Locus 7553

Sequence ID	2L_DroMel_CAF1
Location	20,933,173 – 20,933,333
Length	160
Max. P	0.995499

overview

Window 3

Location	20,933,173 – 20,933,293
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.47
Mean single sequence MFE	-48.53
Consensus MFE	-42.72
Energy contribution	-42.85
Covariance contribution	0.13
Combinations/Pair	1.12
Mean z-score	-2.76
Structure conservation index	0.88
SVM decision value	2.58
SVM RNA-class probability	0.995499
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20933173 120 + 22407834
GGGAUGGCGCGGGGUCACAGCUAGACUCAGAGGCAUGGAGCGAGUGCCAGUGGCAAUGGCAGCGCCAGACCUUGUGCCAUUCGCAUUCCGAAUGGAAGUGGCCUAGGCCAGUGAAAGUUC
.(((((((((((((((...(((.........))).(((.((...(((((.......))))))).))))))))))))))))))((.((((....)))).((((....))))))........ ( -50.50)
>DroSim_CAF1 17787 120 + 1
GGUAUGGCGCGGGGUCACAGCUAGAGUCAGAGGCAUAGAGCGAGUGCCAGUGGCAAUGGCAGCGCCAGACCUUGUGCCAUUCGCAUUCCGAAUGGAAGUGGCCUAGGCCAGUGAAAGUUC
....((((((((((((.........((((..(((((.......)))))..))))..((((...))))))))))))))))(((((.((((....)))).((((....)))))))))..... ( -51.90)
>DroEre_CAF1 16949 90 + 1
GGAAUGGUGCAGGGUCACA------------------------------GUGGCAAUGGCUGCGCCAGACCUUGUGCCACUCGCAUUCCGAAUGGAAGUGGUCUAGGCCAGUGAAAGUUC
....(((..(((((((...------------------------------(..((....))..)....)))))))..))).((((.((((....)))).((((....))))))))...... ( -36.50)
>DroYak_CAF1 17768 120 + 1
GGAAUGGCGCGGGGUCACAGCUCGAGUCAGAGGCAUAGAGCGAGUGCCAGUGGCAAUGGCAGCGCCAGACCUUGUGCCAUUCCCAUUCCGAAUGGAAGUGGCCUAGGCCAGUGAAAGUUC
((((((((((((((((.........((((..(((((.......)))))..))))..((((...))))))))))))))))))))......((((...(.((((....)))).)....)))) ( -55.20)
>consensus
GGAAUGGCGCGGGGUCACAGCUAGAGUCAGAGGCAUAGAGCGAGUGCCAGUGGCAAUGGCAGCGCCAGACCUUGUGCCAUUCGCAUUCCGAAUGGAAGUGGCCUAGGCCAGUGAAAGUUC
.(((((((((((((((...............(((((.......)))))..((((.........))))))))))))))))))).......((((...(.((((....)))).)....)))) (-42.72 = -42.85 +   0.13)

alignment

secondary structure

dotplot

Window 4

Location	20,933,213 – 20,933,333
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.58
Mean single sequence MFE	-35.28
Consensus MFE	-29.80
Energy contribution	-30.67
Covariance contribution	0.88
Combinations/Pair	1.07
Mean z-score	-1.63
Structure conservation index	0.84
SVM decision value	0.07
SVM RNA-class probability	0.568010
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20933213 120 - 22407834
CAUCACGAAGCCAGACAAUAUUAAUGAUGCACAUUGUCAAGAACUUUCACUGGCCUAGGCCACUUCCAUUCGGAAUGCGAAUGGCACAAGGUCUGGCGCUGCCAUUGCCACUGGCACUCG
.....(((.(((((((........((((.......))))...........((((....))))((((((((((.....)))))))...))))))))))..(((((.......))))).))) ( -37.20)
>DroSim_CAF1 17827 120 - 1
CAUCACGAAGCCAGACAAUAUUAAUGAUGCACAUUGUCAAGAACUUUCACUGGCCUAGGCCACUUCCAUUCGGAAUGCGAAUGGCACAAGGUCUGGCGCUGCCAUUGCCACUGGCACUCG
.....(((.(((((((........((((.......))))...........((((....))))((((((((((.....)))))))...))))))))))..(((((.......))))).))) ( -37.20)
>DroEre_CAF1 16968 111 - 1
CAUCACGAAGCCAGACAAUAUUAAUGAUGCACAUUGUCAAGAACUUUCACUGGCCUAGACCACUUCCAUUCGGAAUGCGAGUGGCACAAGGUCUGGCGCAGCCAUUGCCAC---------
.........((..((((((.............))))))...........((((((.(((((....(((((((.....))))))).....)))))))).))).....))...--------- ( -29.42)
>DroYak_CAF1 17808 120 - 1
CAUCACGAAGCCAGACAAUAUUAAUGAUGCACAUUGUCAAGAACUUUCACUGGCCUAGGCCACUUCCAUUCGGAAUGGGAAUGGCACAAGGUCUGGCGCUGCCAUUGCCACUGGCACUCG
.....(((.(((((((........((.(((.((((.(((...........((((....)))).((((....))))))).)))))))))..)))))))..(((((.......))))).))) ( -37.30)
>consensus
CAUCACGAAGCCAGACAAUAUUAAUGAUGCACAUUGUCAAGAACUUUCACUGGCCUAGGCCACUUCCAUUCGGAAUGCGAAUGGCACAAGGUCUGGCGCUGCCAUUGCCACUGGCACUCG
.........(((((..........((((.......))))........((.(((((((((((....(((((((.....))))))).....)))))))....)))).))...)))))..... (-29.80 = -30.67 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:39:42 2006