Locus 5100

Sequence ID	3R_DroMel_CAF1
Location	13,442,093 – 13,442,293
Length	200
Max. P	0.984755

overview

Window 1

Location	13,442,093 – 13,442,213
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	94.44
Mean single sequence MFE	-36.70
Consensus MFE	-32.89
Energy contribution	-33.00
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-2.03
Structure conservation index	0.90
SVM decision value	0.46
SVM RNA-class probability	0.744985
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13442093 120 + 27905053
CUGCGAUUCAGGCGCAAAAGCUUGGUAUCAAACAAACGACUUAAGCGAUGUUCUAGACGAUUAGAACUUGUAGAACCCAUGGAUGUCGAUGAGGAUUACCAAUCGACAUCGAUUGAGCCC
..(((((((((((......)))))).)))...(((.(.......((((.(((((((....)))))))))))..........(((((((((..((....)).)))))))))).))).)).. ( -34.40)
>DroSec_CAF1 11198 120 + 1
CUGCGAUCCAGGCGCAAAAGCUUGGUAUCAAACAAACGACUUAUGCGACGUUCUAGACGAGUCCAACUGGUAGAACCCAUGGAUGUCGAUGAGGAUCACCAAUCGACAUCGAUUGAGCCA
..(((((((((((......)))))).)))..........(((((.(((((((...)))..(((((..(((......)))))))))))))))))......((((((....)))))).)).. ( -36.50)
>DroSim_CAF1 10919 120 + 1
CUGCGAUCCAGGCGCAAAAGCUUGGUAUCAAACAAACGACUUAUGCGACGUUCUAGACGAGUCCAACUGGUAGAACCCAUGGAUGUCGAUGAGGCUCACCAAUCGACAUCGAUUGAGCCA
....(((((((((......)))))).))).......((((........((((...)))).(((((..(((......))))))))))))....((((((...((((....)))))))))). ( -39.20)
>consensus
CUGCGAUCCAGGCGCAAAAGCUUGGUAUCAAACAAACGACUUAUGCGACGUUCUAGACGAGUCCAACUGGUAGAACCCAUGGAUGUCGAUGAGGAUCACCAAUCGACAUCGAUUGAGCCA
..(((((((((((......)))))).)))...(((.(............(((((..((.((.....)).))))))).....(((((((((..((....)).)))))))))).))).)).. (-32.89 = -33.00 +   0.11)

alignment

secondary structure

dotplot

Window 2

Location	13,442,173 – 13,442,293
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	94.44
Mean single sequence MFE	-35.03
Consensus MFE	-32.90
Energy contribution	-33.57
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-3.08
Structure conservation index	0.94
SVM decision value	1.98
SVM RNA-class probability	0.984755
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13442173 120 + 27905053
GGAUGUCGAUGAGGAUUACCAAUCGACAUCGAUUGAGCCCAUGGAUAUUGACUUUGAAUAUGAUUCACAACCGCAAAAUACUCAAAAUCAGUUGAAUCCACAGUCUCGUCAUAAUGUCGA
.(((((((((..((....)).)))))))))(((.(((.(..((((((((((.(((((.(((................))).))))).)))))...)))))..).)))))).......... ( -31.49)
>DroSec_CAF1 11278 120 + 1
GGAUGUCGAUGAGGAUCACCAAUCGACAUCGAUUGAGCCAAUGGAUAUUGAAUUUGAAAAUGAUUCACAACUGCAGAAUACUCAAAUUCAGUUGGAUCCACAGUCUCGUCAUCAUGUCGA
.(((((((((..((....)).)))))))))(((.(((.(..((((((((((((((((.....((((.........))))..)))))))))))...)))))..).)))))).......... ( -35.50)
>DroSim_CAF1 10999 120 + 1
GGAUGUCGAUGAGGCUCACCAAUCGACAUCGAUUGAGCCAAUGGAUAUUGAAUUUGAAAAUGAUUCACAACUGCAGAAUACUCAAAUUCAGUUGGAUCCACAGUCUCGUCAUCAUGUCGA
.((((.(((.((((((((...((((....))))))))))..((((((((((((((((.....((((.........))))..)))))))))))...)))))...))))).))))....... ( -38.10)
>consensus
GGAUGUCGAUGAGGAUCACCAAUCGACAUCGAUUGAGCCAAUGGAUAUUGAAUUUGAAAAUGAUUCACAACUGCAGAAUACUCAAAUUCAGUUGGAUCCACAGUCUCGUCAUCAUGUCGA
.(((((((((..((....)).)))))))))(((.(((.(..((((((((((((((((.....((((.........))))..)))))))))))...)))))..).)))))).......... (-32.90 = -33.57 +   0.67)

alignment

secondary structure

dotplot

Window 3

Location	13,442,173 – 13,442,293
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	94.44
Mean single sequence MFE	-37.83
Consensus MFE	-34.30
Energy contribution	-33.63
Covariance contribution	-0.66
Combinations/Pair	1.06
Mean z-score	-3.48
Structure conservation index	0.91
SVM decision value	1.80
SVM RNA-class probability	0.977714
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13442173 120 - 27905053
UCGACAUUAUGACGAGACUGUGGAUUCAACUGAUUUUGAGUAUUUUGCGGUUGUGAAUCAUAUUCAAAGUCAAUAUCCAUGGGCUCAAUCGAUGUCGAUUGGUAAUCCUCAUCGACAUCC
.............(((.((((((((.....(((((((((((((((..(....)..))..)))))))))))))..)))))))).)))....(((((((((.((....))..))))))))). ( -41.40)
>DroSec_CAF1 11278 120 - 1
UCGACAUGAUGACGAGACUGUGGAUCCAACUGAAUUUGAGUAUUCUGCAGUUGUGAAUCAUUUUCAAAUUCAAUAUCCAUUGGCUCAAUCGAUGUCGAUUGGUGAUCCUCAUCGACAUCC
.......(((...(((...((((((.....((((((((((.((((.((....))))))....))))))))))..))))))...))).)))(((((((((.((....))..))))))))). ( -35.70)
>DroSim_CAF1 10999 120 - 1
UCGACAUGAUGACGAGACUGUGGAUCCAACUGAAUUUGAGUAUUCUGCAGUUGUGAAUCAUUUUCAAAUUCAAUAUCCAUUGGCUCAAUCGAUGUCGAUUGGUGAGCCUCAUCGACAUCC
.......(((...(((...((((((.....((((((((((.((((.((....))))))....))))))))))..))))))...))).)))(((((((((.((....))..))))))))). ( -36.40)
>consensus
UCGACAUGAUGACGAGACUGUGGAUCCAACUGAAUUUGAGUAUUCUGCAGUUGUGAAUCAUUUUCAAAUUCAAUAUCCAUUGGCUCAAUCGAUGUCGAUUGGUGAUCCUCAUCGACAUCC
.............(((...((((((.....((((((((((.((((.((....))))))....))))))))))..))))))...)))....(((((((((.((....))..))))))))). (-34.30 = -33.63 +  -0.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:10 2006