Locus 5040

Sequence ID	X_DroMel_CAF1
Location	13,187,516 – 13,187,624
Length	108
Max. P	0.982281

overview

Window 1

Location	13,187,516 – 13,187,624
Length	108
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	94.99
Mean single sequence MFE	-37.14
Consensus MFE	-32.38
Energy contribution	-33.58
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-1.35
Structure conservation index	0.87
SVM decision value	0.44
SVM RNA-class probability	0.736629
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13187516 108 + 22224390
UGAACAGUUGGCCAUAGAAACGCAGUUGGCCCUUCGUCAUGAAAAGGCGACCACAAUCGUGGGGCCAUCUGGCUGACAUCGACGUCUACAUCGAUGGCCAUCGAGGAC
......(.(((((((.((....(((.((((((.(((((.......))))).(((....))))))))).)))(..(((......)))..).)).))))))).)...... ( -38.70)
>DroSec_CAF1 17179 108 + 1
GGAACAGUUGGCCAUAGAAACGCAGUUGGCCCUUCGUCAUGAAAAGGCGACCACAAUCGUGGGGCCAUCUGGCUGACAUCGACGUCUACAUCGAUGGCCAUCGAGGAC
......(.(((((((.((....(((.((((((.(((((.......))))).(((....))))))))).)))(..(((......)))..).)).))))))).)...... ( -38.70)
>DroSim_CAF1 18556 108 + 1
GGAACAGUUGGCCAUAGAAACGCAGUUGGCCCUUCGUCAUGAAAAGGCGACCACAAUCGUGGGGCCAUCUGGCUGACAUCGACGUCUACAUCGAUGGCCAUCGAGGAC
......(.(((((((.((....(((.((((((.(((((.......))))).(((....))))))))).)))(..(((......)))..).)).))))))).)...... ( -38.70)
>DroEre_CAF1 21254 105 + 1
GGAAGAGCCGGCCAUAGAAACGCAG--GGCCCUUCGUCAUGAAAU-GCGACCACAAUCGUGGGGCCAUCUGGCUGACAUCGACGUCUACAUCGAUGGCCAUCGAGGAC
.((((.(((.((.........))..--))).))))(((.(((...-....((((....))))(((((((..(..(((......)))..)...))))))).)))..))) ( -34.70)
>DroYak_CAF1 23680 105 + 1
GGAACAGCCGGCCAUAGAAACGCAG--GGACCGACGUCAUGAAAA-GCGACCACAAUCGUGGGGCCAUCUGGCUGACAUCGACGUCUACAUCGAUGGCCAUCGAGGAC
((.....))((((((.((......(--....)(((((((((....-....((((....))))((((....))))..))).))))))....)).))))))......... ( -34.90)
>consensus
GGAACAGUUGGCCAUAGAAACGCAGUUGGCCCUUCGUCAUGAAAAGGCGACCACAAUCGUGGGGCCAUCUGGCUGACAUCGACGUCUACAUCGAUGGCCAUCGAGGAC
.........((((((.((....(((.((((((.(((((.......))))).(((....))))))))).)))(..(((......)))..).)).))))))......... (-32.38 = -33.58 +   1.20)

alignment

secondary structure

dotplot

Window 2

Location	13,187,516 – 13,187,624
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	94.99
Mean single sequence MFE	-39.26
Consensus MFE	-36.84
Energy contribution	-37.20
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-1.58
Structure conservation index	0.94
SVM decision value	1.91
SVM RNA-class probability	0.982281
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13187516 108 - 22224390
GUCCUCGAUGGCCAUCGAUGUAGACGUCGAUGUCAGCCAGAUGGCCCCACGAUUGUGGUCGCCUUUUCAUGACGAAGGGCCAACUGCGUUUCUAUGGCCAACUGUUCA
........((((((((((((....)))))))...((((((.((((((..((.(..(((........)))..)))..)))))).))).))).....)))))........ ( -39.80)
>DroSec_CAF1 17179 108 - 1
GUCCUCGAUGGCCAUCGAUGUAGACGUCGAUGUCAGCCAGAUGGCCCCACGAUUGUGGUCGCCUUUUCAUGACGAAGGGCCAACUGCGUUUCUAUGGCCAACUGUUCC
........((((((((((((....)))))))...((((((.((((((..((.(..(((........)))..)))..)))))).))).))).....)))))........ ( -39.80)
>DroSim_CAF1 18556 108 - 1
GUCCUCGAUGGCCAUCGAUGUAGACGUCGAUGUCAGCCAGAUGGCCCCACGAUUGUGGUCGCCUUUUCAUGACGAAGGGCCAACUGCGUUUCUAUGGCCAACUGUUCC
........((((((((((((....)))))))...((((((.((((((..((.(..(((........)))..)))..)))))).))).))).....)))))........ ( -39.80)
>DroEre_CAF1 21254 105 - 1
GUCCUCGAUGGCCAUCGAUGUAGACGUCGAUGUCAGCCAGAUGGCCCCACGAUUGUGGUCGC-AUUUCAUGACGAAGGGCC--CUGCGUUUCUAUGGCCGGCUCUUCC
(((.....((((((((((((....))))))))...))))((..((.((((....))))..))-...))..)))((((((((--..((.........)).)))))))). ( -39.10)
>DroYak_CAF1 23680 105 - 1
GUCCUCGAUGGCCAUCGAUGUAGACGUCGAUGUCAGCCAGAUGGCCCCACGAUUGUGGUCGC-UUUUCAUGACGUCGGUCC--CUGCGUUUCUAUGGCCGGCUGUUCC
........(((((((.(((((((...((((((((((((....))).((((....))))....-......)))))))))...--)))))))...)))))))........ ( -37.80)
>consensus
GUCCUCGAUGGCCAUCGAUGUAGACGUCGAUGUCAGCCAGAUGGCCCCACGAUUGUGGUCGCCUUUUCAUGACGAAGGGCCAACUGCGUUUCUAUGGCCAACUGUUCC
........((((((((((((....)))))))...((((((.((((((..((.(..(((........)))..)))..)))))).))).))).....)))))........ (-36.84 = -37.20 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:44 2006