Locus 6484

Sequence ID	2R_DroMel_CAF1
Location	20,235,331 – 20,235,459
Length	128
Max. P	0.988071

overview

Window 5

Location	20,235,331 – 20,235,421
Length	90
Sequences	3
Columns	90
Reading direction	forward
Mean pairwise identity	90.37
Mean single sequence MFE	-34.70
Consensus MFE	-30.24
Energy contribution	-30.80
Covariance contribution	0.56
Combinations/Pair	1.07
Mean z-score	-1.90
Structure conservation index	0.87
SVM decision value	0.31
SVM RNA-class probability	0.681256
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20235331 90 + 20766785
GUGGCUCUCUCGCCACCCACACACACUUACGUGCGCUUGCUCUCUCGCCUCUUUGGUCCUGCGAGGCAAGCAAGGCAGCGAGGGAGCGAA
...((((((((((..((....(((......))).((((((.(((.((((.....)))...).)))))))))..))..))))))))))... ( -39.90)
>DroSec_CAF1 28169 85 + 1
AUGGCUCUCUCACCACCCACACACACUACCGUGCGCUCGCUCUCUCGCCCAUUUGGUCCUGCGAGGCAAGCAAGGCAGCGAGGGA-----
.....((((((.(..((....(((......))).(((.((...(((((((....))....))))))).)))..))..).))))))----- ( -23.30)
>DroSim_CAF1 27356 90 + 1
GUGGCUCUCUCGCCACCCACACACACUACCGUGCGCUCGCUCUCUCGCCCAUUUGGUCCUGCGAGGCAGGCAAGGCAGCGAGGGAGCGAA
(((((......)))))...(.(((......))).).((((((((((((...((((..(((((...)))))))))...)))))))))))). ( -40.90)
>consensus
GUGGCUCUCUCGCCACCCACACACACUACCGUGCGCUCGCUCUCUCGCCCAUUUGGUCCUGCGAGGCAAGCAAGGCAGCGAGGGAGCGAA
...((((((((((..((....(((......))).(((.((...(((((((....))....))))))).)))..))..))))))))))... (-30.24 = -30.80 +   0.56)

alignment

secondary structure

dotplot

Window 6

Location	20,235,331 – 20,235,421
Length	90
Sequences	3
Columns	90
Reading direction	reverse
Mean pairwise identity	90.37
Mean single sequence MFE	-42.73
Consensus MFE	-40.67
Energy contribution	-41.23
Covariance contribution	0.56
Combinations/Pair	1.07
Mean z-score	-2.77
Structure conservation index	0.95
SVM decision value	2.10
SVM RNA-class probability	0.988071
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20235331 90 - 20766785
UUCGCUCCCUCGCUGCCUUGCUUGCCUCGCAGGACCAAAGAGGCGAGAGAGCAAGCGCACGUAAGUGUGUGUGGGUGGCGAGAGAGCCAC
...((((.(((((..((...((((((((...........))))))))....((.((((((....)))))).))))..))))).))))... ( -47.40)
>DroSec_CAF1 28169 85 - 1
-----UCCCUCGCUGCCUUGCUUGCCUCGCAGGACCAAAUGGGCGAGAGAGCGAGCGCACGGUAGUGUGUGUGGGUGGUGAGAGAGCCAU
-----((.(((((..((((((((..(((((....((....))))))).))))))((((((....))))))...))..))))).))..... ( -37.60)
>DroSim_CAF1 27356 90 - 1
UUCGCUCCCUCGCUGCCUUGCCUGCCUCGCAGGACCAAAUGGGCGAGAGAGCGAGCGCACGGUAGUGUGUGUGGGUGGCGAGAGAGCCAC
.((((((.(((((.......(((((...))))).((....))))))).))))))((((((....))))))....(((((......))))) ( -43.20)
>consensus
UUCGCUCCCUCGCUGCCUUGCUUGCCUCGCAGGACCAAAUGGGCGAGAGAGCGAGCGCACGGUAGUGUGUGUGGGUGGCGAGAGAGCCAC
...((((.(((((..((((((((..(((((............))))).))))))((((((....))))))...))..))))).))))... (-40.67 = -41.23 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	20,235,354 – 20,235,459
Length	105
Sequences	3
Columns	105
Reading direction	forward
Mean pairwise identity	85.03
Mean single sequence MFE	-47.87
Consensus MFE	-37.55
Energy contribution	-37.33
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-3.06
Structure conservation index	0.78
SVM decision value	1.60
SVM RNA-class probability	0.966426
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20235354 105 + 20766785
CACUUACGUGCGCUUGCUCUCUCGCCUCUUUGGUCCUGCGAGGCAAGCAAGGCAGCGAGGGAGCGAAGGUACCAAAGGAGCGAGUGAGCCUGUGUGCGUGAGUAG
.(((((((..(((..((((.(((((..((((((((((.((..((.......))..)).))))((....)).))))))..))))).))))..)))..))))))).. ( -56.50)
>DroSec_CAF1 28192 88 + 1
CACUACCGUGCGCUCGCUCUCUCGCCCAUUUGGUCCUGCGAGGCAAGCAAGGCAGCGAGGGA-----------------GCGAGUGAGCCUGUGUGCGUGAGUAG
(((....((.(((((((((((((((((....)).(((((.......)).)))..))))))))-----------------))))))).))..)))(((....))). ( -40.90)
>DroSim_CAF1 27379 104 + 1
CACUACCGUGCGCUCGCUCUCUCGCCCAUUUGGUCCUGCGAGGCAGGCAAGGCAGCGAGGGAGCGAAGG-AGCAAAGGAGCGAGUGAGCCUGUGUGCGUGAGUAG
.(((..((..(((((((((((((((...((((..(((((...)))))))))...))))))))))))(((-..((..........))..))))))..))..))).. ( -46.20)
>consensus
CACUACCGUGCGCUCGCUCUCUCGCCCAUUUGGUCCUGCGAGGCAAGCAAGGCAGCGAGGGAGCGAAGG_A_CAAAGGAGCGAGUGAGCCUGUGUGCGUGAGUAG
.(((..((..(((..((((.(((((((....))((((.((..((.......))..)).)))).................))))).))))..)))..))..))).. (-37.55 = -37.33 +  -0.22)

alignment

secondary structure

dotplot

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