Locus 1658

Sequence ID	3R_DroMel_CAF1
Location	4,788,101 – 4,788,214
Length	113
Max. P	0.981901

overview

Window 6

Location	4,788,101 – 4,788,214
Length	113
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	95.45
Mean single sequence MFE	-25.84
Consensus MFE	-22.08
Energy contribution	-21.64
Covariance contribution	-0.44
Combinations/Pair	1.12
Mean z-score	-1.55
Structure conservation index	0.85
SVM decision value	0.75
SVM RNA-class probability	0.840868
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4788101 113 + 27905053
GGGAUAUAGAUAUGAAUUGCAGCACUGCAAUCUGGGAUGAUAGUUCCGUAGUGGAUAGUGGUUUAAUUUAGAUUGCUUUCCAAUAUUCUUGGUUUUCUUGGUAUCUGACUUUU
......((((((...((((((....))))))(..(((.(((......(((.((((.((..(((((...)))))..)).)))).))).....))).)))..)))))))...... ( -27.30)
>DroSec_CAF1 23393 108 + 1
GGGAUAUAGAUAUGAAUUGCAGCACUGCAAUCUGGGAUGAUAGUUCCGUAGUGAAUAGUGAUUUAAUUUAGAUUGCUUUCCAAUAUUCUUGGUUUU-----UAUCUGACUUUU
............(((((..(..((((((.....(((((....)))))))))))....)..)))))..((((((......((((.....))))....-----.))))))..... ( -22.20)
>DroSim_CAF1 18860 108 + 1
GGGAUAUAGAUAUGAAUUGCAGCACUGCAAUCUGGGAUGAUAGUUCCGUAGUGGAUAGUGGUUUAAUUUGGAUUGUUUUCCAAUAUUCUUGGUUUU-----UAUCUGACUUUU
.(((((.((((.(((((..(..((((((.....(((((....)))))))))))....)..)))))..(((((......)))))........)))).-----)))))....... ( -24.70)
>DroEre_CAF1 23611 108 + 1
GGGAUAUAGAUAUGAAUUGCAGCACUGCAAUCUGGGAUGAUAGUUCCGUAGUGGAUAGUGGUUUAAUUUAGAUUGCUUUCCAAUAUUCUUGGUUUU-----UAUCUGAUUUUU
.(((((.((((..((((((((....))))))..(((((....)))))(((.((((.((..(((((...)))))..)).)))).)))))...)))).-----)))))....... ( -27.10)
>DroYak_CAF1 24053 108 + 1
GGGAUAUAGAUAUGAAUUGCAGCACUGCAAUCUGGGAUGAUAGUUCCGUAGUGGAUAGUAGUUUAAUUUAGAUUGCUUUCCAAUAUUCUUGGUUUU-----UAUCUGAUCUUU
(((((.((((((.((((((((....))).....(((((....)))))(((.((((.(((((((((...))))))))).)))).)))....))))).-----))))))))))). ( -27.90)
>consensus
GGGAUAUAGAUAUGAAUUGCAGCACUGCAAUCUGGGAUGAUAGUUCCGUAGUGGAUAGUGGUUUAAUUUAGAUUGCUUUCCAAUAUUCUUGGUUUU_____UAUCUGACUUUU
......((((((...((((((....))))))..(((((....)))))(((.((((.(((((((((...))))))))).)))).)))...............))))))...... (-22.08 = -21.64 +  -0.44)

alignment

secondary structure

dotplot

Window 7

Location	4,788,101 – 4,788,214
Length	113
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	95.45
Mean single sequence MFE	-15.93
Consensus MFE	-13.88
Energy contribution	-13.72
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-1.90
Structure conservation index	0.87
SVM decision value	1.90
SVM RNA-class probability	0.981901
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4788101 113 - 27905053
AAAAGUCAGAUACCAAGAAAACCAAGAAUAUUGGAAAGCAAUCUAAAUUAAACCACUAUCCACUACGGAACUAUCAUCCCAGAUUGCAGUGCUGCAAUUCAUAUCUAUAUCCC
....(.(((.(((........((((.....))))...(((((((..............(((.....)))...........))))))).))))))).................. ( -16.51)
>DroSec_CAF1 23393 108 - 1
AAAAGUCAGAUA-----AAAACCAAGAAUAUUGGAAAGCAAUCUAAAUUAAAUCACUAUUCACUACGGAACUAUCAUCCCAGAUUGCAGUGCUGCAAUUCAUAUCUAUAUCCC
.......(((((-----....((((.....))))...(((((((....((......))........(((.......))).)))))))..............)))))....... ( -14.50)
>DroSim_CAF1 18860 108 - 1
AAAAGUCAGAUA-----AAAACCAAGAAUAUUGGAAAACAAUCCAAAUUAAACCACUAUCCACUACGGAACUAUCAUCCCAGAUUGCAGUGCUGCAAUUCAUAUCUAUAUCCC
.......(((((-----........((...(((((......)))))............(((.....)))....))......(((((((....)))))))..)))))....... ( -16.50)
>DroEre_CAF1 23611 108 - 1
AAAAAUCAGAUA-----AAAACCAAGAAUAUUGGAAAGCAAUCUAAAUUAAACCACUAUCCACUACGGAACUAUCAUCCCAGAUUGCAGUGCUGCAAUUCAUAUCUAUAUCCC
.......(((((-----....((((.....))))...(((((((..............(((.....)))...........)))))))..............)))))....... ( -15.91)
>DroYak_CAF1 24053 108 - 1
AAAGAUCAGAUA-----AAAACCAAGAAUAUUGGAAAGCAAUCUAAAUUAAACUACUAUCCACUACGGAACUAUCAUCCCAGAUUGCAGUGCUGCAAUUCAUAUCUAUAUCCC
...(((.(((((-----....((((.....))))...(((((((..............(((.....)))...........)))))))..............)))))..))).. ( -16.21)
>consensus
AAAAGUCAGAUA_____AAAACCAAGAAUAUUGGAAAGCAAUCUAAAUUAAACCACUAUCCACUACGGAACUAUCAUCCCAGAUUGCAGUGCUGCAAUUCAUAUCUAUAUCCC
.......(((((.........((((.....))))........................(((.....)))............(((((((....)))))))..)))))....... (-13.88 = -13.72 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:08 2006