Locus 9678

Sequence ID	dm3.chr3R
Location	8,163,398 – 8,163,492
Length	94
Max. P	0.971047

overview

Window 5

Location	8,163,398 – 8,163,492
Length	94
Sequences	7
Columns	113
Reading direction	forward
Mean pairwise identity	71.38
Shannon entropy	0.52384
G+C content	0.41907
Mean single sequence MFE	-24.54
Consensus MFE	-10.25
Energy contribution	-10.40
Covariance contribution	0.15
Combinations/Pair	1.50
Mean z-score	-1.62
Structure conservation index	0.42
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.21
SVM RNA-class probability	0.592991
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8163398 94 + 27905053
----------CGCUAGUUGAGGUCACAACUGGCA-AUUAG------UUUUAUGGUGGGUGAAGCGACCUCAAAGAAAAUUGAGGGCU--AUGAGGUGGCAGGUUAUUAAAUCC
----------.((((((((......)))))))).-....(------((((((.....)))))))..((((((......))))))(((--((...))))).............. ( -26.70, z-score =  -2.09, R)
>droSim1.chr3R 14291961 94 - 27517382
----------CGCUAGUUGAGGUCACAACUGGCA-AUUAG------UUUUAUGGUGGGUGAAGCGACCUCAAGGAAAAUUGUGGGCU--AUGAGGUGGCAGGUUAUUAAAUCA
----------.((((((((......)))))))).-.....------.....((((..((((.((.((((((.((...........))--.)))))).))...))))...)))) ( -26.70, z-score =  -1.98, R)
>droSec1.super_0 7336801 94 - 21120651
----------CGCUAGUUGAGGUCACAACUGGCA-AUUAG------UUUUAUGGUGGGUGAAGCGACCUCAAGGAAAAUUGUGGGCU--AUGAGGUGGCAGGUUAUUAAAUCA
----------.((((((((......)))))))).-.....------.....((((..((((.((.((((((.((...........))--.)))))).))...))))...)))) ( -26.70, z-score =  -1.98, R)
>droYak2.chr3R 12481752 94 + 28832112
----------CGCUAGUUGAGGUCACAACUGGCA-AUUAG------UUUUAUGGUGGGUGAAGCGACCUCAAGGAAAGUUGAGGGCU--AUAAGGUGGCAGGUUAUUAAAUCA
----------.((((((((......)))))))).-....(------((((((.....)))))))..((((((......))))))(((--((...))))).((((....)))). ( -27.20, z-score =  -2.39, R)
>droEre2.scaffold_4770 4295510 94 - 17746568
----------CGCUAGUUGAGGUCACAACUGGCA-AUUAG------UUUUAUGGUGGGUGAAGCGACCUCAAGGAAAAUUGAGGGCU--AUGUGGUGGCAGGUUAUUAAAUCA
----------.((((((((......)))))))).-....(------((((((.....)))))))..((((((......))))))(((--((...))))).((((....)))). ( -28.10, z-score =  -2.48, R)
>dp4.chr2 22956841 95 + 30794189
----------CGAUAGUUACGGUCAUGCCUAGAA-AUUAC------UUUAAUGGUGGGUGAAGCGACCUUACAAGGAUUUUGGGAUUG-AGGUCAAGGGAGAUCAGAGAAUCA
----------..........((((.(.(((....-.((((------((.......))))))...(((((((((((...))))....))-))))).))).)))))......... ( -18.10, z-score =   0.65, R)
>droGri2.scaffold_14830 2064489 112 + 6267026
CAACAGAAAAGACUAAAUGUACAUAUCUAUGGAAUAUUAAAUACUCUUUUCUGACAGAUUUCA-GAUCACACAGAUAGUUCCGACUUCAAUUAAAUUUUGUGUAAUUUAAUUU
...(((((((((.(((((((.(((....)))..)))))...)).))))))))).........(-(((.((((((((((((........)))))...))))))).))))..... ( -18.30, z-score =  -1.07, R)
>consensus
__________CGCUAGUUGAGGUCACAACUGGCA_AUUAG______UUUUAUGGUGGGUGAAGCGACCUCAAGGAAAAUUGAGGGCU__AUGAGGUGGCAGGUUAUUAAAUCA
...........((((((((......))))))))...................(((.(......).)))............................................. (-10.25 = -10.40 +   0.15)

alignment

secondary structure

dotplot

Window 6

Location	8,163,398 – 8,163,492
Length	94
Sequences	7
Columns	113
Reading direction	reverse
Mean pairwise identity	71.38
Shannon entropy	0.52384
G+C content	0.41907
Mean single sequence MFE	-15.85
Consensus MFE	-9.87
Energy contribution	-9.89
Covariance contribution	0.03
Combinations/Pair	1.50
Mean z-score	-1.63
Structure conservation index	0.62
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.84
SVM RNA-class probability	0.971047
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8163398 94 - 27905053
GGAUUUAAUAACCUGCCACCUCAU--AGCCCUCAAUUUUCUUUGAGGUCGCUUCACCCACCAUAAAA------CUAAU-UGCCAGUUGUGACCUCAACUAGCG----------
..............((.((((((.--((...........)).)))))).))................------.....-.((.(((((......))))).)).---------- ( -17.50, z-score =  -2.16, R)
>droSim1.chr3R 14291961 94 + 27517382
UGAUUUAAUAACCUGCCACCUCAU--AGCCCACAAUUUUCCUUGAGGUCGCUUCACCCACCAUAAAA------CUAAU-UGCCAGUUGUGACCUCAACUAGCG----------
..............((.((((((.--................)))))).))................------.....-.((.(((((......))))).)).---------- ( -17.03, z-score =  -2.63, R)
>droSec1.super_0 7336801 94 + 21120651
UGAUUUAAUAACCUGCCACCUCAU--AGCCCACAAUUUUCCUUGAGGUCGCUUCACCCACCAUAAAA------CUAAU-UGCCAGUUGUGACCUCAACUAGCG----------
..............((.((((((.--................)))))).))................------.....-.((.(((((......))))).)).---------- ( -17.03, z-score =  -2.63, R)
>droYak2.chr3R 12481752 94 - 28832112
UGAUUUAAUAACCUGCCACCUUAU--AGCCCUCAACUUUCCUUGAGGUCGCUUCACCCACCAUAAAA------CUAAU-UGCCAGUUGUGACCUCAACUAGCG----------
........................--(((((((((......))))))..)))...............------.....-.((.(((((......))))).)).---------- ( -15.50, z-score =  -2.10, R)
>droEre2.scaffold_4770 4295510 94 + 17746568
UGAUUUAAUAACCUGCCACCACAU--AGCCCUCAAUUUUCCUUGAGGUCGCUUCACCCACCAUAAAA------CUAAU-UGCCAGUUGUGACCUCAACUAGCG----------
........................--(((((((((......))))))..)))...............------.....-.((.(((((......))))).)).---------- ( -15.60, z-score =  -2.05, R)
>dp4.chr2 22956841 95 - 30794189
UGAUUCUCUGAUCUCCCUUGACCU-CAAUCCCAAAAUCCUUGUAAGGUCGCUUCACCCACCAUUAAA------GUAAU-UUCUAGGCAUGACCGUAACUAUCG----------
.(((....((.((..(((.(((((-(((...........)))..)))))((((............))------))...-....)))...)).)).....))).---------- (  -7.90, z-score =   1.32, R)
>droGri2.scaffold_14830 2064489 112 - 6267026
AAAUUAAAUUACACAAAAUUUAAUUGAAGUCGGAACUAUCUGUGUGAUC-UGAAAUCUGUCAGAAAAGAGUAUUUAAUAUUCCAUAGAUAUGUACAUUUAGUCUUUUCUGUUG
.(((((((((......)))))))))((..(((((((.......))..))-)))..))...(((((((((.((....(((((.....))))).......)).)))))))))... ( -20.40, z-score =  -1.16, R)
>consensus
UGAUUUAAUAACCUGCCACCUCAU__AGCCCUCAAUUUUCCUUGAGGUCGCUUCACCCACCAUAAAA______CUAAU_UGCCAGUUGUGACCUCAACUAGCG__________
.........................................((((((((((....................................))))))))))................ ( -9.87 =  -9.89 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:08:59 2011