Locus 4970

Sequence ID	dm3.chr2R
Location	16,722,375 – 16,722,506
Length	131
Max. P	0.996848

overview

Window 8

Location	16,722,375 – 16,722,476
Length	101
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	79.13
Shannon entropy	0.31982
G+C content	0.40643
Mean single sequence MFE	-28.48
Consensus MFE	-18.38
Energy contribution	-19.00
Covariance contribution	0.62
Combinations/Pair	1.06
Mean z-score	-2.16
Structure conservation index	0.65
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.12
SVM RNA-class probability	0.894451
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16722375 101 + 21146708
-------GAUAUAUUCUGAGGUUUCCAGAUGAGUCGAGAUAACAA-----GUAUUCGAGGUGGCGAAAGCCAACUUCUUCAAAUGCAUAAGCUGAUUAAAAUGUAAGAGACCA
-------............((((((((....((((.((.......-----(((((.((((((((....))))....)))).))))).....))))))....))...)))))). ( -25.10, z-score =  -1.95, R)
>droSim1.chr2R 15375846 101 + 19596830
-------GAUAUAUUCUGAGGUUUCCAGCUGAGUCGAGAUAACAA-----GUAGUCGGGGUGGCGAAAGCCAACCUCUUCGAAUGCAUAAUAUGAUUAACAUGUAUAUGACCA
-------............((((....((....(((((((.....-----...)))((((((((....))).))))).))))..))...(((((.....)))))....)))). ( -27.80, z-score =  -1.86, R)
>droSec1.super_9 48044 96 + 3197100
-------GAUAUAUUCUGAGGUUUCCAGCUGAGUCGAGAUAACAA-----GUAUUCGGGGUGGCGAAAGCCAACCUCUUCGAAUGCAUAAU-----UAACAUGUAUAUGACCA
-------............((((....((((.((.......))..-----((((((((((((((....))).))))...))))))).....-----...)).))....)))). ( -24.70, z-score =  -1.40, R)
>droYak2.chr2R 8660802 113 - 21139217
CAUAUUCUGAAUACUCUCAGCUUUCUGGCUGAGUCGAGAUUACUAUACAUGUAUUCGGGGUGGCGAAAGCCAAUUUCUGCGAAUGCAUAAGCUGAUUAAAGGGUAUAUGACAU
.(((((((.......(((((((....)))))))....(((((((....(((((((((.((((((....))))....)).))))))))).)).)))))..)))))))....... ( -36.30, z-score =  -3.42, R)
>consensus
_______GAUAUAUUCUGAGGUUUCCAGCUGAGUCGAGAUAACAA_____GUAUUCGGGGUGGCGAAAGCCAACCUCUUCGAAUGCAUAAGCUGAUUAAAAUGUAUAUGACCA
................................((((......).......((((((((((((((....))))....))))))))))......................))).. (-18.38 = -19.00 +   0.62)

alignment

secondary structure

dotplot

Window 9

Location	16,722,408 – 16,722,506
Length	98
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	69.03
Shannon entropy	0.50741
G+C content	0.37091
Mean single sequence MFE	-22.88
Consensus MFE	-16.16
Energy contribution	-17.28
Covariance contribution	1.12
Combinations/Pair	1.14
Mean z-score	-2.23
Structure conservation index	0.71
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.99
SVM RNA-class probability	0.996848
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16722408 98 + 21146708
-----AACAAGUAUUCGAGGUGGCGAAAGCCAACUUCUUCAAAUGCAUAAGCUGAUUAAAAUGUAAGAGAC----------CAACCAAAACAUUCAAAGAAACUUAAAAAUCU----
-----...((((.(((((((((((....))).)))))......(((((............)))))......----------.................)))))))........---- ( -17.90, z-score =  -2.08, R)
>droSim1.chr2R 15375879 98 + 19596830
-----AACAAGUAGUCGGGGUGGCGAAAGCCAACCUCUUCGAAUGCAUAAUAUGAUUAACAUGUAUAUGAC----------CAACAAAAACACUCAAAGAAACUUAAAUGUUU----
-----...((((..((((((((((....))).))))).(((.((((((..((....))..)))))).))).----------.................)).))))........---- ( -21.60, z-score =  -2.34, R)
>droSec1.super_9 48077 93 + 3197100
-----AACAAGUAUUCGGGGUGGCGAAAGCCAACCUCUUCGAAUGCAUA-----AUUAACAUGUAUAUGAC----------CAACAAAAACACUCAAAGAAACUUAAAUGUUU----
-----...((((.(((((((((((....))).))))).(((.((((((.-----......)))))).))).----------.................)))))))........---- ( -23.10, z-score =  -3.69, R)
>droYak2.chr2R 8660842 103 - 21139217
UACUAUACAUGUAUUCGGGGUGGCGAAAGCCAAUUUCUGCGAAUGCAUAAGCUGAUUAAAGGGUAUAUGAC----------AUAGCAAAACAUUCACAGAAACUUAAAUGGUU----
...........((((..((.((((....)))).((((((.(((((((((.(((........))).))))..----------.........))))).))))))))..))))...---- ( -24.90, z-score =  -2.30, R)
>droEre2.scaffold_4845 10862294 103 + 22589142
--------------UCGGGGUGGCGAAAGCCGACUUCUUCGAAUGCAUAAACUGAUUAAGGUGUUUACAGCAGUAUUCUAUCAAGCUGGAUAUAUUCGGCGGCAUGAAUGAUCGUAA
--------------..((((((((....))).)))))..(((.(((.(((((..........)))))..))).(((((......((((((....)))))).....))))).)))... ( -26.90, z-score =  -0.75, R)
>consensus
_____AACAAGUAUUCGGGGUGGCGAAAGCCAACUUCUUCGAAUGCAUAAGCUGAUUAAAAUGUAUAUGAC__________CAACCAAAACAUUCAAAGAAACUUAAAUGUUU____
..........((((((((((((((....))))....))))))))))....................................................................... (-16.16 = -17.28 +   1.12)

alignment

secondary structure

dotplot

Window 0

Location	16,722,408 – 16,722,506
Length	98
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	69.03
Shannon entropy	0.50741
G+C content	0.37091
Mean single sequence MFE	-22.76
Consensus MFE	-11.81
Energy contribution	-12.53
Covariance contribution	0.72
Combinations/Pair	1.33
Mean z-score	-2.23
Structure conservation index	0.52
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.12
SVM RNA-class probability	0.983041
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16722408 98 - 21146708
----AGAUUUUUAAGUUUCUUUGAAUGUUUUGGUUG----------GUCUCUUACAUUUUAAUCAGCUUAUGCAUUUGAAGAAGUUGGCUUUCGCCACCUCGAAUACUUGUU-----
----.......((((((((((..(((((...(((((----------((.............)))))))...)))))..)))))(.((((....)))).)......)))))..----- ( -24.52, z-score =  -2.75, R)
>droSim1.chr2R 15375879 98 - 19596830
----AAACAUUUAAGUUUCUUUGAGUGUUUUUGUUG----------GUCAUAUACAUGUUAAUCAUAUUAUGCAUUCGAAGAGGUUGGCUUUCGCCACCCCGACUACUUGUU-----
----.((((....(((((((((((((((......((----------(((((....)))...))))......)))))))))))((.((((....)))).)).))))...))))----- ( -24.40, z-score =  -2.65, R)
>droSec1.super_9 48077 93 - 3197100
----AAACAUUUAAGUUUCUUUGAGUGUUUUUGUUG----------GUCAUAUACAUGUUAAU-----UAUGCAUUCGAAGAGGUUGGCUUUCGCCACCCCGAAUACUUGUU-----
----.......(((((.(((((((((((....((((----------(.(((....))))))))-----...)))))))))))((.((((....)))).)).....)))))..----- ( -24.80, z-score =  -3.08, R)
>droYak2.chr2R 8660842 103 + 21139217
----AACCAUUUAAGUUUCUGUGAAUGUUUUGCUAU----------GUCAUAUACCCUUUAAUCAGCUUAUGCAUUCGCAGAAAUUGGCUUUCGCCACCCCGAAUACAUGUAUAGUA
----.........(((((((((((((((...(((((----------...............)).)))....)))))))))))))))(((....)))..................... ( -24.56, z-score =  -3.28, R)
>droEre2.scaffold_4845 10862294 103 - 22589142
UUACGAUCAUUCAUGCCGCCGAAUAUAUCCAGCUUGAUAGAAUACUGCUGUAAACACCUUAAUCAGUUUAUGCAUUCGAAGAAGUCGGCUUUCGCCACCCCGA--------------
.................(((((...((((......))))(((...(((.((((((..........)))))))))))).......)))))..............-------------- ( -15.50, z-score =   0.61, R)
>consensus
____AAACAUUUAAGUUUCUUUGAAUGUUUUGGUUG__________GUCAUAUACAUGUUAAUCAGCUUAUGCAUUCGAAGAAGUUGGCUUUCGCCACCCCGAAUACUUGUU_____
.............(((((((((((((((...........................................)))))))))))))))(((....)))..................... (-11.81 = -12.53 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:39:27 2011