Locus 6437

Sequence ID	2L_DroMel_CAF1
Location	18,085,524 – 18,085,672
Length	148
Max. P	0.598831

overview

Window 1

Location	18,085,524 – 18,085,632
Length	108
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.11
Mean single sequence MFE	-36.25
Consensus MFE	-25.80
Energy contribution	-25.68
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-2.46
Structure conservation index	0.71
SVM decision value	0.13
SVM RNA-class probability	0.598831
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18085524 108 + 22407834
UCGAGAGGGAAAGUAGUCGAAGACGAUGUCGAUGUCG------------AUGUCAGACCAAAAGAGCUGGCUCACAUUGUUUGGCAUCGUGUCGGAGCAUAUGACUAUGCAUAUUUGAAA
(((((...........((((..((((((((((...((------------((((.((.(((.......))))).)))))).)))))))))).)))).(((((....)))))...))))).. ( -34.00)
>DroSec_CAF1 292858 108 + 1
UCGAGAGGGGAAGUAGUCGAAGGCGAUGUCGAUGUCG------------AUGUCAGACCAAAAGAGCUGGCUCACAUUGUUUGGCAUCGUGUCGGAGCAUAUGACUAUGCAUAUUUGAAA
(((((...(...(((((((...((....((((((.((------------(((((((((.....(((....))).....))))))))))))))))).))...))))))).)...))))).. ( -36.00)
>DroSim_CAF1 294904 108 + 1
UCGAGAGGGAAAGCAGUCGAAGGCGAUGUCGAUGUCG------------AUGUCAGACCAAAAGAGCUGGCUCACAUUGUUUGGCAUCGUGUCGGAGCAUAUGACUAUGCAUAUUUGAAA
(((((...........((((..((((((((((...((------------((((.((.(((.......))))).)))))).)))))))))).)))).(((((....)))))...))))).. ( -34.30)
>DroYak_CAF1 310294 120 + 1
UCGAGAGGGAAAGUAGUCGAAAGCAAUGUCGAUGUCGAUGCCGAUGCCGAUGUCGGACCAAAAGAGCUGGCUCACAUUGUUUGGCAUCGUGUCGGAGCAUAUGACUAUGCAUAUUUGAAA
(((((...(...(((((((...((....((((((.(((((((((...((((((.((.(((.......))))).)))))).))))))))))))))).))...))))))).)...))))).. ( -40.70)
>consensus
UCGAGAGGGAAAGUAGUCGAAGGCGAUGUCGAUGUCG____________AUGUCAGACCAAAAGAGCUGGCUCACAUUGUUUGGCAUCGUGUCGGAGCAUAUGACUAUGCAUAUUUGAAA
(((((...........((((..((((((((((.................((((.((.(((.......))))).))))...)))))))))).)))).(((((....)))))...))))).. (-25.80 = -25.68 +  -0.12)

alignment

secondary structure

dotplot

Window 2

Location	18,085,561 – 18,085,672
Length	111
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.24
Mean single sequence MFE	-32.67
Consensus MFE	-29.23
Energy contribution	-28.85
Covariance contribution	-0.38
Combinations/Pair	1.06
Mean z-score	-1.46
Structure conservation index	0.89
SVM decision value	-0.05
SVM RNA-class probability	0.509892
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18085561 111 + 22407834
---------AUGUCAGACCAAAAGAGCUGGCUCACAUUGUUUGGCAUCGUGUCGGAGCAUAUGACUAUGCAUAUUUGAAAGGCAAUUUCCCCAGUGUUCUGGUCAUCGAUGCAAAUGCAA
---------..(((((..(....)..))))).....((((...((((((((((((((((((((......)))....((((.....))))....))))))))).)).))))))....)))) ( -29.70)
>DroSec_CAF1 292895 111 + 1
---------AUGUCAGACCAAAAGAGCUGGCUCACAUUGUUUGGCAUCGUGUCGGAGCAUAUGACUAUGCAUAUUUGAAAGGCAAUUUCCCCAGUGUUUUGGUCAUCGAUGCAAAUGCAA
---------......((((((((..(((((.....((((((((((.....)))...(((((....))))).........)))))))....))))).)))))))).....(((....))). ( -31.00)
>DroSim_CAF1 294941 111 + 1
---------AUGUCAGACCAAAAGAGCUGGCUCACAUUGUUUGGCAUCGUGUCGGAGCAUAUGACUAUGCAUAUUUGAAAGGCAAUUUCCCCAGUGUUCUGGUCAUCGAUGCAAAUGCAA
---------..(((((..(....)..))))).....((((...((((((((((((((((((((......)))....((((.....))))....))))))))).)).))))))....)))) ( -29.70)
>DroYak_CAF1 310334 120 + 1
CCGAUGCCGAUGUCGGACCAAAAGAGCUGGCUCACAUUGUUUGGCAUCGUGUCGGAGCAUAUGACUAUGCAUAUUUGAAAGGCAAUUUCCCCAGUGUUCUGGUCAUCGAUGCAAAUGCAA
(((((((.((((((((((.....(((....))).....))))))))))))))))).(((((((((((.((((....((((.....))))....))))..)))))))..))))........ ( -40.30)
>consensus
_________AUGUCAGACCAAAAGAGCUGGCUCACAUUGUUUGGCAUCGUGUCGGAGCAUAUGACUAUGCAUAUUUGAAAGGCAAUUUCCCCAGUGUUCUGGUCAUCGAUGCAAAUGCAA
...........(((((..(....)..))))).....((((...((((((((((((((((((((......)))....((((.....))))....))))))))).)).))))))....)))) (-29.23 = -28.85 +  -0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:12 2006