Locus 1966

Sequence ID	X_DroMel_CAF1
Location	5,382,410 – 5,382,521
Length	111
Max. P	0.916991

overview

Window 2

Location	5,382,410 – 5,382,521
Length	111
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.66
Mean single sequence MFE	-33.72
Consensus MFE	-31.52
Energy contribution	-31.77
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.90
Structure conservation index	0.93
SVM decision value	1.11
SVM RNA-class probability	0.916991
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5382410 111 + 22224390
UCACUCGAUCGGGGAACUAAUAAUCUUAUUAGAAUUAAUGAUGGAAUUUCCAAUU---------UGCGGCGACAGGCAGCUGCCGGCGAUUUAAUGUUAAUAAGUCCCGCGUUCCUCGAG
........(((((((((........................(((.....)))...---------.((((.(((.(((....)))((((......)))).....)))))))))))))))). ( -33.50)
>DroSec_CAF1 63684 111 + 1
UCACUCGAUCGGGGAACUAAUAAUCUUAUUACAAUUAAUGAUGGAAUUUCCAAUU---------UGCGGCGACAGGCAGCUGCCGGCGAUUUAAUGUUAAUAAGUCCCGCGUUCCUCGAG
........(((((((((........((((((....))))))(((.....)))...---------.((((.(((.(((....)))((((......)))).....)))))))))))))))). ( -33.50)
>DroEre_CAF1 56746 120 + 1
UCACUCGAUCGGGGAACUAAUAAUCUUAUUAGAAUUAAUGAUGGAAUUUCCAAUUUGCGAAAUUUGCGGCGACAGGCAGCUGCCGGCGAUUUAAUGUUAAUAAGUGCCGCGUUCCUCGAG
........(((((((((..........................((((((((.....).)))))))(((((.((.(((....)))((((......)))).....)))))))))))))))). ( -34.60)
>DroYak_CAF1 56431 111 + 1
UCAGUCGAUCGGGGAACUAAUAAUCUUAUUAGAAUUAAUGAUGGAAUUUCCAAUU---------UGCGGCGACAGGCAGCUGCCGGCGAUUUAAUGUUAAUAAGUGCCGCGUUCCUCGAG
........(((((((((........................(((.....)))...---------.(((((.((.(((....)))((((......)))).....)))))))))))))))). ( -33.30)
>consensus
UCACUCGAUCGGGGAACUAAUAAUCUUAUUAGAAUUAAUGAUGGAAUUUCCAAUU_________UGCGGCGACAGGCAGCUGCCGGCGAUUUAAUGUUAAUAAGUCCCGCGUUCCUCGAG
........(((((((((.......((((((((.(((((...(((.....)))..............((.((.(((....))).)).))..))))).))))))))......))))))))). (-31.52 = -31.77 +   0.25)

alignment

secondary structure

dotplot

Window 3

Location	5,382,410 – 5,382,521
Length	111
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.66
Mean single sequence MFE	-29.11
Consensus MFE	-27.30
Energy contribution	-27.55
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.94
SVM decision value	0.36
SVM RNA-class probability	0.702484
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5382410 111 - 22224390
CUCGAGGAACGCGGGACUUAUUAACAUUAAAUCGCCGGCAGCUGCCUGUCGCCGCA---------AAUUGGAAAUUCCAUCAUUAAUUCUAAUAAGAUUAUUAGUUCCCCGAUCGAGUGA
((((((((((....(((((((((..(((((...((.(((.((.....)).))))).---------...(((.....)))...)))))..))))))).))....)))))....)))))... ( -29.40)
>DroSec_CAF1 63684 111 - 1
CUCGAGGAACGCGGGACUUAUUAACAUUAAAUCGCCGGCAGCUGCCUGUCGCCGCA---------AAUUGGAAAUUCCAUCAUUAAUUGUAAUAAGAUUAUUAGUUCCCCGAUCGAGUGA
((((((((((....(((((((((..(((((...((.(((.((.....)).))))).---------...(((.....)))...)))))..))))))).))....)))))....)))))... ( -29.50)
>DroEre_CAF1 56746 120 - 1
CUCGAGGAACGCGGCACUUAUUAACAUUAAAUCGCCGGCAGCUGCCUGUCGCCGCAAAUUUCGCAAAUUGGAAAUUCCAUCAUUAAUUCUAAUAAGAUUAUUAGUUCCCCGAUCGAGUGA
(((((((((((((((..(((.......)))......(((((....))))))))))...........(((((((.............)))))))..........)))))....)))))... ( -29.32)
>DroYak_CAF1 56431 111 - 1
CUCGAGGAACGCGGCACUUAUUAACAUUAAAUCGCCGGCAGCUGCCUGUCGCCGCA---------AAUUGGAAAUUCCAUCAUUAAUUCUAAUAAGAUUAUUAGUUCCCCGAUCGACUGA
.(((.((((((((((..(((.......)))......(((((....)))))))))).---------.(((((((.............)))))))..........))))).)))........ ( -28.22)
>consensus
CUCGAGGAACGCGGCACUUAUUAACAUUAAAUCGCCGGCAGCUGCCUGUCGCCGCA_________AAUUGGAAAUUCCAUCAUUAAUUCUAAUAAGAUUAUUAGUUCCCCGAUCGAGUGA
((((((((((......(((((((..(((((...((.(((.((.....)).))))).............(((.....)))...)))))..))))))).......)))))....)))))... (-27.30 = -27.55 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:05 2006