Locus 1603

Sequence ID	3R_DroMel_CAF1
Location	4,617,741 – 4,617,841
Length	100
Max. P	0.606798

overview

Window 4

Location	4,617,741 – 4,617,841
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	84.11
Mean single sequence MFE	-24.60
Consensus MFE	-21.46
Energy contribution	-23.12
Covariance contribution	1.66
Combinations/Pair	1.10
Mean z-score	-1.49
Structure conservation index	0.87
SVM decision value	0.10
SVM RNA-class probability	0.583746
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4617741 100 + 27905053
GAACUGUUAAAUCGAAUUCGAUCACUGGAACGUAACGCGGCUAUAUGGCUAUAUGGCUAUAUGGCCACGAAUUGCCAGUUGGUGGCAGAAGGAGAGAUGG
...((((((.((((....)))).(((((.......((.((((((((((((....)))))))))))).)).....)))))...))))))............ ( -34.60)
>DroSec_CAF1 16575 92 + 1
GAACUGUAAAAUCGAAUUCGAUCACUGGAACGUAACGCGGCUAUAUGG--------CUAUAUGGCCACAAAUUGCCAGUCGGUGGCAGAAGGAGAGAUGG
...((((...((((....))))((((((...((((.(.((((((((..--------..)))))))).)...))))...))))))))))............ ( -25.00)
>DroSim_CAF1 17862 92 + 1
GAACUGUAAAAUCGAAUUCGAUCACUGGAACGUAACGCGGCUAUAUGG--------CUAUAUGGCCACAAAUUGCCAGUCGGUGGCAGAAGGAGAGAUGG
...((((...((((....))))((((((...((((.(.((((((((..--------..)))))))).)...))))...))))))))))............ ( -25.00)
>DroEre_CAF1 17692 84 + 1
GAACUGUAAAAUCGAAUUCGAUCACUGGAACGUAGUGCGGCUA----------------UAUGGCCACAAAUUGCACGUUGUUGGCAGAAAGAGAGAAGA
...((((...((((....))))..(.(.(((((..((.((((.----------------...)))).))......))))).).)))))............ ( -17.00)
>DroYak_CAF1 17479 84 + 1
GAACUGUAAAAUCGAAUUCGAUCACUGGAACGUAGUGCGGCUA----------------UAUGGCCACAAAUUGCACGUUGUUCGCAGAGAGAGAGAAGA
................(((..((.((((((((..((((((((.----------------...)))).......))))..))))).))).))..))).... ( -21.41)
>consensus
GAACUGUAAAAUCGAAUUCGAUCACUGGAACGUAACGCGGCUAUAUGG________CUAUAUGGCCACAAAUUGCCAGUUGGUGGCAGAAGGAGAGAUGG
...((((...((((....))))((((((...((((((.(((((((((((......))))))))))).))..))))...))))))))))............ (-21.46 = -23.12 +   1.66)

alignment

secondary structure

dotplot

Window 5

Location	4,617,741 – 4,617,841
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	84.11
Mean single sequence MFE	-20.52
Consensus MFE	-14.74
Energy contribution	-15.90
Covariance contribution	1.16
Combinations/Pair	1.12
Mean z-score	-1.68
Structure conservation index	0.72
SVM decision value	0.15
SVM RNA-class probability	0.606798
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4617741 100 - 27905053
CCAUCUCUCCUUCUGCCACCAACUGGCAAUUCGUGGCCAUAUAGCCAUAUAGCCAUAUAGCCGCGUUACGUUCCAGUGAUCGAAUUCGAUUUAACAGUUC
............(((......(((((.(((.((((((.((((.((......)).)))).))))))....))))))))(((((....)))))...)))... ( -25.80)
>DroSec_CAF1 16575 92 - 1
CCAUCUCUCCUUCUGCCACCGACUGGCAAUUUGUGGCCAUAUAG--------CCAUAUAGCCGCGUUACGUUCCAGUGAUCGAAUUCGAUUUUACAGUUC
............(((......(((((.(((.((((((.((((..--------..)))).))))))....))))))))(((((....)))))...)))... ( -21.00)
>DroSim_CAF1 17862 92 - 1
CCAUCUCUCCUUCUGCCACCGACUGGCAAUUUGUGGCCAUAUAG--------CCAUAUAGCCGCGUUACGUUCCAGUGAUCGAAUUCGAUUUUACAGUUC
............(((......(((((.(((.((((((.((((..--------..)))).))))))....))))))))(((((....)))))...)))... ( -21.00)
>DroEre_CAF1 17692 84 - 1
UCUUCUCUCUUUCUGCCAACAACGUGCAAUUUGUGGCCAUA----------------UAGCCGCACUACGUUCCAGUGAUCGAAUUCGAUUUUACAGUUC
............(((.....((((((.....((((((....----------------..)))))).)))))).....(((((....)))))...)))... ( -16.20)
>DroYak_CAF1 17479 84 - 1
UCUUCUCUCUCUCUGCGAACAACGUGCAAUUUGUGGCCAUA----------------UAGCCGCACUACGUUCCAGUGAUCGAAUUCGAUUUUACAGUUC
................((((((((((.....((((((....----------------..)))))).))))))...(((((((....)))))..)).)))) ( -18.60)
>consensus
CCAUCUCUCCUUCUGCCACCAACUGGCAAUUUGUGGCCAUAUAG________CCAUAUAGCCGCGUUACGUUCCAGUGAUCGAAUUCGAUUUUACAGUUC
.............(((((.....)))))...((((((.((((.((......)).)))).))))))..........(((((((....)))))..))..... (-14.74 = -15.90 +   1.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:39 2006