Locus 5165

Sequence ID	dm3.chr2R
Location	18,255,768 – 18,255,925
Length	157
Max. P	0.908123

overview

Window 3

Location	18,255,768 – 18,255,925
Length	157
Sequences	6
Columns	168
Reading direction	forward
Mean pairwise identity	86.10
Shannon entropy	0.26241
G+C content	0.41113
Mean single sequence MFE	-39.37
Consensus MFE	-27.82
Energy contribution	-28.27
Covariance contribution	0.45
Combinations/Pair	1.11
Mean z-score	-2.19
Structure conservation index	0.71
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.08
SVM RNA-class probability	0.886523
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18255768 157 + 21146708
AUUUCCCCACAGAUGUCAUCGAGAUGGUAUUUUAAUUCAUUUAAUUAAAAGUUUAAUUACAUUUCUGUACAGCGCCGGAUUUGGCAGCCAUGAACUC-------GGUGACAUCUGCCAGGCCCAUUAAGGC---AAUACGGAUUUCAAAAUGCCAGCAG-CGAAUAUC
...(((...(((((((((((((((((((.((((((((.....))))))))(((....((((....)))).)))((((....)))).)))))...)))-------)))))))))))....(((......)))---.....)))........(((.....)-))...... ( -42.30, z-score =  -2.46, R)
>droAna3.scaffold_13266 12383026 167 - 19884421
AUUUCCCCACAGAUGUCAUCGAGAUGGUAUAUUAAUUCAUUUAAUUAAAAGUUUAAUUACGUUUCUGUUUUGCACCGGAUUCGCCAGCCAUGAACUCUCUCCGCCGUGACAUCUGCAAUGCCCAUUAGGGCUCUACUACAAAUUUCAUAACACAAUCCC-CGAAAAUA
.((((....((((((((((.((((.(((.............(((((((....)))))))((..((((........))))..))..........))).))))....))))))))))....((((....))))............................-.))))... ( -34.50, z-score =  -2.03, R)
>droEre2.scaffold_4845 12395756 136 + 22589142
AUUUCCCCACAGAUGUCAUCGAGAUGGUAUUUUAAUUCAUUUAAUUAAAAGUUUAAUUACAUUUCAACACUGCGCCAGAUUUGGCGGCCAUGAACUC-------CGUGACAUCUGCCAGGCCCAUUAGGGC---AAUACGGAUUUC----------------------
...(((...((((((((((.((((((((.((((((((.....))))))))......................((((......)))))))))...)))-------.))))))))))....((((....))))---.....)))....---------------------- ( -42.50, z-score =  -4.34, R)
>droYak2.chr2R 18003834 158 + 21139217
AUUUCCCCACAGAUGUCAUCGAGAUGGUAUUUUAAUUCAUUUAAUUAAAAGUUUAAUUACAUUUGUGUACUGCGCCGGUUUUGGCGGCCAUGAACUC-------CGUGACAUCUGCCAGGCCCAUUAAGGC---AAUACGGAUUUCAAAAUGCCAGCAAACGACUAAC
...(((...((((((((((.((((((((.((((((((.....)))))))).......((((....))))...(((((....))))))))))...)))-------.))))))))))....(((......)))---.....))).......................... ( -38.70, z-score =  -1.12, R)
>droSec1.super_9 1563735 157 + 3197100
AUUUCCCCACAGAUGUCAUCGAGAUGGUAUUUUAAUUCAUUUAGUUAAAAGUUUAAUUACAUUUCUGUACAGCGCCGGAUUUGGCAGCCAUGAACUC-------CGUGACAUCUGCCAGGCCCAUUAAGGC---AAUACGGAUUUCAAAAUGCCAGCAG-CGACUAUC
...(((...((((((((((.((((((((.((((((((.....))))))))(((....((((....)))).)))((((....)))).)))))...)))-------.))))))))))....(((......)))---.....)))........(((.....)-))...... ( -37.30, z-score =  -1.20, R)
>droSim1.chr2R 16853225 157 + 19596830
AUUUCCCCACAGAUGUCAUCGAGAUGGUAUUUUAAUUCAUUUAAUUAAAAGUUUAAUUACAUUUCUGUACAGCGCCGGAUUUGGCAGCCAUGAACUC-------CGUGACAUCUGCCAGGCCCAUUAGGGC---AAUACGGAUUUCAAAAUGCCAGCAG-CGACUAUC
...(((...((((((((((.((((((((.((((((((.....))))))))(((....((((....)))).)))((((....)))).)))))...)))-------.))))))))))....((((....))))---.....)))........(((.....)-))...... ( -40.90, z-score =  -1.97, R)
>consensus
AUUUCCCCACAGAUGUCAUCGAGAUGGUAUUUUAAUUCAUUUAAUUAAAAGUUUAAUUACAUUUCUGUACAGCGCCGGAUUUGGCAGCCAUGAACUC_______CGUGACAUCUGCCAGGCCCAUUAAGGC___AAUACGGAUUUCAAAAUGCCAGCAG_CGACUAUC
...(((...((((((((((.((((((...((((((((.....)))))))).........))))))......((((((....)))).)).................))))))))))....(((......)))........))).......................... (-27.82 = -28.27 +   0.45)

alignment

secondary structure

dotplot

Window 4

Location	18,255,768 – 18,255,925
Length	157
Sequences	6
Columns	168
Reading direction	reverse
Mean pairwise identity	86.10
Shannon entropy	0.26241
G+C content	0.41113
Mean single sequence MFE	-44.12
Consensus MFE	-34.65
Energy contribution	-34.48
Covariance contribution	-0.17
Combinations/Pair	1.11
Mean z-score	-1.96
Structure conservation index	0.79
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.20
SVM RNA-class probability	0.908123
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18255768 157 - 21146708
GAUAUUCG-CUGCUGGCAUUUUGAAAUCCGUAUU---GCCUUAAUGGGCCUGGCAGAUGUCACC-------GAGUUCAUGGCUGCCAAAUCCGGCGCUGUACAGAAAUGUAAUUAAACUUUUAAUUAAAUGAAUUAAAAUACCAUCUCGAUGACAUCUGUGGGGAAAU
........-.....((((...((.....))...)---)))........(((.((((((((((.(-------(((...((((..(((......)))....((((....)))).......((((((((.....))))))))..)))))))).)))))))))).))).... ( -46.10, z-score =  -2.57, R)
>droAna3.scaffold_13266 12383026 167 + 19884421
UAUUUUCG-GGGAUUGUGUUAUGAAAUUUGUAGUAGAGCCCUAAUGGGCAUUGCAGAUGUCACGGCGGAGAGAGUUCAUGGCUGGCGAAUCCGGUGCAAAACAGAAACGUAAUUAAACUUUUAAUUAAAUGAAUUAAUAUACCAUCUCGAUGACAUCUGUGGGGAAAU
..((..((-.((((.((((..(((.(((((((((...((((....))))))))))))).)))..)).((((.(((((((.(((((.....)))))..............(((((((....))))))).))))))).........))))....)))))).))..))... ( -44.60, z-score =  -1.55, R)
>droEre2.scaffold_4845 12395756 136 - 22589142
----------------------GAAAUCCGUAUU---GCCCUAAUGGGCCUGGCAGAUGUCACG-------GAGUUCAUGGCCGCCAAAUCUGGCGCAGUGUUGAAAUGUAAUUAAACUUUUAAUUAAAUGAAUUAAAAUACCAUCUCGAUGACAUCUGUGGGGAAAU
----------------------....(((.....---((((....)))).(.((((((((((..-------(((...((((.(((((....)))))((..(((((((.((......)))))))))....))..........)))))))..)))))))))).))))... ( -42.10, z-score =  -2.94, R)
>droYak2.chr2R 18003834 158 - 21139217
GUUAGUCGUUUGCUGGCAUUUUGAAAUCCGUAUU---GCCUUAAUGGGCCUGGCAGAUGUCACG-------GAGUUCAUGGCCGCCAAAACCGGCGCAGUACACAAAUGUAAUUAAACUUUUAAUUAAAUGAAUUAAAAUACCAUCUCGAUGACAUCUGUGGGGAAAU
.....(((((....((((...((.....))...)---)))..))))).(((.((((((((((..-------(((...((((.((((......))))...((((....)))).......((((((((.....))))))))..)))))))..)))))))))).))).... ( -43.90, z-score =  -1.52, R)
>droSec1.super_9 1563735 157 - 3197100
GAUAGUCG-CUGCUGGCAUUUUGAAAUCCGUAUU---GCCUUAAUGGGCCUGGCAGAUGUCACG-------GAGUUCAUGGCUGCCAAAUCCGGCGCUGUACAGAAAUGUAAUUAAACUUUUAACUAAAUGAAUUAAAAUACCAUCUCGAUGACAUCUGUGGGGAAAU
........-.....((((...((.....))...)---)))........(((.((((((((((((-------(((((((((((.(((......)))))).((((....)))).................)))))))...........))).)))))))))).))).... ( -43.00, z-score =  -1.42, R)
>droSim1.chr2R 16853225 157 - 19596830
GAUAGUCG-CUGCUGGCAUUUUGAAAUCCGUAUU---GCCCUAAUGGGCCUGGCAGAUGUCACG-------GAGUUCAUGGCUGCCAAAUCCGGCGCUGUACAGAAAUGUAAUUAAACUUUUAAUUAAAUGAAUUAAAAUACCAUCUCGAUGACAUCUGUGGGGAAAU
......((-(((.((((((..((((.(((((...---((((....))))..(((....))))))-------)).))))..).)))))....)))))((.((((((..(((........((((((((.....))))))))...(((....)))))))))))).)).... ( -45.00, z-score =  -1.79, R)
>consensus
GAUAGUCG_CUGCUGGCAUUUUGAAAUCCGUAUU___GCCCUAAUGGGCCUGGCAGAUGUCACG_______GAGUUCAUGGCUGCCAAAUCCGGCGCAGUACAGAAAUGUAAUUAAACUUUUAAUUAAAUGAAUUAAAAUACCAUCUCGAUGACAUCUGUGGGGAAAU
..........................(((........((((....))))...((((((((((((........(((((((.((.(((......)))))............(((((((....))))))).)))))))............)).))))))))))..)))... (-34.65 = -34.48 +  -0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:43:02 2011