Locus 3726

Sequence ID	2R_DroMel_CAF1
Location	12,333,953 – 12,334,055
Length	102
Max. P	0.991493

overview

Window 2

Location	12,333,953 – 12,334,055
Length	102
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.54
Mean single sequence MFE	-32.27
Consensus MFE	-28.80
Energy contribution	-28.67
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-2.61
Structure conservation index	0.89
SVM decision value	2.27
SVM RNA-class probability	0.991493
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12333953 102 + 20766785
------------------AAGCAAAAGCACCAGCGACCGAGCACGCAUUUCGAAAUGCGAGUGCGAGUGUCGGAGGCAAUUGAAAUGCUUUGCAGCAAAAGCAAAUCGAACUGCUCUGAA
------------------...((...((((..((......)).((((((....)))))).))))...))((((((.((.((((..((((((......))))))..))))..)))))))). ( -31.40)
>DroSec_CAF1 32579 101 + 1
------------------AAGCAAAAGCACCAGCGACCGAGCACGCAUUUCGAAAUGCGAGUGCGAGUGUCGGAGGCAAUUGAAAUGCUUUGCAGCAAAAGCAAAUCGAACUGCACUGA-
------------------..((....))..((((((((..(((((((((....)))))..))))..).))))...(((.((((..((((((......))))))..))))..))).))).- ( -30.10)
>DroSim_CAF1 30965 101 + 1
------------------AAGCAAAAGCACCAGCGACCGAGCACGCAUUUCGAAAUGCGAGUGCGAGUGUCGGAGGCAAUUGAAAUGCUUUGCAGCAAAAGCAAAUCGAACUGCACUGA-
------------------..((....))..((((((((..(((((((((....)))))..))))..).))))...(((.((((..((((((......))))))..))))..))).))).- ( -30.10)
>DroYak_CAF1 32064 119 + 1
GGAGCAAGAGCAAAAGCAAAGCAAAAGCGCCAGCAAGCGAAAACGCAUUUCGAAAUGCGAGUGCGAGUGUCGGAGGCAAUUGAAAUGCUUUGCAGCAAAAGCAAAUCGAACUGCUCUGA-
......((((((...((((((((...((((..(((..(((((.....)))))...)))..))))...(((.....))).......)))))))).((....)).........))))))..- ( -37.50)
>consensus
__________________AAGCAAAAGCACCAGCGACCGAGCACGCAUUUCGAAAUGCGAGUGCGAGUGUCGGAGGCAAUUGAAAUGCUUUGCAGCAAAAGCAAAUCGAACUGCACUGA_
....................(((...((.((.(((..((.((.((((((....)))))).)).))..))).))..))..((((..((((((......))))))..))))..)))...... (-28.80 = -28.67 +  -0.12)

alignment

secondary structure

dotplot

Window 3

Location	12,333,953 – 12,334,055
Length	102
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.54
Mean single sequence MFE	-31.30
Consensus MFE	-26.89
Energy contribution	-26.82
Covariance contribution	-0.06
Combinations/Pair	1.11
Mean z-score	-2.22
Structure conservation index	0.86
SVM decision value	1.52
SVM RNA-class probability	0.961036
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12333953 102 - 20766785
UUCAGAGCAGUUCGAUUUGCUUUUGCUGCAAAGCAUUUCAAUUGCCUCCGACACUCGCACUCGCAUUUCGAAAUGCGUGCUCGGUCGCUGGUGCUUUUGCUU------------------
....((((((...((..((((((......))))))..))....(((..((((....((((..(((((....)))))))))...))))..)))....))))))------------------ ( -31.30)
>DroSec_CAF1 32579 101 - 1
-UCAGUGCAGUUCGAUUUGCUUUUGCUGCAAAGCAUUUCAAUUGCCUCCGACACUCGCACUCGCAUUUCGAAAUGCGUGCUCGGUCGCUGGUGCUUUUGCUU------------------
-(((((((((((.((..((((((......))))))..))))))))....(((....((((..(((((....)))))))))...)))))))).((....))..------------------ ( -30.70)
>DroSim_CAF1 30965 101 - 1
-UCAGUGCAGUUCGAUUUGCUUUUGCUGCAAAGCAUUUCAAUUGCCUCCGACACUCGCACUCGCAUUUCGAAAUGCGUGCUCGGUCGCUGGUGCUUUUGCUU------------------
-(((((((((((.((..((((((......))))))..))))))))....(((....((((..(((((....)))))))))...)))))))).((....))..------------------ ( -30.70)
>DroYak_CAF1 32064 119 - 1
-UCAGAGCAGUUCGAUUUGCUUUUGCUGCAAAGCAUUUCAAUUGCCUCCGACACUCGCACUCGCAUUUCGAAAUGCGUUUUCGCUUGCUGGCGCUUUUGCUUUGCUUUUGCUCUUGCUCC
-..(((((((........((....)).((((((((....((.((((..(((....((....((((((....))))))....)).)))..)))).)).))))))))..)))))))...... ( -32.50)
>consensus
_UCAGAGCAGUUCGAUUUGCUUUUGCUGCAAAGCAUUUCAAUUGCCUCCGACACUCGCACUCGCAUUUCGAAAUGCGUGCUCGGUCGCUGGUGCUUUUGCUU__________________
......((((...((..((((((......))))))..))....(((..((((....((((..(((((....)))))))))...))))..)))....)))).................... (-26.89 = -26.82 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:50 2006