Locus 5314

Sequence ID	3R_DroMel_CAF1
Location	13,900,907 – 13,901,050
Length	143
Max. P	0.994104

overview

Window 6

Location	13,900,907 – 13,900,997
Length	90
Sequences	3
Columns	91
Reading direction	forward
Mean pairwise identity	65.91
Mean single sequence MFE	-27.03
Consensus MFE	-12.02
Energy contribution	-13.13
Covariance contribution	1.11
Combinations/Pair	1.06
Mean z-score	-2.84
Structure conservation index	0.44
SVM decision value	2.45
SVM RNA-class probability	0.994104
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13900907 90 + 27905053
GAUGAGGAUCUGGAGAUCUGGAGAUCUGGGUAUCUGCGGAUCUGCGGAUCUA-CAGAUCGUCAGAUCGGGAAUCGCGAGCAGAGAGUCGGG
..(((.((((((.(((((((.(((((((........))))))).))))))).-)))))).)))..((((...((.......))...)))). ( -37.30)
>DroSim_CAF1 172034 68 + 1
GAUGAGGAUCUGGAGAUCUGGGGAUCUGCGGAU--------CUGGAGAUCGG-AUGAUCGGGA--------AUCGCGAGCUGAGA------
.....(((((((.(((((....))))).)))))--------)).....((((-....(((.(.--------..).))).))))..------ ( -22.70)
>DroYak_CAF1 183639 83 + 1
GAUGAGGAUCUGGAGAUCAGGUGAUCAAGAGAUCUGGAGAUCCGAAGAUCGAGAAGAUCGGGA--------AUCGCGAACUUAGUGUCGGG
(((..((((((..(((((............)))))..))))))...((((.....))))....--------))).(((.(.....)))).. ( -21.10)
>consensus
GAUGAGGAUCUGGAGAUCUGGAGAUCUGGGGAUCUG__GAUCUGAAGAUCGA_AAGAUCGGGA________AUCGCGAGCUGAGAGUCGGG
(((..((((((..(((((....)))))..))))))...........((((.....))))............)))................. (-12.02 = -13.13 +   1.11)

alignment

secondary structure

dotplot

Window 7

Location	13,900,907 – 13,900,997
Length	90
Sequences	3
Columns	91
Reading direction	reverse
Mean pairwise identity	65.91
Mean single sequence MFE	-18.33
Consensus MFE	-7.60
Energy contribution	-8.60
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.92
Structure conservation index	0.41
SVM decision value	1.77
SVM RNA-class probability	0.976572
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13900907 90 - 27905053
CCCGACUCUCUGCUCGCGAUUCCCGAUCUGACGAUCUG-UAGAUCCGCAGAUCCGCAGAUACCCAGAUCUCCAGAUCUCCAGAUCCUCAUC
...((...((((...(.((((...((((((...(((((-..((((....))))..)))))...))))))....)))).)))))...))... ( -25.20)
>DroSim_CAF1 172034 68 - 1
------UCUCAGCUCGCGAU--------UCCCGAUCAU-CCGAUCUCCAG--------AUCCGCAGAUCCCCAGAUCUCCAGAUCCUCAUC
------..............--------....((((..-..))))....(--------(((.(.(((((....))))).).))))...... ( -12.10)
>DroYak_CAF1 183639 83 - 1
CCCGACACUAAGUUCGCGAU--------UCCCGAUCUUCUCGAUCUUCGGAUCUCCAGAUCUCUUGAUCACCUGAUCUCCAGAUCCUCAUC
.........(((.(((.(..--------..)))).)))...((((....))))....(((((...((((....))))...)))))...... ( -17.70)
>consensus
CCCGACUCUCAGCUCGCGAU________UCCCGAUCUU_UCGAUCUCCAGAUC__CAGAUCCCCAGAUCACCAGAUCUCCAGAUCCUCAUC
................................((((.....((((....))))............((((....))))....))))...... ( -7.60 =  -8.60 +   1.00)

alignment

secondary structure

dotplot

Window 8

Location	13,900,959 – 13,901,050
Length	91
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	80.77
Mean single sequence MFE	-18.24
Consensus MFE	-12.21
Energy contribution	-13.05
Covariance contribution	0.84
Combinations/Pair	1.23
Mean z-score	-2.07
Structure conservation index	0.67
SVM decision value	0.93
SVM RNA-class probability	0.883668
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13900959 91 - 27905053
CGCUGACAGUUGGGCUACCACACUUUUCAUUUGU--CCCUCCAAUCUUUUCGAUGCCCGACUCUCUGCUCGCGAU-UCCCGAUCUGACGAUCUG-
.((.((.((((((((................((.--.....))(((.....))))))))))).)).)).......-....((((....))))..- ( -20.00)
>DroSec_CAF1 163174 92 - 1
CGCUGACAGUUGGGCUACCACACUUUUCAUUUGU--CCCUCCAAUCUUUUCGAUGCCCGACUCUCAGCUCGCGAUCUACCGAUCUCCCGAUCUA-
.(((((.((((((((................((.--.....))(((.....))))))))))).)))))(((.((((....))))...)))....- ( -25.40)
>DroEre_CAF1 163835 83 - 1
CGCUGACAGUUGGGCUACCACACUUUUCAUUUGU--CCCUCCAAUCUUUUCGAUGCCCGACUCUCAGUUCGCGAU---------GCCCGAUCUU-
.(((((.((((((((................((.--.....))(((.....))))))))))).)))))(((.(..---------..))))....- ( -19.40)
>DroYak_CAF1 183691 84 - 1
CGCUGACAGUUGGGCUACCACACUUUUCAUUUGU--CCCUCCAAUCUUUUCGAUGCCCGACACUAAGUUCGCGAU---------UCCCGAUCUUC
(((.(((.(((((((................((.--.....))(((.....)))))))))).....))).)))..---------........... ( -14.80)
>DroAna_CAF1 163972 84 - 1
CGCUGACAGUUGGGCUACCACACUUUCCAUUUAUUCCCCUCGAAUCCUCCCGAUUCUAGAUUCCCAAUCCCCGUU---------UCCCGAUU--C
.......(((((((..((.......................(((((.....)))))..(((.....)))...)).---------.)))))))--. ( -11.60)
>consensus
CGCUGACAGUUGGGCUACCACACUUUUCAUUUGU__CCCUCCAAUCUUUUCGAUGCCCGACUCUCAGUUCGCGAU_________UCCCGAUCUU_
.(((((.((((((((.......................................)))))))).)))))........................... (-12.21 = -13.05 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:47 2006