Locus 6482

Sequence ID	2R_DroMel_CAF1
Location	20,234,163 – 20,234,320
Length	157
Max. P	0.632228

overview

Window 2

Location	20,234,163 – 20,234,283
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	99.50
Mean single sequence MFE	-45.75
Consensus MFE	-45.40
Energy contribution	-45.40
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-0.69
Structure conservation index	0.99
SVM decision value	0.20
SVM RNA-class probability	0.632228
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20234163 120 - 20766785
CCAUCAUUAUUCGCAUUGAAUUGGAGUCGCAAGCGCGUCUCAAGCGGGCCUGCACCAUGCUAGCACCGCCGAACCCGAGGUCAAUAUGCGGCCAGGACCCGGGCUGGUCGUGAUGGCGCU
(((((((.....(((((((.((((((.(((....))).)))..((((((..((.....))..)).))))......)))..)))..))))((((((........))))))))))))).... ( -45.40)
>DroPse_CAF1 27098 120 - 1
CCAUCAUUACUCGCAUUGAAUUGGAGUCGCAAGCGCGUCUCAAGCGGGCCUGCACCAUGCUAGCACCGCCGAACCCGAGGUCAAUAUGCGGCCAGGACCCGGGCUGGUCGUGAUGGCGCU
(((((((.(((.((......((((((.(((....))).)))..((((((..((.....))..)).)))))))..(((.((((....((....)).))))))))).))).))))))).... ( -46.10)
>DroEre_CAF1 28136 120 - 1
CCAUCAUUAUUCGCAUUGAAUUGGAGUCGCAAGCGCGUCUCAAGCGGGCCUGCACCAUGCUAGCACCGCCGAACCCGAGGUCAAUAUGCGGCCAGGACCCGGGCUGGUCGUGAUGGCGCU
(((((((.....(((((((.((((((.(((....))).)))..((((((..((.....))..)).))))......)))..)))..))))((((((........))))))))))))).... ( -45.40)
>DroYak_CAF1 26866 120 - 1
CCAUCAUUAUUCGCAUUGAAUUGGAGUCGCAAGCGCGUCUCAAGCGGGCCUGCACCAUGCUAGCACCGCCGAACCCGAGGUCAAUAUGCGGCCAGGACCCGGGCUGGUCGUGAUGGCGCU
(((((((.....(((((((.((((((.(((....))).)))..((((((..((.....))..)).))))......)))..)))..))))((((((........))))))))))))).... ( -45.40)
>DroAna_CAF1 24909 120 - 1
CCAUCAUUACUCGCAUUGAAUUGGAGUCGCAAGCGCGUCUCAAGCGGGCCUGCACCAUGCUAGCACCGCCGAACCCGAGGUCAAUAUGCGGCCAGGACCCGGGCUGGUCGUGAUGGCGCU
(((((((.(((.((......((((((.(((....))).)))..((((((..((.....))..)).)))))))..(((.((((....((....)).))))))))).))).))))))).... ( -46.10)
>DroPer_CAF1 27405 120 - 1
CCAUCAUUACUCGCAUUGAAUUGGAGUCGCAAGCGCGUCUCAAGCGGGCCUGCACCAUGCUAGCACCGCCGAACCCGAGGUCAAUAUGCGGCCAGGACCCGGGCUGGUCGUGAUGGCGCU
(((((((.(((.((......((((((.(((....))).)))..((((((..((.....))..)).)))))))..(((.((((....((....)).))))))))).))).))))))).... ( -46.10)
>consensus
CCAUCAUUACUCGCAUUGAAUUGGAGUCGCAAGCGCGUCUCAAGCGGGCCUGCACCAUGCUAGCACCGCCGAACCCGAGGUCAAUAUGCGGCCAGGACCCGGGCUGGUCGUGAUGGCGCU
(((((((.....(((((((.((((((.(((....))).)))..((((((..((.....))..)).))))......)))..)))..))))((((((........))))))))))))).... (-45.40 = -45.40 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	20,234,203 – 20,234,320
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	97.29
Mean single sequence MFE	-39.60
Consensus MFE	-38.85
Energy contribution	-38.60
Covariance contribution	-0.25
Combinations/Pair	1.03
Mean z-score	-0.68
Structure conservation index	0.98
SVM decision value	0.13
SVM RNA-class probability	0.597719
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20234203 117 - 20766785
CGCAGCCCACACU---ACUGAUGAUGAUGGGGCCAUGAGCCCAUCAUUAUUCGCAUUGAAUUGGAGUCGCAAGCGCGUCUCAAGCGGGCCUGCACCAUGCUAGCACCGCCGAACCCGAGG
.(((((((.(...---...((((((((((((........))))))))))))............(((.(((....))).)))..).))).))))............((..((....)).)) ( -39.30)
>DroPse_CAF1 27138 117 - 1
CGAAUCCCACACU---UCUGAUGAUGAUGGGGCCAUGAGCCCAUCAUUACUCGCAUUGAAUUGGAGUCGCAAGCGCGUCUCAAGCGGGCCUGCACCAUGCUAGCACCGCCGAACCCGAGG
.............---.....((((((((((........))))))))))((((..(((.....(((.(((....))).)))..((((((..((.....))..)).)))))))...)))). ( -39.90)
>DroEre_CAF1 28176 117 - 1
CGCAGCCCACACU---ACUGAUGAUGAUGGGGCCAUGAGCCCAUCAUUAUUCGCAUUGAAUUGGAGUCGCAAGCGCGUCUCAAGCGGGCCUGCACCAUGCUAGCACCGCCGAACCCGAGG
.(((((((.(...---...((((((((((((........))))))))))))............(((.(((....))).)))..).))).))))............((..((....)).)) ( -39.30)
>DroYak_CAF1 26906 117 - 1
CGCAGCCCACACU---ACUGAUGAUGAUGGGGCCAUGAGCCCAUCAUUAUUCGCAUUGAAUUGGAGUCGCAAGCGCGUCUCAAGCGGGCCUGCACCAUGCUAGCACCGCCGAACCCGAGG
.(((((((.(...---...((((((((((((........))))))))))))............(((.(((....))).)))..).))).))))............((..((....)).)) ( -39.30)
>DroAna_CAF1 24949 120 - 1
CGCAGCCCACACUACUACUGAUGAUGAUGGGGCCAUGAGCCCAUCAUUACUCGCAUUGAAUUGGAGUCGCAAGCGCGUCUCAAGCGGGCCUGCACCAUGCUAGCACCGCCGAACCCGAGG
.....................((((((((((........))))))))))((((..(((.....(((.(((....))).)))..((((((..((.....))..)).)))))))...)))). ( -39.90)
>DroPer_CAF1 27445 117 - 1
CGAAUCCCACACU---UCUGAUGAUGAUGGGGCCAUGAGCCCAUCAUUACUCGCAUUGAAUUGGAGUCGCAAGCGCGUCUCAAGCGGGCCUGCACCAUGCUAGCACCGCCGAACCCGAGG
.............---.....((((((((((........))))))))))((((..(((.....(((.(((....))).)))..((((((..((.....))..)).)))))))...)))). ( -39.90)
>consensus
CGCAGCCCACACU___ACUGAUGAUGAUGGGGCCAUGAGCCCAUCAUUACUCGCAUUGAAUUGGAGUCGCAAGCGCGUCUCAAGCGGGCCUGCACCAUGCUAGCACCGCCGAACCCGAGG
.....................((((((((((........))))))))))((((..(((.....(((.(((....))).)))..((((((..((.....))..)).)))))))...)))). (-38.85 = -38.60 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:01 2006