Locus 9827

Sequence ID	3R_DroMel_CAF1
Location	26,134,644 – 26,134,745
Length	101
Max. P	0.951004

overview

Window 5

Location	26,134,644 – 26,134,745
Length	101
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	88.28
Mean single sequence MFE	-39.08
Consensus MFE	-24.55
Energy contribution	-26.03
Covariance contribution	1.48
Combinations/Pair	1.03
Mean z-score	-4.59
Structure conservation index	0.63
SVM decision value	1.41
SVM RNA-class probability	0.951004
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26134644 101 + 27905053
CGAGGGAAAUCCUUAUCGCCAUCGCAUCCGGCUUGAAUUC------GAGUUCGAAUUCGAAUUCGCAUUCGAAUUGGAGACUGGAGGAAUUUCCGCUCGCCUGUCAU
((((((((((((.....((....)).((((((((.(((((------((((.(((((....))))).))))))))).))).))))))).)))))).))))........ ( -40.50)
>DroSec_CAF1 125175 95 + 1
CGAGGGAAAUCCUUAUCGCCAUUGCAUCCGGCUUGAAUUC------GAGUUCGAAUUCGAAU------UCGAAUUGGAGACUGGAGGAAUUUCCGCUCGCCUGUCAU
((((((((((((.....((....)).((((((((.(((((------(((((((....)))))------))))))).))).))))))).)))))).))))........ ( -42.20)
>DroSim_CAF1 131072 95 + 1
CGAGGGAAAUCCUUAUCGCCAUUGCAUCCGGCUUGAAUUC------GAGUUCGAAUUCGAAU------UCGAAUUGGAAACUGGAGGAAUUUCCGCUCGCCUGUCAU
((((((((((((.....((....)).(((((.((.(((((------(((((((....)))))------))))))).))..))))))).)))))).))))........ ( -37.40)
>DroEre_CAF1 133885 100 + 1
-GUGGGAAAUCCUUAUCGCCAUUGCAUCCGGCUUGAAUUCGUUUUCGAGUUCGAACUCGAAG------UCGAAUUCGAGACUGGAGGAAUUUCCGCUCGCCUGUCAU
-(((((((.(((.....((....)).(((((((((((((((.((((((((....))))))))------.)))))))))).)))))))).)))))))........... ( -44.40)
>DroYak_CAF1 132675 89 + 1
AGUGGGAAAUCCUUAUCGCCAUUGCAUCCGGCUUGAAUU------------UGAAUUCAAAU------UCGAAUUGGAGACUGAAGGAAUUUCCGCUCGCCUGUCAU
((((((((.(((((.((((....)).(((((.(((((((------------((....)))))------)))).)))))))...))))).)))))))).......... ( -30.90)
>consensus
CGAGGGAAAUCCUUAUCGCCAUUGCAUCCGGCUUGAAUUC______GAGUUCGAAUUCGAAU______UCGAAUUGGAGACUGGAGGAAUUUCCGCUCGCCUGUCAU
.(((((((((((.....((....)).((((((((.(((((........(((((....)))))........))))).))).))))))).)))))).)))......... (-24.55 = -26.03 +   1.48)

alignment

secondary structure

dotplot

Window 6

Location	26,134,644 – 26,134,745
Length	101
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	88.28
Mean single sequence MFE	-30.66
Consensus MFE	-22.18
Energy contribution	-22.50
Covariance contribution	0.32
Combinations/Pair	1.11
Mean z-score	-2.49
Structure conservation index	0.72
SVM decision value	1.05
SVM RNA-class probability	0.906883
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26134644 101 - 27905053
AUGACAGGCGAGCGGAAAUUCCUCCAGUCUCCAAUUCGAAUGCGAAUUCGAAUUCGAACUC------GAAUUCAAGCCGGAUGCGAUGGCGAUAAGGAUUUCCCUCG
........((((.((((((.(((...(((.(((..(((.((.((..((.(((((((....)------))))))))..)).)).)))))).))).))))))))))))) ( -33.90)
>DroSec_CAF1 125175 95 - 1
AUGACAGGCGAGCGGAAAUUCCUCCAGUCUCCAAUUCGA------AUUCGAAUUCGAACUC------GAAUUCAAGCCGGAUGCAAUGGCGAUAAGGAUUUCCCUCG
........((((.((((((.(((...(((...(((((((------.((((....)))).))------)))))...((((.......))))))).))))))))))))) ( -31.30)
>DroSim_CAF1 131072 95 - 1
AUGACAGGCGAGCGGAAAUUCCUCCAGUUUCCAAUUCGA------AUUCGAAUUCGAACUC------GAAUUCAAGCCGGAUGCAAUGGCGAUAAGGAUUUCCCUCG
........((((.((((((((.(((.((((..(((((((------.((((....)))).))------))))).)))).)))(((....)))....)))))))))))) ( -31.70)
>DroEre_CAF1 133885 100 - 1
AUGACAGGCGAGCGGAAAUUCCUCCAGUCUCGAAUUCGA------CUUCGAGUUCGAACUCGAAAACGAAUUCAAGCCGGAUGCAAUGGCGAUAAGGAUUUCCCAC-
...........(.((((((.(((...(((..(((((((.------.(((((((....)))))))..)))))))..((((.......))))))).))))))))))..- ( -32.80)
>DroYak_CAF1 132675 89 - 1
AUGACAGGCGAGCGGAAAUUCCUUCAGUCUCCAAUUCGA------AUUUGAAUUCA------------AAUUCAAGCCGGAUGCAAUGGCGAUAAGGAUUUCCCACU
...........(.((((((.((((..(((.(((....((------(((((....))------------)))))..((.....))..))).))))))))))))))... ( -23.60)
>consensus
AUGACAGGCGAGCGGAAAUUCCUCCAGUCUCCAAUUCGA______AUUCGAAUUCGAACUC______GAAUUCAAGCCGGAUGCAAUGGCGAUAAGGAUUUCCCUCG
.........(((.((((((.(((...(((((.(((((((........))))))).))..................((((.......))))))).)))))))))))). (-22.18 = -22.50 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:43:06 2006