Locus 4994

Sequence ID	X_DroMel_CAF1
Location	13,046,202 – 13,046,335
Length	133
Max. P	0.734810

overview

Window 3

Location	13,046,202 – 13,046,295
Length	93
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	76.36
Mean single sequence MFE	-23.12
Consensus MFE	-10.26
Energy contribution	-11.90
Covariance contribution	1.64
Combinations/Pair	1.29
Mean z-score	-1.94
Structure conservation index	0.44
SVM decision value	0.43
SVM RNA-class probability	0.734810
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13046202 93 - 22224390
GUGGUGCUAGAGGUGGAAGAAAAAGAAUAAUCGAUGCUUAUC-GAUAGCGUCGAAGUUUGCAGAAAUUUUGCAAAUUAAUACCCCACAAGUAUC
..((((((.(.((.((..............((((((((....-...))))))))((((((((((...))))))))))....)))).).)))))) ( -28.70)
>DroSec_CAF1 15628 93 - 1
GUGGUGCUAGAGGUGGAGAAAAAAGUCUAAUCGAUACCUAUC-GAUAGCGUCGAAGUUUGCAGAAAUUUUGCAAAUGAAUACCGCACGCGGAUC
(((((((((.(((((..((...........))..)))))...-..))))......(((((((((...)))))))))....)))))......... ( -24.10)
>DroSim_CAF1 15168 93 - 1
GUGGUGCUAGAGGUGGAGAAAAAAGACUAAUCGAUACCUAUC-GAUAGCGUCGAAGUUUGCAGAAAUUUUGCAAAUGAAUACCGCACGAGGAUC
(((((((((.(((((..((...........))..)))))...-..))))......(((((((((...)))))))))....)))))......... ( -24.10)
>DroEre_CAF1 16333 91 - 1
GUGGUGUUAGAGGUGGUGGAAAAAAAAUAAUCGAUAUUUAUCCGCUGCUAUCGCAAU-UGCAGAAAUUUCUUAAGAAAAUACCAGA--AAUUGC
.(((((((.((((..(((((....(((((.....))))).)))))..)).))((...-.))................)))))))..--...... ( -20.30)
>DroYak_CAF1 16735 89 - 1
GUGGUGCUAGAGGUGGGGAAAAAUUAAUAAUCGAUGUUUAUGCG---CUAUCGCAAUUUGCUGAAAUUUCGCAAGAAAAUACCAGA--AAUUCU
(((((((((((.((.((.............)).)).)))).)))---)))).(.(((((.(((...((((....))))....))))--))))). ( -18.42)
>consensus
GUGGUGCUAGAGGUGGAGAAAAAAGAAUAAUCGAUACUUAUC_GAUAGCGUCGAAGUUUGCAGAAAUUUUGCAAAUAAAUACCACAC_AGUAUC
((((((........................(((((((..........)))))))..((((((((...))))))))....))))))......... (-10.26 = -11.90 +   1.64)

alignment

secondary structure

dotplot

Window 4

Location	13,046,217 – 13,046,335
Length	118
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	85.51
Mean single sequence MFE	-28.26
Consensus MFE	-18.56
Energy contribution	-18.12
Covariance contribution	-0.44
Combinations/Pair	1.29
Mean z-score	-1.87
Structure conservation index	0.66
SVM decision value	0.05
SVM RNA-class probability	0.559718
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13046217 118 - 22224390
ACUUACCGACAAAUUUUGAUGCCCAAGCAACAACACGCAUGUGGUGCUAGAGGUGGAAGAAAAAGAAUAAUCGAUGCUUAUC-GAUAGCGUCGAAGUUUGCAGAAAUUUUGCAAAUUAA
.(((.(((.....(((((..(((((.((........)).)).)))..))))).))))))...........((((((((....-...))))))))((((((((((...)))))))))).. ( -31.30)
>DroSec_CAF1 15643 118 - 1
ACUUACUGACAAAUUUUGAUGCCCAAGCAACAACACACAUGUGGUGCUAGAGGUGGAGAAAAAAGUCUAAUCGAUACCUAUC-GAUAGCGUCGAAGUUUGCAGAAAUUUUGCAAAUGAA
.....(((.((((((((((((((((((((....(((....))).)))).....))).............((((((....)))-))).))))))))))))))))................ ( -32.80)
>DroSim_CAF1 15183 118 - 1
ACUUACCGACAAAUUUUGAUGCCCAAGCAACAACACACAUGUGGUGCUAGAGGUGGAGAAAAAAGACUAAUCGAUACCUAUC-GAUAGCGUCGAAGUUUGCAGAAAUUUUGCAAAUGAA
......((((...((((..(((((.((((....(((....))).)))).).))))..))))...(.(((.(((((....)))-))))))))))..(((((((((...)))))))))... ( -31.60)
>DroEre_CAF1 16346 118 - 1
ACUUACCGACAAAUUUUGAUGCCCAAGCAACAACACACAUGUGGUGUUAGAGGUGGUGGAAAAAAAAUAAUCGAUAUUUAUCCGCUGCUAUCGCAAU-UGCAGAAAUUUCUUAAGAAAA
.((((.....(((((((..(((....((((((.(((....))).)))).((((..(((((....(((((.....))))).)))))..)).))))...-.))))))))))..)))).... ( -23.50)
>DroYak_CAF1 16748 116 - 1
ACUUACCGACAAUUUUUGAUGCCCAAGCAACAACACACAUGUGGUGCUAGAGGUGGGGAAAAAUUAAUAAUCGAUGUUUAUGCG---CUAUCGCAAUUUGCUGAAAUUUCGCAAGAAAA
......((.((((((((..(((((.((((....(((....))).)))).).))))..)))))..................((((---....))))..))).))...((((....)))). ( -22.10)
>consensus
ACUUACCGACAAAUUUUGAUGCCCAAGCAACAACACACAUGUGGUGCUAGAGGUGGAGAAAAAAGAAUAAUCGAUACUUAUC_GAUAGCGUCGAAGUUUGCAGAAAUUUUGCAAAUAAA
.......(.(((((((((((((...((((....(((....))).))))..(((((..((...........))..)))))........)))))))))))))).................. (-18.56 = -18.12 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:42 2006