Locus 5469

Sequence ID	3L_DroMel_CAF1
Location	14,945,648 – 14,945,757
Length	109
Max. P	0.970917

overview

Window 5

Location	14,945,648 – 14,945,757
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	91.65
Mean single sequence MFE	-28.39
Consensus MFE	-25.36
Energy contribution	-25.00
Covariance contribution	-0.36
Combinations/Pair	1.10
Mean z-score	-1.34
Structure conservation index	0.89
SVM decision value	0.61
SVM RNA-class probability	0.799786
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14945648 109 + 23771897
CGGUGAACGAUUGUUUUGGAAAAUUGUCGCCAAAUGGCAGAAGGAAAUCGACGACAGGUUCCUGAUCCAAAAUCUCUUCGUGGUGAUUAUGACGACAGAGAAUGGACGG
.......((....(((((((...((((((((....))).((......)))))))(((....))).)))))))(((((((((.((....)).)))).))))).....)). ( -30.30)
>DroSec_CAF1 125980 109 + 1
CGGAGAUCGAUUGUUUUGGAAAAUUGUCGCCAAAUGGCAGAAGGAAAUCGACGACAGGUUCUUGAUCCAAAAUCUCUUCGUGGUAAUUAUGACGACAGAGAAUGGACGA
......(((....(((((((...((((((((....))).((......)))))))(((....))).)))))))(((((((((.((....)).)))).))))).....))) ( -27.70)
>DroSim_CAF1 123708 109 + 1
CGGAGAUCGAUUGUUUUGGAAAAUUGUCGCCAAAUGGCAAAAGGAAAUCGACGACAGGUUCCUGAUCCAAAAUCUCUUCGUGGUGAUUAUGACGACAGAGAAUGGACGA
......(((....(((((((...((((((((....))).....(....))))))(((....))).)))))))(((((((((.((....)).)))).))))).....))) ( -29.70)
>DroEre_CAF1 120762 109 + 1
CGGGGAAAAAUUGUUUUGGAAAACUGCCGCCAAAUGGCAGAAGGAAAUCGACGAUAAGUUCCUGAUCCAAAAUCUUUUCGUGGUGUUAAUGACGACAGAGGAUGGACGA
((((((...((((((........((((((.....)))))).........))))))...)))))).((((...(((((((((.((....)).)))).))))).))))... ( -29.43)
>DroYak_CAF1 122592 109 + 1
CGGAGAAAAAUUGUUUUGGAAAAUAACCGCCAAAUGGCAGAAGGAAAUCGACGAUAGGUUCCUGAUCCAAAAUCUUUUCGUGGUAAUAAUGACGACAGAGAAUGGACGA
((...........(((((((........(((....)))...(((((.((.......)))))))..)))))))(((((((((.((....)).)))).))))).....)). ( -24.80)
>consensus
CGGAGAACGAUUGUUUUGGAAAAUUGUCGCCAAAUGGCAGAAGGAAAUCGACGACAGGUUCCUGAUCCAAAAUCUCUUCGUGGUGAUUAUGACGACAGAGAAUGGACGA
((...........(((((((........(((....)))...(((((.((.......)))))))..)))))))(((((((((.((....)).)))).))))).....)). (-25.36 = -25.00 +  -0.36)

alignment

secondary structure

dotplot

Window 6

Location	14,945,648 – 14,945,757
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	91.65
Mean single sequence MFE	-23.91
Consensus MFE	-21.92
Energy contribution	-22.64
Covariance contribution	0.72
Combinations/Pair	1.07
Mean z-score	-1.61
Structure conservation index	0.92
SVM decision value	1.67
SVM RNA-class probability	0.970917
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14945648 109 - 23771897
CCGUCCAUUCUCUGUCGUCAUAAUCACCACGAAGAGAUUUUGGAUCAGGAACCUGUCGUCGAUUUCCUUCUGCCAUUUGGCGACAAUUUUCCAAAACAAUCGUUCACCG
..(((((.(((((.((((..........)))))))))...)))))..((((..(((((((((..............)))))))))...))))................. ( -27.94)
>DroSec_CAF1 125980 109 - 1
UCGUCCAUUCUCUGUCGUCAUAAUUACCACGAAGAGAUUUUGGAUCAAGAACCUGUCGUCGAUUUCCUUCUGCCAUUUGGCGACAAUUUUCCAAAACAAUCGAUCUCCG
..(((((.(((((.((((..........)))))))))...)))))...(((..(((((((((..............)))))))))...))).................. ( -23.74)
>DroSim_CAF1 123708 109 - 1
UCGUCCAUUCUCUGUCGUCAUAAUCACCACGAAGAGAUUUUGGAUCAGGAACCUGUCGUCGAUUUCCUUUUGCCAUUUGGCGACAAUUUUCCAAAACAAUCGAUCUCCG
..(((((.(((((.((((..........)))))))))...)))))..((((..(((((((((..............)))))))))...))))................. ( -27.94)
>DroEre_CAF1 120762 109 - 1
UCGUCCAUCCUCUGUCGUCAUUAACACCACGAAAAGAUUUUGGAUCAGGAACUUAUCGUCGAUUUCCUUCUGCCAUUUGGCGGCAGUUUUCCAAAACAAUUUUUCCCCG
..(((((...(((.((((..........))))..)))...)))))..((((......(((((......)).(((....)))))).((((....)))).....))))... ( -19.70)
>DroYak_CAF1 122592 109 - 1
UCGUCCAUUCUCUGUCGUCAUUAUUACCACGAAAAGAUUUUGGAUCAGGAACCUAUCGUCGAUUUCCUUCUGCCAUUUGGCGGUUAUUUUCCAAAACAAUUUUUCUCCG
..(((((.(((...((((..........))))..)))...)))))..((((...((((((((..............))))))))....))))................. ( -20.24)
>consensus
UCGUCCAUUCUCUGUCGUCAUAAUCACCACGAAGAGAUUUUGGAUCAGGAACCUGUCGUCGAUUUCCUUCUGCCAUUUGGCGACAAUUUUCCAAAACAAUCGUUCUCCG
..(((((.(((((.((((..........)))))))))...)))))..((((..(((((((((..............)))))))))...))))................. (-21.92 = -22.64 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:11 2006