Locus 4024

Sequence ID	3L_DroMel_CAF1
Location	11,740,491 – 11,740,591
Length	100
Max. P	0.927706

overview

Window 9

Location	11,740,491 – 11,740,591
Length	100
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	74.66
Mean single sequence MFE	-17.65
Consensus MFE	-2.54
Energy contribution	-2.78
Covariance contribution	0.24
Combinations/Pair	1.15
Mean z-score	-1.94
Structure conservation index	0.14
SVM decision value	1.19
SVM RNA-class probability	0.927706
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11740491 100 + 23771897
CAUAGUUUUUACCCUAAAUGGAUCAUCUUACUCAGAUUGACUACACUGGAUGUAAGAUUCCACAAUUCCAACUCUGGCUAAAA-AGCCACUGAAAAAUGGU
....((((((........((((..(((((((((((..........))))..))))))))))).........(..(((((....-)))))..)))))))... ( -19.30)
>DroSec_CAF1 53338 80 + 1
CAUAGUUUUUACCCUAAGUGGAUCAUCUUACUCAG--------------------GAUUCCACAAUUCCAGCUCUGGCUAAAA-AGCCACUGAAAAAUGGG
...........(((...(((((..(((((....))--------------------)))))))).....(((...(((((....-))))))))......))) ( -20.40)
>DroSim_CAF1 49154 80 + 1
CAUAGUUUUUACCCUAAGUGGAUCAUCUUACUCAG--------------------GAUUCCACAAUUCCAGCUCUGGCUAAAA-AGCCACUGAAAAAUGGG
...........(((...(((((..(((((....))--------------------)))))))).....(((...(((((....-))))))))......))) ( -20.40)
>DroEre_CAF1 50213 99 + 1
CAUAGUAUUUUU-CCAACUGAAACAUCUUACUCAGAUGCACAAUGCUGGAUGUAAGAUACCCCUAUUUAAACUCUAGCUAAAA-AGGCACUGAAAAAUGGG
.....(((((((-(...((((..........)))).(((.....((((((.((.(((((....)))))..)))))))).....-..)))..)))))))).. ( -17.40)
>DroYak_CAF1 50772 84 + 1
CAUAGUUUUCAU-CUAACUGAAACAUCUUACUCAGA--------------AGUAAGAUU--CCAAUUUCAACUCUAUCUAAAAAAAACACUGAAAAAUGGG
..(((((.....-..)))))....((((((((....--------------)))))))).--(((.(((((....................)))))..))). ( -10.75)
>consensus
CAUAGUUUUUACCCUAACUGGAUCAUCUUACUCAGA_______________GUAAGAUUCCACAAUUCCAACUCUGGCUAAAA_AGCCACUGAAAAAUGGG
...............................((((....................((((....)))).......(((((.....)))))))))........ ( -2.54 =  -2.78 +   0.24)

alignment

secondary structure

dotplot

Window 0

Location	11,740,491 – 11,740,591
Length	100
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	74.66
Mean single sequence MFE	-22.44
Consensus MFE	-7.98
Energy contribution	-8.22
Covariance contribution	0.24
Combinations/Pair	1.33
Mean z-score	-1.85
Structure conservation index	0.36
SVM decision value	0.40
SVM RNA-class probability	0.722905
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11740491 100 - 23771897
ACCAUUUUUCAGUGGCU-UUUUAGCCAGAGUUGGAAUUGUGGAAUCUUACAUCCAGUGUAGUCAAUCUGAGUAAGAUGAUCCAUUUAGGGUAAAAACUAUG
.((((.(((((((((((-....)))))...))))))..)))).(((((((...(((..........))).))))))).((((.....)))).......... ( -23.70)
>DroSec_CAF1 53338 80 - 1
CCCAUUUUUCAGUGGCU-UUUUAGCCAGAGCUGGAAUUGUGGAAUC--------------------CUGAGUAAGAUGAUCCACUUAGGGUAAAAACUAUG
.((((.(((((((((((-....))))...)))))))..)))).(((--------------------((((((..........))))))))).......... ( -25.40)
>DroSim_CAF1 49154 80 - 1
CCCAUUUUUCAGUGGCU-UUUUAGCCAGAGCUGGAAUUGUGGAAUC--------------------CUGAGUAAGAUGAUCCACUUAGGGUAAAAACUAUG
.((((.(((((((((((-....))))...)))))))..)))).(((--------------------((((((..........))))))))).......... ( -25.40)
>DroEre_CAF1 50213 99 - 1
CCCAUUUUUCAGUGCCU-UUUUAGCUAGAGUUUAAAUAGGGGUAUCUUACAUCCAGCAUUGUGCAUCUGAGUAAGAUGUUUCAGUUGG-AAAAAUACUAUG
...........((((((-((..(((....))).....))))))))......((((((.....((((((.....))))))....)))))-)........... ( -21.40)
>DroYak_CAF1 50772 84 - 1
CCCAUUUUUCAGUGUUUUUUUUAGAUAGAGUUGAAAUUGG--AAUCUUACU--------------UCUGAGUAAGAUGUUUCAGUUAG-AUGAAAACUAUG
.(((..(((((((((((.....)))))...)))))).)))--.((((((((--------------....)))))))).(((((.....-.)))))...... ( -16.30)
>consensus
CCCAUUUUUCAGUGGCU_UUUUAGCCAGAGUUGGAAUUGUGGAAUCUUAC_______________UCUGAGUAAGAUGAUCCACUUAGGGUAAAAACUAUG
.((((.(((((((((((.....)))))...))))))..))))........................((((((..........))))))............. ( -7.98 =  -8.22 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:41 2006