Locus 6646

Sequence ID	3R_DroMel_CAF1
Location	17,459,562 – 17,459,699
Length	137
Max. P	0.993768

overview

Window 6

Location	17,459,562 – 17,459,659
Length	97
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	95.71
Mean single sequence MFE	-29.30
Consensus MFE	-25.68
Energy contribution	-25.36
Covariance contribution	-0.32
Combinations/Pair	1.08
Mean z-score	-1.70
Structure conservation index	0.88
SVM decision value	1.43
SVM RNA-class probability	0.953319
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17459562 97 + 27905053
ACCGCUUCACCAUCUUCUUUAUCUUUAUCAGUUGUGUGCCAAGUGUUGCAUUGCGUUGCAGUGACGAC--AUUGUUGUAGUUGCAGCAGCACAGCAGCG
..............................(((((((((..(((((((((((((...)))))).))))--)))(((((....))))).))))).)))). ( -29.00)
>DroSec_CAF1 11989 97 + 1
UCCGCUUCCCCAUCUUCUUUAUCUUUAUCAGUUGUGUGCCAAGUGUUGCAUUGCGUUGCAGUGACGAC--AUUGUUGUAGUUGCAGCAGCGCUGCAGCG
..............................(((((((((..(((((((((((((...)))))).))))--)))(((((....))))).)))).))))). ( -28.20)
>DroSim_CAF1 13147 97 + 1
UCCGCUUCCCCAUCUUCUUUAUCUUUAUCAGUUGUGUGCCAAGUGUUGCAUUGCGUUGCAGUGACGAC--AUUGUUGUAGUUGCAGCAGCGCUGCAGCG
..............................(((((((((..(((((((((((((...)))))).))))--)))(((((....))))).)))).))))). ( -28.20)
>DroEre_CAF1 12149 97 + 1
UCCUCUUCCCCAUCUUAUUUAUCUUUAUCAGUUGUGUGCCAAGUGUUGCAUUGCGUUGCAGUGACGAC--AUUGUUGCAGUUGCAGCAGCGCUGCAGCG
..............................(((((((((..(((((((((((((...)))))).))))--)))(((((....))))).)))).))))). ( -30.40)
>DroYak_CAF1 12151 99 + 1
UCCUCUUCCCCAUCUUCCUUAUCUUUAUCAGUUGUGUGCCAAGUGUUGCAUUGCGUUGCAGUGACGACACAUUGUUGUAGUUGCAGCAGCGCUGCAGCG
..............................(((((((((...((((((((((((...)))))).))))))..((((((....)))))))))).))))). ( -30.70)
>consensus
UCCGCUUCCCCAUCUUCUUUAUCUUUAUCAGUUGUGUGCCAAGUGUUGCAUUGCGUUGCAGUGACGAC__AUUGUUGUAGUUGCAGCAGCGCUGCAGCG
..............................(((((((((.....((((((((((...)))))).))))....((((((....)))))))))).))))). (-25.68 = -25.36 +  -0.32)

alignment

secondary structure

dotplot

Window 7

Location	17,459,595 – 17,459,699
Length	104
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	94.85
Mean single sequence MFE	-39.22
Consensus MFE	-33.44
Energy contribution	-33.84
Covariance contribution	0.40
Combinations/Pair	1.06
Mean z-score	-2.25
Structure conservation index	0.85
SVM decision value	2.42
SVM RNA-class probability	0.993768
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17459595 104 + 27905053
GUGUGCCAAGUGUUGCAUUGCGUUGCAGUGACGAC--AUUGUUGUAGUUGCAGCAGCACAGCAGCGUUGCCGAUUUUCAGCGCCCCAUCAACAAGGGGUACACUUU
(((((((...((((((..((((((((((..(((((--...)))))..))))))).)))..)).((((((........))))))......))))...)))))))... ( -40.50)
>DroSec_CAF1 12022 104 + 1
GUGUGCCAAGUGUUGCAUUGCGUUGCAGUGACGAC--AUUGUUGUAGUUGCAGCAGCGCUGCAGCGUUGCCGAUUUUCAGCGCCCCAUCAACAAGGGGUUCACUUU
(((.(((...(((((((..(((((((.(..((.((--(....))).))..).)))))))))).((((((........))))))......))))...))).)))... ( -39.70)
>DroSim_CAF1 13180 104 + 1
GUGUGCCAAGUGUUGCAUUGCGUUGCAGUGACGAC--AUUGUUGUAGUUGCAGCAGCGCUGCAGCGUUGCCGAUUUUCAGCGCCCCAUCAACAAGGGGUUCACUUU
(((.(((...(((((((..(((((((.(..((.((--(....))).))..).)))))))))).((((((........))))))......))))...))).)))... ( -39.70)
>DroEre_CAF1 12182 104 + 1
GUGUGCCAAGUGUUGCAUUGCGUUGCAGUGACGAC--AUUGUUGCAGUUGCAGCAGCGCUGCAGCGUUGCCGAUUUUCAGAGCGCCACCAUCAAGGGGUUCAUUUU
...(((..(((((((((((((...)))))).))))--)))...)))((((((((...))))))))..............((((.((........)).))))..... ( -37.30)
>DroYak_CAF1 12184 106 + 1
GUGUGCCAAGUGUUGCAUUGCGUUGCAGUGACGACACAUUGUUGUAGUUGCAGCAGCGCUGCAGCGUUGCCGAUUUUCAGAGCCCCAUCAUCAAGGGGUUGAUUUU
...((.(((.(((((((.((((((((((..(((((.....)))))..))))))).))).)))))))))).))........((((((........))))))...... ( -38.90)
>consensus
GUGUGCCAAGUGUUGCAUUGCGUUGCAGUGACGAC__AUUGUUGUAGUUGCAGCAGCGCUGCAGCGUUGCCGAUUUUCAGCGCCCCAUCAACAAGGGGUUCACUUU
(((((.(((.(((((((.((((((((((..(((((.....)))))..))))))).))).)))))))))).)).........(((((........))))).)))... (-33.44 = -33.84 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:42 2006