Locus 1184

Sequence ID	2R_DroMel_CAF1
Location	4,705,777 – 4,705,931
Length	154
Max. P	0.956562

overview

Window 0

Location	4,705,777 – 4,705,891
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.33
Mean single sequence MFE	-23.26
Consensus MFE	-19.88
Energy contribution	-20.92
Covariance contribution	1.04
Combinations/Pair	1.04
Mean z-score	-1.77
Structure conservation index	0.85
SVM decision value	1.45
SVM RNA-class probability	0.955053
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4705777 114 + 20766785
GCUCGUAAAAGAUUUCAAACACCCAAACGUGACCAAUGCCAAUUUGCGCUCCAAUCAAUGGACGCCUCGUCACUUAUGGCCAAAAAUUUGGUCAAUUACGAUCAAUU------AAGCCAU
(.((((((....................(((((....((......))((((((.....)))).))...)))))...(((((((....))))))).)))))).)....------....... ( -26.20)
>DroSec_CAF1 15492 114 + 1
GCUCGUAAAAGAUUUCAAACAUCCAAACGUGACCAAUGCCAAUUUGCGCUCCAAUCAAUGGACACCUCGACACUUAUGGCCAAAAAUUUGGUCAACUACGAUCAAUU------AAGCCAC
(.(((((.....................(((......((......))(.((((.....))))).......)))...(((((((....)))))))..))))).)....------....... ( -18.60)
>DroSim_CAF1 15821 114 + 1
GCUCGUAAAAGAUUUCAAACACCCAAACGUGACCAAUGCCAAUUUGCGCUCCAAUCAAUGGACGCCUCGACACUUAUGGCCAAAAAUUUGGUCAAUUACGAUCAAUU------AAGCCAU
(.(((((((((........(((......)))..............(((.((((.....))))))).......))).(((((((....))))))).)))))).)....------....... ( -22.90)
>DroEre_CAF1 15216 114 + 1
GCUCGUAAAAGAUUUCAAACACCGAAACGUGACCAAUGCCAAUUUUCGCUCCAAUCAAUGGACGCCUCGUCACUUAUGGCCAAAAAUUUGGUCAAUUACGAUCAAUU------AAGCCAU
(.((((((....................(((((.(((....)))...((((((.....)))).))...)))))...(((((((....))))))).)))))).)....------....... ( -23.40)
>DroYak_CAF1 15321 120 + 1
GCUCGUAAAAGAUUUCAAACACCCAAACGUGACCAAUGCCAAUUCGCGCUCCAAUCAAUGGACGCCUCUUCACUUAUGGCCAAAAAUUUGGUCAAUUAUGAUCAAUUACGAUCAAGCCAU
(.((((((..((((..............((((.....((......))((((((.....)))).))....))))...(((((((....))))))).....))))..)))))).)....... ( -25.20)
>consensus
GCUCGUAAAAGAUUUCAAACACCCAAACGUGACCAAUGCCAAUUUGCGCUCCAAUCAAUGGACGCCUCGUCACUUAUGGCCAAAAAUUUGGUCAAUUACGAUCAAUU______AAGCCAU
(.((((((....................(((((....((......))((((((.....)))).))...)))))...(((((((....))))))).)))))).)................. (-19.88 = -20.92 +   1.04)

alignment

secondary structure

dotplot

Window 1

Location	4,705,817 – 4,705,931
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.10
Mean single sequence MFE	-27.32
Consensus MFE	-21.59
Energy contribution	-22.15
Covariance contribution	0.56
Combinations/Pair	1.10
Mean z-score	-2.23
Structure conservation index	0.79
SVM decision value	1.47
SVM RNA-class probability	0.956562
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4705817 114 + 20766785
AAUUUGCGCUCCAAUCAAUGGACGCCUCGUCACUUAUGGCCAAAAAUUUGGUCAAUUACGAUCAAUU------AAGCCAUACACAUGCAAAUUAUUGCCACCUGCUGCGCGAAGAACGAU
..(((((((..((....(((((((...))))...((((((.......((((((......))))))..------..))))))..)))((((....))))....))..)))))))....... ( -28.50)
>DroSec_CAF1 15532 114 + 1
AAUUUGCGCUCCAAUCAAUGGACACCUCGACACUUAUGGCCAAAAAUUUGGUCAACUACGAUCAAUU------AAGCCACACACAUGCAAAUUAUUGCCACCUGCUGGGCGAAGAACGAU
((((((((.((((.....))))).............((((.......((((((......))))))..------..)))).......))))))).(((((........)))))........ ( -24.70)
>DroSim_CAF1 15861 114 + 1
AAUUUGCGCUCCAAUCAAUGGACGCCUCGACACUUAUGGCCAAAAAUUUGGUCAAUUACGAUCAAUU------AAGCCAUACACAUGCAAAUUAUUGCCACCUGCUGGGCAAAGAACGAU
(((((((((((((.....)))).)).........((((((.......((((((......))))))..------..)))))).....))))))).(((((........)))))........ ( -29.70)
>DroEre_CAF1 15256 114 + 1
AAUUUUCGCUCCAAUCAAUGGACGCCUCGUCACUUAUGGCCAAAAAUUUGGUCAAUUACGAUCAAUU------AAGCCAUACACAUGCAAAUUAUUGCCACCUGCUGCGUGAAAAGCAAU
..(((((((((((.....)))).((.........((((((.......((((((......))))))..------..)))))).....((((....))))........)))))))))..... ( -24.30)
>DroYak_CAF1 15361 120 + 1
AAUUCGCGCUCCAAUCAAUGGACGCCUCUUCACUUAUGGCCAAAAAUUUGGUCAAUUAUGAUCAAUUACGAUCAAGCCAUACACAUGCAAAUGAUUGCCACCUGCUGCGUGAAAAACGAU
..(((((((..((....((((.(.............(((((((....)))))))....(((((......))))).)))))......((((....))))....))..)))))))....... ( -29.40)
>consensus
AAUUUGCGCUCCAAUCAAUGGACGCCUCGUCACUUAUGGCCAAAAAUUUGGUCAAUUACGAUCAAUU______AAGCCAUACACAUGCAAAUUAUUGCCACCUGCUGCGCGAAGAACGAU
..(((((((((((.....)))).((.........((((((.......((((((......))))))..........)))))).....((((....)))).....)).)))))))....... (-21.59 = -22.15 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	4,705,817 – 4,705,931
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.10
Mean single sequence MFE	-33.32
Consensus MFE	-28.46
Energy contribution	-27.78
Covariance contribution	-0.68
Combinations/Pair	1.20
Mean z-score	-1.61
Structure conservation index	0.85
SVM decision value	1.08
SVM RNA-class probability	0.912573
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4705817 114 - 20766785
AUCGUUCUUCGCGCAGCAGGUGGCAAUAAUUUGCAUGUGUAUGGCUU------AAUUGAUCGUAAUUGACCAAAUUUUUGGCCAUAAGUGACGAGGCGUCCAUUGAUUGGAGCGCAAAUU
.((((((((.(((((((((((.......)))))).)))))((((((.------((((..(((....)))...))))...))))))))).))))).(((((((.....)))).)))..... ( -34.10)
>DroSec_CAF1 15532 114 - 1
AUCGUUCUUCGCCCAGCAGGUGGCAAUAAUUUGCAUGUGUGUGGCUU------AAUUGAUCGUAGUUGACCAAAUUUUUGGCCAUAAGUGUCGAGGUGUCCAUUGAUUGGAGCGCAAAUU
.........(((((((..(((((((....(((((((...(((((((.------((((..(((....)))...))))...))))))).))).)))).)).)))))..)))).)))...... ( -31.50)
>DroSim_CAF1 15861 114 - 1
AUCGUUCUUUGCCCAGCAGGUGGCAAUAAUUUGCAUGUGUAUGGCUU------AAUUGAUCGUAAUUGACCAAAUUUUUGGCCAUAAGUGUCGAGGCGUCCAUUGAUUGGAGCGCAAAUU
.(((....((((((.....).)))))......((((...(((((((.------((((..(((....)))...))))...))))))).))))))).(((((((.....)))).)))..... ( -30.10)
>DroEre_CAF1 15256 114 - 1
AUUGCUUUUCACGCAGCAGGUGGCAAUAAUUUGCAUGUGUAUGGCUU------AAUUGAUCGUAAUUGACCAAAUUUUUGGCCAUAAGUGACGAGGCGUCCAUUGAUUGGAGCGAAAAUU
....(((.(((((((((((((.......)))))).))).(((((((.------((((..(((....)))...))))...))))))).)))).)))((.((((.....))))))....... ( -31.50)
>DroYak_CAF1 15361 120 - 1
AUCGUUUUUCACGCAGCAGGUGGCAAUCAUUUGCAUGUGUAUGGCUUGAUCGUAAUUGAUCAUAAUUGACCAAAUUUUUGGCCAUAAGUGAAGAGGCGUCCAUUGAUUGGAGCGCGAAUU
.((.((((((((((((((((((.....))))))).))).((((((.((((((....))))))........(((....))))))))).))))))))(((((((.....)))).)))))... ( -39.40)
>consensus
AUCGUUCUUCGCGCAGCAGGUGGCAAUAAUUUGCAUGUGUAUGGCUU______AAUUGAUCGUAAUUGACCAAAUUUUUGGCCAUAAGUGACGAGGCGUCCAUUGAUUGGAGCGCAAAUU
....(((.((((...(((.(((.(((....)))))).)))((((((.........(((.(((....))).)))......))))))..)))).)))(((((((.....)))).)))..... (-28.46 = -27.78 +  -0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:32 2006