Locus 4100

Sequence ID	3R_DroMel_CAF1
Location	11,200,249 – 11,200,353
Length	104
Max. P	0.938852

overview

Window 5

Location	11,200,249 – 11,200,353
Length	104
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	95.96
Mean single sequence MFE	-35.06
Consensus MFE	-34.20
Energy contribution	-33.36
Covariance contribution	-0.84
Combinations/Pair	1.14
Mean z-score	-1.12
Structure conservation index	0.98
SVM decision value	0.40
SVM RNA-class probability	0.719737
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11200249 104 + 27905053
GGGAGAGAAUUGCCCGUUUUUCAGUGUCAUUUGGCAGAAAAAUCGAUUCCCCGCACACUGAAUAGUGGGCACUGGGUACUGAGUGCUCGGCUCUGGGUUCUCUG
...(((((((((((((((.((((((((....(((..(((.......))).))).)))))))).))))))).((((((((...)))))))).....)))))))). ( -36.80)
>DroSec_CAF1 2374 104 + 1
GGGAGAGAAUUGCCCGUUUUUCAGUGUCAUUUGGCAGAAAAAUCGAUUCCCCGCACACUGGAUAGUGGGCAUUGGGUACUGAGUGCUCGGCUCUGGGUUCUCUG
...(((((((((((((((.((((((((....(((..(((.......))).))).)))))))).))))))).((((((((...)))))))).....)))))))). ( -34.10)
>DroSim_CAF1 2546 104 + 1
GGGAGAGAAUUGCCCGUUUUUCAGUGUCAUUUGGCAGAAAAAUCGAUUCCCCGCACACUGGAUAGUGGGCAUUGGGUACUGAGUGCUCGGCUCUGGGUUCUCUG
...(((((((((((((((.((((((((....(((..(((.......))).))).)))))))).))))))).((((((((...)))))))).....)))))))). ( -34.10)
>DroEre_CAF1 7370 104 + 1
GGGAGAAAAUUGCCCGUUUUUCAGUGUCAUUUGGCUGAAAAAUCGAUUCCCCGCACACUGGAUGGUGGGCACUGGGUACUGAGUGCUCGGUUCUGGGUUCUCUG
.(((((((((((...((((((((((........))))))))))))))).(((((.((((....)))).))(((((((((...)))))))))...))))))))). ( -36.40)
>DroYak_CAF1 2598 104 + 1
GGGAGAAAAUUGCCCGUUUUUCAGUGUCAUUUGGCUGAAAAAUCGAUUCCCCGCACACUGGAUGGUGGGCACUGGGUACUGAGUACUGGGUUCUGGGUUCUCUG
.(((((((((((...((((((((((........))))))))))))))).(((((.((((....)))).))(((.(((((...))))).)))...))))))))). ( -33.90)
>consensus
GGGAGAGAAUUGCCCGUUUUUCAGUGUCAUUUGGCAGAAAAAUCGAUUCCCCGCACACUGGAUAGUGGGCACUGGGUACUGAGUGCUCGGCUCUGGGUUCUCUG
.((((((...((((((((.((((((((....(((..(((.......))).))).)))))))).))))))))((((((((...)))))))).......)))))). (-34.20 = -33.36 +  -0.84)

alignment

secondary structure

dotplot

Window 6

Location	11,200,249 – 11,200,353
Length	104
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	95.96
Mean single sequence MFE	-28.30
Consensus MFE	-25.36
Energy contribution	-25.92
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-1.57
Structure conservation index	0.90
SVM decision value	1.27
SVM RNA-class probability	0.938852
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11200249 104 - 27905053
CAGAGAACCCAGAGCCGAGCACUCAGUACCCAGUGCCCACUAUUCAGUGUGCGGGGAAUCGAUUUUUCUGCCAAAUGACACUGAAAAACGGGCAAUUCUCUCCC
.(((((((((......(.(((((........))))).)....((((((((((((..((.....))..))))......))))))))....)))...))))))... ( -32.60)
>DroSec_CAF1 2374 104 - 1
CAGAGAACCCAGAGCCGAGCACUCAGUACCCAAUGCCCACUAUCCAGUGUGCGGGGAAUCGAUUUUUCUGCCAAAUGACACUGAAAAACGGGCAAUUCUCUCCC
.((((((....(((.......))).........(((((......((((((((((..((.....))..))))......))))))......))))).))))))... ( -29.70)
>DroSim_CAF1 2546 104 - 1
CAGAGAACCCAGAGCCGAGCACUCAGUACCCAAUGCCCACUAUCCAGUGUGCGGGGAAUCGAUUUUUCUGCCAAAUGACACUGAAAAACGGGCAAUUCUCUCCC
.((((((....(((.......))).........(((((......((((((((((..((.....))..))))......))))))......))))).))))))... ( -29.70)
>DroEre_CAF1 7370 104 - 1
CAGAGAACCCAGAACCGAGCACUCAGUACCCAGUGCCCACCAUCCAGUGUGCGGGGAAUCGAUUUUUCAGCCAAAUGACACUGAAAAACGGGCAAUUUUCUCCC
..((((((((......(.(((((........))))).)......((((((.((.((....((....))..))...))))))))......))).....))))).. ( -24.50)
>DroYak_CAF1 2598 104 - 1
CAGAGAACCCAGAACCCAGUACUCAGUACCCAGUGCCCACCAUCCAGUGUGCGGGGAAUCGAUUUUUCAGCCAAAUGACACUGAAAAACGGGCAAUUUUCUCCC
..((((((((.((.(((.((((...)))).....((.(((......))).)))))...))(.((((((((..........)))))))))))).....))))).. ( -25.00)
>consensus
CAGAGAACCCAGAGCCGAGCACUCAGUACCCAGUGCCCACUAUCCAGUGUGCGGGGAAUCGAUUUUUCUGCCAAAUGACACUGAAAAACGGGCAAUUCUCUCCC
.((((((....(((.......))).........(((((......((((((((((..((.....))..))))......))))))......))))).))))))... (-25.36 = -25.92 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:07 2006