Locus 5259

Sequence ID	3R_DroMel_CAF1
Location	13,715,789 – 13,715,905
Length	116
Max. P	0.999826

overview

Window 5

Location	13,715,789 – 13,715,905
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	68.62
Mean single sequence MFE	-32.19
Consensus MFE	-13.29
Energy contribution	-14.57
Covariance contribution	1.28
Combinations/Pair	1.30
Mean z-score	-3.49
Structure conservation index	0.41
SVM decision value	4.18
SVM RNA-class probability	0.999826
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13715789 116 + 27905053
CCAGGCUGAUUCUGGCCUUCACUUUCA-UCCAUUUACCUUAAAUCUUACGAUC-UUA--AGAUACAAAGCUAUUAGGAAAUUUACGAGAGAGACCUAAGAAAGUGAAGACUAGAUCCACC
...((.((..(((((.((((((((((.-..............((((((.....-.))--)))).........(((((...(((.(....))))))))))))))))))).)))))..)))) ( -30.50)
>DroSec_CAF1 25567 116 + 1
CCAGGUUGAUUCUGGCCUUCACUUUCA-UCCAUUUACCUUAAAUCUUACGAUC-UUA--AGAAACAAAGCUAUUAGGAAGUUUUAGAUUGUGAGCUGGGAAAGUCCCCCCCAAAUUCACC
...(((.((((.(((.....((((((.-.(((............(((((((((-(..--.(((((....((....))..))))))))))))))).))))))))).....))))))).))) ( -22.32)
>DroSim_CAF1 29312 116 + 1
CCAGGUUGAUUCUGGCCUUCACUUUCA-UCCAUUUACCUUAAAUCUCACGAUC-UUA--AGUUACAAAGCUAUUAGGAAGUUAUAGAUUGUGAGCUGGGAAAGUGAAGACCAAAUCCACC
...(((.((((.(((.((((((((((.-.(((............(((((((((-(((--(.((.(.((....)).).)).))).)))))))))).))))))))))))).))))))).))) ( -35.12)
>DroEre_CAF1 26078 112 + 1
CCAGGUCGGUUCUGGCCUUCACUUUCA-UCAAUUCAGCUUAAAUCGUACGAU-------AGCUACAAAGCUAUUCGGAUACUUCAGAUUGAGACCUGAGAAAGUGAAGACUAGAGCCGCC
...((.(((((((((.((((((((((.-(((......(((((.((...((((-------((((....))))).)))((....)).)))))))...))))))))))))).))))))))))) ( -44.00)
>DroAna_CAF1 15216 106 + 1
CCAAGCUGGAUCCGUCUUUCAGUUCAGGACUAUGUGAGUUUAAUAUUAAAACUUUUAAUAUAUUCAAAGUU--UCG------------UAAAAUCUGUAAAACUGAAAGUCGGAUCAUCC
........((((((.(((((((((((((..((((.((.(((.(((((((.....)))))))....))).))--.))------------))...))))...))))))))).)))))).... ( -29.00)
>consensus
CCAGGUUGAUUCUGGCCUUCACUUUCA_UCCAUUUACCUUAAAUCUUACGAUC_UUA__AGAUACAAAGCUAUUAGGAAAUUUUAGAUUGAGACCUGAGAAAGUGAAGACCAGAUCCACC
...((.(((.(((((.((((((((((........................................................................)))))))))).))))).))))) (-13.29 = -14.57 +   1.28)

alignment

secondary structure

dotplot

Window 6

Location	13,715,789 – 13,715,905
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	68.62
Mean single sequence MFE	-35.42
Consensus MFE	-21.48
Energy contribution	-21.44
Covariance contribution	-0.04
Combinations/Pair	1.50
Mean z-score	-3.32
Structure conservation index	0.61
SVM decision value	4.03
SVM RNA-class probability	0.999764
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13715789 116 - 27905053
GGUGGAUCUAGUCUUCACUUUCUUAGGUCUCUCUCGUAAAUUUCCUAAUAGCUUUGUAUCU--UAA-GAUCGUAAGAUUUAAGGUAAAUGGA-UGAAAGUGAAGGCCAGAAUCAGCCUGG
(((.(((((.(((((((((((((((((................)))))...((...(((((--((.-((((....)))))))))))...)).-.)))))))))))).)).))).)))... ( -38.39)
>DroSec_CAF1 25567 116 - 1
GGUGAAUUUGGGGGGGACUUUCCCAGCUCACAAUCUAAAACUUCCUAAUAGCUUUGUUUCU--UAA-GAUCGUAAGAUUUAAGGUAAAUGGA-UGAAAGUGAAGGCCAGAAUCAACCUGG
(((((.(((((..(((.....)))...((((..((.......(((.....((((((..(((--((.-.....)))))..))))))....)))-.))..))))...))))).)).)))... ( -28.50)
>DroSim_CAF1 29312 116 - 1
GGUGGAUUUGGUCUUCACUUUCCCAGCUCACAAUCUAUAACUUCCUAAUAGCUUUGUAACU--UAA-GAUCGUGAGAUUUAAGGUAAAUGGA-UGAAAGUGAAGGCCAGAAUCAACCUGG
(((.(((((((((((((((((((((....((((.((((.........))))..)))).(((--(.(-((((....))))).))))...))).-.))))))))))))))).))).)))... ( -42.10)
>DroEre_CAF1 26078 112 - 1
GGCGGCUCUAGUCUUCACUUUCUCAGGUCUCAAUCUGAAGUAUCCGAAUAGCUUUGUAGCU-------AUCGUACGAUUUAAGCUGAAUUGA-UGAAAGUGAAGGCCAGAACCGACCUGG
(((((.(((.((((((((((((((((((....))))))......(((.(((((....))))-------))))..((((((.....)))))).-.)))))))))))).))).))).))... ( -42.40)
>DroAna_CAF1 15216 106 - 1
GGAUGAUCCGACUUUCAGUUUUACAGAUUUUA------------CGA--AACUUUGAAUAUAUUAAAAGUUUUAAUAUUAAACUCACAUAGUCCUGAACUGAAAGACGGAUCCAGCUUGG
....((((((.(((((((((...(((......------------.((--((((((..........))))))))........(((.....))).)))))))))))).))))))........ ( -25.70)
>consensus
GGUGGAUCUGGUCUUCACUUUCCCAGCUCUCAAUCUAAAACUUCCUAAUAGCUUUGUAUCU__UAA_GAUCGUAAGAUUUAAGGUAAAUGGA_UGAAAGUGAAGGCCAGAAUCAACCUGG
(((((.((((((((((((((((...(....)....................................((((....))))...............)))))))))))))))).))).))... (-21.48 = -21.44 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:30 2006