Locus 4079

Sequence ID	X_DroMel_CAF1
Location	10,779,593 – 10,779,702
Length	109
Max. P	0.854674

overview

Window 7

Location	10,779,593 – 10,779,702
Length	109
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	85.66
Mean single sequence MFE	-25.86
Consensus MFE	-20.14
Energy contribution	-20.30
Covariance contribution	0.16
Combinations/Pair	1.05
Mean z-score	-1.95
Structure conservation index	0.78
SVM decision value	0.80
SVM RNA-class probability	0.854674
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10779593 109 + 22224390
CAACAUGGCGCGCAUAUUUUUUUCUUCUUUUUUUUUUUACCAAAGGUUUAUUGGCCUUUUGGCUUACUCUCUGCAC----GCGCCUGUGUGUGUGUCGCCAUUUUAGCUCGAA
....(((((((((..........................(((((((((....)))).)))))..........((((----((....))))))))).))))))........... ( -27.30)
>DroPse_CAF1 46538 105 + 1
CAACAUGGCGCGCU-----UUUUU---CUAUAUUUUUCUCCAAAGGUUUAUUGGCCUUUUGGCUUACUCUUGCCAGUUCUCUGCGUGUGUGUGUGUCGCCAUUUUAGCUCGAA
....(((((((((.-----.....---............(((((((((....)))).)))))..(((.(.(((.((....))))).).))).))).))))))........... ( -23.60)
>DroSec_CAF1 29126 106 + 1
CAACAUGGCGCGCAUAUUUUUUUU---UUUCAUUUUUUACCAAAGGUUUAUUGGCCUUUUGGCUUACUCUCUGCAC----GCGCCUGUGUGUGUGUCGCCAUUUUAGCUCGAA
....(((((((((...........---............(((((((((....)))).)))))..........((((----((....))))))))).))))))........... ( -27.30)
>DroSim_CAF1 27794 106 + 1
CAACAUGGCGCGCAUAUUUUUUUU---UUUCAUUUUUUACCAAAGGUUUAUUGGCCCUUUGGCUUACUCUCUGCAC----GCGCCUGUGUGUGUGUCGCCAUUUUAGCUCGAA
....(((((((((...........---............(((((((.........)))))))..........((((----((....))))))))).))))))........... ( -27.50)
>DroPer_CAF1 40595 104 + 1
CAACAUGGCGCGCU-----UUUUU----UAUAUUUUUCUCCAAAGGUUUAUUGGCCUUUUGGCUUACUCUUGCCAGUUCUCUGCGUGUGUGUGUGUCGCCAUUUUAGCUCGAA
....(((((((((.-----.....----(((((........(((((((....)))))))((((........)))).........)))))...))).))))))........... ( -23.60)
>consensus
CAACAUGGCGCGCAUAUUUUUUUU___UUUUAUUUUUUACCAAAGGUUUAUUGGCCUUUUGGCUUACUCUCUGCAC____GCGCCUGUGUGUGUGUCGCCAUUUUAGCUCGAA
....(((((((((..........................(((((((((....)))).)))))..................((((....))))))).))))))........... (-20.14 = -20.30 +   0.16)

alignment

secondary structure

dotplot

Window 8

Location	10,779,593 – 10,779,702
Length	109
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	85.66
Mean single sequence MFE	-23.00
Consensus MFE	-17.62
Energy contribution	-17.54
Covariance contribution	-0.08
Combinations/Pair	1.15
Mean z-score	-1.71
Structure conservation index	0.77
SVM decision value	0.33
SVM RNA-class probability	0.692462
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10779593 109 - 22224390
UUCGAGCUAAAAUGGCGACACACACACAGGCGC----GUGCAGAGAGUAAGCCAAAAGGCCAAUAAACCUUUGGUAAAAAAAAAAAGAAGAAAAAAAUAUGCGCGCCAUGUUG
.....(((.....))).........((((((((----((((.....))..((((((.((........)))))))).........................))))))).))).. ( -24.10)
>DroPse_CAF1 46538 105 - 1
UUCGAGCUAAAAUGGCGACACACACACACGCAGAGAACUGGCAAGAGUAAGCCAAAAGGCCAAUAAACCUUUGGAGAAAAAUAUAG---AAAAA-----AGCGCGCCAUGUUG
...........((((((...........(((.......((((........))))(((((........)))))..............---.....-----.))))))))).... ( -19.20)
>DroSec_CAF1 29126 106 - 1
UUCGAGCUAAAAUGGCGACACACACACAGGCGC----GUGCAGAGAGUAAGCCAAAAGGCCAAUAAACCUUUGGUAAAAAAUGAAA---AAAAAAAAUAUGCGCGCCAUGUUG
.....(((.....))).........((((((((----((((.....))..((((((.((........))))))))...........---...........))))))).))).. ( -24.10)
>DroSim_CAF1 27794 106 - 1
UUCGAGCUAAAAUGGCGACACACACACAGGCGC----GUGCAGAGAGUAAGCCAAAGGGCCAAUAAACCUUUGGUAAAAAAUGAAA---AAAAAAAAUAUGCGCGCCAUGUUG
.....(((.....))).........((((((((----((((.....))..((((((((.........))))))))...........---...........))))))).))).. ( -28.40)
>DroPer_CAF1 40595 104 - 1
UUCGAGCUAAAAUGGCGACACACACACACGCAGAGAACUGGCAAGAGUAAGCCAAAAGGCCAAUAAACCUUUGGAGAAAAAUAUA----AAAAA-----AGCGCGCCAUGUUG
...........((((((...........(((.......((((........))))(((((........))))).............----.....-----.))))))))).... ( -19.20)
>consensus
UUCGAGCUAAAAUGGCGACACACACACAGGCGC____GUGCAGAGAGUAAGCCAAAAGGCCAAUAAACCUUUGGUAAAAAAUAAAA___AAAAAAAAUAUGCGCGCCAUGUUG
...........((((((.(.(........((((....)))).........(((((.(((........)))))))).........................).))))))).... (-17.62 = -17.54 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:53 2006