Locus 6810

Sequence ID	2L_DroMel_CAF1
Location	19,033,272 – 19,033,457
Length	185
Max. P	0.840334

overview

Window 8

Location	19,033,272 – 19,033,377
Length	105
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.93
Mean single sequence MFE	-34.17
Consensus MFE	-23.60
Energy contribution	-23.73
Covariance contribution	0.12
Combinations/Pair	1.07
Mean z-score	-1.77
Structure conservation index	0.69
SVM decision value	-0.05
SVM RNA-class probability	0.509730
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19033272 105 + 22407834
UGGAGAGUUUAUUUUUGGACCUUGGUAUUCCUCCGACUGG-------GGUGUGUUGAAAAUAGACAUAAACAAAUUUUCAGAUGGGAGCCCAGCCAUCGGUGCUCCC--------AUUCC
.((((.(((((((((..(((((..((.........))..)-------)))...)..))))))))).................(((((((((.......)).))))))--------))))) ( -35.00)
>DroSim_CAF1 34938 105 + 1
UGGAGAGUUUAUUUUUGGACCUUGGUAUUCCUCCGACUGG-------GGUGUGUUGAAAAUAGACAUAAACAAAUUUUCAGAUGGGAGCCCAGCCAGCGGUGCUCCC--------AUUCC
.((((.(((((((((..(((((..((.........))..)-------)))...)..))))))))).................(((((((((.......)).))))))--------))))) ( -35.00)
>DroEre_CAF1 35456 113 + 1
UGGAGAGUUUAUUUUUGGACCUUGGUAUUCCUCCGACUGG-------GGUGUGUUGAAAAUAGACAUAAACAAAAUUUCAGAUGGCGGCCCUGCCAGCGGUGCUCCCAUUCUCCCAUUCC
.((((((((((((((..(((((..((.........))..)-------)))...)..)))))))))................((((.(((.(((....))).))).)))))))))...... ( -34.90)
>DroYak_CAF1 31604 112 + 1
UGGAGAGUUUAUUUUUGGACUUUGGUAUUCUUCCGACUGGGGUCUGGGGUGUGUUGAAAAUAGACAUAAACAAAAUUUCAGAUGGCAGCCCAGCCAGCGGUGCUCCC--------AUUCC
.((((((((((....))))))...........(((.((((...(((((.(((.((((((................))))))...))).))))))))))))..)))).--------..... ( -31.79)
>consensus
UGGAGAGUUUAUUUUUGGACCUUGGUAUUCCUCCGACUGG_______GGUGUGUUGAAAAUAGACAUAAACAAAAUUUCAGAUGGCAGCCCAGCCAGCGGUGCUCCC________AUUCC
.((((.(((((((((..((((((((.......))))...........)))...)..)))))))))..................((((((((.......)).)))))).........)))) (-23.60 = -23.73 +   0.12)

alignment

secondary structure

dotplot

Window 9

Location	19,033,345 – 19,033,457
Length	112
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.82
Mean single sequence MFE	-44.39
Consensus MFE	-39.47
Energy contribution	-40.48
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.80
Structure conservation index	0.89
SVM decision value	0.75
SVM RNA-class probability	0.840334
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19033345 112 - 22407834
CUGCUCUAUAAUUACCCCGUAUCACGGGUGUGGAUGUGGAAUCGUUCUCUAGAGGGUGACAUUUGAUGUUGGCCUGGGGAGGAAU--------GGGAGCACCGAUGGCUGGGCUCCCAUC
....((((((.((((((((.....)))).)))).))))))....((((((..(((.((((((...)))))).)))..))))))((--------((((((.(((.....))))))))))). ( -47.20)
>DroSim_CAF1 35011 112 - 1
CUGCUCUAUAAUUACCCCGUAUCACGGGUGUGGAUGUGGAAUCGUUCUCUAGAGGGUGACAUUUGAUGUUGGCCUGGGGAGGAAU--------GGGAGCACCGCUGGCUGGGCUCCCAUC
....((((((.((((((((.....)))).)))).))))))....((((((..(((.((((((...)))))).)))..))))))((--------((((((.(((.....))))))))))). ( -46.90)
>DroEre_CAF1 35529 120 - 1
CUGCUCUAUAAUUACCCCGUAUCACGGGUGUGGAUGUGGAAUCGUUCUGUAGAGGGUGACAUUUGAUGUUGGCCUGGGGAGGAAUGGGAGAAUGGGAGCACCGCUGGCAGGGCCGCCAUC
..((((((((.((((((((.....)))).)))).))))))...(((((((..((((((.(((((........(((....))).......)))))....)))).)).))))))).)).... ( -38.26)
>DroYak_CAF1 31684 112 - 1
CUGCUCUAUAAUUACCCCGUAUCACGGGUGUGGAUGUGGAAGCGUUCUCUAGAGGGUGACAUUUGAUGUUGGCCUGGGGAGGAAU--------GGGAGCACCGCUGGCUGGGCUGCCAUC
..((((((((.((((((((.....)))).)))).))))).))).((((((..(((.((((((...)))))).)))..))))))((--------((.(((.(((.....)))))).)))). ( -45.20)
>consensus
CUGCUCUAUAAUUACCCCGUAUCACGGGUGUGGAUGUGGAAUCGUUCUCUAGAGGGUGACAUUUGAUGUUGGCCUGGGGAGGAAU________GGGAGCACCGCUGGCUGGGCUCCCAUC
....((((((.((((((((.....)))).)))).))))))....((((((..(((.((((((...)))))).)))..))))))..........((((((.((.......))))))))... (-39.47 = -40.48 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:28 2006