...)).)..)))..))).))))...)))... ( -27.20)
>consensus
UUUUUCUUUGUUGGAAAGAUCAUCAUUAAGCAUUCAUCCAUUGAAUGCGUGGGAGCAUUCGAUUUUAAUUUUGAUUUUGAUUUCACAUUGAAGGUCACGCCACUC
...........(((...((((.(((....(((((((.....)))))))(((..(.((.((((........))))...)).)..)))..))).))))...)))... (-27.20 = -27.20 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	7,479,472 – 7,479,589
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.99
Mean single sequence MFE	-28.29
Consensus MFE	-25.86
Energy contribution	-26.12
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.36
Structure conservation index	0.91
SVM decision value	-0.03
SVM RNA-class probability	0.519333
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7479472 117 + 22224390
UUAAGCAUUCAUCCAUUGAAUGCGUGGGAGCAUUCGAUUUUAAUUUUGAUUUUGAUUUCACAUUGAAGGUCAUGCCACUCAUCGUCUGCUCAACCGUUGAGGAAUUGAUAA-AUACAU--
....(((((((.....)))))))(((.(((((..((((........(((((((.(........).)))))))........))))..)))))..((.....)).........-.)))..-- ( -28.99)
>DroSec_CAF1 12635 118 + 1
UUAAGCAUUCAUCCAUUGAAUGCGUGGGAGCAUUCGAUUUUAAUUUUGAUUUUGAUUUCACAUUGAAGGUCACGCCACUCAUCGUCUGCUCAACCGUUGAGGAAUUGAUAA-AAACAUU-
....(((((((.....)))))))(((.(((((..((((........(((((((.(........).)))))))........))))..)))))..((.....)).........-...))).- ( -27.69)
>DroSim_CAF1 12662 119 + 1
UUAAGCAUUCAUCCAUUGAAUGCGUGGGAGCAUUCGAUUUUAAUUUUGAUUUUGAUUUCACAUUGAAGGUCACGCCACUCAUCGUCUGCUCAACCGUUGAGGAAUUGAUAA-AAACAUUU
....(((((((.....)))))))(((.(((((..((((........(((((((.(........).)))))))........))))..)))))..((.....)).........-...))).. ( -27.69)
>DroEre_CAF1 13519 120 + 1
UUAAGCAUUCAUCCAUUGAAUGCGUGGGAGCAUUCGAUUUUAAUUUUGAUUUUGAUUUCGCAUUGAAGGUCACGCCACUCAUCGACCGCUCGCCCGCCGAGGAAUUGAUAAGAAACAAAC
....(((((((.....)))))))((((((((..(((((........(((((((.(........).)))))))........)))))..)))..)))))....................... ( -28.79)
>consensus
UUAAGCAUUCAUCCAUUGAAUGCGUGGGAGCAUUCGAUUUUAAUUUUGAUUUUGAUUUCACAUUGAAGGUCACGCCACUCAUCGUCUGCUCAACCGUUGAGGAAUUGAUAA_AAACAUU_
....(((((((.....)))))))((..(((((..((((........(((((((.(........).)))))))........))))..)))))..((.....))............)).... (-25.86 = -26.12 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:24 2006