Locus 7459

Sequence ID	3L_DroMel_CAF1
Location	20,016,828 – 20,016,933
Length	105
Max. P	0.997949

overview

Window 0

Location	20,016,828 – 20,016,933
Length	105
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	81.52
Mean single sequence MFE	-31.80
Consensus MFE	-22.40
Energy contribution	-25.28
Covariance contribution	2.88
Combinations/Pair	1.18
Mean z-score	-3.20
Structure conservation index	0.70
SVM decision value	2.97
SVM RNA-class probability	0.997949
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20016828 105 + 23771897
----------AUUCAAUGGAACUCUGCAUACAAAUUUUCUAUUUAGCUGCCCUUUCAAUUGAAAGGUAGAGUAUCUUCUGCGAAUCUCGGAGCCCGUUUGUGUGCAAAGUUCCCU
----------.......((((((.(((((((((((...........(((((.((((....)))))))))........((.((.....)).))...))))))))))).)))))).. ( -34.20)
>DroSec_CAF1 8746 105 + 1
----------AUUCAACGGCACUCUGCACACAAAUUUUCUAUUGGGCUGUCCUUUCAAUUGAAAGGUAGAGUAUCUCCUGCGAAUCUCGAGGCCCGUUUGUGUGCAAAGUUCCCU
----------.......((.(((.(((((((((((........(((((..((((((....))))))..(((..((......))..)))..)))))))))))))))).))).)).. ( -37.30)
>DroSim_CAF1 3421 105 + 1
----------AUUCAAUGGCACUCUGCAUACAAAUUUUCUAUUGGGCUGCCCUUUCAAUUGAAAGGUAGAGUAUUUCCUGCGAAUCUCGAGGCCCGUUUGUGUGCAAAGUUCCCU
----------.......((.(((.(((((((((((........(((((..((((((....))))))..(((...(((....))).)))..)))))))))))))))).))).)).. ( -35.60)
>DroYak_CAF1 10202 106 + 1
CUCCCUUUUCAUUCAAUGACACUUUGAAUAUUUAUUUUCUAUUGGGUUGCCCAUGCAAUUGAAAGGUAGAGUAUCUCCUGCGAAUCUCGGAGCCCGUCUG--------U-UCCCU
....((((((((((((.......))))))...............((((((....))))))))))))..(((..((......))..)))(((((......)--------)-))).. ( -20.10)
>consensus
__________AUUCAAUGGCACUCUGCAUACAAAUUUUCUAUUGGGCUGCCCUUUCAAUUGAAAGGUAGAGUAUCUCCUGCGAAUCUCGAAGCCCGUUUGUGUGCAAAGUUCCCU
.................((.(((.(((((((((((........(((((.(((((((....))))))..(((..((......))..)))).)))))))))))))))).))).)).. (-22.40 = -25.28 +   2.88)

alignment

secondary structure

dotplot

Window 1

Location	20,016,828 – 20,016,933
Length	105
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	81.52
Mean single sequence MFE	-31.40
Consensus MFE	-18.40
Energy contribution	-22.27
Covariance contribution	3.88
Combinations/Pair	1.07
Mean z-score	-2.79
Structure conservation index	0.59
SVM decision value	1.50
SVM RNA-class probability	0.959389
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20016828 105 - 23771897
AGGGAACUUUGCACACAAACGGGCUCCGAGAUUCGCAGAAGAUACUCUACCUUUCAAUUGAAAGGGCAGCUAAAUAGAAAAUUUGUAUGCAGAGUUCCAUUGAAU----------
..(((((((((((.(((((..((((.((((..((......))..)))..((((((....))))))).))))..........))))).))))))))))).......---------- ( -34.90)
>DroSec_CAF1 8746 105 - 1
AGGGAACUUUGCACACAAACGGGCCUCGAGAUUCGCAGGAGAUACUCUACCUUUCAAUUGAAAGGACAGCCCAAUAGAAAAUUUGUGUGCAGAGUGCCGUUGAAU----------
..((.((((((((((((((.((((...(((..((......))..)))..((((((....))))))...)))).........)))))))))))))).)).......---------- ( -38.90)
>DroSim_CAF1 3421 105 - 1
AGGGAACUUUGCACACAAACGGGCCUCGAGAUUCGCAGGAAAUACUCUACCUUUCAAUUGAAAGGGCAGCCCAAUAGAAAAUUUGUAUGCAGAGUGCCAUUGAAU----------
..((.((((((((.(((((.((((...(((.(((....)))...)))..((((((....))))))...)))).........))))).)))))))).)).......---------- ( -31.80)
>DroYak_CAF1 10202 106 - 1
AGGGA-A--------CAGACGGGCUCCGAGAUUCGCAGGAGAUACUCUACCUUUCAAUUGCAUGGGCAACCCAAUAGAAAAUAAAUAUUCAAAGUGUCAUUGAAUGAAAAGGGAG
.(...-.--------)(((.(..((((..........))))...)))).(((((((((.((((((....)).....(((........)))...)))).))))).....))))... ( -20.00)
>consensus
AGGGAACUUUGCACACAAACGGGCCCCGAGAUUCGCAGGAGAUACUCUACCUUUCAAUUGAAAGGGCAGCCCAAUAGAAAAUUUGUAUGCAGAGUGCCAUUGAAU__________
..((.((((((((.(((((.((((...(((..((......))..)))..((((((....))))))...)))).........))))).)))))))).))................. (-18.40 = -22.27 +   3.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:47:38 2006