Locus 4846

Sequence ID	X_DroMel_CAF1
Location	12,599,133 – 12,599,270
Length	137
Max. P	0.994478

overview

Window 8

Location	12,599,133 – 12,599,236
Length	103
Sequences	3
Columns	117
Reading direction	forward
Mean pairwise identity	79.49
Mean single sequence MFE	-26.21
Consensus MFE	-21.46
Energy contribution	-21.80
Covariance contribution	0.34
Combinations/Pair	1.10
Mean z-score	-2.52
Structure conservation index	0.82
SVM decision value	2.48
SVM RNA-class probability	0.994478
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12599133 103 + 22224390
AUGAAAAAAAA--------------AAAUAGACAUCGAUGUUUCGGAAAAUCGAUAAAAACAUCGAUGCAUCGAUGUUAGCUUCGAUAUUUCGGUACCGCUAGUUGCCACGAAAGUC
..((((.....--------------.....(.(((((((((((((......)))....)))))))))))(((((........))))).))))((((.(....).))))((....)). ( -26.40)
>DroSec_CAF1 7988 109 + 1
AUAAAUAUAAAUUGUCCGUAGUCUAUAAUAAACAUCGAUAUUUCGGGAAAUUGAUAAAAACAU--------CGAUGUUAACAUCGAUGUUUCGGCACCUCUAGUUGCCACGAAAGUC
.....(((.((((..(((..(((.............)))....)))..)))).))).((((((--------(((((....))))))))))).((((.(....).))))((....)). ( -26.52)
>DroSim_CAF1 7421 117 + 1
AUAAAUAUAAAUUGUCCGUAGUCUAUAAUAAACAUCGAUAUUUCGGGAAAUUGAUAAAAACAUCGCUGCAUCGAUGUUAUCAUCGAUGUUUCGGCACCUCUAGUUGCCACGAAAGUC
.....((((.((((....)))).))))..((((((((((...((((....))))....(((((((......)))))))...)))))))))).((((.(....).))))((....)). ( -25.70)
>consensus
AUAAAUAUAAAUUGUCCGUAGUCUAUAAUAAACAUCGAUAUUUCGGGAAAUUGAUAAAAACAUCG_UGCAUCGAUGUUAACAUCGAUGUUUCGGCACCUCUAGUUGCCACGAAAGUC
....................................(((.(((((((((((((((...(((((((......)))))))...)))))).))))((((.(....).)))).)))))))) (-21.46 = -21.80 +   0.34)

alignment

secondary structure

dotplot

Window 9

Location	12,599,133 – 12,599,236
Length	103
Sequences	3
Columns	117
Reading direction	reverse
Mean pairwise identity	79.49
Mean single sequence MFE	-26.07
Consensus MFE	-17.84
Energy contribution	-19.07
Covariance contribution	1.23
Combinations/Pair	1.08
Mean z-score	-1.96
Structure conservation index	0.68
SVM decision value	0.92
SVM RNA-class probability	0.881866
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12599133 103 - 22224390
GACUUUCGUGGCAACUAGCGGUACCGAAAUAUCGAAGCUAACAUCGAUGCAUCGAUGUUUUUAUCGAUUUUCCGAAACAUCGAUGUCUAUUU--------------UUUUUUUUCAU
(((..(((((((.....))....(.((((.(((((....((((((((....))))))))....))))))))).)...)).))).))).....--------------........... ( -23.30)
>DroSec_CAF1 7988 109 - 1
GACUUUCGUGGCAACUAGAGGUGCCGAAACAUCGAUGUUAACAUCG--------AUGUUUUUAUCAAUUUCCCGAAAUAUCGAUGUUUAUUAUAGACUACGGACAAUUUAUAUUUAU
...(((((.((((.(....).))))((((((((((((....)))))--------)))))))...........)))))..(((..(((((...)))))..)))............... ( -26.00)
>DroSim_CAF1 7421 117 - 1
GACUUUCGUGGCAACUAGAGGUGCCGAAACAUCGAUGAUAACAUCGAUGCAGCGAUGUUUUUAUCAAUUUCCCGAAAUAUCGAUGUUUAUUAUAGACUACGGACAAUUUAUAUUUAU
....(((((((((.(....).)))).((((((((((((.(((((((......))))))).)))))........((....)))))))))..........))))).............. ( -28.90)
>consensus
GACUUUCGUGGCAACUAGAGGUGCCGAAACAUCGAUGAUAACAUCGAUGCA_CGAUGUUUUUAUCAAUUUCCCGAAAUAUCGAUGUUUAUUAUAGACUACGGACAAUUUAUAUUUAU
........(((((.(....).)))))(((((((((((..(((((((......)))))))....((........))..)))))))))))............................. (-17.84 = -19.07 +   1.23)

alignment

secondary structure

dotplot

Window 0

Location	12,599,159 – 12,599,270
Length	111
Sequences	3
Columns	111
Reading direction	forward
Mean pairwise identity	89.79
Mean single sequence MFE	-33.53
Consensus MFE	-28.59
Energy contribution	-28.93
Covariance contribution	0.34
Combinations/Pair	1.09
Mean z-score	-2.64
Structure conservation index	0.85
SVM decision value	1.08
SVM RNA-class probability	0.912200
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12599159 111 + 22224390
UUUCGGAAAAUCGAUAAAAACAUCGAUGCAUCGAUGUUAGCUUCGAUAUUUCGGUACCGCUAGUUGCCACGAAAGUCGCUCGAACGCCGGUAACGGAAAUUCUCAGCAAAC
..((((((.(((((....((((((((....))))))))....))))).))))))....(((....((.((....)).))..(((..(((....)))...)))..))).... ( -33.80)
>DroSec_CAF1 8028 103 + 1
UUUCGGGAAAUUGAUAAAAACAU--------CGAUGUUAACAUCGAUGUUUCGGCACCUCUAGUUGCCACGAAAGUCGCGCGAACGCCGGUAACGGAAAUUCUCAGCAAAC
....(((((..((....((((((--------(((((....)))))))))))...))..(((.((((((((....)).(((....))).)))))))))..)))))....... ( -32.70)
>DroSim_CAF1 7461 111 + 1
UUUCGGGAAAUUGAUAAAAACAUCGCUGCAUCGAUGUUAUCAUCGAUGUUUCGGCACCUCUAGUUGCCACGAAAGUCGCGCGAACGCCGGUAACGGAAAUUCUCAGCAAAC
....(((((...............((((((((((((....)))))))))...)))...(((.((((((((....)).(((....))).)))))))))..)))))....... ( -34.10)
>consensus
UUUCGGGAAAUUGAUAAAAACAUCG_UGCAUCGAUGUUAACAUCGAUGUUUCGGCACCUCUAGUUGCCACGAAAGUCGCGCGAACGCCGGUAACGGAAAUUCUCAGCAAAC
(((((((((((((((...(((((((......)))))))...)))))).))))((((.(....).)))).)))))...((..(((..(((....)))...)))...)).... (-28.59 = -28.93 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:28 2006