Locus 3137

Sequence ID	2L_DroMel_CAF1
Location	8,922,934 – 8,923,077
Length	143
Max. P	0.741319

overview

Window 4

Location	8,922,934 – 8,923,039
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.37
Mean single sequence MFE	-30.26
Consensus MFE	-21.16
Energy contribution	-21.02
Covariance contribution	-0.14
Combinations/Pair	1.11
Mean z-score	-1.50
Structure conservation index	0.70
SVM decision value	0.21
SVM RNA-class probability	0.636032
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8922934 105 + 22407834
---------------CAGAUAUCCGACUCCCAAAACAUCUCACAGCCAAAUGGCACACAGCACACGCAACGCAAACAGUUGGAGGUGCUGAAGGCCCGCACCGCCAACGGCGCCAUGCAG
---------------......(((((((................(((....))).....((....)).........)))))))(((((((..(((.......)))..)))))))...... ( -31.80)
>DroVir_CAF1 102191 114 + 1
UCUUGCCCGAUUUUGCAGAUAUCAGAUUCCCAAAAUAUCUCACAGCCGAAUGGCACACAGCACACACAGCGCAAACAAAUGGAGGUGCUG------CGCACCGCCAAUGGCGCCAUGCAG
...(((.......(((((((((............))))))....(((....))).....)))......((((.......(((.(((((..------.))))).)))...))))...))). ( -27.60)
>DroGri_CAF1 101536 111 + 1
U---GAUCAACAUUGCAGAUAUCGGAUUCACAAAAUAUCUCACAGCCGAAUGGCACACAGCACAUACAGCGCAAACAAAUGGAGGUACUA------CGAAGCGCCAAUGGUGCCAUGCAG
.---.........(((.....((((....................))))(((((((.((((.(.....).))...........((..((.------...))..))..)))))))))))). ( -23.85)
>DroWil_CAF1 196850 105 + 1
---------------CAGAUAUCCGAUUCCCAAAACAUCUCACAGCCAAAUGGCACACAGCACACACAGCGCAAACAGUUGGAGGUGCUGCAGGCACGCACCGCCAACGGCGCCAUGCAA
---------------.............................(((....))).....(((......((((.....(((((.(((((((....)).))))).))))).))))..))).. ( -31.40)
>DroYak_CAF1 137404 105 + 1
---------------CAGAUAUCCGACUCCCAAAACAUCUCACAGCCGAAUGGCACACAGCACACGCAGCGCAAACAGUUGGAGGUGCUGAAGGCCCGCACCGCCAACGGCGCCAUGCAG
---------------......(((((((................(((....))).....((.(.....).))....)))))))(((((((..(((.......)))..)))))))...... ( -31.50)
>DroMoj_CAF1 164964 114 + 1
UCUCGUGCGAUAUUGCAGAUAUCCGAUUCCCAAAAUAUCUCACAGCCGAAUGGCACACAGCACACACAGCGCAAGCAAAUGGAGGUGCUG------CGCACCGCCAAUGGCGCCAUGCAG
....(((.((((((...((........))....)))))).))).((...(((((.(.((((((.((..((....))...))...))))))------.)....(((...)))))))))).. ( -35.40)
>consensus
_______________CAGAUAUCCGAUUCCCAAAACAUCUCACAGCCGAAUGGCACACAGCACACACAGCGCAAACAAAUGGAGGUGCUG______CGCACCGCCAACGGCGCCAUGCAG
............................................(((....))).....(((......((((.....(.(((.(((((.........))))).))).).))))..))).. (-21.16 = -21.02 +  -0.14)

alignment

secondary structure

dotplot

Window 5

Location	8,922,959 – 8,923,077
Length	118
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	96.84
Mean single sequence MFE	-40.50
Consensus MFE	-37.10
Energy contribution	-37.43
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.15
Structure conservation index	0.92
SVM decision value	0.45
SVM RNA-class probability	0.741319
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8922959 118 + 22407834
CACAGCCAAAUGGCACACAGCACACGCAACGCAAACAGUUGGAGGUGCUGAAGGCCCGCACCGCCAACGGCGCCAUGCAGGUGAUCCGCACCCAGACAGUGCAAAAGAGUUCGUCCUC
....(((....))).....((((..(((.(((.....(((((.(((((.(.....).))))).))))).)))...))).((((.....))))......))))....(((......))) ( -39.50)
>DroSec_CAF1 133141 118 + 1
CACAGCCGAAUGGCACACAGCACACGCAACGCAAACAGUUGGAGGUGCUGAAGGCCCGCACCGCCAACGGCGCCAUGCAGGUGAUCCGCACCCAGACAGUCCAAAAGAGCUCGUCCUC
....((((..((((...((((((...((((.......))))...))))))..((......)))))).))))........((((.....))))..(((((..(....)..)).)))... ( -37.20)
>DroSim_CAF1 132183 118 + 1
CACAGCCGAAUGGCACACAGCACACGCAACGCAAACAGUUGGAGGUGCUGAAGGCCCGCACCGCCAACGGCGCCAUGCAGGUGAUCCGCACCCAGACCGUGCAAAAGAGCUCGUCCUC
....(((....))).....((((..(((.(((.....(((((.(((((.(.....).))))).))))).)))...))).((((.....))))......))))................ ( -38.60)
>DroEre_CAF1 141028 118 + 1
CACAGCCGAAUGGCACACAGCACACGCAGCGCAAACAGUUGGAGGUGCUGAAGGCCCGCACCGCCAACGGCGCCAUGCAGGUGAUCCGCACCCAGACCGUGCAAAAGAGCUCGUCCUC
....(((....))).....((((..(((((((.....(((((.(((((.(.....).))))).))))).))))..))).((((.....))))......))))................ ( -42.10)
>DroYak_CAF1 137429 118 + 1
CACAGCCGAAUGGCACACAGCACACGCAGCGCAAACAGUUGGAGGUGCUGAAGGCCCGCACCGCCAACGGCGCCAUGCAGGUGAUCCGCACCCAGACGGUGCAAAAGAGCUCGUCCUC
....(((....)))..(((((.((((((((((.....(((((.(((((.(.....).))))).))))).))))..)))..)))....(((((.....)))))......))).)).... ( -43.40)
>DroAna_CAF1 135493 118 + 1
CACAGCCGAACGGCACACAGCACACACAGCGCAAACAGUUGGAGGUGCUGAAGGCCCGCACCGCCAACGGCGCCAUGCAGGUGAUCCGCACCCAGACGGUGCAGAAGAGCUCCUCCUC
....(((....)))....(((.(((.((((((.....(((((.(((((.(.....).))))).))))).))))..))...))).((.(((((.....))))).))...)))....... ( -42.20)
>consensus
CACAGCCGAAUGGCACACAGCACACGCAACGCAAACAGUUGGAGGUGCUGAAGGCCCGCACCGCCAACGGCGCCAUGCAGGUGAUCCGCACCCAGACAGUGCAAAAGAGCUCGUCCUC
....(((....))).....((((..(((.(((.....(((((.(((((.(.....).))))).))))).)))...))).((((.....))))......))))....(((......))) (-37.10 = -37.43 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:11 2006