Locus 1061

Sequence ID	3R_DroMel_CAF1
Location	3,284,456 – 3,284,594
Length	138
Max. P	0.995236

overview

Window 4

Location	3,284,456 – 3,284,576
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	90.94
Mean single sequence MFE	-25.60
Consensus MFE	-23.21
Energy contribution	-23.77
Covariance contribution	0.56
Combinations/Pair	1.06
Mean z-score	-2.40
Structure conservation index	0.91
SVM decision value	2.55
SVM RNA-class probability	0.995236
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3284456 120 - 27905053
GGUUGCAUGCAAUCUAGAAACGAUUCUAAACAAAAGGAAUCCGCUUUCAUAAUUUCCCCAUGGAACGCGCAUUCUUUUUAUUGCCACUAAGCGACCGAACAAACGACCAACCGACCCACC
((((((..(((((.(((((....)))))...(((((((((.(((((((((.........)))))).))).))))))))))))))......)))))).......((......))....... ( -27.70)
>DroSec_CAF1 37533 120 - 1
CGUUGCAUGCAAUCUAGAAACGAUUCUAAACAAAAGGAAUCCGCUUUCAUAAUUUCCCCAUGGAACGCGCAUUCUUUUUAUUGCCACUAAGCGACCGAACAAACGACCAACCGACCCACC
.(((((..(((((.(((((....)))))...(((((((((.(((((((((.........)))))).))).))))))))))))))......)))))........((......))....... ( -23.80)
>DroSim_CAF1 38739 120 - 1
CGUUGCAUGCAAUCUAGAAACGAUUCUAAACAAAAGGAAUCCGCUUUCAUAAUUUCCCCAUGGAACGCGCAUUCUUUUUAUUGCCACUAAGCGACCGAACAAACGACCAACCGACCCACC
.(((((..(((((.(((((....)))))...(((((((((.(((((((((.........)))))).))).))))))))))))))......)))))........((......))....... ( -23.80)
>DroEre_CAF1 39115 120 - 1
GGUCGCAUGCAAUCUAGAAACGAUUCUAAACAAAAGGAAUCCGCUUUCAUAAUUUCCCCAUGGAGCGCGCAUUCUUUUUAUUGCCACUAAGCGACCGAACAAACGACCAACCGACCCACC
((((((..(((((.(((((....)))))...(((((((((.(((((((((.........)))))).))).))))))))))))))......)))))).......((......))....... ( -29.50)
>DroWil_CAF1 147259 96 - 1
GGCUGAAUGCAAUCUAGAAACGAUUCUAAACAAAAGAAAUCCGCUUUCAUAAUUUCCCUAUGGAAUGCGCAUUCUUUUUAUUGCCACUAAGCGACC------------------------
.(((....(((((.(((((....)))))...(((((((...((((((((((.......))))))).)))..))))))).))))).....)))....------------------------ ( -21.10)
>DroYak_CAF1 56867 120 - 1
GGUUGCAUGCAAUCUAGAAACGAUUCUAAACAAAAGGAAUCCGCUUUCAUAAUUUCCCCAUGGAACGCGCAUUCUUUUUAUUGCCACUAAGCGACCGAACAAACGACCAACCGACCCACC
((((((..(((((.(((((....)))))...(((((((((.(((((((((.........)))))).))).))))))))))))))......)))))).......((......))....... ( -27.70)
>consensus
GGUUGCAUGCAAUCUAGAAACGAUUCUAAACAAAAGGAAUCCGCUUUCAUAAUUUCCCCAUGGAACGCGCAUUCUUUUUAUUGCCACUAAGCGACCGAACAAACGACCAACCGACCCACC
((((((..(((((.(((((....)))))...(((((((((.(((((((((.........)))))).))).))))))))))))))......))))))........................ (-23.21 = -23.77 +   0.56)

alignment

secondary structure

dotplot

Window 5

Location	3,284,496 – 3,284,594
Length	98
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	96.94
Mean single sequence MFE	-27.88
Consensus MFE	-26.26
Energy contribution	-27.46
Covariance contribution	1.20
Combinations/Pair	1.13
Mean z-score	-1.53
Structure conservation index	0.94
SVM decision value	1.49
SVM RNA-class probability	0.958193
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3284496 98 + 27905053
UAAAAAGAAUGCGCGUUCCAUGGGGAAAUUAUGAAAGCGGAUUCCUUUUGUUUAGAAUCGUUUCUAGAUUGCAUGCAACCAAGCGGUACGAGCGCGUG
..........(((((((((((((((((.(..(....)..).)))))...((((((((....))))))))..))))..(((....)))..)))))))). ( -27.70)
>DroSec_CAF1 37573 98 + 1
UAAAAAGAAUGCGCGUUCCAUGGGGAAAUUAUGAAAGCGGAUUCCUUUUGUUUAGAAUCGUUUCUAGAUUGCAUGCAACGAAGCGGCACGAGCGCGUG
..........((((((((((..(((((.(..(....)..).)))))..))(((((((....))))))).(((.(((......)))))).)))))))). ( -28.80)
>DroSim_CAF1 38779 98 + 1
UAAAAAGAAUGCGCGUUCCAUGGGGAAAUUAUGAAAGCGGAUUCCUUUUGUUUAGAAUCGUUUCUAGAUUGCAUGCAACGAAGCGGCACGAGCGCGUG
..........((((((((((..(((((.(..(....)..).)))))..))(((((((....))))))).(((.(((......)))))).)))))))). ( -28.80)
>DroEre_CAF1 39155 98 + 1
UAAAAAGAAUGCGCGCUCCAUGGGGAAAUUAUGAAAGCGGAUUCCUUUUGUUUAGAAUCGUUUCUAGAUUGCAUGCGACCAAGCGGUACGAGCGUGUG
..........(((((((((((((((((.(..(....)..).)))))...((((((((....))))))))..))))..(((....)))..)))))))). ( -28.30)
>DroYak_CAF1 56907 98 + 1
UAAAAAGAAUGCGCGUUCCAUGGGGAAAUUAUGAAAGCGGAUUCCUUUUGUUUAGAAUCGUUUCUAGAUUGCAUGCAACCAAGCGGUACGAACGUGUG
..........(((((((((((((((((.(..(....)..).)))))...((((((((....))))))))..))))..(((....)))..)))))))). ( -25.80)
>consensus
UAAAAAGAAUGCGCGUUCCAUGGGGAAAUUAUGAAAGCGGAUUCCUUUUGUUUAGAAUCGUUUCUAGAUUGCAUGCAACCAAGCGGUACGAGCGCGUG
..........((((((((((..(((((.(..(....)..).)))))..))(((((((....))))))).(((.(((......)))))).)))))))). (-26.26 = -27.46 +   1.20)

alignment

secondary structure

dotplot

Window 6

Location	3,284,496 – 3,284,594
Length	98
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	96.94
Mean single sequence MFE	-21.70
Consensus MFE	-20.92
Energy contribution	-21.36
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.53
Structure conservation index	0.96
SVM decision value	1.70
SVM RNA-class probability	0.972927
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3284496 98 - 27905053
CACGCGCUCGUACCGCUUGGUUGCAUGCAAUCUAGAAACGAUUCUAAACAAAAGGAAUCCGCUUUCAUAAUUUCCCCAUGGAACGCGCAUUCUUUUUA
.......((((....((.(((((....))))).))..))))........(((((((((.(((((((((.........)))))).))).))))))))). ( -22.40)
>DroSec_CAF1 37573 98 - 1
CACGCGCUCGUGCCGCUUCGUUGCAUGCAAUCUAGAAACGAUUCUAAACAAAAGGAAUCCGCUUUCAUAAUUUCCCCAUGGAACGCGCAUUCUUUUUA
...((((....)).((......))..))....(((((....)))))...(((((((((.(((((((((.........)))))).))).))))))))). ( -21.30)
>DroSim_CAF1 38779 98 - 1
CACGCGCUCGUGCCGCUUCGUUGCAUGCAAUCUAGAAACGAUUCUAAACAAAAGGAAUCCGCUUUCAUAAUUUCCCCAUGGAACGCGCAUUCUUUUUA
...((((....)).((......))..))....(((((....)))))...(((((((((.(((((((((.........)))))).))).))))))))). ( -21.30)
>DroEre_CAF1 39155 98 - 1
CACACGCUCGUACCGCUUGGUCGCAUGCAAUCUAGAAACGAUUCUAAACAAAAGGAAUCCGCUUUCAUAAUUUCCCCAUGGAGCGCGCAUUCUUUUUA
.....((.((.(((....)))))...))....(((((....)))))...(((((((((.(((((((((.........)))))).))).))))))))). ( -21.00)
>DroYak_CAF1 56907 98 - 1
CACACGUUCGUACCGCUUGGUUGCAUGCAAUCUAGAAACGAUUCUAAACAAAAGGAAUCCGCUUUCAUAAUUUCCCCAUGGAACGCGCAUUCUUUUUA
.......((((....((.(((((....))))).))..))))........(((((((((.(((((((((.........)))))).))).))))))))). ( -22.50)
>consensus
CACGCGCUCGUACCGCUUGGUUGCAUGCAAUCUAGAAACGAUUCUAAACAAAAGGAAUCCGCUUUCAUAAUUUCCCCAUGGAACGCGCAUUCUUUUUA
.......((((....((.(((((....))))).))..))))........(((((((((.(((((((((.........)))))).))).))))))))). (-20.92 = -21.36 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:33 2006