Locus 1029

Sequence ID	3R_DroMel_CAF1
Location	3,219,021 – 3,219,152
Length	131
Max. P	0.997916

overview

Window 4

Location	3,219,021 – 3,219,123
Length	102
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	96.67
Mean single sequence MFE	-23.36
Consensus MFE	-21.68
Energy contribution	-22.12
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.45
Structure conservation index	0.93
SVM decision value	1.13
SVM RNA-class probability	0.919765
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3219021 102 + 27905053
CAGCGAAAAUAUAUCAAUUGCAUGGCGCAAAGUAUUUCGCCAUCGAAACUUCAGUUCGGCAACUUUCUCAUCGAGCACUUAGAUGGGACUUGCCAAACUUUU
.................(((.((((((.((....)).)))))))))......((((.(((((...(((((((.........))))))).))))).))))... ( -25.70)
>DroSec_CAF1 43754 102 + 1
CAUCGAAAAUAUAUCAAUUGCAUGGCGCAAAGUAUUUCGCCAUUGAAACUUCAGUUCGGCAACUUUCUCAUCGAGCACUUAGAUGGGACUUGCCAAACUUUU
.............(((.....((((((.((....)).)))))))))......((((.(((((...(((((((.........))))))).))))).))))... ( -23.90)
>DroSim_CAF1 45103 102 + 1
CAUCGAAAAUAUAUCAAUUGCAUGGCGCAAAGUAUUUCGCCAUCGAAACUUCAGUUCGGCAACUUUCUCAUCGAGCACUUAGAUGGGACUUGCCAAACUUUU
.................(((.((((((.((....)).)))))))))......((((.(((((...(((((((.........))))))).))))).))))... ( -25.70)
>DroEre_CAF1 38069 102 + 1
CUGCGAAAAUAUAUCAAUUGCAUGGCGCAAAGUAUUUCGCCAUCGAAACUUUAGUUCGGCAACUUUCACAUCGAGCACUUAGAUGGGACUUGGCAAACUUUU
.(((.((....((((..(((.((((((.((....)).))))))))).......((((((...........)))))).....))))....)).)))....... ( -20.50)
>DroYak_CAF1 28394 102 + 1
CUGCGAAAAUAUAUCAAUUGCAUGGCGCAAAGUAUUUCGCCAUCGAAACUUUAGUUCGGCAACUUUCUCAUCGAGCACUUAAAUGGGACUUGCCAAACUUUU
.................(((.((((((.((....)).)))))))))......((((.(((((...((((((...........)))))).))))).))))... ( -21.00)
>consensus
CAGCGAAAAUAUAUCAAUUGCAUGGCGCAAAGUAUUUCGCCAUCGAAACUUCAGUUCGGCAACUUUCUCAUCGAGCACUUAGAUGGGACUUGCCAAACUUUU
.................(((.((((((.((....)).)))))))))......((((.(((((...(((((((.........))))))).))))).))))... (-21.68 = -22.12 +   0.44)

alignment

secondary structure

dotplot

Window 5

Location	3,219,021 – 3,219,123
Length	102
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	96.67
Mean single sequence MFE	-25.57
Consensus MFE	-24.10
Energy contribution	-24.14
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.11
Structure conservation index	0.94
SVM decision value	0.06
SVM RNA-class probability	0.562249
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3219021 102 - 27905053
AAAAGUUUGGCAAGUCCCAUCUAAGUGCUCGAUGAGAAAGUUGCCGAACUGAAGUUUCGAUGGCGAAAUACUUUGCGCCAUGCAAUUGAUAUAUUUUCGCUG
...((((((((((.((.((((.........)))).))...))))))))))...........(((((((....((((.....)))).........))))))). ( -26.92)
>DroSec_CAF1 43754 102 - 1
AAAAGUUUGGCAAGUCCCAUCUAAGUGCUCGAUGAGAAAGUUGCCGAACUGAAGUUUCAAUGGCGAAAUACUUUGCGCCAUGCAAUUGAUAUAUUUUCGAUG
...((((((((((.((.((((.........)))).))...)))))))))).........((((((.((....)).))))))...(((((.......))))). ( -27.80)
>DroSim_CAF1 45103 102 - 1
AAAAGUUUGGCAAGUCCCAUCUAAGUGCUCGAUGAGAAAGUUGCCGAACUGAAGUUUCGAUGGCGAAAUACUUUGCGCCAUGCAAUUGAUAUAUUUUCGAUG
...((((((((((.((.((((.........)))).))...)))))))))).........((((((.((....)).))))))...(((((.......))))). ( -27.90)
>DroEre_CAF1 38069 102 - 1
AAAAGUUUGCCAAGUCCCAUCUAAGUGCUCGAUGUGAAAGUUGCCGAACUAAAGUUUCGAUGGCGAAAUACUUUGCGCCAUGCAAUUGAUAUAUUUUCGCAG
.........................(((..((((((..(((((((((((....).))))((((((.((....)).))))))))))))..))))))...))). ( -21.50)
>DroYak_CAF1 28394 102 - 1
AAAAGUUUGGCAAGUCCCAUUUAAGUGCUCGAUGAGAAAGUUGCCGAACUAAAGUUUCGAUGGCGAAAUACUUUGCGCCAUGCAAUUGAUAUAUUUUCGCAG
...((((((((((.((.((((.........)))).))...))))))))))............((((((....((((.....)))).........)))))).. ( -23.72)
>consensus
AAAAGUUUGGCAAGUCCCAUCUAAGUGCUCGAUGAGAAAGUUGCCGAACUGAAGUUUCGAUGGCGAAAUACUUUGCGCCAUGCAAUUGAUAUAUUUUCGCUG
...((((((((((.((.((((.........)))).))...))))))))))..((((.(.((((((.((....)).))))))).))))............... (-24.10 = -24.14 +   0.04)

alignment

secondary structure

dotplot

Window 6

Location	3,219,043 – 3,219,152
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	97.61
Mean single sequence MFE	-28.26
Consensus MFE	-27.28
Energy contribution	-27.72
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-2.00
Structure conservation index	0.97
SVM decision value	2.96
SVM RNA-class probability	0.997916
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3219043 109 + 27905053
UGGCGCAAAGUAUUUCGCCAUCGAAACUUCAGUUCGGCAACUUUCUCAUCGAGCACUUAGAUGGGACUUGCCAAACUUUUCGAUUUUGCGGCAACUUAAAAAUUUGAAU
((.((((((((.(((((....)))))....((((.(((((...(((((((.........))))))).))))).)))).....)))))))).))................ ( -31.00)
>DroSec_CAF1 43776 109 + 1
UGGCGCAAAGUAUUUCGCCAUUGAAACUUCAGUUCGGCAACUUUCUCAUCGAGCACUUAGAUGGGACUUGCCAAACUUUUCGAUUUUGCGGCAACUUAAAAAUUUGAAU
((.((((((((.(((((....)))))....((((.(((((...(((((((.........))))))).))))).)))).....)))))))).))................ ( -29.70)
>DroSim_CAF1 45125 109 + 1
UGGCGCAAAGUAUUUCGCCAUCGAAACUUCAGUUCGGCAACUUUCUCAUCGAGCACUUAGAUGGGACUUGCCAAACUUUUCGAUUUUGCGGCAACUUAAAAAUUUGAAU
((.((((((((.(((((....)))))....((((.(((((...(((((((.........))))))).))))).)))).....)))))))).))................ ( -31.00)
>DroEre_CAF1 38091 109 + 1
UGGCGCAAAGUAUUUCGCCAUCGAAACUUUAGUUCGGCAACUUUCACAUCGAGCACUUAGAUGGGACUUGGCAAACUUUUCGAUUUUGCGGCAACUUCAAAAUUUGAAU
((.((((((((.(((((....)))))....((((.(.(((..(((.((((.........))))))).))).).)))).....)))))))).))..((((.....)))). ( -23.30)
>DroYak_CAF1 28416 109 + 1
UGGCGCAAAGUAUUUCGCCAUCGAAACUUUAGUUCGGCAACUUUCUCAUCGAGCACUUAAAUGGGACUUGCCAAACUUUUCGAUUUUGCGGCAACUUAAAAAUUUGAAU
((.((((((((.(((((....)))))....((((.(((((...((((((...........)))))).))))).)))).....)))))))).))................ ( -26.30)
>consensus
UGGCGCAAAGUAUUUCGCCAUCGAAACUUCAGUUCGGCAACUUUCUCAUCGAGCACUUAGAUGGGACUUGCCAAACUUUUCGAUUUUGCGGCAACUUAAAAAUUUGAAU
((.((((((((.(((((....)))))....((((.(((((...(((((((.........))))))).))))).)))).....)))))))).))................ (-27.28 = -27.72 +   0.44)

alignment

secondary structure

dotplot

Window 7

Location	3,219,043 – 3,219,152
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	97.61
Mean single sequence MFE	-27.58
Consensus MFE	-26.68
Energy contribution	-26.92
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.46
Structure conservation index	0.97
SVM decision value	1.32
SVM RNA-class probability	0.942198
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3219043 109 - 27905053
AUUCAAAUUUUUAAGUUGCCGCAAAAUCGAAAAGUUUGGCAAGUCCCAUCUAAGUGCUCGAUGAGAAAGUUGCCGAACUGAAGUUUCGAUGGCGAAAUACUUUGCGCCA
............((((...(((...(((((((((((((((((.((.((((.........)))).))...))))))))))....))))))).)))....))))....... ( -29.70)
>DroSec_CAF1 43776 109 - 1
AUUCAAAUUUUUAAGUUGCCGCAAAAUCGAAAAGUUUGGCAAGUCCCAUCUAAGUGCUCGAUGAGAAAGUUGCCGAACUGAAGUUUCAAUGGCGAAAUACUUUGCGCCA
................((.((((((.......((((((((((.((.((((.........)))).))...))))))))))...(((((......)))))..)))))).)) ( -26.90)
>DroSim_CAF1 45125 109 - 1
AUUCAAAUUUUUAAGUUGCCGCAAAAUCGAAAAGUUUGGCAAGUCCCAUCUAAGUGCUCGAUGAGAAAGUUGCCGAACUGAAGUUUCGAUGGCGAAAUACUUUGCGCCA
............((((...(((...(((((((((((((((((.((.((((.........)))).))...))))))))))....))))))).)))....))))....... ( -29.70)
>DroEre_CAF1 38091 109 - 1
AUUCAAAUUUUGAAGUUGCCGCAAAAUCGAAAAGUUUGCCAAGUCCCAUCUAAGUGCUCGAUGUGAAAGUUGCCGAACUAAAGUUUCGAUGGCGAAAUACUUUGCGCCA
...........(((((...(((...(((((((((((((.(((.((.((((.........)))).))...))).))))))....))))))).)))....)))))...... ( -24.30)
>DroYak_CAF1 28416 109 - 1
AUUCAAAUUUUUAAGUUGCCGCAAAAUCGAAAAGUUUGGCAAGUCCCAUUUAAGUGCUCGAUGAGAAAGUUGCCGAACUAAAGUUUCGAUGGCGAAAUACUUUGCGCCA
............((((...(((...(((((((((((((((((.((.((((.........)))).))...))))))))))....))))))).)))....))))....... ( -27.30)
>consensus
AUUCAAAUUUUUAAGUUGCCGCAAAAUCGAAAAGUUUGGCAAGUCCCAUCUAAGUGCUCGAUGAGAAAGUUGCCGAACUGAAGUUUCGAUGGCGAAAUACUUUGCGCCA
............((((...(((...(((((((((((((((((.((.((((.........)))).))...))))))))))....))))))).)))....))))....... (-26.68 = -26.92 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:46 2006