Locus 8543

Sequence ID	3L_DroMel_CAF1
Location	22,322,843 – 22,323,002
Length	159
Max. P	0.588498

overview

Window 2

Location	22,322,843 – 22,322,962
Length	119
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	88.89
Mean single sequence MFE	-31.03
Consensus MFE	-26.62
Energy contribution	-26.73
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-1.75
Structure conservation index	0.86
SVM decision value	0.11
SVM RNA-class probability	0.588498
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22322843 119 - 23771897
GCAGCGCUGCCCAACCAAUUUACAAUUUAAUAGCGCGCCGCAAAAUCGAACGAUCUUCGAAGAUCUUCUUCCCCGAGAAGAUCCCAAAGACGUCGAGGCACGCAGUGGA-AAAAGAUGCA
(((((((((.....................)))))).((((....((((.((.((((.(..(((((((((....))))))))).).)))))))))).(....).)))).-......))). ( -32.70)
>DroSec_CAF1 2037 120 - 1
GCAGCGCUGCCCAACCAAUUUACAAUUUAAUAGCGCGCCGCAAAAUCGAACGAUCUUCGAAGAUCUUCUUCCCCGAGAAGAUCCCAAAGACGUCGAGGCACGCAGUGGACAAAAGAUGCA
(((((((((.....................))))))(((((....((((.((.((((.(..(((((((((....))))))))).).)))))))))).(....).)))).)......))). ( -33.00)
>DroEre_CAF1 131 108 - 1
GCAGCGCUGCCCAACCAAUUUACAAUUUAAUAGUGCGCCGCAAAAUCGAACGAUCUUCGAAGAUCUUCUGCCCCGAGAAGAUCCCAAAC------------ACAGUAGGCAGAAGAUGCA
(((((((((.....................))))))(((((....(((((.....))))).((((((((......))))))))......------------...)).)))......))). ( -27.40)
>consensus
GCAGCGCUGCCCAACCAAUUUACAAUUUAAUAGCGCGCCGCAAAAUCGAACGAUCUUCGAAGAUCUUCUUCCCCGAGAAGAUCCCAAAGACGUCGAGGCACGCAGUGGACAAAAGAUGCA
(((((((((.....................)))))).((((....(((((.....))))).((((((((......)))))))).....................))))........))). (-26.62 = -26.73 +   0.11)

alignment

secondary structure

dotplot

Window 3

Location	22,322,882 – 22,323,002
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	96.67
Mean single sequence MFE	-34.60
Consensus MFE	-32.71
Energy contribution	-32.93
Covariance contribution	0.23
Combinations/Pair	1.06
Mean z-score	-1.52
Structure conservation index	0.95
SVM decision value	-0.03
SVM RNA-class probability	0.519242
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22322882 120 - 23771897
GUUCAAUACGAUGUGGCAUUCAGACACGUUUGCCGCUGCAGCAGCGCUGCCCAACCAAUUUACAAUUUAAUAGCGCGCCGCAAAAUCGAACGAUCUUCGAAGAUCUUCUUCCCCGAGAAG
((((........((((((..(......)..))))))(((.((.((((((.....................)))))))).))).....))))(((((....)))))(((((....))))). ( -33.00)
>DroSec_CAF1 2077 120 - 1
GUUCAAUACGAUGUGGCAUUCAGACACGUUUGCCGCUGCGGCAGCGCUGCCCAACCAAUUUACAAUUUAAUAGCGCGCCGCAAAAUCGAACGAUCUUCGAAGAUCUUCUUCCCCGAGAAG
((((........((((((..(......)..))))))((((((.((((((.....................)))))))))))).....))))(((((....)))))(((((....))))). ( -39.10)
>DroEre_CAF1 159 120 - 1
GUUUAAUACGAUGUGGCAUUCAGACACGUUUGCCGGAGCGGCAGCGCUGCCCAACCAAUUUACAAUUUAAUAGUGCGCCGCAAAAUCGAACGAUCUUCGAAGAUCUUCUGCCCCGAGAAG
........((((.(((((..(......)..)))))..(((((.((((((.....................)))))))))))...))))...(((((....)))))((((......)))). ( -31.70)
>consensus
GUUCAAUACGAUGUGGCAUUCAGACACGUUUGCCGCUGCGGCAGCGCUGCCCAACCAAUUUACAAUUUAAUAGCGCGCCGCAAAAUCGAACGAUCUUCGAAGAUCUUCUUCCCCGAGAAG
((((........((((((..(......)..)))))).(((((.((((((.....................)))))))))))......))))(((((....)))))((((......)))). (-32.71 = -32.93 +   0.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:18:39 2006