Locus 6320

Sequence ID	2L_DroMel_CAF1
Location	17,617,543 – 17,617,648
Length	105
Max. P	0.998675

overview

Window 3

Location	17,617,543 – 17,617,648
Length	105
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.79
Mean single sequence MFE	-24.07
Consensus MFE	-15.31
Energy contribution	-14.87
Covariance contribution	-0.44
Combinations/Pair	1.26
Mean z-score	-3.36
Structure conservation index	0.64
SVM decision value	3.18
SVM RNA-class probability	0.998675
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17617543 105 + 22407834
CCCAAAUGUGCAUUUAAACUAGCAAGGGAGCCACCCCAC-----------ACCACA----CACACACUUUGUUCGCACAACUGCAAUGUCAUUUCUAUGCACAAUGAAUGCAUAAAUCAU
......((((((((((.....(((.(((......)))..-----------......----........((((....)))).)))..((((((....))).))).))))))))))...... ( -20.50)
>DroSim_CAF1 3112 116 + 1
CCCAAAUGUGCAUUUAAACUAGCAAGGGAUCCCCCCCACCUUUCAAUCCCACACCA----CACACACUUUGUUCGCACAACUGCAAUGUCAUUUCUAUGCACAAUGAAUGCAUAAAUCAU
......((((((((((.....(((.(((((...............)))))......----........((((....)))).)))..((((((....))).))).))))))))))...... ( -21.16)
>DroEre_CAF1 1359 99 + 1
CCCAAAUGUGCAUUUAAACUAGCAGGGGAUCCCC--C---------------ACCA----CACACACUUUGCUCGCACAACUGCAAUGUCAUUUCUAUGCACAAUGAAUGCAUAAAUCAU
......((((((((((.....(((((((....))--)---------------....----.........((....))...))))..((((((....))).))).))))))))))...... ( -22.80)
>DroYak_CAF1 12869 114 + 1
CCCAAAUGUGCAUUUAAACUAGCAGGGCAUCCCC--CACCUUUCGAUCCCACACCA----CACACACUUUGCUUGCACAACUGCAAUGUCAUUUCUAUGCACAAUGAAUGCAUAAAUCAU
......((((((((((.....((((((.(((...--........))))))......----..........(((((((....))))).))........)))....))))))))))...... ( -21.40)
>DroPer_CAF1 4372 112 + 1
CCCAAAUGUGCAUUUCAAUUAGUAGAG-AGCCCCUCCCCCUGGAGCUCCUGC-CCAGGGGCACCCCUUCUGG------UACUGCAAUGUCAUUUCUAUGCACAAUGAAUGCAUAAAUCAU
......((((((((.((....((((..-........(((((((.((....))-))))))).(((......))------).))))..((((((....))).))).))))))))))...... ( -34.50)
>consensus
CCCAAAUGUGCAUUUAAACUAGCAGGGGAUCCCC_CCACCU_____UCC_ACACCA____CACACACUUUGCUCGCACAACUGCAAUGUCAUUUCUAUGCACAAUGAAUGCAUAAAUCAU
......((((((((((....(((((((.......................................))))))).............((((((....))).))).))))))))))...... (-15.31 = -14.87 +  -0.44)

alignment

secondary structure

dotplot

Window 4

Location	17,617,543 – 17,617,648
Length	105
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.79
Mean single sequence MFE	-32.34
Consensus MFE	-17.60
Energy contribution	-18.36
Covariance contribution	0.76
Combinations/Pair	1.24
Mean z-score	-1.95
Structure conservation index	0.54
SVM decision value	0.26
SVM RNA-class probability	0.655918
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17617543 105 - 22407834
AUGAUUUAUGCAUUCAUUGUGCAUAGAAAUGACAUUGCAGUUGUGCGAACAAAGUGUGUG----UGUGGU-----------GUGGGGUGGCUCCCUUGCUAGUUUAAAUGCACAUUUGGG
....(((((((((.....))))))))).......(((((....))))).(.(((((((((----(.(((.-----------(..(((......)))..)....))).)))))))))).). ( -28.20)
>DroSim_CAF1 3112 116 - 1
AUGAUUUAUGCAUUCAUUGUGCAUAGAAAUGACAUUGCAGUUGUGCGAACAAAGUGUGUG----UGGUGUGGGAUUGAAAGGUGGGGGGGAUCCCUUGCUAGUUUAAAUGCACAUUUGGG
....(((((((((.....)))))))))....((((.(((.((((....))))..))))))----)((((((.(.(((((.((..((((....))))..))..))))).).)))))).... ( -33.30)
>DroEre_CAF1 1359 99 - 1
AUGAUUUAUGCAUUCAUUGUGCAUAGAAAUGACAUUGCAGUUGUGCGAGCAAAGUGUGUG----UGGU---------------G--GGGGAUCCCCUGCUAGUUUAAAUGCACAUUUGGG
....(((((((((.....)))))))))..((...(((((....))))).))(((((((((----(((.---------------.--(((....)))..)).......))))))))))... ( -31.61)
>DroYak_CAF1 12869 114 - 1
AUGAUUUAUGCAUUCAUUGUGCAUAGAAAUGACAUUGCAGUUGUGCAAGCAAAGUGUGUG----UGGUGUGGGAUCGAAAGGUG--GGGGAUGCCCUGCUAGUUUAAAUGCACAUUUGGG
....(((((((((.....)))))))))..((...(((((....))))).))(((((((((----((((.....)))....((..--(((....)))..)).......))))))))))... ( -32.10)
>DroPer_CAF1 4372 112 - 1
AUGAUUUAUGCAUUCAUUGUGCAUAGAAAUGACAUUGCAGUA------CCAGAAGGGGUGCCCCUGG-GCAGGAGCUCCAGGGGGAGGGGCU-CUCUACUAAUUGAAAUGCACAUUUGGG
....(((((((((.....)))))))))...............------(((((....((((((((((-((....)).))))))((((.....-))))............)))).))))). ( -36.50)
>consensus
AUGAUUUAUGCAUUCAUUGUGCAUAGAAAUGACAUUGCAGUUGUGCGAACAAAGUGUGUG____UGGUGU_GGA_____AGGUGG_GGGGAUCCCCUGCUAGUUUAAAUGCACAUUUGGG
....(((((((((.....)))))))))..........(((.((((((.((.....))..........................(.((((....)))).).........)))))).))).. (-17.60 = -18.36 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:15 2006