Locus 6249

Sequence ID	3R_DroMel_CAF1
Location	16,298,800 – 16,298,956
Length	156
Max. P	0.985852

overview

Window 4

Location	16,298,800 – 16,298,916
Length	116
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.22
Mean single sequence MFE	-37.51
Consensus MFE	-35.65
Energy contribution	-35.65
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.33
Structure conservation index	0.95
SVM decision value	1.22
SVM RNA-class probability	0.931960
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16298800 116 + 27905053
UCACCCUGCCCCACAAUGGU---UCCGUUUCACUUCCAGGCUUCCAGACUUCCAGG-UUGCAGGCGGCAUGUUAACGUGCCGCCGCCCCUCGUUGCUGUCUCAAUAGUGACACUCACAUC
....((((........(((.---.((............))...)))......))))-..((.(((((((((....))))))))))).....((..((((....))))..))......... ( -34.54)
>DroSec_CAF1 20011 120 + 1
UCACCCUGCCCCACAAUGGUGGCUCCGUUUCACUUCCAGGCUUCCAGACUUCCAGGCUUGCAGGCGGCAUGAUAACGUGCCGCCGCCCCUCGUUGCUGUCUCAAUAGUGACACUCACAUC
.......(((((.....)).)))...((.(((((...((((.....(((....(((...((.(((((((((....))))))))))).))).)))...))))....))))).))....... ( -38.60)
>DroSim_CAF1 12185 120 + 1
UCACCCUGCCCCACAAUGGUGGCUCCGUUUCACUUCCAGGCUUCCAGACUUCCAGGCUUGCAGGCGGCAUGUUAACGUGCCGCCGCCCCUCGUUGCUGUCUCAAUAGUGACACUCACAUC
.......(((((.....)).)))...((.(((((...((((.....(((....(((...((.(((((((((....))))))))))).))).)))...))))....))))).))....... ( -39.40)
>consensus
UCACCCUGCCCCACAAUGGUGGCUCCGUUUCACUUCCAGGCUUCCAGACUUCCAGGCUUGCAGGCGGCAUGUUAACGUGCCGCCGCCCCUCGUUGCUGUCUCAAUAGUGACACUCACAUC
....((((......(((((.....))))).......)))).............(((...((.(((((((((....))))))))))).))).((..((((....))))..))......... (-35.65 = -35.65 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	16,298,837 – 16,298,956
Length	119
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	95.56
Mean single sequence MFE	-41.30
Consensus MFE	-39.57
Energy contribution	-39.90
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.94
Structure conservation index	0.96
SVM decision value	2.02
SVM RNA-class probability	0.985852
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16298837 119 + 27905053
CUUCCAGACUUCCAGG-UUGCAGGCGGCAUGUUAACGUGCCGCCGCCCCUCGUUGCUGUCUCAAUAGUGACACUCACAUCCGUGAAAUGCAAAUGUAUGCGUGCCUCCUGAACAUUAUGA
............((((-..((((((((((((....)))))))))((.....((..((((....))))..))..((((....)))).((((....)))))).)))..)))).......... ( -41.70)
>DroSec_CAF1 20051 120 + 1
CUUCCAGACUUCCAGGCUUGCAGGCGGCAUGAUAACGUGCCGCCGCCCCUCGUUGCUGUCUCAAUAGUGACACUCACAUCCGUGAAAUGCAAAUGUAUGCGUGCCUCCUGAACAUUAUGA
....(((......((((.(((((((((((((....)))))))))((.....((..((((....))))..))..((((....))))...)).......)))).)))).))).......... ( -40.70)
>DroSim_CAF1 12225 114 + 1
CUUCCAGACUUCCAGGCUUGCAGGCGGCAUGUUAACGUGCCGCCGCCCCUCGUUGCUGUCUCAAUAGUGACACUCACAUCCGUGAAAUGCAAAUGUAUGCGUGCCUCCUGAACA------
....(((......((((.(((((((((((((....)))))))))((.....((..((((....))))..))..((((....))))...)).......)))).)))).)))....------ ( -41.50)
>consensus
CUUCCAGACUUCCAGGCUUGCAGGCGGCAUGUUAACGUGCCGCCGCCCCUCGUUGCUGUCUCAAUAGUGACACUCACAUCCGUGAAAUGCAAAUGUAUGCGUGCCUCCUGAACAUUAUGA
....(((......((((.(((((((((((((....)))))))))((.....((..((((....))))..))..((((....))))...)).......)))).)))).))).......... (-39.57 = -39.90 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:16:43 2006