Locus 2705

Sequence ID	X_DroMel_CAF1
Location	7,252,858 – 7,253,015
Length	157
Max. P	0.874071

overview

Window 5

Location	7,252,858 – 7,252,975
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	77.36
Mean single sequence MFE	-39.08
Consensus MFE	-25.69
Energy contribution	-27.00
Covariance contribution	1.31
Combinations/Pair	1.21
Mean z-score	-1.86
Structure conservation index	0.66
SVM decision value	0.77
SVM RNA-class probability	0.844919
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7252858 117 + 22224390
CCGA---CGAGCCAUGCUGGCUAAACAUCCGGAUCGAAACGGCUCACCAUAUCUGGCGGGAAAAAUCCACAAGCCCAAGAAUGGGCUGCUGGAGGGAAGAAAUCGGUUCAGAUAGAAAUC
((((---.(((((...((((........))))........))))).((...((..((.(((....)))...((((((....))))))))..)).))......)))).............. ( -37.60)
>DroSec_CAF1 3103 117 + 1
CCGA---CGAGUCAUGCUGGCUAAAGAUCUGGAUCGAAGCGGCUCACCAUAUCUGGCAGGAAAAAUCCACAAGCCCAAGAAUGGGCUGUUGGACGAAAGAAAUCGGUUCAGAUAGAAAUC
....---..((((.....))))....(((((((((((...((....))...((..((.(((....)))...((((((....))))))))..))(....)...)))))))))))....... ( -36.80)
>DroSim_CAF1 1545 117 + 1
CCGA---CGUUCCAUGCUGGCUAAAGAUCCGGAUCGAAACGGCUCACCAUAUCUGGCGGGAAAAAUCCACAAGCCCAAGAAUGGGCUGUUGGACUAAAGAAAUCGGUUCAGAUAGAAAUC
((((---..((((.(((..(.((..((.(((........))).))....)).)..)))))))...((((..((((((....))))))..)))).........)))).............. ( -33.70)
>DroAna_CAF1 5088 118 + 1
CCACAGGCAGGUCAUGCUGGCCAACCAUCCGGACCGCUGUGGCUCUCCCUAUUUGGCGUCCAAAAUCAACGAGGCCAAGGAGCUGCUAAUGUCGCGGAGGCAGCGGUCCCGGUAGGGA--
((...((..((((.....))))..))(((.((((((((((....((((...((((((.((..........)).))))))..((.((....)).)))))))))))))))).))).))..-- ( -48.20)
>consensus
CCGA___CGAGCCAUGCUGGCUAAACAUCCGGAUCGAAACGGCUCACCAUAUCUGGCGGGAAAAAUCCACAAGCCCAAGAAUGGGCUGUUGGACGAAAGAAAUCGGUUCAGAUAGAAAUC
.........((((.....))))....(((.(((((((.....(((.((......)).))).....((((..(((((......)))))..)))).........))))))).)))....... (-25.69 = -27.00 +   1.31)

alignment

secondary structure

dotplot

Window 6

Location	7,252,895 – 7,253,015
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	92.07
Mean single sequence MFE	-35.72
Consensus MFE	-28.01
Energy contribution	-28.01
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-3.37
Structure conservation index	0.78
SVM decision value	0.88
SVM RNA-class probability	0.874071
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7252895 120 + 22224390
GGCUCACCAUAUCUGGCGGGAAAAAUCCACAAGCCCAAGAAUGGGCUGCUGGAGGGAAGAAAUCGGUUCAGAUAGAAAUCGAAAGAUUAGGCACUAGAUGGCAGGAUGUGAAGUUCAACA
......((...((..((.(((....)))...((((((....))))))))..)).))..(((.(((((((.......((((....))))..((.(.....))).)))).)))..))).... ( -31.90)
>DroSec_CAF1 3140 113 + 1
GGCUCACCAUAUCUGGCAGGAAAAAUCCACAAGCCCAAGAAUGGGCUGUUGGACGAAAGAAAUCGGUUCAGAUAGAAAUCGAAAGAUUAGG-------UGGCAGGAAUUGAAGUUCAACA
.((.((((.((((((((..((....((((..((((((....))))))..))))(....)...)).).)))))))..((((....)))).))-------))))..((((....)))).... ( -38.60)
>DroSim_CAF1 1582 113 + 1
GGCUCACCAUAUCUGGCGGGAAAAAUCCACAAGCCCAAGAAUGGGCUGUUGGACUAAAGAAAUCGGUUCAGAUAGAAAUCGAAAGAUUAGG-------UGGCAGGAAUUGAAGUUCAACA
.((.((((.((((((((((......((((..((((((....))))))..)))).........)))..)))))))..((((....)))).))-------))))..((((....)))).... ( -36.66)
>consensus
GGCUCACCAUAUCUGGCGGGAAAAAUCCACAAGCCCAAGAAUGGGCUGUUGGACGAAAGAAAUCGGUUCAGAUAGAAAUCGAAAGAUUAGG_______UGGCAGGAAUUGAAGUUCAACA
..((..(((((((((((.((.....((((..((((((....))))))..)))).........)).).)))))))..((((....))))..........)))..))............... (-28.01 = -28.01 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	7,252,895 – 7,253,015
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	92.07
Mean single sequence MFE	-28.97
Consensus MFE	-23.00
Energy contribution	-23.33
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.43
Structure conservation index	0.79
SVM decision value	0.31
SVM RNA-class probability	0.680740
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7252895 120 - 22224390
UGUUGAACUUCACAUCCUGCCAUCUAGUGCCUAAUCUUUCGAUUUCUAUCUGAACCGAUUUCUUCCCUCCAGCAGCCCAUUCUUGGGCUUGUGGAUUUUUCCCGCCAGAUAUGGUGAGCC
.(..(((.((((((...(((............((((.((((((....))).)))..))))...........)))(((((....))))).)))))).)))..)(((((....))))).... ( -25.40)
>DroSec_CAF1 3140 113 - 1
UGUUGAACUUCAAUUCCUGCCA-------CCUAAUCUUUCGAUUUCUAUCUGAACCGAUUUCUUUCGUCCAACAGCCCAUUCUUGGGCUUGUGGAUUUUUCCUGCCAGAUAUGGUGAGCC
.((((.....))))....((((-------((.((((....))))..((((((...(((......)))((((..((((((....))))))..))))..........)))))).)))).)). ( -31.30)
>DroSim_CAF1 1582 113 - 1
UGUUGAACUUCAAUUCCUGCCA-------CCUAAUCUUUCGAUUUCUAUCUGAACCGAUUUCUUUAGUCCAACAGCCCAUUCUUGGGCUUGUGGAUUUUUCCCGCCAGAUAUGGUGAGCC
.((((.....))))....((((-------((.((((....))))..((((((...((........((((((..((((((....))))))..)))))).....)).)))))).)))).)). ( -30.22)
>consensus
UGUUGAACUUCAAUUCCUGCCA_______CCUAAUCUUUCGAUUUCUAUCUGAACCGAUUUCUUUCGUCCAACAGCCCAUUCUUGGGCUUGUGGAUUUUUCCCGCCAGAUAUGGUGAGCC
..................((((..........((((....))))..((((((....(....)....(((((..((((((....))))))..))))).........))))))))))..... (-23.00 = -23.33 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:21 2006