Locus 3277

Sequence ID	X_DroMel_CAF1
Location	8,714,190 – 8,714,359
Length	169
Max. P	0.960429

overview

Window 0

Location	8,714,190 – 8,714,280
Length	90
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	80.48
Mean single sequence MFE	-18.57
Consensus MFE	-14.31
Energy contribution	-14.88
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-2.16
Structure conservation index	0.77
SVM decision value	1.51
SVM RNA-class probability	0.960429
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8714190 90 + 22224390
CCACAUCCA------------------------------CAGCCAAGAUCACAUCCACAACCACGAGUUUAAAUAUCUUAAAUGCCUCGAGAAGCUCACUCGAUGGCUUCGCGGAAAUUC
.........------------------------------.....................((.(((((((((.....))))))((((((((.......))))).))).))).))...... ( -17.50)
>DroSec_CAF1 149272 90 + 1
CCACAUCCA------------------------------CAACCAAGAUCGCAUCCACAUCCACGAGUUUAAAUAUCUUAAAUGCCUCGAGAAGCUCACUCGAUGGCUUCGAGGAAAUUC
.........------------------------------....................(((.(((((((((.....))))))((((((((.......))))).))).))).)))..... ( -18.10)
>DroSim_CAF1 114358 90 + 1
CCACAUCCA------------------------------CAACCAAGAUCACAUCCACAUCCACGAGUUUAAAUGUCUUAAAUGCCUCGAGAAGCUCACUCGAUGGCUUCGCGGAAAUUC
.........------------------------------....................(((.(((((((((.....))))))((((((((.......))))).))).))).)))..... ( -18.90)
>DroYak_CAF1 157015 120 + 1
CCACAUCCACAUCCACAUCCUCAUCCACAUCCACUUCAACAACGAAGAGCACAUGCACAUCCAUGAGUUUAAAUAUCUUAAAUGCCUCUAGAAGCUCACUCGCUGGCUUCGCGGAAAUUC
...........(((.(...(((((.........((((......)))).((....))......))))).......................((((((........))))))).)))..... ( -19.80)
>consensus
CCACAUCCA______________________________CAACCAAGAUCACAUCCACAUCCACGAGUUUAAAUAUCUUAAAUGCCUCGAGAAGCUCACUCGAUGGCUUCGCGGAAAUUC
...........................................................(((.(((((((((.....))))))((((((((.......))))).))).))).)))..... (-14.31 = -14.88 +   0.56)

alignment

secondary structure

dotplot

Window 1

Location	8,714,240 – 8,714,359
Length	119
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	88.11
Mean single sequence MFE	-38.42
Consensus MFE	-25.48
Energy contribution	-26.80
Covariance contribution	1.32
Combinations/Pair	1.10
Mean z-score	-2.31
Structure conservation index	0.66
SVM decision value	0.18
SVM RNA-class probability	0.622350
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8714240 119 + 22224390
AAUGCCUCGAGAAGCUCACUCGAUGGCUUCGCGGAAAUUCUGCUUUGAAAAGUGCCGCCUAGCCAGGCUGUCACCAUCGAUAAAGUUGGAAAAGCUGCCUGGCGAAGUGGAAAAAUAUU
...((((((((.......))))).)))...((((.....))))...........((((...(((((((.((..(((.(......).)))....)).)))))))...))))......... ( -40.40)
>DroSec_CAF1 149322 118 + 1
AAUGCCUCGAGAAGCUCACUCGAUGGCUUCGAGGAAAUUCUGCUUUGAAAAGUGCCGCCUAGCCAGGCUGUCACCAUCGAUAAAGGUGGAAAAGCUGGCUGGCAAGGUGGAA-AAUAUU
...((((((((.......))))).)))(((((((........))))))).....((((((.(((((.(.((..(((((......)))))....)).).))))).))))))..-...... ( -44.80)
>DroSim_CAF1 114408 119 + 1
AAUGCCUCGAGAAGCUCACUCGAUGGCUUCGCGGAAAUUCUGCUUUGAAAAGUGCCGCCUAGCCAGGCUGUCACCAUCGAUAAAAGUGGAAAAGCUGGCUGGCAAAGUGGAAAAAUAUU
...((((((((.......))))).)))(((((((...(((......))).....))(((.((((((.((....((((........))))...)))))))))))...)))))........ ( -38.20)
>DroEre_CAF1 163701 107 + 1
AAUGCCUCUAGAAGCUCAA-CGAUGGCUUCGCGGAAAUUCUGCUUUGAAAAGUGCCGC----------UGUCACCGUCGAUAGAGGUGGAAAAGCUGCCUGGCAAGGGGGAA-AGUAUU
(((((.(((.(((((.((.-...)))))))..)))..((((.(((((...((.((.((----------(.(((((.((....)))))))...))).))))..))))).))))-.))))) ( -36.50)
>DroYak_CAF1 157095 108 + 1
AAUGCCUCUAGAAGCUCACUCGCUGGCUUCGCGGAAAUUCUGCUUUGAAAAGUGCCGC----------CGUCACCAUCGAUAAAGGUGGAAAAGCUGCCUGGCAAAGUGGAG-AAAAUU
......(((.((((((........))))))..)))..(((..(((((...((.((.((----------.....(((((......)))))....)).))))..)))))..)))-...... ( -32.20)
>consensus
AAUGCCUCGAGAAGCUCACUCGAUGGCUUCGCGGAAAUUCUGCUUUGAAAAGUGCCGCCUAGCCAGGCUGUCACCAUCGAUAAAGGUGGAAAAGCUGCCUGGCAAAGUGGAA_AAUAUU
..((((....((((((........))))))((((...(((((((((.....((((.((((....)))).).)))........)))))))))...))))..))))............... (-25.48 = -26.80 +   1.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:27 2006