Locus 5803

Sequence ID	3R_DroMel_CAF1
Location	15,152,706 – 15,152,866
Length	160
Max. P	0.992946

overview

Window 5

Location	15,152,706 – 15,152,826
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	94.44
Mean single sequence MFE	-28.41
Consensus MFE	-25.25
Energy contribution	-26.37
Covariance contribution	1.11
Combinations/Pair	1.03
Mean z-score	-1.87
Structure conservation index	0.89
SVM decision value	0.18
SVM RNA-class probability	0.620987
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15152706 120 + 27905053
GAUCAAAAUCGAAUGAGUUUCACUUCGCUAAAAACAACUUCUGCUGAAGACGUUUUCAGAGACGGAAAAUGCAUCAUCAUAUGAAUUUUUUUGGCUCUGAUAACUUCUCCAGGACUGUCG
(((......((((((.....)).))))................(((.(((.(((.((((((.(((((((..(((......)))...))))))).)))))).))).))).)))....))). ( -25.60)
>DroSec_CAF1 76305 120 + 1
GAUCAAAAUCGAAUGAGCUUCACUUCGCUAAAAUCAACUUCUGCUGAAGAAAUUUUCAGAGACUGAAAAUGCAUCAUCAUAUGAAUUUUGUUGGCUCUGAAAACUUCUCCAGGUCUGCCG
((((......((...(((........)))....)).........((.((((.(((((((((.(..(.......((((...))))......)..)))))))))).)))).))))))..... ( -24.32)
>DroSim_CAF1 75333 120 + 1
GAUCAAAAUCGAAUGAGCUUCACUUCGCUAAAAUCAACUUCUGUUGAAGAAGUUUUCAGAGACUGAAAAUGCAUCAUCAUAUGAAUUUUUUUGGCUCUGAAAACUUCUCCAGGUCUGCCG
((((.....((((((.....)).))))......(((((....)))))((((((((((((((.(..((((....((((...))))...))))..)))))))))))))))...))))..... ( -35.30)
>consensus
GAUCAAAAUCGAAUGAGCUUCACUUCGCUAAAAUCAACUUCUGCUGAAGAAGUUUUCAGAGACUGAAAAUGCAUCAUCAUAUGAAUUUUUUUGGCUCUGAAAACUUCUCCAGGUCUGCCG
.........((((((.....)).))))................(((.((((((((((((((.(..((((....((((...))))...))))..))))))))))))))).)))........ (-25.25 = -26.37 +   1.11)

alignment

secondary structure

dotplot

Window 6

Location	15,152,706 – 15,152,826
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	94.44
Mean single sequence MFE	-32.50
Consensus MFE	-30.61
Energy contribution	-31.17
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-2.39
Structure conservation index	0.94
SVM decision value	1.37
SVM RNA-class probability	0.946951
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15152706 120 - 27905053
CGACAGUCCUGGAGAAGUUAUCAGAGCCAAAAAAAUUCAUAUGAUGAUGCAUUUUCCGUCUCUGAAAACGUCUUCAGCAGAAGUUGUUUUUAGCGAAGUGAAACUCAUUCGAUUUUGAUC
(((.(((((((((((.(((.((((((.(...(((((.(((......))).)))))..).)))))).))).)))))))..(((...(((((.........)))))...))))))))))... ( -27.10)
>DroSec_CAF1 76305 120 - 1
CGGCAGACCUGGAGAAGUUUUCAGAGCCAACAAAAUUCAUAUGAUGAUGCAUUUUCAGUCUCUGAAAAUUUCUUCAGCAGAAGUUGAUUUUAGCGAAGUGAAGCUCAUUCGAUUUUGAUC
........((((((((((((((((((.(...(((((.(((......))).)))))..).))))))))))))))))))..((((((((....(((........)))...)))))))).... ( -35.10)
>DroSim_CAF1 75333 120 - 1
CGGCAGACCUGGAGAAGUUUUCAGAGCCAAAAAAAUUCAUAUGAUGAUGCAUUUUCAGUCUCUGAAAACUUCUUCAACAGAAGUUGAUUUUAGCGAAGUGAAGCUCAUUCGAUUUUGAUC
.((....))(((((((((((((((((.(...(((((.(((......))).)))))..).)))))))))))))))))...((((((((....(((........)))...)))))))).... ( -35.30)
>consensus
CGGCAGACCUGGAGAAGUUUUCAGAGCCAAAAAAAUUCAUAUGAUGAUGCAUUUUCAGUCUCUGAAAACUUCUUCAGCAGAAGUUGAUUUUAGCGAAGUGAAGCUCAUUCGAUUUUGAUC
((((....((((((((((((((((((.(...(((((.(((......))).)))))..).)))))))))))))))))).....)))).......(((((((((.....))).))))))... (-30.61 = -31.17 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	15,152,746 – 15,152,866
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-39.21
Consensus MFE	-38.01
Energy contribution	-39.23
Covariance contribution	1.23
Combinations/Pair	1.05
Mean z-score	-3.35
Structure conservation index	0.97
SVM decision value	2.36
SVM RNA-class probability	0.992946
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15152746 120 + 27905053
CUGCUGAAGACGUUUUCAGAGACGGAAAAUGCAUCAUCAUAUGAAUUUUUUUGGCUCUGAUAACUUCUCCAGGACUGUCGCUCUUAUGGAGGUGAAACUCCUUCGAGUUUGGGCAUACUA
...(((.(((.(((.((((((.(((((((..(((......)))...))))))).)))))).))).))).)))...((((((((....((((......))))...))))...))))..... ( -35.20)
>DroSec_CAF1 76345 120 + 1
CUGCUGAAGAAAUUUUCAGAGACUGAAAAUGCAUCAUCAUAUGAAUUUUGUUGGCUCUGAAAACUUCUCCAGGUCUGCCGCUCCUAUGGAGGUGAAACUCCUUCGAGUUUGGGCAUACUA
...(((.((((.(((((((((.(..(.......((((...))))......)..)))))))))).)))).)))((.((((((((....((((......))))...))))...)))).)).. ( -37.62)
>DroSim_CAF1 75373 120 + 1
CUGUUGAAGAAGUUUUCAGAGACUGAAAAUGCAUCAUCAUAUGAAUUUUUUUGGCUCUGAAAACUUCUCCAGGUCUGCCGCUCCUAUGGAGGUGAAACUCCUUCGAGUUUGGGCAUACUA
....((.((((((((((((((.(..((((....((((...))))...))))..))))))))))))))).))(((.((((((((....((((......))))...))))...)))).))). ( -44.80)
>consensus
CUGCUGAAGAAGUUUUCAGAGACUGAAAAUGCAUCAUCAUAUGAAUUUUUUUGGCUCUGAAAACUUCUCCAGGUCUGCCGCUCCUAUGGAGGUGAAACUCCUUCGAGUUUGGGCAUACUA
...(((.((((((((((((((.(..((((....((((...))))...))))..))))))))))))))).)))((.((((((((....((((......))))...))))...)))).)).. (-38.01 = -39.23 +   1.23)

alignment

secondary structure

dotplot

Window 8

Location	15,152,746 – 15,152,866
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	95.00
Mean single sequence MFE	-38.47
Consensus MFE	-36.75
Energy contribution	-37.87
Covariance contribution	1.11
Combinations/Pair	1.02
Mean z-score	-3.93
Structure conservation index	0.96
SVM decision value	2.19
SVM RNA-class probability	0.989884
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15152746 120 - 27905053
UAGUAUGCCCAAACUCGAAGGAGUUUCACCUCCAUAAGAGCGACAGUCCUGGAGAAGUUAUCAGAGCCAAAAAAAUUCAUAUGAUGAUGCAUUUUCCGUCUCUGAAAACGUCUUCAGCAG
..((......((((((....))))))..((((.....))).)))....(((((((.(((.((((((.(...(((((.(((......))).)))))..).)))))).))).)))))))... ( -29.30)
>DroSec_CAF1 76345 120 - 1
UAGUAUGCCCAAACUCGAAGGAGUUUCACCUCCAUAGGAGCGGCAGACCUGGAGAAGUUUUCAGAGCCAACAAAAUUCAUAUGAUGAUGCAUUUUCAGUCUCUGAAAAUUUCUUCAGCAG
..((.((((.((((((....))))))...((((...)))).)))).))((((((((((((((((((.(...(((((.(((......))).)))))..).))))))))))))))))))... ( -43.10)
>DroSim_CAF1 75373 120 - 1
UAGUAUGCCCAAACUCGAAGGAGUUUCACCUCCAUAGGAGCGGCAGACCUGGAGAAGUUUUCAGAGCCAAAAAAAUUCAUAUGAUGAUGCAUUUUCAGUCUCUGAAAACUUCUUCAACAG
..((.((((.((((((....))))))...((((...)))).)))).)).(((((((((((((((((.(...(((((.(((......))).)))))..).))))))))))))))))).... ( -43.00)
>consensus
UAGUAUGCCCAAACUCGAAGGAGUUUCACCUCCAUAGGAGCGGCAGACCUGGAGAAGUUUUCAGAGCCAAAAAAAUUCAUAUGAUGAUGCAUUUUCAGUCUCUGAAAACUUCUUCAGCAG
.....((((.((((((....))))))...(((.....))).))))...((((((((((((((((((.(...(((((.(((......))).)))))..).))))))))))))))))))... (-36.75 = -37.87 +   1.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:10 2006