Locus 5196

Sequence ID	dm3.chr2R
Location	18,462,168 – 18,462,295
Length	127
Max. P	0.967724

overview

Window 8

Location	18,462,168 – 18,462,268
Length	100
Sequences	4
Columns	100
Reading direction	forward
Mean pairwise identity	57.35
Shannon entropy	0.66753
G+C content	0.44433
Mean single sequence MFE	-26.18
Consensus MFE	-13.31
Energy contribution	-13.99
Covariance contribution	0.69
Combinations/Pair	1.35
Mean z-score	-1.17
Structure conservation index	0.51
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.49
SVM RNA-class probability	0.943434
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18462168 100 + 21146708
UUUAUAUAUAUUGUAGGUUGGUUGGUAUACGUACAUAUGUAUACGUACUGUAUGUACCGUAUAUACCGAUGCCUGUUGCCAGGUGCCAACUUGGCUCUUG
.............(((((..(((((((((.(((((((((((....))).))))))))....))))))))))))))..(((((((....)))))))..... ( -33.10, z-score =  -2.07, R)
>droSim1.chr2R 17052496 79 + 19596830
---------UUUAUAUAUAGGUUGGUGUACGUACGUA------UGUACCGUAUACC----GUAUACCGAUGCCUGUUGCCAGGUGCCAACUUGGCUCU--
---------.......(((((((((((((((((((..------.....))))...)----))))))))..)))))).(((((((....)))))))...-- ( -29.50, z-score =  -2.80, R)
>droSec1.super_9 1767054 79 + 3197100
---------AUAAUAUAUAGGAUGGUGUACGUACGUA------CGUCCCGUAUGCA----GUAUACCGAUGACUGUGACCAGGUGCCAACUUAGCUCU--
---------......(((((..((((((((...((((------((...))))))..----))))))))....)))))...((((....))))......-- ( -19.30, z-score =   0.16, R)
>droMoj3.scaffold_6496 19846035 88 + 26866924
-----UACAGAUACACACUUGUCGGCUU-UGCAGGUAAAAAUUUGUAUCUGUUGGACUUUGGAUUUGGUUGCCUGUUGCCAGGUGCCUUGGCGG------
-----.(((((((((.((((((......-.)))))).......)))))))))..(.((..(((((((((........))))))).))..)))..------ ( -22.80, z-score =   0.03, R)
>consensus
_________AUUAUAUAUAGGUUGGUGUACGUACGUA______CGUACCGUAUGCA____GUAUACCGAUGCCUGUUGCCAGGUGCCAACUUGGCUCU__
.................(((((((((...((((((.............))))))................(((((....))))))))))))))....... (-13.31 = -13.99 +   0.69)

alignment

secondary structure

dotplot

Window 9

Location	18,462,168 – 18,462,268
Length	100
Sequences	4
Columns	100
Reading direction	reverse
Mean pairwise identity	57.35
Shannon entropy	0.66753
G+C content	0.44433
Mean single sequence MFE	-21.93
Consensus MFE	-8.41
Energy contribution	-8.72
Covariance contribution	0.31
Combinations/Pair	1.14
Mean z-score	-1.38
Structure conservation index	0.38
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.58
SVM RNA-class probability	0.749697
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18462168 100 - 21146708
CAAGAGCCAAGUUGGCACCUGGCAACAGGCAUCGGUAUAUACGGUACAUACAGUACGUAUACAUAUGUACGUAUACCAACCAACCUACAAUAUAUAUAAA
..........(((((..((((....))))....(((((((...(((((((..(((....))).))))))))))))))..)))))................ ( -27.70, z-score =  -2.76, R)
>droSim1.chr2R 17052496 79 - 19596830
--AGAGCCAAGUUGGCACCUGGCAACAGGCAUCGGUAUAC----GGUAUACGGUACA------UACGUACGUACACCAACCUAUAUAUAAA---------
--.(((((.....))).((((....))))..))(((....----(((.((((.(((.------...))))))).))).)))..........--------- ( -23.30, z-score =  -1.98, R)
>droSec1.super_9 1767054 79 - 3197100
--AGAGCUAAGUUGGCACCUGGUCACAGUCAUCGGUAUAC----UGCAUACGGGACG------UACGUACGUACACCAUCCUAUAUAUUAU---------
--.(((((.....)))..(((....)))...))(((.(((----(((.((((...))------)).))).))).)))..............--------- ( -14.70, z-score =   1.24, R)
>droMoj3.scaffold_6496 19846035 88 - 26866924
------CCGCCAAGGCACCUGGCAACAGGCAACCAAAUCCAAAGUCCAACAGAUACAAAUUUUUACCUGCA-AAGCCGACAAGUGUGUAUCUGUA-----
------..((....)).((((....))))...................(((((((((.((((((..((...-.))..)).)))).))))))))).----- ( -22.00, z-score =  -2.04, R)
>consensus
__AGAGCCAAGUUGGCACCUGGCAACAGGCAUCGGUAUAC____UGCAUACGGUACA______UACGUACGUACACCAACCAAUAUAUAAU_________
.....(((.....))).((((....))))....................................................................... ( -8.41 =  -8.72 +   0.31)

alignment

secondary structure

dotplot

Window 0

Location	18,462,204 – 18,462,295
Length	91
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	75.43
Shannon entropy	0.41592
G+C content	0.46071
Mean single sequence MFE	-18.94
Consensus MFE	-11.04
Energy contribution	-11.48
Covariance contribution	0.44
Combinations/Pair	1.10
Mean z-score	-2.29
Structure conservation index	0.58
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.79
SVM RNA-class probability	0.967724
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18462204 91 - 21146708
AAAAAGAAAAUCAAUACGAGGCAGACACAAGAGCCAAGUUGGCACCUGGCAACAGG-CAUCGGUAUAUACGGUACAUACA-GUACGUAUACAU
................(((.((..........(((.....)))..(((....))))-).)))((((((...((((.....-)))))))))).. ( -22.80, z-score =  -3.69, R)
>droSim1.chr2R 17052521 80 - 19596830
-AAAAGAAAAUCAAUACGAGGCAG--ACAAGAGCCAAGUUGGCACCUGGCAACAGG-CAUCGGUAUAC----GGUAUACG-GUACAUAC----
-...............(((.((..--......(((.....)))..(((....))))-).)))((((.(----(.....))-))))....---- ( -19.40, z-score =  -2.66, R)
>droSec1.super_9 1767079 80 - 3197100
-UAAAGAAAAUCAAUACGAGGCAG--ACUAGAGCUAAGUUGGCACCUGGUCACAGU-CAUCGGUAUAC----UGCAUACG-GGACGUAC----
-.............((((.(((.(--(((((.(((.....)))..))))))...))-).((.((((..----...)))).-)).)))).---- ( -17.20, z-score =  -0.66, R)
>droYak2.chr2R 15931714 80 - 21139217
-AAAAGAAAAUCAAUACGAGGCAG--ACAAGAGCCAAGUUGGCACCUGGCAACAGG-CAUCGGCAUA-----UACAUACAUACUCCUAC----
-..................(((..--......)))..(((((..((((....))))-..)))))...-----.................---- ( -17.50, z-score =  -2.28, R)
>droAna3.scaffold_13266 12595327 86 + 19884421
-AAAAUAAAAUCAAUACAAGGCAG--ACAAGAGCCAACCUGGCACCUGGCAACAGGCCUUCCCCGCCCCACUCACUCACAUACCUCUAU----
-..................(((.(--..(((.(((.....))).((((....)))).)))..).)))......................---- ( -17.80, z-score =  -2.16, R)
>consensus
_AAAAGAAAAUCAAUACGAGGCAG__ACAAGAGCCAAGUUGGCACCUGGCAACAGG_CAUCGGUAUAC____UACAUACA_GCACCUAC____
................(((.............(((.....))).((((....))))...)))............................... (-11.04 = -11.48 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:43:40 2011