Locus 3581

Sequence ID	3L_DroMel_CAF1
Location	10,540,150 – 10,540,244
Length	94
Max. P	0.654549

overview

Window 2

Location	10,540,150 – 10,540,244
Length	94
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	88.15
Mean single sequence MFE	-21.32
Consensus MFE	-15.94
Energy contribution	-15.78
Covariance contribution	-0.16
Combinations/Pair	1.13
Mean z-score	-1.68
Structure conservation index	0.75
SVM decision value	0.20
SVM RNA-class probability	0.631450
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10540150 94 + 23771897
UUUUUCAUUUAUUUUUUUUUCUGCUCACGCUGUUUAGUUUUACGUUGAUAUAUAGGUGUAGUAGCAUGUAUGUGCGAGCAUAGGAGUGCGCAU------A
....................((((((((.((((...(((.......)))..))))))).)))))....((((((((..(....)..)))))))------) ( -18.90)
>DroSec_CAF1 419654 91 + 1
UUUUUCAUUUAUUUUUUUUUCUGCACACGCUGUUUAGUUUUACGUUGAUAUAUAGGUGU---AGCAUGUAUGUGCGAGCAUAAGAGUGCGCAU------A
.....................(((((((.((((...(((.......)))..))))))))---.)))..((((((((..(....)..)))))))------) ( -18.40)
>DroSim_CAF1 428013 91 + 1
UUUUUCAUUUAUUUUUUUUUCUGCACACGCUGUUUAGUUUUACGUUGAUAUAUAGGUGU---AGCAUGAAUGUGCGAGCAUAAGAGUGCGCAU------A
...................(((((((((.((((...(((.......)))..))))))))---.))).))(((((((..(....)..)))))))------. ( -18.90)
>DroEre_CAF1 428724 90 + 1
UUUAUGCUUU-UUUCUCUUUCUGCACACGCUGUUUAGUUUUACGCUAAUAUAUAGGUGU---GGCAUGUAUGCGCGAGCAUAGGAGUGCGCAU------A
..(((((...-............(((((.(((((((((.....)))))...))))))))---)((((.(((((....)))))...))))))))------) ( -28.30)
>DroYak_CAF1 428923 95 + 1
UUUUUUCUCU-UUUUU-UUUUUGCACACGCUGUUUAGUUUUACGUUGAUAUAUAGGUGU---AGCAUGUAUGUGCGAGUAUAAGAGUGCGCAUAUACAUA
..........-.....-.....((((((.((((...(((.......)))..))))))))---.))(((((((((((..(......)..))))))))))). ( -22.10)
>consensus
UUUUUCAUUUAUUUUUUUUUCUGCACACGCUGUUUAGUUUUACGUUGAUAUAUAGGUGU___AGCAUGUAUGUGCGAGCAUAAGAGUGCGCAU______A
.....................(((.(((.((((........))(((..((((((.((((....)))).))))))..)))...)).))).)))........ (-15.94 = -15.78 +  -0.16)

alignment

secondary structure

dotplot

Window 3

Location	10,540,150 – 10,540,244
Length	94
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	88.15
Mean single sequence MFE	-13.69
Consensus MFE	-10.96
Energy contribution	-11.00
Covariance contribution	0.04
Combinations/Pair	1.08
Mean z-score	-1.54
Structure conservation index	0.80
SVM decision value	0.25
SVM RNA-class probability	0.654549
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10540150 94 - 23771897
U------AUGCGCACUCCUAUGCUCGCACAUACAUGCUACUACACCUAUAUAUCAACGUAAAACUAAACAGCGUGAGCAGAAAAAAAAAUAAAUGAAAAA
.------.............((((((((......)))..................((((...........)))))))))..................... ( -10.90)
>DroSec_CAF1 419654 91 - 1
U------AUGCGCACUCUUAUGCUCGCACAUACAUGCU---ACACCUAUAUAUCAACGUAAAACUAAACAGCGUGUGCAGAAAAAAAAAUAAAUGAAAAA
.------.(((((((.((.......(((......))).---................((........)))).)))))))..................... ( -12.50)
>DroSim_CAF1 428013 91 - 1
U------AUGCGCACUCUUAUGCUCGCACAUUCAUGCU---ACACCUAUAUAUCAACGUAAAACUAAACAGCGUGUGCAGAAAAAAAAAUAAAUGAAAAA
.------.(((((((.((.......(((......))).---................((........)))).)))))))..................... ( -12.50)
>DroEre_CAF1 428724 90 - 1
U------AUGCGCACUCCUAUGCUCGCGCAUACAUGCC---ACACCUAUAUAUUAGCGUAAAACUAAACAGCGUGUGCAGAAAGAGAAA-AAAGCAUAAA
(------((((...(((...(((.(((((.........---..(((((.....))).))...........))))).)))....)))...-...))))).. ( -19.65)
>DroYak_CAF1 428923 95 - 1
UAUGUAUAUGCGCACUCUUAUACUCGCACAUACAUGCU---ACACCUAUAUAUCAACGUAAAACUAAACAGCGUGUGCAAAAA-AAAAA-AGAGAAAAAA
..(((((((((..............(((......))).---................((........)).)))))))))....-.....-.......... ( -12.90)
>consensus
U______AUGCGCACUCUUAUGCUCGCACAUACAUGCU___ACACCUAUAUAUCAACGUAAAACUAAACAGCGUGUGCAGAAAAAAAAAUAAAUGAAAAA
........(((((((..........(((......)))....................((........))...)))))))..................... (-10.96 = -11.00 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:28 2006