Locus 8374

Sequence ID	3R_DroMel_CAF1
Location	22,335,392 – 22,335,557
Length	165
Max. P	0.730931

overview

Window 1

Location	22,335,392 – 22,335,491
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	94.55
Mean single sequence MFE	-20.38
Consensus MFE	-17.36
Energy contribution	-17.24
Covariance contribution	-0.12
Combinations/Pair	1.17
Mean z-score	-1.40
Structure conservation index	0.85
SVM decision value	0.42
SVM RNA-class probability	0.730931
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22335392 99 + 27905053
UACACUCAACCUGAAGGAGAGACACGCUCAACCUGUUUGCCCCAUAACUCAUCUGAAGAGCGCUCUUCACGGAAAAAUAUAAAUUUUCCGCUACGAAAU
.....((........((((((...(((((.....(((........)))((....)).))))))))))).(((((((.......)))))))....))... ( -20.50)
>DroSec_CAF1 52236 99 + 1
UACACUCAACCUGAAGGAGAGACACGCUCAACCUGUUUGCCCCAUAACUCAUCUGAAGAGCACUCUUCACGGGAAAUUAUAAAUUUUCCGCUACGAAAU
.....((........((((((....((((.....(((........)))((....)).)))).)))))).((((((((.....))))))))....))... ( -18.90)
>DroSim_CAF1 51310 99 + 1
CACACUCAACCUGAAGGAGAGACACGCUCAACCUGUUUGCCCCAUAACUCAUCUGAAGAGCGCUCUUCACGGGAAAAUAUAAAUUUUCCGCUACGAAAU
.....((........((((((...(((((.....(((........)))((....)).)))))))))))...(((((((....))))))).....))... ( -20.50)
>DroEre_CAF1 54308 99 + 1
UACACUCCACCUGAAGGGGAGACACGUUCAACCUGUUUGCCUCAUAACUCAUCUGAAGAGCGUUCUUCACGGGAAAAUAUAAAUUUUCCGCUACGAAAU
....((((.((....))))))............(((..((.............(((((......)))))..(((((((....))))))))).))).... ( -20.60)
>DroYak_CAF1 53730 96 + 1
UACACUCCACCUGA---GGAGACACGCUCAACCUGUUUGCCUCAUAACUCAUCUGAAGAGCGCUCUUCACGGGAAAAUAUAAAUUUUCCGCUACGAAAU
.........(.(((---((((...(((((.....(((........)))((....)).)))))))))))).)(((((((....))))))).......... ( -21.40)
>consensus
UACACUCAACCUGAAGGAGAGACACGCUCAACCUGUUUGCCCCAUAACUCAUCUGAAGAGCGCUCUUCACGGGAAAAUAUAAAUUUUCCGCUACGAAAU
...............((((((...(((((.....(((........)))((....)).))))))))))).(((((((.......)))))))......... (-17.36 = -17.24 +  -0.12)

alignment

secondary structure

dotplot

Window 2

Location	22,335,464 – 22,335,557
Length	93
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	85.67
Mean single sequence MFE	-20.58
Consensus MFE	-12.92
Energy contribution	-14.36
Covariance contribution	1.44
Combinations/Pair	1.05
Mean z-score	-2.11
Structure conservation index	0.63
SVM decision value	0.09
SVM RNA-class probability	0.580507
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22335464 93 + 27905053
AAAAAUAUAAAUUUUCCGCUACGAAAUCCUGCCCUGAAGAGCCUCCAGCUCACCUGUGCCAUC---------CAGGCCAUCCGGGCCUUUAGAACAAAACAA
..............................((((.((.((((.....))))...((.(((...---------..))))))).))))................ ( -18.40)
>DroSec_CAF1 52308 102 + 1
GAAAUUAUAAAUUUUCCGCUACGAAAUCCUGCCCUGAAGAGCCUCCAGCUCACCUGUGCCAUCUUGGCCAACCAGGCCAUCCGGGCCAUCAGAACAAAACAA
((((........)))).............((..((((.((((.....))))...((.(((....(((((.....)))))....)))))))))..))...... ( -25.20)
>DroSim_CAF1 51382 102 + 1
GAAAAUAUAAAUUUUCCGCUACGAAAUCCUGCCCUGAAGAGCCUCCAGCUCACCUGAGCCAUCCAGGCCAACCAGGCCAUCCGGGCCAUCAGAACAAAACAA
((((((....)))))).............((..((((.(.((((...((((....))))......((((.....))))....))))).))))..))...... ( -25.50)
>DroEre_CAF1 54380 84 + 1
GAAAAUAUAAAUUUUCCGCUACGAAAUCCAGCCCUGAAGAGCCUCCAGCUCACCUGUGCCA------------------UCCGGGCCAUCAGAACAAAACAA
((((((....)))))).(((.........))).((((.((((.....))))...((.(((.------------------....))))))))).......... ( -15.90)
>DroYak_CAF1 53799 84 + 1
GAAAAUAUAAAUUUUCCGCUACGAAAUCCUGCCCUGAAGAGCCUCCAGCUCACCUGCGCCA------------------UGCGGGCCAUCAGAACAAAACAA
((((((....)))))).............((..((((.((((.....)))).(((((....------------------.)))))...))))..))...... ( -17.90)
>consensus
GAAAAUAUAAAUUUUCCGCUACGAAAUCCUGCCCUGAAGAGCCUCCAGCUCACCUGUGCCAUC_________CAGGCCAUCCGGGCCAUCAGAACAAAACAA
((((((....)))))).................((((.((((.....))))....(.(((.....((((.....)))).....)))).)))).......... (-12.92 = -14.36 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:01 2006