Locus 2309

Sequence ID	3L_DroMel_CAF1
Location	6,503,405 – 6,503,535
Length	130
Max. P	0.918000

overview

Window 4

Location	6,503,405 – 6,503,510
Length	105
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	87.81
Mean single sequence MFE	-30.13
Consensus MFE	-25.17
Energy contribution	-25.87
Covariance contribution	0.70
Combinations/Pair	1.20
Mean z-score	-2.57
Structure conservation index	0.84
SVM decision value	1.12
SVM RNA-class probability	0.918000
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6503405 105 - 23771897
GAAAGCUGAUGGAAAAGCAGAGCAGAGGAAAAGGCUUACGGCCAUGAGCGUGGCCAAGGCUUAUUAGUCAAGUUGAAAGACAUGACGCGGAACGGUUUUAUUGAA
.(((((((......((((.((((..........))))..((((((....))))))...))))....((((.(((....))).))))......)))))))...... ( -31.50)
>DroSec_CAF1 37647 105 - 1
GCAAGCUGAUGGAAAAGCAGAGCAGAGGAAAAGGCUUACGGCCAUGAGCGUGGCCAAGGCUUAUUAGUCAAGUUGAAAGACAUGACGCGGAACGGUUUUAUUGAA
..((((((......((((.((((..........))))..((((((....))))))...))))....((((.(((....))).))))......))))))....... ( -29.90)
>DroSim_CAF1 38071 105 - 1
GCAAGCUGAUGGAGAAGCAGAGCAGAGGAAAAGGCUUACGGCCAUGAGCGUGGCCAAGGCUUAUUAGUCAAGUUGAAAGACAUGACGCGGAACGGUUUUAUUGAA
..((((((......((((.((((..........))))..((((((....))))))...))))....((((.(((....))).))))......))))))....... ( -30.00)
>DroEre_CAF1 40005 105 - 1
AAAAGCUGGAGGAAAAACACAGCAGAGGAAAAGGCUUACGGCCAUGAGCGUGGCCAAGGCUUAUUAGUCAAGUUGAAAGACAUGACGCGGGACGGUUUUAUUGAA
.(((((((..(......)...((........((((((..((((((....)))))).))))))....((((.(((....))).))))))....)))))))...... ( -31.30)
>DroYak_CAF1 39527 105 - 1
GAAAAGUGGUGGAAAAACACAGCGGAGGAAAAGGCUUACGGCCAUAAGCGUGGCCAAGGCUUAUUAGUCAAGUUGAAAGGCAUGACGCGGGACGGUUUUAUUGAA
.((((.(((((......))).((........((((((..((((((....)))))).))))))....((((.(((....))).))))))....)).))))...... ( -30.20)
>DroAna_CAF1 39376 92 - 1
AGGAGCCGG--GAAA----UAGC-GAGAAA------CAAGGCCAUGAGCGUGGCCAAGGCUUAUUAGUCAAGUUGGCAGACAUGACGCGGGGCGGUUUUAUUGAA
.((((((..--....----....-......------...((((((....))))))...((((....((((.(((....))).))))...))))))))))...... ( -27.90)
>consensus
GAAAGCUGAUGGAAAAGCAGAGCAGAGGAAAAGGCUUACGGCCAUGAGCGUGGCCAAGGCUUAUUAGUCAAGUUGAAAGACAUGACGCGGAACGGUUUUAUUGAA
.(((((((.......................(((((...((((((....))))))..)))))....((((.(((....))).))))......)))))))...... (-25.17 = -25.87 +   0.70)

alignment

secondary structure

dotplot

Window 5

Location	6,503,441 – 6,503,535
Length	94
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	80.68
Mean single sequence MFE	-25.47
Consensus MFE	-15.09
Energy contribution	-14.98
Covariance contribution	-0.11
Combinations/Pair	1.14
Mean z-score	-1.65
Structure conservation index	0.59
SVM decision value	-0.06
SVM RNA-class probability	0.505213
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6503441 94 - 23771897
ACGAAGCUGGGA---GAAA--AGUG----GCGGG-----GAAAGCUGAUGGAAAAGCAGAGCAGAGGAAAAGGCUUACGGCCAUGAGCGUGGCCAAGGCUUAUUAGUC
.((..(((....---....--))).----.))..-----....(((((((....(((.((((..........))))..((((((....))))))...)))))))))). ( -25.10)
>DroSec_CAF1 37683 94 - 1
ACGAAGCUGGGA---GAAA--AGUG----GCGGG-----GCAAGCUGAUGGAAAAGCAGAGCAGAGGAAAAGGCUUACGGCCAUGAGCGUGGCCAAGGCUUAUUAGUC
.((..(((....---....--))).----.)).(-----((..(((.((((..((((....(....).....))))....)))).)))...)))..((((....)))) ( -26.00)
>DroSim_CAF1 38107 94 - 1
ACGAAGCUGGGA---GAAA--AGUG----GCGGG-----GCAAGCUGAUGGAGAAGCAGAGCAGAGGAAAAGGCUUACGGCCAUGAGCGUGGCCAAGGCUUAUUAGUC
.((..(((....---....--))).----.)).(-----((..(((.((((..((((....(....).....))))....)))).)))...)))..((((....)))) ( -27.10)
>DroEre_CAF1 40041 94 - 1
ACGAAGCUGGCA---GAAA--AGGG----GCGGG-----AAAAGCUGGAGGAAAAACACAGCAGAGGAAAAGGCUUACGGCCAUGAGCGUGGCCAAGGCUUAUUAGUC
......(((.(.---....--...)----.))).-----....((((..(......).)))).((..((.((((((..((((((....)))))).)))))).))..)) ( -24.30)
>DroYak_CAF1 39563 102 - 1
ACGAAGCUGGAAAACGAAA--AGAG----GUGGAAUGAGGAAAAGUGGUGGAAAAACACAGCGGAGGAAAAGGCUUACGGCCAUAAGCGUGGCCAAGGCUUAUUAGUC
.....(((((.........--....----...............((.(((......))).))........((((((..((((((....)))))).)))))).))))). ( -21.10)
>DroAna_CAF1 39412 87 - 1
ACGAAGCUGGGC---CAGAGCCGUGGGAGCCGGG-----AGGAGCCGG--GAAA----UAGC-GAGAAA------CAAGGCCAUGAGCGUGGCCAAGGCUUAUUAGUC
...(((((.(((---((..(((((((...((((.-----.....))))--(...----...)-......------.....))))).)).)))))..)))))....... ( -29.20)
>consensus
ACGAAGCUGGGA___GAAA__AGUG____GCGGG_____GAAAGCUGAUGGAAAAGCAGAGCAGAGGAAAAGGCUUACGGCCAUGAGCGUGGCCAAGGCUUAUUAGUC
...(((((......................(((...........)))...............................((((((....))))))..)))))....... (-15.09 = -14.98 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:12 2006