Locus 9648

Sequence ID	3R_DroMel_CAF1
Location	25,512,061 – 25,512,185
Length	124
Max. P	0.989913

overview

Window 3

Location	25,512,061 – 25,512,165
Length	104
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	85.02
Mean single sequence MFE	-26.29
Consensus MFE	-21.20
Energy contribution	-21.40
Covariance contribution	0.20
Combinations/Pair	1.07
Mean z-score	-2.17
Structure conservation index	0.81
SVM decision value	1.36
SVM RNA-class probability	0.946141
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25512061 104 - 27905053
CGCAGGCCGGAAAAUUCCGAUCAGGCUUGACUCAAUGUGUACCUUGAUAUAGGGGGUUACAAAAUGAAUU-------------AACAAAACAAUUUGUAGUCAAGCAAAAAACGAUG
....(..((((....))))..)..((((((((...((((..((((......))))..)))).........-------------.(((((....)))))))))))))........... ( -26.10)
>DroSec_CAF1 5849 104 - 1
CGCAGGUCGGAAAAUUCCGAUCGGGGUUGACUCAAUGUGUACCUUGAUAUAGAGGGUUACAAAAUAAAUU-------------AACAAAACAAUUUGCAGUCAAGCAAAAAACGAUC
.((.(((((((....)))))))....(((((((((..(((.((((......))))((((..........)-------------)))...)))..))).))))))))........... ( -26.20)
>DroSim_CAF1 6866 104 - 1
CGCAGGUCGGAAAAUUCCGAUCGGGGUUGACUCAAUGUGUACCUUGAUAUAGAGGGUUACAAAAUAAAUU-------------AACAAAACAAUUUGUAGUCAAGCAAAAAACGAUG
.((.(((((((....)))))))....((((((...((((..((((......))))..))))..(((((((-------------........)))))))))))))))........... ( -26.70)
>DroEre_CAF1 6022 116 - 1
CGCAGGUCGGAAAAUUCCGAUCGGAGUUGACUCAAUGUGUACCUUGAUAUAGAGGGUUACAAAAUAAAUUGAAUCAGAGGCAUAAGCAAACAAAUUGCAGGCAAGCGAA-AACGGCG
(((.(((((((....)))))))....((((.(((((.((((((((.......)))).))))......))))).))))..((....((((.....))))..))..)))..-....... ( -29.40)
>DroYak_CAF1 6011 114 - 1
CGCAGGUCUGA--AUUCCGAUCAGAGUUGACUCAAUGUGUACCUUGAUAUAGGGGGUUACAAAACAAAUUG-AUCAGAGACAUAACAAAACAAUUUGUAGUCAAGCAAAAAACAAUG
.((...(((((--.......))))).((((((...((((..((((......))))..))))..((((((((-..................))))))))))))))))........... ( -23.07)
>consensus
CGCAGGUCGGAAAAUUCCGAUCGGGGUUGACUCAAUGUGUACCUUGAUAUAGAGGGUUACAAAAUAAAUU_____________AACAAAACAAUUUGUAGUCAAGCAAAAAACGAUG
.((.(((((((....)))))))....(((((((((..(((.((((......))))(((....)))........................)))..))).))))))))........... (-21.20 = -21.40 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	25,512,095 – 25,512,185
Length	90
Sequences	4
Columns	100
Reading direction	reverse
Mean pairwise identity	91.05
Mean single sequence MFE	-23.33
Consensus MFE	-21.31
Energy contribution	-21.25
Covariance contribution	-0.06
Combinations/Pair	1.11
Mean z-score	-2.47
Structure conservation index	0.91
SVM decision value	2.19
SVM RNA-class probability	0.989913
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25512095 90 - 27905053
AUAAUUUAUCAUUUAUUUAACGCAGGCCGGAAAAUUCCGAUCAGGCUUGACUCAAUGUGUACCUUGAUAUAGGGGGUUACAAAAUGAAUU----------
........((((((.......((.(..((((....))))..)..)).((((((..(((((......)))))..))))))..))))))...---------- ( -20.10)
>DroSec_CAF1 5883 90 - 1
AUAAUUUAUCAUUUAUUUAACGCAGGUCGGAAAAUUCCGAUCGGGGUUGACUCAAUGUGUACCUUGAUAUAGAGGGUUACAAAAUAAAUU----------
..........((((((((.((((((((((((....)))))))(((.....)))..))))).((((......))))......)))))))).---------- ( -23.90)
>DroSim_CAF1 6900 90 - 1
AUAAUUUAUCAUUUAUUUAACGCAGGUCGGAAAAUUCCGAUCGGGGUUGACUCAAUGUGUACCUUGAUAUAGAGGGUUACAAAAUAAAUU----------
..........((((((((.((((((((((((....)))))))(((.....)))..))))).((((......))))......)))))))).---------- ( -23.90)
>DroEre_CAF1 6058 100 - 1
AUAACUUAUCAUUUAUUUAACGCAGGUCGGAAAAUUCCGAUCGGAGUUGACUCAAUGUGUACCUUGAUAUAGAGGGUUACAAAAUAAAUUGAAUCAGAGG
........((((((((((.((((((((((((....))))))).(((....)))..))))).((((......))))......))))))).)))........ ( -25.40)
>consensus
AUAAUUUAUCAUUUAUUUAACGCAGGUCGGAAAAUUCCGAUCGGGGUUGACUCAAUGUGUACCUUGAUAUAGAGGGUUACAAAAUAAAUU__________
..........((((((((.((((((((((((....))))))).(((....)))..))))).((((......))))......))))))))........... (-21.31 = -21.25 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:39:05 2006