Locus 3693

Sequence ID	3L_DroMel_CAF1
Location	10,759,304 – 10,759,442
Length	138
Max. P	0.698277

overview

Window 5

Location	10,759,304 – 10,759,410
Length	106
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	85.31
Mean single sequence MFE	-20.90
Consensus MFE	-13.68
Energy contribution	-13.80
Covariance contribution	0.12
Combinations/Pair	1.09
Mean z-score	-1.93
Structure conservation index	0.65
SVM decision value	0.35
SVM RNA-class probability	0.698277
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10759304 106 + 23771897
AGUAAAAAAAUGAUAAUAAAAUCUCUUGGGUAACAAAAUUUGUUGUUUGUUGUUGCAAAUACAUUAAUUGUUGUUGCGGAAGCGGAUGCAAAAACAGAAGAAAA--AA
.....................(((..((..((((((....(((.((((((....)))))))))....))))))((((....)))).........))..)))...--.. ( -17.80)
>DroSec_CAF1 93040 104 + 1
AGUAAAAAAAUGAUAAUAAAAUCUCUUGGGUAACACAAUUUGUUGUUUGUUGUUGCUAAUACAUUAAUUGUUGUUGCGGAAGCGGAUGCAAAAACCGAAAGAAA----
.....................(((.(((((((((((((........))).))))))...........((((..((((....))))..))))...)))).)))..---- ( -21.90)
>DroSim_CAF1 95853 104 + 1
AGUAAAAAAAUGAUAAUAAAAUCUCUUGGGUAACACAAUUUGUUGUUUGUUGUUGCUAAUACAUUAAUUGUUGUUGCGGAAGCGGAUGCAAAAACCGAAAGAAA----
.....................(((.(((((((((((((........))).))))))...........((((..((((....))))..))))...)))).)))..---- ( -21.90)
>DroEre_CAF1 97738 93 + 1
-----------AAUAUUAAAAUCCCUUGGGUAACAAAAUUUGUUGUCUGCUGUUGCUAAUACAAUAAUUGUUGUUGCGGAAGCGGAUGCAAAAACAGAAG----AAAA
-----------.........(((((((..(((((((...(((((((..((....))....)))))))...)))))))..))).)))).............----.... ( -22.00)
>consensus
AGUAAAAAAAUGAUAAUAAAAUCUCUUGGGUAACAAAAUUUGUUGUUUGUUGUUGCUAAUACAUUAAUUGUUGUUGCGGAAGCGGAUGCAAAAACAGAAAGAAA____
....................(((((((..(((((((((((...(((..((....))....)))..))))).))))))..))).))))..................... (-13.68 = -13.80 +   0.12)

alignment

secondary structure

dotplot

Window 6

Location	10,759,339 – 10,759,442
Length	103
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	82.62
Mean single sequence MFE	-18.48
Consensus MFE	-16.08
Energy contribution	-15.60
Covariance contribution	-0.48
Combinations/Pair	1.14
Mean z-score	-1.58
Structure conservation index	0.87
SVM decision value	0.34
SVM RNA-class probability	0.696253
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10759339 103 + 23771897
AAAUUUGUUGUUUGUUGUUGCAAAUACAUUAAUUGUUGUUGCGGAAGCGGAUGCAAAAACAGAAGAAAA---------AAAAAACAUUUGAAAAAAAGCUGGAGAAGAGCAG
...(((....((((((.(((((...(((.....)))..((((....)))).))))).))))))....))---------)..................(((.......))).. ( -18.00)
>DroSec_CAF1 93075 89 + 1
CAAUUUGUUGUUUGUUGUUGCUAAUACAUUAAUUGUUGUUGCGGAAGCGGAUGCAAAAACCGAAAGAAA-----------------------AAAAAGCUGGAGAAGAGCAG
.....((((.(((......(((..........((((..((((....))))..))))....(....)...-----------------------....)))....))).)))). ( -16.80)
>DroSim_CAF1 95888 89 + 1
CAAUUUGUUGUUUGUUGUUGCUAAUACAUUAAUUGUUGUUGCGGAAGCGGAUGCAAAAACCGAAAGAAA-----------------------AAAAAGCUGGAGAAGAGCAG
.....((((.(((......(((..........((((..((((....))))..))))....(....)...-----------------------....)))....))).)))). ( -16.80)
>DroEre_CAF1 97762 100 + 1
AAAUUUGUUGUCUGCUGUUGCUAAUACAAUAAUUGUUGUUGCGGAAGCGGAUGCAAAAACAGAAG-----------AAAAAAAGCAUUUGA-AAAAAGCUGGAGAAGAGCAG
...(((((.(((((((.((((....(((((....))))).)))).))))))))))))........-----------......(((.(((..-..))))))............ ( -21.60)
>DroYak_CAF1 108809 111 + 1
AAAUUUGUUGUUUGUUGCUGCUAAUACAAUAAUUGUUGUUGCGGAAGCGGAUGCAAAAACAGAAAGAAAAAACAGAAAAAAAAACAUUUGA-AAAAAGCUGGAGAAGAGCAG
...((((((.((((((..(((....(((((....)))))(((....)))...)))..)))))).......))))))...............-.....(((.......))).. ( -19.20)
>consensus
AAAUUUGUUGUUUGUUGUUGCUAAUACAUUAAUUGUUGUUGCGGAAGCGGAUGCAAAAACAGAAAGAAA_________AAAAA_CAUUUGA_AAAAAGCUGGAGAAGAGCAG
...(((((.(((((((.((((....(((.....)))....)))).))))))))))))........................................(((.......))).. (-16.08 = -15.60 +  -0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:25 2006