Locus 7190

Sequence ID	3R_DroMel_CAF1
Location	18,959,397 – 18,959,525
Length	128
Max. P	0.999289

overview

Window 5

Location	18,959,397 – 18,959,494
Length	97
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	98.56
Mean single sequence MFE	-31.06
Consensus MFE	-31.10
Energy contribution	-30.94
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-2.25
Structure conservation index	1.00
SVM decision value	3.49
SVM RNA-class probability	0.999289
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18959397 97 - 27905053
GCACGUAAGCAUGGGCAAAUAAGCCUUUGGCCAAAAGGGAACUGGGCAAAUAAGAUCGCCUGUUUGUUGAGGUUGCAGCAACAGGUUCAAAGGAUGC
(((.....((....)).......(((((((((...((....)).)))..........(((((((.((((......))))))))))).)))))).))) ( -29.70)
>DroSec_CAF1 70804 97 - 1
GCGCAUAAGCAUGGGCAAAUAAGCCUUUGGCCAAAAGGGAACUGGGCAAACAAGAUCGCCUGUUUGUUGAGGUUGCAGCAACAGGUUCAAAGGAUGC
((.(((....))).)).......(((((((((...((....)).)))..........(((((((.((((......))))))))))).)))))).... ( -32.10)
>DroSim_CAF1 72410 97 - 1
GCGCGUAAGCAUGGGCAAAUAAGCCUUUGGCCAAAAGGGAACUGGGCAAACAAGAUCGCCUGUUUGUUGAGGUUGCAGCAACAGGUUCAAAGGAUGC
((((....)).............(((((((((...((....)).)))..........(((((((.((((......))))))))))).))))))..)) ( -31.90)
>DroEre_CAF1 70989 97 - 1
GCACGUAAGCAUGGGCAAAUAAGCCUUUGGCCAAAAGGGAACUGGGCAAACAAGAUCGCCUGUUUGUUGAGGUUGCAGCAACAGGUUCAAAGGAUGC
(((.....((....)).......(((((((((...((....)).)))..........(((((((.((((......))))))))))).)))))).))) ( -29.70)
>DroYak_CAF1 73150 97 - 1
GCGCGUAAGCAUGGGCAAAUAAGCCUUUGGCCAAAAGGGAACUGGGCAAACAAGAUCGCCUGUUUGUUGAGGUUGCAGCAACAGGUUCAAAGGAUGC
((((....)).............(((((((((...((....)).)))..........(((((((.((((......))))))))))).))))))..)) ( -31.90)
>consensus
GCGCGUAAGCAUGGGCAAAUAAGCCUUUGGCCAAAAGGGAACUGGGCAAACAAGAUCGCCUGUUUGUUGAGGUUGCAGCAACAGGUUCAAAGGAUGC
((.(((....))).)).......(((((((((...((....)).)))..........(((((((.((((......))))))))))).)))))).... (-31.10 = -30.94 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	18,959,435 – 18,959,525
Length	90
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	90.13
Mean single sequence MFE	-26.88
Consensus MFE	-25.86
Energy contribution	-25.70
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.37
Structure conservation index	0.96
SVM decision value	0.96
SVM RNA-class probability	0.889636
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18959435 90 - 27905053
---------AUCGCCAUCGUCGAGGGUCAGUGUUUGAACUGCACGUAAGCAUGGGCAAAUAAGCCUUUGGCCAAAAGGGAACUGGGCAAAUAAGAUCGC
---------...((.(((..(((((((...((((((..((((......))).)..)))))).)))))))(((...((....)).)))......))).)) ( -28.70)
>DroSec_CAF1 70842 90 - 1
---------AUCGCCAUCGUCGAGGGUCAGUGUUUGAACUGCGCAUAAGCAUGGGCAAAUAAGCCUUUGGCCAAAAGGGAACUGGGCAAACAAGAUCGC
---------...((.(((..(((((((...((((((..((((......))).)..)))))).)))))))(((...((....)).)))......))).)) ( -29.40)
>DroSim_CAF1 72448 86 - 1
-------------CCAUCGUCGAGGGUCAGUGUUUGAACUGCGCGUAAGCAUGGGCAAAUAAGCCUUUGGCCAAAAGGGAACUGGGCAAACAAGAUCGC
-------------..(((..(((((((...((((((..((((......))).)..)))))).)))))))(((...((....)).)))......)))... ( -26.70)
>DroEre_CAF1 71027 86 - 1
-------------CCAUCGUUGAGGGUCAGUGUUUGGACUGCACGUAAGCAUGGGCAAAUAAGCCUUUGGCCAAAAGGGAACUGGGCAAACAAGAUCGC
-------------.....(((((((((...((((((..((((......))).)..)))))).)))))).(((...((....)).))).)))........ ( -22.90)
>DroYak_CAF1 73188 99 - 1
CACAUCCACAUCCACAUCAUCGAGGGUCAGUGUUUGAACUGCGCGUAAGCAUGGGCAAAUAAGCCUUUGGCCAAAAGGGAACUGGGCAAACAAGAUCGC
...............(((..(((((((...((((((..((((......))).)..)))))).)))))))(((...((....)).)))......)))... ( -26.70)
>consensus
_________AUC_CCAUCGUCGAGGGUCAGUGUUUGAACUGCGCGUAAGCAUGGGCAAAUAAGCCUUUGGCCAAAAGGGAACUGGGCAAACAAGAUCGC
...............(((..(((((((...((((((..((((......))).)..)))))).)))))))(((...((....)).)))......)))... (-25.86 = -25.70 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:39:44 2006