Locus 7331

Sequence ID	2L_DroMel_CAF1
Location	20,475,523 – 20,475,683
Length	160
Max. P	0.998646

overview

Window 6

Location	20,475,523 – 20,475,643
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.67
Mean single sequence MFE	-25.46
Consensus MFE	-24.14
Energy contribution	-23.98
Covariance contribution	-0.16
Combinations/Pair	1.02
Mean z-score	-1.31
Structure conservation index	0.95
SVM decision value	0.35
SVM RNA-class probability	0.700607
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20475523 120 - 22407834
GAAGGCGAAAUGCGAUCCGUAUUACACAAAAUCCCAUUUGUAUAUUUAUACACCAGGGCCCACAUGUGUGUGCUCUUCAAAUACACGAAAAUAUUUUUGAAAAUAUCUCGAAUGUUUGUU
(((((((.((((((...))))))(((((....(((...(((((....)))))...)))......))))).))).))))..........((((((((..((.....))..))))))))... ( -24.20)
>DroSec_CAF1 28533 120 - 1
GAAGGCGAAAUGCGAUCCGUAUUACACAAAAUCCCAUUUGUAUAUUUAUACACCAGGGCCCACAUGUGUGUGCUCUUCAAAUACACGAAAAUAUUUUUGAAAAUAUCUCGAAUGUUUGUU
(((((((.((((((...))))))(((((....(((...(((((....)))))...)))......))))).))).))))..........((((((((..((.....))..))))))))... ( -24.20)
>DroSim_CAF1 32308 120 - 1
GAAGGCGAAAUGCGAUCCGUAUUACACAAAAUCCCAUUUGUAUAUUUAUACACCAGGGCCCACAUGUGUGUGCUCUUCAAAUACACGAAAAUAUUUUUGAAAAUAUCUCGAAUGUUUGUU
(((((((.((((((...))))))(((((....(((...(((((....)))))...)))......))))).))).))))..........((((((((..((.....))..))))))))... ( -24.20)
>DroEre_CAF1 30720 120 - 1
GAAGGCGAAAUGCGAUCCGUAUUACACAAAAUCCCAUUUGUGUAUUUAUACACCGGGGCCCACAUGUGUGUGCUCUUCAAAUACACGAGAAUAUUUUUGAAAAUAUCUCGAAUGUUUGUU
...((.(.((((((...))))))(((((((......))))))).......).))(((((.(((....))).))))).((((((..(((((.(((((....))))))))))..)))))).. ( -30.60)
>DroYak_CAF1 27929 120 - 1
GAAGGCGAAAUGCGAUCCGUAUUACACAAAAUCCCAUUUGUAUAUUUAUACACCAGGGCCCACAUGUGUGUGCUCUUCAAAUACACGAAAAUAUUUUUCAAAAUAUCUCGAAUGUUUGUU
(((((((.((((((...))))))(((((....(((...(((((....)))))...)))......))))).))).))))(((((..(((..((((((....)))))).)))..)))))... ( -24.10)
>consensus
GAAGGCGAAAUGCGAUCCGUAUUACACAAAAUCCCAUUUGUAUAUUUAUACACCAGGGCCCACAUGUGUGUGCUCUUCAAAUACACGAAAAUAUUUUUGAAAAUAUCUCGAAUGUUUGUU
(((((((.((((((...))))))(((((....(((...(((((....)))))...)))......))))).))).))))(((((..(((..((((((....)))))).)))..)))))... (-24.14 = -23.98 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	20,475,563 – 20,475,683
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.99
Mean single sequence MFE	-30.46
Consensus MFE	-29.26
Energy contribution	-29.66
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.20
Structure conservation index	0.96
SVM decision value	0.46
SVM RNA-class probability	0.743528
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20475563 120 + 22407834
UUGAAGAGCACACACAUGUGGGCCCUGGUGUAUAAAUAUACAAAUGGGAUUUUGUGUAAUACGGAUCGCAUUUCGCCUUCUGUCUGUCCGACGUUGUUUAAAAAUAAAUCCAUUCGGACU
..((((.((..(((((......(((...(((((....)))))...)))....))))).....(((......))))))))).....((((((....(((((....)))))....)))))). ( -30.80)
>DroSec_CAF1 28573 120 + 1
UUGAAGAGCACACACAUGUGGGCCCUGGUGUAUAAAUAUACAAAUGGGAUUUUGUGUAAUACGGAUCGCAUUUCGCCUUCUGUCUGUCCGACGUUGUUUAAAAAUAAAUCCAUUCGGACU
..((((.((..(((((......(((...(((((....)))))...)))....))))).....(((......))))))))).....((((((....(((((....)))))....)))))). ( -30.80)
>DroSim_CAF1 32348 120 + 1
UUGAAGAGCACACACAUGUGGGCCCUGGUGUAUAAAUAUACAAAUGGGAUUUUGUGUAAUACGGAUCGCAUUUCGCCUUCUGUCUGUCCGACGUUGUUUAAAAAUAAAUCCAUUCGGACU
..((((.((..(((((......(((...(((((....)))))...)))....))))).....(((......))))))))).....((((((....(((((....)))))....)))))). ( -30.80)
>DroEre_CAF1 30760 116 + 1
UUGAAGAGCACACACAUGUGGGCCCCGGUGUAUAAAUACACAAAUGGGAUUUUGUGUAAUACGGAUCGCAUUUCGCCUUCU----GUCCGCCGUUGUUUAAAAAUAAAUCCAUUCGGACU
(((((.(((.(((....)))......((((......((((((((......))))))))..(((((..((.....))..)))----)).))))))).))))).......(((....))).. ( -29.10)
>DroYak_CAF1 27969 116 + 1
UUGAAGAGCACACACAUGUGGGCCCUGGUGUAUAAAUAUACAAAUGGGAUUUUGUGUAAUACGGAUCGCAUUUCGCCUUCU----GUCCGACGUUGUUUAAAAAUAAAUCCAUUCGGACU
..((((.((..(((((......(((...(((((....)))))...)))....))))).....(((......))))))))).----((((((....(((((....)))))....)))))). ( -30.80)
>consensus
UUGAAGAGCACACACAUGUGGGCCCUGGUGUAUAAAUAUACAAAUGGGAUUUUGUGUAAUACGGAUCGCAUUUCGCCUUCUGUCUGUCCGACGUUGUUUAAAAAUAAAUCCAUUCGGACU
..((((.((..(((((......(((...(((((....)))))...)))....))))).....(((......))))))))).....((((((....(((((....)))))....)))))). (-29.26 = -29.66 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	20,475,563 – 20,475,683
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.99
Mean single sequence MFE	-30.86
Consensus MFE	-29.66
Energy contribution	-29.70
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.03
Structure conservation index	0.96
SVM decision value	3.17
SVM RNA-class probability	0.998646
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20475563 120 - 22407834
AGUCCGAAUGGAUUUAUUUUUAAACAACGUCGGACAGACAGAAGGCGAAAUGCGAUCCGUAUUACACAAAAUCCCAUUUGUAUAUUUAUACACCAGGGCCCACAUGUGUGUGCUCUUCAA
.((((((...(.((((....)))))....)))))).....(((((((.((((((...))))))(((((....(((...(((((....)))))...)))......))))).))).)))).. ( -30.90)
>DroSec_CAF1 28573 120 - 1
AGUCCGAAUGGAUUUAUUUUUAAACAACGUCGGACAGACAGAAGGCGAAAUGCGAUCCGUAUUACACAAAAUCCCAUUUGUAUAUUUAUACACCAGGGCCCACAUGUGUGUGCUCUUCAA
.((((((...(.((((....)))))....)))))).....(((((((.((((((...))))))(((((....(((...(((((....)))))...)))......))))).))).)))).. ( -30.90)
>DroSim_CAF1 32348 120 - 1
AGUCCGAAUGGAUUUAUUUUUAAACAACGUCGGACAGACAGAAGGCGAAAUGCGAUCCGUAUUACACAAAAUCCCAUUUGUAUAUUUAUACACCAGGGCCCACAUGUGUGUGCUCUUCAA
.((((((...(.((((....)))))....)))))).....(((((((.((((((...))))))(((((....(((...(((((....)))))...)))......))))).))).)))).. ( -30.90)
>DroEre_CAF1 30760 116 - 1
AGUCCGAAUGGAUUUAUUUUUAAACAACGGCGGAC----AGAAGGCGAAAUGCGAUCCGUAUUACACAAAAUCCCAUUUGUGUAUUUAUACACCGGGGCCCACAUGUGUGUGCUCUUCAA
.(((((....(.((((....))))).....)))))----.(((((((.((((((...))))))(((((....(((....(((((....)))))..)))......))))).))).)))).. ( -30.70)
>DroYak_CAF1 27969 116 - 1
AGUCCGAAUGGAUUUAUUUUUAAACAACGUCGGAC----AGAAGGCGAAAUGCGAUCCGUAUUACACAAAAUCCCAUUUGUAUAUUUAUACACCAGGGCCCACAUGUGUGUGCUCUUCAA
.((((((...(.((((....)))))....))))))----.(((((((.((((((...))))))(((((....(((...(((((....)))))...)))......))))).))).)))).. ( -30.90)
>consensus
AGUCCGAAUGGAUUUAUUUUUAAACAACGUCGGACAGACAGAAGGCGAAAUGCGAUCCGUAUUACACAAAAUCCCAUUUGUAUAUUUAUACACCAGGGCCCACAUGUGUGUGCUCUUCAA
.((((((...(.((((....)))))....)))))).....(((((((.((((((...))))))(((((....(((...(((((....)))))...)))......))))).))).)))).. (-29.66 = -29.70 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:51 2006