Locus 5238

Sequence ID	2L_DroMel_CAF1
Location	14,786,639 – 14,786,774
Length	135
Max. P	0.999774

overview

Window 7

Location	14,786,639 – 14,786,737
Length	98
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	97.55
Mean single sequence MFE	-30.72
Consensus MFE	-28.90
Energy contribution	-29.30
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.71
Structure conservation index	0.94
SVM decision value	4.05
SVM RNA-class probability	0.999774
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14786639 98 + 22407834
CAGUCCAGCGCACAACUUCACAGGUGCCAAAUGACAACAACAAAUUGCCCGAUUGCCUUCGCUCCUGGGCAAAAGUGUUGUCCUUUCCGCUCCUGUCG
...................(((((.((.(((.(((((((.....(((((((...((....))...)))))))...))))))).)))..)).))))).. ( -30.10)
>DroSec_CAF1 33145 98 + 1
CAGUCCAGCGCACAACUUUACAGGUGCCAAAUGACAACAACAAAUUGCCCGAUUGCCUUCGCUACUGGGCAAAAGUGUUGUCCUUUCCGCUCCUGUCG
...................(((((.((.(((.(((((((.....(((((((...((....))...)))))))...))))))).)))..)).))))).. ( -30.00)
>DroSim_CAF1 31217 98 + 1
CAGUCCAGCGCACAACUUCACAGGUGCCAAAUGACAACAACAAAUUGCCCGAUUGCCUUCGCUACUGGGCAAAAGUGUUGUCCUUUCCGCUCCUGUCG
...................(((((.((.(((.(((((((.....(((((((...((....))...)))))))...))))))).)))..)).))))).. ( -30.10)
>DroEre_CAF1 25950 98 + 1
CAGUGCAGCGCACAACUUCACAGGUGCCAACUGACAACAACAAAUUGCCCGAUUGCCUUCGCUCCUGGGCAAAAGUGUUGUCCUUUCCGCUCCUGUCG
..((((...))))......(((((.((.....(((((((.....(((((((...((....))...)))))))...)))))))......)).))))).. ( -33.50)
>DroYak_CAF1 30304 98 + 1
CAGUGCAGCGCACAACUUCACAGGUGCCAAAUGACAACAACAAAUUGCCCGAUUGCCUUCGCUCCUGGGCAAAAGUGUCGUCCUUUCCGCUCCUGUCG
..((((...))))......(((((.((.(((.(((.(((.....(((((((...((....))...)))))))...))).))).)))..)).))))).. ( -29.90)
>consensus
CAGUCCAGCGCACAACUUCACAGGUGCCAAAUGACAACAACAAAUUGCCCGAUUGCCUUCGCUCCUGGGCAAAAGUGUUGUCCUUUCCGCUCCUGUCG
...................(((((.((.(((.(((((((.....(((((((...((....))...)))))))...))))))).)))..)).))))).. (-28.90 = -29.30 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	14,786,639 – 14,786,737
Length	98
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	97.55
Mean single sequence MFE	-38.08
Consensus MFE	-35.32
Energy contribution	-35.16
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-2.76
Structure conservation index	0.93
SVM decision value	3.91
SVM RNA-class probability	0.999697
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14786639 98 - 22407834
CGACAGGAGCGGAAAGGACAACACUUUUGCCCAGGAGCGAAGGCAAUCGGGCAAUUUGUUGUUGUCAUUUGGCACCUGUGAAGUUGUGCGCUGGACUG
..(((((.((.(((..((((((((..((((((.(..((....))..).))))))...).))))))).))).)).)))))..((((........)))). ( -36.60)
>DroSec_CAF1 33145 98 - 1
CGACAGGAGCGGAAAGGACAACACUUUUGCCCAGUAGCGAAGGCAAUCGGGCAAUUUGUUGUUGUCAUUUGGCACCUGUAAAGUUGUGCGCUGGACUG
..(((((.((.(((..((((((((..((((((.((.((....)).)).))))))...).))))))).))).)).)))))..((((........)))). ( -37.70)
>DroSim_CAF1 31217 98 - 1
CGACAGGAGCGGAAAGGACAACACUUUUGCCCAGUAGCGAAGGCAAUCGGGCAAUUUGUUGUUGUCAUUUGGCACCUGUGAAGUUGUGCGCUGGACUG
..(((((.((.(((..((((((((..((((((.((.((....)).)).))))))...).))))))).))).)).)))))..((((........)))). ( -37.70)
>DroEre_CAF1 25950 98 - 1
CGACAGGAGCGGAAAGGACAACACUUUUGCCCAGGAGCGAAGGCAAUCGGGCAAUUUGUUGUUGUCAGUUGGCACCUGUGAAGUUGUGCGCUGCACUG
..(((((.((.((...((((((((..((((((.(..((....))..).))))))...).)))))))..)).)).)))))......((((...)))).. ( -39.70)
>DroYak_CAF1 30304 98 - 1
CGACAGGAGCGGAAAGGACGACACUUUUGCCCAGGAGCGAAGGCAAUCGGGCAAUUUGUUGUUGUCAUUUGGCACCUGUGAAGUUGUGCGCUGCACUG
..(((((.((.(((..((((((((..((((((.(..((....))..).))))))...).))))))).))).)).)))))......((((...)))).. ( -38.70)
>consensus
CGACAGGAGCGGAAAGGACAACACUUUUGCCCAGGAGCGAAGGCAAUCGGGCAAUUUGUUGUUGUCAUUUGGCACCUGUGAAGUUGUGCGCUGGACUG
..(((((.((.((...((((((((..((((((....((....))....))))))...).)))))))..)).)).)))))................... (-35.32 = -35.16 +  -0.16)

alignment

secondary structure

dotplot

Window 9

Location	14,786,669 – 14,786,774
Length	105
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	96.00
Mean single sequence MFE	-33.57
Consensus MFE	-31.49
Energy contribution	-32.18
Covariance contribution	0.70
Combinations/Pair	1.03
Mean z-score	-1.88
Structure conservation index	0.94
SVM decision value	2.72
SVM RNA-class probability	0.996604
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14786669 105 + 22407834
AUGACAACAACAAAUUGCCCGAUUGCCUUCGCUCCUGGGCAAAAGUGUUGUCCUUUCCGCUCCUGUCGAUGACGAUGUCGACAUAUGGAAAUGCUGAUGGAUGCA
..(((((((.....(((((((...((....))...)))))))...))))))).((((((....(((((((......)))))))..))))))(((........))) ( -34.80)
>DroSec_CAF1 33175 105 + 1
AUGACAACAACAAAUUGCCCGAUUGCCUUCGCUACUGGGCAAAAGUGUUGUCCUUUCCGCUCCUGUCGAUGACGAUGUCGACAUAUGGAAAUGCUGAUGGAUGCA
..(((((((.....(((((((...((....))...)))))))...))))))).((((((....(((((((......)))))))..))))))(((........))) ( -34.80)
>DroSim_CAF1 31247 105 + 1
AUGACAACAACAAAUUGCCCGAUUGCCUUCGCUACUGGGCAAAAGUGUUGUCCUUUCCGCUCCUGUCGAUGACGAUGUCGACAUAUGGAAAUGCUGAUGGAUGCA
..(((((((.....(((((((...((....))...)))))))...))))))).((((((....(((((((......)))))))..))))))(((........))) ( -34.80)
>DroEre_CAF1 25980 105 + 1
CUGACAACAACAAAUUGCCCGAUUGCCUUCGCUCCUGGGCAAAAGUGUUGUCCUUUCCGCUCCUGUCGAUGACGAUGUCGACAUAUGGAAAUGCUGAUGGAUGCA
..(((((((.....(((((((...((....))...)))))))...))))))).((((((....(((((((......)))))))..))))))(((........))) ( -34.80)
>DroYak_CAF1 30334 105 + 1
AUGACAACAACAAAUUGCCCGAUUGCCUUCGCUCCUGGGCAAAAGUGUCGUCCUUUCCGCUCCUGUCGAUGACGAUGUCGACAUAUGGAAAUGCUGAUGGAUGCA
..((((........(((((((...((....))...)))))))...))))((((..((.((((((((((((......)))))))...)))...)).)).))))... ( -31.60)
>DroAna_CAF1 22829 105 + 1
AUGACAACAACAAAUUGCCCGAUUGCCUCCGCUCCAGGGCAAGAGGGUUGUCCUUGCCGAUGCUGUCGAUGACGAUGUCGACAUAUGGAAAUACUGAUGGAUGCG
..((((((......((((((....((....))....))))))....))))))....((.(((.(((((((......))))))))))))................. ( -30.60)
>consensus
AUGACAACAACAAAUUGCCCGAUUGCCUUCGCUCCUGGGCAAAAGUGUUGUCCUUUCCGCUCCUGUCGAUGACGAUGUCGACAUAUGGAAAUGCUGAUGGAUGCA
..(((((((.....(((((((...((....))...)))))))...))))))).((((((....(((((((......)))))))..))))))(((........))) (-31.49 = -32.18 +   0.70)

alignment

secondary structure

dotplot

Window 0

Location	14,786,669 – 14,786,774
Length	105
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	96.00
Mean single sequence MFE	-35.52
Consensus MFE	-33.03
Energy contribution	-33.25
Covariance contribution	0.22
Combinations/Pair	1.06
Mean z-score	-2.43
Structure conservation index	0.93
SVM decision value	3.61
SVM RNA-class probability	0.999449
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14786669 105 - 22407834
UGCAUCCAUCAGCAUUUCCAUAUGUCGACAUCGUCAUCGACAGGAGCGGAAAGGACAACACUUUUGCCCAGGAGCGAAGGCAAUCGGGCAAUUUGUUGUUGUCAU
(((........)))(((((...((((((........)))))).....))))).((((((((..((((((.(..((....))..).))))))...).))))))).. ( -36.10)
>DroSec_CAF1 33175 105 - 1
UGCAUCCAUCAGCAUUUCCAUAUGUCGACAUCGUCAUCGACAGGAGCGGAAAGGACAACACUUUUGCCCAGUAGCGAAGGCAAUCGGGCAAUUUGUUGUUGUCAU
(((........)))(((((...((((((........)))))).....))))).((((((((..((((((.((.((....)).)).))))))...).))))))).. ( -37.20)
>DroSim_CAF1 31247 105 - 1
UGCAUCCAUCAGCAUUUCCAUAUGUCGACAUCGUCAUCGACAGGAGCGGAAAGGACAACACUUUUGCCCAGUAGCGAAGGCAAUCGGGCAAUUUGUUGUUGUCAU
(((........)))(((((...((((((........)))))).....))))).((((((((..((((((.((.((....)).)).))))))...).))))))).. ( -37.20)
>DroEre_CAF1 25980 105 - 1
UGCAUCCAUCAGCAUUUCCAUAUGUCGACAUCGUCAUCGACAGGAGCGGAAAGGACAACACUUUUGCCCAGGAGCGAAGGCAAUCGGGCAAUUUGUUGUUGUCAG
(((........)))(((((...((((((........)))))).....))))).((((((((..((((((.(..((....))..).))))))...).))))))).. ( -36.10)
>DroYak_CAF1 30334 105 - 1
UGCAUCCAUCAGCAUUUCCAUAUGUCGACAUCGUCAUCGACAGGAGCGGAAAGGACGACACUUUUGCCCAGGAGCGAAGGCAAUCGGGCAAUUUGUUGUUGUCAU
(((........)))(((((...((((((........)))))).....))))).((((((((..((((((.(..((....))..).))))))...).))))))).. ( -35.80)
>DroAna_CAF1 22829 105 - 1
CGCAUCCAUCAGUAUUUCCAUAUGUCGACAUCGUCAUCGACAGCAUCGGCAAGGACAACCCUCUUGCCCUGGAGCGGAGGCAAUCGGGCAAUUUGUUGUUGUCAU
.((........((((....))))(((((........))))).))...(((((.((((((((..((((((((...))).)))))..)))....))))).))))).. ( -30.70)
>consensus
UGCAUCCAUCAGCAUUUCCAUAUGUCGACAUCGUCAUCGACAGGAGCGGAAAGGACAACACUUUUGCCCAGGAGCGAAGGCAAUCGGGCAAUUUGUUGUUGUCAU
(((........)))(((((...((((((........)))))).....))))).((((((((..((((((.(..((....))..).))))))...).))))))).. (-33.03 = -33.25 +   0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:27 2006