Locus 10253

Sequence ID	3R_DroMel_CAF1
Location	27,466,061 – 27,466,197
Length	136
Max. P	0.925944

overview

Window 1

Location	27,466,061 – 27,466,157
Length	96
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.83
Mean single sequence MFE	-34.02
Consensus MFE	-21.62
Energy contribution	-22.18
Covariance contribution	0.56
Combinations/Pair	1.11
Mean z-score	-1.98
Structure conservation index	0.64
SVM decision value	1.17
SVM RNA-class probability	0.925944
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27466061 96 - 27905053
GGCAGGAAACUGCCUCGAGGAGCUAUAGCGAUU--CCAGC----------------------CCGACUCCAAGGAUCUGGCUGGGCCAGCAAUUAAUGUCAAAGUCAAUAUGCCUUAUCG
(((((....))))).(((.(((.((((((...(--(((((----------------------(.((.((....)))).)))))))...))......((.......)).)))).))).))) ( -33.50)
>DroSec_CAF1 21961 96 - 1
GGCAGGAAACUGCCUCGAGGAGCUACAGCGAUU--CCAGC----------------------CCGACUCCAAGGAUCUGGCUGGGCCAGCAAUUAAUGUCAAAGUCAACAUGCCUUAUCG
(((((....)))))..((((.......((...(--(((((----------------------(.((.((....)))).)))))))...)).....((((........)))).)))).... ( -34.70)
>DroSim_CAF1 21832 96 - 1
GGCAGGAAACUGCCUCGAGGAGCUACAGCGAUU--CCAGC----------------------CCGACUCCAAGGAUCUGGCUGGGCCAGCAAUUAAUGUCAAAGUCAAUAUGCCUUAUCG
(((((....)))))..((((.......((...(--(((((----------------------(.((.((....)))).)))))))...)).....((((........)))).)))).... ( -32.80)
>DroEre_CAF1 21800 110 - 1
GGCAGGAAACUGCCUCGAGGAGCUCGAGCAGCU--CGAGGAGCUCGAGGAGCUACAG------CGACUCCA--GAUCUGGCUGGGCCAGCAAUUAAUGUCAAAGUCAAUAUGCCUUAUCG
(((((....)))))..(((..(((..(((..((--((((...))))))..)))..))------)..)))..--(((..(((..(((..(((.....)))....))).....)))..))). ( -41.10)
>DroYak_CAF1 22831 109 - 1
GGCAGGAAACUGCCUCGAGGAGCUCGAGAAGCU-----------CGAGAAGCUACAGAGAUUCCGACUCCAAGGAUCUGGCUGGGCCAGCAAUUAAUGUCAAAGUCAAUAUGCCUUAUCG
(((((....))))).(((((((.(((.(((.((-----------(...........))).))))))))))((((...(((((..(.((........)).)..))))).....)))).))) ( -36.80)
>DroPer_CAF1 25394 94 - 1
GGCAGGAAACUGCCUCGGGGCUCCGUCUCUCUUUCUCUAU----------------------CCGACUCC----CUCUAGUUGGGCCCGCAAUUAAUGUCGAAGUCAAUAUGCCUUAUCG
(((((....)))))..(((((..................(----------------------((((((..----....)))))))..((((.....)).))..........))))).... ( -25.20)
>consensus
GGCAGGAAACUGCCUCGAGGAGCUACAGCGAUU__CCAGC______________________CCGACUCCAAGGAUCUGGCUGGGCCAGCAAUUAAUGUCAAAGUCAAUAUGCCUUAUCG
(((((....)))))..((((.((....))...................................(((.........(((((...)))))........)))............)))).... (-21.62 = -22.18 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	27,466,101 – 27,466,197
Length	96
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	78.27
Mean single sequence MFE	-32.34
Consensus MFE	-19.55
Energy contribution	-20.61
Covariance contribution	1.06
Combinations/Pair	1.10
Mean z-score	-1.56
Structure conservation index	0.60
SVM decision value	0.23
SVM RNA-class probability	0.645561
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27466101 96 - 27905053
UGCUGACGUUAAUGACCGCCAAUAAAAUGCGUGCUCAAGUGGCAGGAAACUGCCUCGAGGAGCUAUAGCGAUUCCAGC----------------------CCGACUCCAAGGAUCUGG
.((((.(((((.....(((.........))).((((..(.(((((....))))).)...))))..)))))....))))----------------------(((..((....))..))) ( -31.40)
>DroSec_CAF1 22001 96 - 1
UGCUGACGUUAAUGACCGCCAAUAAAAUGCGUGCUCAAGUGGCAGGAAACUGCCUCGAGGAGCUACAGCGAUUCCAGC----------------------CCGACUCCAAGGAUCUGG
.((((((((...................))))((((..(.(((((....))))).)...))))..))))....((((.----------------------((........))..)))) ( -32.91)
>DroSim_CAF1 21872 96 - 1
UGCUGACGUUAAUGACCGCCAAUAAAAUGCGUGCUCAAGUGGCAGGAAACUGCCUCGAGGAGCUACAGCGAUUCCAGC----------------------CCGACUCCAAGGAUCUGG
.((((((((...................))))((((..(.(((((....))))).)...))))..))))....((((.----------------------((........))..)))) ( -32.91)
>DroEre_CAF1 21840 110 - 1
UGCUGACGUUAAUGACCGCCAAUAAAAUGCGUGCUCAAGUGGCAGGAAACUGCCUCGAGGAGCUCGAGCAGCUCGAGGAGCUCGAGGAGCUACAG------CGACUCCA--GAUCUGG
.((((........................((.((((..(.(((((....))))).)...)))).))(((..((((((...))))))..))).)))------)....(((--....))) ( -41.00)
>DroYak_CAF1 22871 109 - 1
UGCUGACGUUAAUGACCGCCAAUAAAAUGCGUGCUCAAGUGGCAGGAAACUGCCUCGAGGAGCUCGAGAAGCU---------CGAGAAGCUACAGAGAUUCCGACUCCAAGGAUCUGG
.(((.((((...................))))((((..(.(((((....))))).)...))))(((((...))---------)))..)))..((((...(((........))))))). ( -34.01)
>DroAna_CAF1 24471 77 - 1
UGCUGACGUUAAUGACCGCCAAUAAAAUGCGUGCUCAAGUGGCAGGAAACUGCCUCGAGGC---------------------------------------CC-AACCGAAGGAACUC-
............(((.(((((......)).))).))).(.(((((....))))).)(((..---------------------------------------((-.......))..)))- ( -21.80)
>consensus
UGCUGACGUUAAUGACCGCCAAUAAAAUGCGUGCUCAAGUGGCAGGAAACUGCCUCGAGGAGCUACAGCGAUUCCAGC______________________CCGACUCCAAGGAUCUGG
((((.((((...................))))((((..(.(((((....))))).)...))))...))))....................................(((......))) (-19.55 = -20.61 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:52:43 2006