Locus 4327

Sequence ID	X_DroMel_CAF1
Location	11,395,120 – 11,395,334
Length	214
Max. P	0.830476

overview

Window 6

Location	11,395,120 – 11,395,217
Length	97
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	90.85
Mean single sequence MFE	-31.96
Consensus MFE	-25.04
Energy contribution	-24.88
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-1.81
Structure conservation index	0.78
SVM decision value	0.71
SVM RNA-class probability	0.830476
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11395120 97 - 22224390
GC-----GAUGCGAUCCGGCAGCCAGAACAGGAGCCAGAGCCAACCCAGAGCGGUGGCCAGAGGAAAGAAGCUUUGGUGACAAAGCUGGCAUACCAAAUAGU
..-----.((((..((((((..((......)).))).(.((((.((......)))))))...)))....(((((((....))))))).)))).......... ( -33.10)
>DroSec_CAF1 48394 97 - 1
GC-----GAUGCGAUCCGGCAGCCAGAACAGGAGCCAGAGCCAACCCAGAGCGGUGGCCAGAGGAAAGAAGCUUUGGUGACAAAGCUGGCAUACCAAAUACU
..-----.((((..((((((..((......)).))).(.((((.((......)))))))...)))....(((((((....))))))).)))).......... ( -33.10)
>DroSim_CAF1 19860 97 - 1
GC-----GAUGCGAUCCGGCAGCCAGAACAGGAGCCAGAGCCAACCCAGAGCGGUGGCCAGAGGAAAGAAGCUUUGGUGACAAAGCUGGCAUACCAAAUACU
..-----.((((..((((((..((......)).))).(.((((.((......)))))))...)))....(((((((....))))))).)))).......... ( -33.10)
>DroEre_CAF1 54537 91 - 1
GC-----GAUGCGAUGCGGCAGCCAGAACAGGAG------CCAACCCAGAGCGGUGGCCGGGGAAAAGAAGCUUUGGUGACAAAGCUGGCAUACCAAAUAGU
..-----..((..(((((((..((......)).)------))..(((.(.((....))).)))......(((((((....))))))).))))..))...... ( -28.70)
>DroYak_CAF1 53896 96 - 1
GCGAGCCGAUGCGAUGCGGCAGCCAGAACAGGAG------CCAAGCCAGAGCGGUGGCCGGAGGAAAGAGGCUUUGGUGACAAAGCUGGCAUACCAAAUAGU
....((((........)))).(((.......(.(------(((.((....))..)))))..........(((((((....))))))))))............ ( -31.80)
>consensus
GC_____GAUGCGAUCCGGCAGCCAGAACAGGAGCCAGAGCCAACCCAGAGCGGUGGCCAGAGGAAAGAAGCUUUGGUGACAAAGCUGGCAUACCAAAUAGU
........((((.....(((.(((.(..(.((.............)).)..)))).)))..........(((((((....))))))).)))).......... (-25.04 = -24.88 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	11,395,217 – 11,395,334
Length	117
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	91.88
Mean single sequence MFE	-19.67
Consensus MFE	-16.44
Energy contribution	-17.44
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.35
Structure conservation index	0.84
SVM decision value	0.20
SVM RNA-class probability	0.631702
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11395217 117 - 22224390
UGACAAAGUACGUGCCAUAAUGAAGCAAUUGCGCUUCCGGCAACAGGCAAACUACUAAAACAACUAAAACAGCAACACUACGAAGUAUUGCCAACACCCAAAGCGACACAACAACUG
......((((..((((.....(((((......))))).(....).))))...))))...............((((.(((....))).)))).......................... ( -21.50)
>DroSec_CAF1 48491 116 - 1
UGACAAAGUACGUGCCAUAAUGAAGCAAUUGCGCUUCCGGCAACAGGCAAACUACUAAAACAACUAAAACAGCAACACUACGA-GUAUUGCCAACACCCGAAGCGACACAACAACUG
...........(((.(........((....))(((((.((.....((((((((..........((.....))..........)-)).)))))....)).)))))).)))........ ( -20.65)
>DroSim_CAF1 19957 116 - 1
UGACAAAGUACGUGCCAUAAUGAAGCAAUUGCGCUUCCUGCUACAGGCAAACUACUAAAACAACUAAAACAGCAACACUACGA-GUAUUGCCAACACCCAAAGCGACACAACAACUG
......((((..((((.....(((((......)))))........))))...))))...............((((.((.....-)).)))).......................... ( -16.92)
>DroEre_CAF1 54628 109 - 1
UGACAAAGUACGUGCCAUAAUGAAGCAAUUGCGCUUCCGGCAACAGGCAAACUACUAA-ACAACUAAAACAGCAACGCU-------AUUGCCAACACUUAAAGCAGCAGAACCACUG
......((((..((((.....(((((......))))).(....).))))...))))..-..........(((.....((-------.((((...........)))).)).....))) ( -20.80)
>DroYak_CAF1 53992 109 - 1
UGACAAAGUACGUGCCAUAAUGAAGCAAUUGCGCUUCCGGCAACAGGCAAACUACUAA-ACAACUAAAACAGCAACGCU-------AUUGCCAACACUUAAAGCAACACAACAACUG
......((((..((((.....(((((......))))).(....).))))...))))..-............((((....-------.)))).......................... ( -18.50)
>consensus
UGACAAAGUACGUGCCAUAAUGAAGCAAUUGCGCUUCCGGCAACAGGCAAACUACUAAAACAACUAAAACAGCAACACUACGA_GUAUUGCCAACACCCAAAGCGACACAACAACUG
......((((..((((.....(((((......))))).(....).))))...))))...............((((.((......)).)))).......................... (-16.44 = -17.44 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:11 2006