Locus 706

Sequence ID	2L_DroMel_CAF1
Location	2,045,388 – 2,045,487
Length	99
Max. P	0.795113

overview

Window 5

Location	2,045,388 – 2,045,487
Length	99
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	84.02
Mean single sequence MFE	-26.46
Consensus MFE	-17.80
Energy contribution	-19.12
Covariance contribution	1.32
Combinations/Pair	1.25
Mean z-score	-2.11
Structure conservation index	0.67
SVM decision value	0.60
SVM RNA-class probability	0.795113
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2045388 99 + 22407834
AAAAACCGUUUGGUUUUAUAAUUUAAUCGAUCCUU-UCCCUGCUGCCACAGCUGAUCGCCGAGUGCUGCCACUUGUAUCCUCUUCUGUGGCAGCGUUGCC
.((((((....))))))..................-.....((((((((((..((....((((((....)))))).....))..))))))))))...... ( -31.40)
>DroSec_CAF1 62845 96 + 1
AAAAACCGUAUGGUUUUAAAAUUUAAUUGAUCCUU-UCAGCGCUGACACAGCUGAUCUCAAAGUGCUGCCAUCUGUAU---CUUCUGUGGCAGCGUUGCC
.((((((....))))))..................-.((((((((.(((((..(((..((..(((....))).)).))---)..))))).)))))))).. ( -26.00)
>DroSim_CAF1 61241 96 + 1
AAAAACCGUUUGGUUUUAAAAUUUAAUUGAUCCUU-UCGGCGCUGCUACAGCUGAUCUCCAAGUGCUGCCAUCUGUAU---CUUCUGUGGCAGCGUUGCC
.((((((....))))))..................-.((((((((((((((..(((...((..((....))..)).))---)..)))))))))))))).. ( -30.90)
>DroEre_CAF1 61737 96 + 1
AAAAACCGUUGCGUUUUAUAAUUUAAUCGAUCCUU-UCGGCGCUGCCACUGUUGAUCGCCCAGUGCUGCCACUUCUAU---CUGCUGAUGCAGCGUUGCC
......(((((((((.............((.....-))((((..((.((((.........))))))))))........---.....)))))))))..... ( -20.60)
>DroYak_CAF1 65047 92 + 1
AAAAACCGUUUCGUUUCAUAAUUUAAUCGAUCCUUUUUGGCGCUGCCACUGUUGAUCGCCAAGUGCUGCC-----CAU---CUUUUGCGGCAGCGUUGCC
...........................(((((..(..((((...))))..)..))))).(((.(((((((-----((.---....)).)))))))))).. ( -23.40)
>consensus
AAAAACCGUUUGGUUUUAUAAUUUAAUCGAUCCUU_UCGGCGCUGCCACAGCUGAUCGCCAAGUGCUGCCACCUGUAU___CUUCUGUGGCAGCGUUGCC
.(((((......)))))....................((((((((((((((..(........((((........))))...)..)))))))))))))).. (-17.80 = -19.12 +   1.32)

alignment

secondary structure

dotplot

Window 6

Location	2,045,388 – 2,045,487
Length	99
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	84.02
Mean single sequence MFE	-27.36
Consensus MFE	-16.85
Energy contribution	-18.05
Covariance contribution	1.20
Combinations/Pair	1.14
Mean z-score	-1.96
Structure conservation index	0.62
SVM decision value	0.09
SVM RNA-class probability	0.577787
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2045388 99 - 22407834
GGCAACGCUGCCACAGAAGAGGAUACAAGUGGCAGCACUCGGCGAUCAGCUGUGGCAGCAGGGA-AAGGAUCGAUUAAAUUAUAAAACCAAACGGUUUUU
(....)((((((((((.....(((.(.((((....)))).)...)))..)))))))))).....-..................((((((....)))))). ( -31.60)
>DroSec_CAF1 62845 96 - 1
GGCAACGCUGCCACAGAAG---AUACAGAUGGCAGCACUUUGAGAUCAGCUGUGUCAGCGCUGA-AAGGAUCAAUUAAAUUUUAAAACCAUACGGUUUUU
(....)((((((((.....---.....).))))))).((((.((....((((...)))).)).)-)))...............((((((....)))))). ( -25.70)
>DroSim_CAF1 61241 96 - 1
GGCAACGCUGCCACAGAAG---AUACAGAUGGCAGCACUUGGAGAUCAGCUGUAGCAGCGCCGA-AAGGAUCAAUUAAAUUUUAAAACCAAACGGUUUUU
.....((((((.((((..(---((.(((.((....)).)))...)))..)))).))))))((..-..))..............((((((....)))))). ( -28.50)
>DroEre_CAF1 61737 96 - 1
GGCAACGCUGCAUCAGCAG---AUAGAAGUGGCAGCACUGGGCGAUCAACAGUGGCAGCGCCGA-AAGGAUCGAUUAAAUUAUAAAACGCAACGGUUUUU
.((..((((((....((..---.........))..(((((.........)))))))))))((..-..))...................)).......... ( -24.20)
>DroYak_CAF1 65047 92 - 1
GGCAACGCUGCCGCAAAAG---AUG-----GGCAGCACUUGGCGAUCAACAGUGGCAGCGCCAAAAAGGAUCGAUUAAAUUAUGAAACGAAACGGUUUUU
(....)((((((.((....---.))-----))))))..(((((((((.....((((...)))).....))))).)))).....(((((......))))). ( -26.80)
>consensus
GGCAACGCUGCCACAGAAG___AUACAAAUGGCAGCACUUGGCGAUCAGCUGUGGCAGCGCCGA_AAGGAUCGAUUAAAUUAUAAAACCAAACGGUUUUU
(....)(((((((................))))))).......((((.....((((...)))).....))))...........(((((......))))). (-16.85 = -18.05 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:25 2006