Locus 6445

Sequence ID	3R_DroMel_CAF1
Location	16,886,349 – 16,886,491
Length	142
Max. P	0.874261

overview

Window 2

Location	16,886,349 – 16,886,468
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.95
Mean single sequence MFE	-24.74
Consensus MFE	-19.72
Energy contribution	-20.28
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-1.82
Structure conservation index	0.80
SVM decision value	0.88
SVM RNA-class probability	0.874261
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16886349 119 + 27905053
ACUCACUCGCCUCUCACAUGCACACUGUCUUUUCGUCUGUGCCCAAUGUGGCAACCUGCGGCCACUCUCUCUUCUUUGACUUGCCGAAAUCUGGCAACACUCGACAAGAGUACUA-ACCU
....(((((((...((((((((((.((......))..)))))...)))))((.....))))).............((((.((((((.....))))))...))))...))))....-.... ( -26.80)
>DroSec_CAF1 16684 119 + 1
ACUCUUUCGCCUCUCACACGCACACUGUCUUUUCGUCUGUGCCCAAUGUGGCAACCUGCGGCCACUCUCUCUUCUUUUACUUGCCGAAAUCUGGCAACACUCGACAAGAGUACUA-ACCU
(((((((((((...((((.(((((.((......))..)))))....))))((.....)))))..................((((((.....)))))).....)).))))))....-.... ( -26.60)
>DroSim_CAF1 17220 119 + 1
ACUCACUCGCCUCUCACACGCACACUGUCUUUUCGUCUGUGCCCAAUGUGGCAACCUGCGGCCACUCUCUCUCCUUUUACUUGCCGAAAUCUGGCAACACUCGACAAGAGUACUA-ACCU
....(((((((...((((.(((((.((......))..)))))....))))((.....)))))..................((((((.....))))))..........))))....-.... ( -24.30)
>DroEre_CAF1 16609 115 + 1
ACUCACUCGCCUCUCACACACACACUGCCU--UCGUCUGUGCCCAAUGUGGCAACCUGCGACCACUCUCU---CUUUGACUCGCCAAAAUCUGGCAACACUCGAAACGAGUACUAUACCU
....(((((..((.................--((((...((((......))))....)))).........---.........((((.....)))).......))..)))))......... ( -21.60)
>DroYak_CAF1 17554 119 + 1
ACUCACUCGCCCAUCACACGCACACUGUCUUUUCGUCUUUGCCCAAUGUGGCAACAUGCGGCCACUCUCUUUUCUUUGGCUUGCCAAAAUCUGGCAACACCCGACCCGAGUACUA-ACCU
....((((((.........))...........(((...(((((....(((((........))))).........(((((....)))))....)))))....)))...))))....-.... ( -24.40)
>consensus
ACUCACUCGCCUCUCACACGCACACUGUCUUUUCGUCUGUGCCCAAUGUGGCAACCUGCGGCCACUCUCUCUUCUUUGACUUGCCGAAAUCUGGCAACACUCGACAAGAGUACUA_ACCU
((((....(((...((((.(((((.((......))..)))))....))))((.....)))))..................((((((.....))))))..........))))......... (-19.72 = -20.28 +   0.56)

alignment

secondary structure

dotplot

Window 3

Location	16,886,389 – 16,886,491
Length	102
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	93.36
Mean single sequence MFE	-22.69
Consensus MFE	-20.10
Energy contribution	-20.46
Covariance contribution	0.36
Combinations/Pair	1.06
Mean z-score	-1.25
Structure conservation index	0.89
SVM decision value	0.32
SVM RNA-class probability	0.685785
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16886389 102 + 27905053
GCCCAAUGUGGCAACCUGCGGCCACUCUCUCUUCUUUGACUUGCCGAAAUCUGGCAACACUCGACAAGAGUACUA-ACCUUAUCGGCCAAACUGAAGUUUUAA
(((....(((((........)))))...(((((..((((.((((((.....))))))...)))).))))).....-........)))................ ( -23.50)
>DroSec_CAF1 16724 102 + 1
GCCCAAUGUGGCAACCUGCGGCCACUCUCUCUUCUUUUACUUGCCGAAAUCUGGCAACACUCGACAAGAGUACUA-ACCUUAUCGGCCAAACUGAAGUUUUAA
.......(((((........))))).....((((........(((((.....(....)((((.....))))....-......)))))......))))...... ( -23.24)
>DroSim_CAF1 17260 102 + 1
GCCCAAUGUGGCAACCUGCGGCCACUCUCUCUCCUUUUACUUGCCGAAAUCUGGCAACACUCGACAAGAGUACUA-ACCUUAUCGGCCAAACUGAAGUUUUAA
(((......))).......((((.................((((((.....)))))).((((.....))))....-........))))............... ( -23.10)
>DroEre_CAF1 16647 100 + 1
GCCCAAUGUGGCAACCUGCGACCACUCUCU---CUUUGACUCGCCAAAAUCUGGCAACACUCGAAACGAGUACUAUACCUUAUCGGCCAAACUGAAGUUUUAA
(((....(((((.......).)))).....---....((...((((.....))))...(((((...)))))...........)))))................ ( -17.40)
>DroYak_CAF1 17594 102 + 1
GCCCAAUGUGGCAACAUGCGGCCACUCUCUUUUCUUUGGCUUGCCAAAAUCUGGCAACACCCGACCCGAGUACUA-ACCUUAUCGGCCAAACUGAAGUUUUAA
.......(((((........)))))...((((..((((((((((((.....)))))).........(((......-......)))))))))..))))...... ( -26.20)
>consensus
GCCCAAUGUGGCAACCUGCGGCCACUCUCUCUUCUUUGACUUGCCGAAAUCUGGCAACACUCGACAAGAGUACUA_ACCUUAUCGGCCAAACUGAAGUUUUAA
(((......))).......((((.................((((((.....)))))).((((.....)))).............))))............... (-20.10 = -20.46 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:21:42 2006