Locus 5885

Sequence ID	3L_DroMel_CAF1
Location	15,828,459 – 15,828,559
Length	100
Max. P	0.998433

overview

Window 1

Location	15,828,459 – 15,828,559
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	92.40
Mean single sequence MFE	-21.99
Consensus MFE	-20.18
Energy contribution	-20.34
Covariance contribution	0.16
Combinations/Pair	1.06
Mean z-score	-1.61
Structure conservation index	0.92
SVM decision value	1.76
SVM RNA-class probability	0.976182
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15828459 100 + 23771897
UAAAUGUCAACUCGACCUGUAGGCAACUGUAAUUACCUUAAGAAACAAGGCCGGAAUUAUGCAUUAUGCAAAUUCGGCCAAGGGUUAACACACGCACACA
....(((.(((((......(((....)))...................(((((.((((.(((.....))))))))))))..))))).))).......... ( -24.20)
>DroSec_CAF1 35816 100 + 1
UAAAUGUCAACUCGACCUGUAGGCAACUGUAAUUACCUUAAGAAACAAGGCCGGAAUUAUGCGUUAUGCAAAUUCGGCCAAGGGUUAACACACGCACACA
....(((.(((((......(((....)))...................(((((.((((.(((.....))))))))))))..))))).))).......... ( -23.50)
>DroSim_CAF1 37048 100 + 1
UAAAUGUCAACUCGACCUGUAGGCAACUGUAAUUACCUUAAGAAACAAGGCCGGAAUUAUGCGUUAUGCAAAUUCGGCCAAGGGUUAACACACGCACACA
....(((.(((((......(((....)))...................(((((.((((.(((.....))))))))))))..))))).))).......... ( -23.50)
>DroEre_CAF1 35012 100 + 1
UAAAUGUCAACUCGACCUGUAGGCAACUGUAAUUACCUUAAGAAACAAGGCCGGAAUUAUGCAUUAUGCAAAUUCGGCCAAAGGUUAACACACGCACACA
.............(((((.(((....)))...................(((((.((((.(((.....))))))))))))..))))).............. ( -22.60)
>DroYak_CAF1 77319 100 + 1
UAAAUGUCAACUCGACCUGUAGGCAACUGUAAUUACCUUAACAAACCAGGCCGGAAUUAGGCAUUAUGCAACUUCAGCCCAAGGUUAACANNNNNNNNNN
.............(((((...(((..(((.................)))(((.......)))..............)))..))))).............. ( -16.13)
>consensus
UAAAUGUCAACUCGACCUGUAGGCAACUGUAAUUACCUUAAGAAACAAGGCCGGAAUUAUGCAUUAUGCAAAUUCGGCCAAGGGUUAACACACGCACACA
.............(((((.(((....)))...................(((((((....(((.....)))..)))))))..))))).............. (-20.18 = -20.34 +   0.16)

alignment

secondary structure

dotplot

Window 2

Location	15,828,459 – 15,828,559
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	92.40
Mean single sequence MFE	-28.59
Consensus MFE	-26.10
Energy contribution	-26.30
Covariance contribution	0.20
Combinations/Pair	1.07
Mean z-score	-2.08
Structure conservation index	0.91
SVM decision value	3.10
SVM RNA-class probability	0.998433
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15828459 100 - 23771897
UGUGUGCGUGUGUUAACCCUUGGCCGAAUUUGCAUAAUGCAUAAUUCCGGCCUUGUUUCUUAAGGUAAUUACAGUUGCCUACAGGUCGAGUUGACAUUUA
.........((((((((....((((((((((((.....))).)))).)))))(((..(((..(((((((....)))))))..))).)))))))))))... ( -28.70)
>DroSec_CAF1 35816 100 - 1
UGUGUGCGUGUGUUAACCCUUGGCCGAAUUUGCAUAACGCAUAAUUCCGGCCUUGUUUCUUAAGGUAAUUACAGUUGCCUACAGGUCGAGUUGACAUUUA
.........((((((((....((((((((((((.....))).)))).)))))(((..(((..(((((((....)))))))..))).)))))))))))... ( -28.40)
>DroSim_CAF1 37048 100 - 1
UGUGUGCGUGUGUUAACCCUUGGCCGAAUUUGCAUAACGCAUAAUUCCGGCCUUGUUUCUUAAGGUAAUUACAGUUGCCUACAGGUCGAGUUGACAUUUA
.........((((((((....((((((((((((.....))).)))).)))))(((..(((..(((((((....)))))))..))).)))))))))))... ( -28.40)
>DroEre_CAF1 35012 100 - 1
UGUGUGCGUGUGUUAACCUUUGGCCGAAUUUGCAUAAUGCAUAAUUCCGGCCUUGUUUCUUAAGGUAAUUACAGUUGCCUACAGGUCGAGUUGACAUUUA
.........((((((((....((((((((((((.....))).)))).)))))(((..(((..(((((((....)))))))..))).)))))))))))... ( -28.70)
>DroYak_CAF1 77319 100 - 1
NNNNNNNNNNUGUUAACCUUGGGCUGAAGUUGCAUAAUGCCUAAUUCCGGCCUGGUUUGUUAAGGUAAUUACAGUUGCCUACAGGUCGAGUUGACAUUUA
..........(((((((.((((((..............))))))...(((((((........(((((((....))))))).))))))).))))))).... ( -28.74)
>consensus
UGUGUGCGUGUGUUAACCCUUGGCCGAAUUUGCAUAAUGCAUAAUUCCGGCCUUGUUUCUUAAGGUAAUUACAGUUGCCUACAGGUCGAGUUGACAUUUA
.........((((((((.(..((((((((((((.....))).)))).)))))..).......(((((((....))))))).........))))))))... (-26.10 = -26.30 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:55 2006