Locus 3644

Sequence ID	2R_DroMel_CAF1
Location	12,092,386 – 12,092,476
Length	90
Max. P	0.961804

overview

Window 1

Location	12,092,386 – 12,092,476
Length	90
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	89.02
Mean single sequence MFE	-32.46
Consensus MFE	-27.34
Energy contribution	-28.38
Covariance contribution	1.04
Combinations/Pair	1.04
Mean z-score	-1.36
Structure conservation index	0.84
SVM decision value	0.08
SVM RNA-class probability	0.572706
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12092386 90 + 20766785
AUUCGCUGGGCCAGUGACGUUGUUGGCCAAGUGGCAUUAGUUUGUCGAUUUCAAGAC------------CCGUCUUGGCCGUGUCAAUGGCCAACCGGUUGC
..(((...(((((.(((((....(((((((((((.........(((........)))------------))).))))))))))))).)))))...))).... ( -33.50)
>DroSec_CAF1 5773 90 + 1
AUUCGUUGGGCCAGUGACGUUGUUGGCCAAGUGGCAUUAGUUUGUCGAUUUCGAGAC------------CCGUCUUGGCCGUGUCAAUGGCCAACCGGUUGC
..(((...(((((.(((((....(((((((((((.....(((..(((....))))))------------))).))))))))))))).)))))...))).... ( -34.10)
>DroSim_CAF1 4911 90 + 1
AUUCGUUGGGCCAGUGACGUUGUUGGCCAAGUGGCAUUAGUUUGUCGAUUUCGAGAC------------CCGUCUUGGCCGUGUCAAUGGCCAACCGGUUGC
..(((...(((((.(((((....(((((((((((.....(((..(((....))))))------------))).))))))))))))).)))))...))).... ( -34.10)
>DroEre_CAF1 5852 89 + 1
GUUCGAAGAGCCAGUGACGUUGUUGGCCAAGUGGCAUUAGCUU-UCGAUUUCAAGAC------------CCGUCUUGGCCGUGUCAAUGGCCAACCGGUUGC
..((((.((((.(((..((....))(((....)))))).))))-))))......(((------------(.((..(((((((....))))))))).)))).. ( -27.20)
>DroYak_CAF1 6348 101 + 1
AUGCGAAGAGCCAGUGACGUUGUUGGCCAAGUGGCAUUAGUUU-UCGAUUUCAAGACUCGGAUUUGGACUCGUCGCGGCCGUGUCAAUGGCCAACCGGUUGC
..((((.(((((((...((......(((....)))...(((((-(.(....)))))))))...)))).))).))))((((((....)))))).......... ( -33.40)
>consensus
AUUCGAUGGGCCAGUGACGUUGUUGGCCAAGUGGCAUUAGUUUGUCGAUUUCAAGAC____________CCGUCUUGGCCGUGUCAAUGGCCAACCGGUUGC
...((...(((((.(((((....(((((((((((.........(((........)))............))).))))))))))))).)))))...))..... (-27.34 = -28.38 +   1.04)

alignment

secondary structure

dotplot

Window 2

Location	12,092,386 – 12,092,476
Length	90
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	89.02
Mean single sequence MFE	-29.24
Consensus MFE	-23.62
Energy contribution	-23.22
Covariance contribution	-0.40
Combinations/Pair	1.10
Mean z-score	-2.13
Structure conservation index	0.81
SVM decision value	1.53
SVM RNA-class probability	0.961804
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12092386 90 - 20766785
GCAACCGGUUGGCCAUUGACACGGCCAAGACGG------------GUCUUGAAAUCGACAAACUAAUGCCACUUGGCCAACAACGUCACUGGCCCAGCGAAU
.....((.(.(((((.((((..(((((((...(------------((.(((............))).))).)))))))......)))).))))).).))... ( -29.80)
>DroSec_CAF1 5773 90 - 1
GCAACCGGUUGGCCAUUGACACGGCCAAGACGG------------GUCUCGAAAUCGACAAACUAAUGCCACUUGGCCAACAACGUCACUGGCCCAACGAAU
.......((((((((.((((..(((((((...(------------((.(((....))).........))).)))))))......)))).))).))))).... ( -29.60)
>DroSim_CAF1 4911 90 - 1
GCAACCGGUUGGCCAUUGACACGGCCAAGACGG------------GUCUCGAAAUCGACAAACUAAUGCCACUUGGCCAACAACGUCACUGGCCCAACGAAU
.......((((((((.((((..(((((((...(------------((.(((....))).........))).)))))))......)))).))).))))).... ( -29.60)
>DroEre_CAF1 5852 89 - 1
GCAACCGGUUGGCCAUUGACACGGCCAAGACGG------------GUCUUGAAAUCGA-AAGCUAAUGCCACUUGGCCAACAACGUCACUGGCUCUUCGAAC
.....(((..(((((.((((..(((((((...(------------((.(((....(..-..).))).))).)))))))......)))).)))))..)))... ( -30.60)
>DroYak_CAF1 6348 101 - 1
GCAACCGGUUGGCCAUUGACACGGCCGCGACGAGUCCAAAUCCGAGUCUUGAAAUCGA-AAACUAAUGCCACUUGGCCAACAACGUCACUGGCUCUUCGCAU
..........((((........))))((((.(((.(((....(((((.(((....)))-..)))...(((....)))......))....)))))).)))).. ( -26.60)
>consensus
GCAACCGGUUGGCCAUUGACACGGCCAAGACGG____________GUCUUGAAAUCGACAAACUAAUGCCACUUGGCCAACAACGUCACUGGCCCAACGAAU
....((((((((((........))))).((((................(((....))).........(((....)))......))))))))).......... (-23.62 = -23.22 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:41 2006