Locus 6865

Sequence ID	3R_DroMel_CAF1
Location	18,168,114 – 18,168,334
Length	220
Max. P	0.642799

overview

Window 0

Location	18,168,114 – 18,168,221
Length	107
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	95.51
Mean single sequence MFE	-21.75
Consensus MFE	-20.76
Energy contribution	-20.82
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-0.85
Structure conservation index	0.95
SVM decision value	0.23
SVM RNA-class probability	0.642799
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18168114 107 + 27905053
AGCUAAUUAUACAUGCACAUUAAUAUGCAAAUAUUAUGAAGUGUGAACAUUUUGAUGUGCCCCAUUGGUUUCGGUAUGAUAAUUACCAGUUCGGCUUUACAGAUCCA
(((((((((.....(((((((((.(((...(((((....)))))...))).))))))))).....)))))..((((.......)))).....))))........... ( -21.70)
>DroSec_CAF1 196380 107 + 1
AGCUAAUUAUACAUGCACAUUAAUAUGCAAAUAUUAUGAAGUGUGAACAUUUUGAUGUGCCCCAUUGGUUUCGGUAUGAUAAUUACCAGUUCGGCUUUACAGAUCCA
(((((((((.....(((((((((.(((...(((((....)))))...))).))))))))).....)))))..((((.......)))).....))))........... ( -21.70)
>DroSim_CAF1 204188 107 + 1
AGCUAAUUAUACAUGCACAUUAAUAUGCAAAUAUUAUGAAGUGUGAACAUUUUGAUGUGCCCCAUUGGUUUCGGUAUGAUAAUUACCAGUUCGGCUUUACAGAUCCA
(((((((((.....(((((((((.(((...(((((....)))))...))).))))))))).....)))))..((((.......)))).....))))........... ( -21.70)
>DroEre_CAF1 212198 107 + 1
GGCUAAUUAUACAUGCACAUUAAUAUGCAAAUAUUAUGAAGUGUGAACAUUUUGAUGUGCCCCAUUGGUUUCGGUAUGAUAAUUACCAGCUCGGCCUUACAGAUCCA
(((((((((.....(((((((((.(((...(((((....)))))...))).))))))))).....)))))..((((.......)))).....))))........... ( -24.50)
>DroYak_CAF1 206740 105 + 1
AGCUAAUUAUACAUGCACAUUAAUAUGCAAAUAUUAUGAAGUGUGAACAUUUUGAUGUGCCCCAUUGGUUUCGGUAUGAUAAUUACCAGCUCGGCUUUACAGAUC--
(((((((((.....(((((((((.(((...(((((....)))))...))).))))))))).....)))))..((((.......))))))))..............-- ( -21.70)
>DroAna_CAF1 192800 107 + 1
AGCUAAUUAUAUAUGCACAUUAAUAUGCAAAUAUUAUGAAGUGUGAACAUUUUGAUAUGCCCCAUUGGUUCUGGCAUGGUAAUUACCAUUUCGGCUUUACACAUCCG
........((((.((((........)))).))))...((.(((((((...........(((.....))).((((.(((((....))))).)))).))))))).)).. ( -19.20)
>consensus
AGCUAAUUAUACAUGCACAUUAAUAUGCAAAUAUUAUGAAGUGUGAACAUUUUGAUGUGCCCCAUUGGUUUCGGUAUGAUAAUUACCAGUUCGGCUUUACAGAUCCA
(((((((((.....(((((((((.(((...(((((....)))))...))).))))))))).....)))))..((((.......)))).....))))........... (-20.76 = -20.82 +   0.06)

alignment

secondary structure

dotplot

Window 1

Location	18,168,221 – 18,168,334
Length	113
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	86.32
Mean single sequence MFE	-25.27
Consensus MFE	-16.65
Energy contribution	-15.77
Covariance contribution	-0.88
Combinations/Pair	1.27
Mean z-score	-1.72
Structure conservation index	0.66
SVM decision value	0.10
SVM RNA-class probability	0.583343
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18168221 113 + 27905053
ACUGGAGGCCCGACAGCGGUUC---UCGAUUGAGUGGAUCUCAAUUAGCCGGCUACAAAAAAUAUGACUAGCUAAUUGGCUUAAUCAAAUAGUAAAAAUAAGCUAAUAGAAACUAA
.((((((..(((....)))..)---))((((((((......((((((((..((............).)..))))))))))))))))...((((........)))).)))....... ( -27.40)
>DroSec_CAF1 196487 113 + 1
ACUGGGGACACGACAGCGUUUA---UCGAUUGAGUGGAUCUCAAUUAGUCGGCUACAAAAAAUAUGAAUAGAUAAUUGUCCCAAUCAAAUAGUACAAAUAAGCUAAUGGAAACAAA
....((((((((((...(....---.)(((((((.....))))))).))))...........(((......)))..)))))).......((((........)))).((....)).. ( -23.10)
>DroSim_CAF1 204295 113 + 1
ACUGGGGGCACGACAGCGUUUA---UCGAUUGAGUGGAUCUCAAUUAGCCGGCUACAAAAAAUAUGACUAGCUAAUUGGCUUAAUCAAAUAGUAAAAAUAAGCUAAUGGAAACUAA
......((((((....)))...---..(((((((.....))))))).)))(((((.............))))).(((((((((...............)))))))))(....)... ( -22.68)
>DroEre_CAF1 212305 114 + 1
ACUGGGGGCACGGCAGCGAUUCGAUUCGAUAGGGUGGAUUCCAAUUAGCCGGCUACAAAA--AAUGACUAGCUAAUUGGCCCAAUCAAAUAGUAUAAAAAAACUAAUGAUAACUAA
..(((((((........((.((.((((....)))).)).))((((((((..((.......--...).)..)))))))))))).((((..((((........)))).))))..))). ( -27.90)
>consensus
ACUGGGGGCACGACAGCGUUUA___UCGAUUGAGUGGAUCUCAAUUAGCCGGCUACAAAAAAUAUGACUAGCUAAUUGGCCCAAUCAAAUAGUAAAAAUAAGCUAAUGGAAACUAA
..((((((((((....)))........(((((((.....))))))).)))(((((.............)))))......))))......((((........))))........... (-16.65 = -15.77 +  -0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:51 2006