Locus 11274

Sequence ID	dm3.chr3R
Location	19,948,151 – 19,948,351
Length	200
Max. P	0.750932

overview

Window 3

Location	19,948,151 – 19,948,249
Length	98
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.42
Shannon entropy	0.28351
G+C content	0.48047
Mean single sequence MFE	-34.18
Consensus MFE	-23.15
Energy contribution	-24.27
Covariance contribution	1.11
Combinations/Pair	1.13
Mean z-score	-1.94
Structure conservation index	0.68
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.58
SVM RNA-class probability	0.750932
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 19948151 98 + 27905053
-----------UUUUCCGAGUGUGGAUGUCAAGGCGGAUUGGGGGCGGAUC--GUUGAUAACUCGAUUAGUCUGCGUCUGCCUCUGA--UUACGCCGUAGAUUGUAUAUAAUA-------
-----------........(((((.(.(((..(((((((..((((((((.(--((.(((..........))).)))))))))))..)--)).))))...)))).)))))....------- ( -34.00, z-score =  -2.35, R)
>droSim1.chr3R 19779783 98 + 27517382
-----------UUUUCCGAGUGUGGAUGUCAAGGCGGAUUGGGGGCGGAUC--GUUGAUAACUCGAUUAGUCUGCGUCUGCCUCUGA--UUACGCAGUAGAUUGUAUACAAUA-------
-----------........(((((.(.((((..((((((..((((((((.(--((.(((..........))).)))))))))))..)--)).)))..).)))).)))))....------- ( -32.60, z-score =  -2.02, R)
>droSec1.super_0 20286194 98 + 21120651
-----------UUUUCCGAGUGUGGAUGUCAAGGCGGAUUGGGGGCGGAUC--GUUGAUAACUCGAUUAGUCUGCGUCUGCCUCUGA--UUACGCCGUAGAUUGUAUACAAUA-------
-----------........(((((.(.(((..(((((((..((((((((.(--((.(((..........))).)))))))))))..)--)).))))...)))).)))))....------- ( -36.20, z-score =  -2.90, R)
>droYak2.chr3R 2277225 105 - 28832112
-----------UUUUCCGAGUGUGGAUGUCAAGGCGGAUUGGGGGCGGAUC--GUUGAUAACUCGAUUAGUCUGCGUCUGCCGCUGA--UUACGCCGCAGAUUGUCUAUAAUAAUUAUAA
-----------.........((((((((((..(((((((..(.((((((.(--((.(((..........))).))))))))).)..)--)).))))...)).)))))))).......... ( -35.30, z-score =  -2.04, R)
>droEre2.scaffold_4820 2359067 98 - 10470090
-----------UUUUCCGAGUGUGGAUGUCAAGGCGGAUUGGGGGCGGAUC--GUUGAUAACUCGAUUAGUCUGCGUCUGCCUCUGA--UUACGCCGUAGAUUGUGUAUAAUA-------
-----------...((((....)))).(((..(((((((..((((((((.(--((.(((..........))).)))))))))))..)--)).))))...)))...........------- ( -33.40, z-score =  -2.08, R)
>droAna3.scaffold_13340 1149398 110 - 23697760
CACCGACUCGCCAUUGCGAGUGCAAGUGUCAAGGAAGAU-GGGGGCGGCUGCGAGAGAUAACUCGAUUAGUCUGCGUCUGGGUCUGAGAUUACGGCGUACAUUUCAUAUUA---------
(.(((((((((....))))))...(((.(((.((.((((-(.((((.....((((......))))....)))).)))))...))))).))).))).)..............--------- ( -33.60, z-score =  -0.27, R)
>consensus
___________UUUUCCGAGUGUGGAUGUCAAGGCGGAUUGGGGGCGGAUC__GUUGAUAACUCGAUUAGUCUGCGUCUGCCUCUGA__UUACGCCGUAGAUUGUAUAUAAUA_______
................((.((((((...(((((((((((.....((((((...(((((....)))))..)))))))))))))).)))..))))))))....................... (-23.15 = -24.27 +   1.11)

alignment

secondary structure

dotplot

Window 4

Location	19,948,249 – 19,948,351
Length	102
Sequences	7
Columns	120
Reading direction	reverse
Mean pairwise identity	71.42
Shannon entropy	0.53023
G+C content	0.43115
Mean single sequence MFE	-25.09
Consensus MFE	-8.79
Energy contribution	-11.59
Covariance contribution	2.80
Combinations/Pair	1.35
Mean z-score	-1.99
Structure conservation index	0.35
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.26
SVM RNA-class probability	0.616175
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 19948249 102 - 27905053
------UGCAAU--UUCCACUCACGCCGGCUGCAAAUGCAAUCUUCGCAGCCAUAAUUUGUAACUC-----AUCGCAGACAUGGCAUCACCCCGGAUUUGAGUUGGAAACAUCAU-----
------.....(--(((((((((..((((.(((....))).........(((((..(((((.....-----...))))).)))))......))))...)))).))))))......----- ( -29.40, z-score =  -2.40, R)
>droWil1.scaffold_181089 6409481 90 + 12369635
--------------UACAUUCUACAUUCACCUAUAAUGCCAAUUCUAUUAUUA-AAUUUGGCAUUC-----UUAAUGGCUUUAUUAUUUUUAGGCAUUC-ACUUGGACUAA---------
--------------...............((...((((((((...........-...)))))))).-----..((((.((..(.....)..)).)))).-....)).....--------- ( -11.84, z-score =  -1.42, R)
>droSim1.chr3R 19779881 102 - 27517382
------UGCCAU--UUCCACUCACGCCGGCUGCAAUUGCAAUCUUCGCAUCCAUAAUUUGUAACUC-----AUCGCAGACAUGGCAUCACCCCGGAUUUGAGUUGGAAACAUCAU-----
------.....(--(((((((((..((((.(((....)))..........((((..(((((.....-----...))))).)))).......))))...)))).))))))......----- ( -24.60, z-score =  -1.15, R)
>droSec1.super_0 20286292 102 - 21120651
------UGCCAU--UUCCACUCACGCCGGCUGCAAUUGCAAUCUUCGCAGCCAUAAUUUGUAACUC-----AUCGCAGACAUGGCAUUACCCCGGAUUUGAGUUGGAAACAUCAU-----
------.....(--(((((((((..((((.(((....))).........(((((..(((((.....-----...))))).)))))......))))...)))).))))))......----- ( -29.40, z-score =  -2.47, R)
>droYak2.chr3R 2277330 107 + 28832112
------UGUCAU--UUCCACUCACGCCGGCUGCAAAUGCAAUCUUCGCAGCCAUAAUUUGUAACUC-----AUCGCAGACAUGGCAUCACCCCGGAUUUGAGUUGGAAACAUCAUCAUUA
------.....(--(((((((((..((((.(((....))).........(((((..(((((.....-----...))))).)))))......))))...)))).))))))........... ( -29.40, z-score =  -2.46, R)
>droEre2.scaffold_4820 2359165 102 + 10470090
------UGUCAU--UUCCACUCACGCCGGCUGCAAAUGCAAUCUUCGCCGCCAUAAUUUGUAACUC-----AUCGCAGACAUGGCAUCACCCCGGAUUUAAGUUGGAAACAUCAU-----
------.....(--(((((((....((((.(((....))).........(((((..(((((.....-----...))))).)))))......)))).....)).))))))......----- ( -24.40, z-score =  -1.35, R)
>droAna3.scaffold_13340 1149508 115 + 23697760
UACUCUUUCCAUAAUGGAAUUCGCCAUUAUGAGAACUGCAAUCUUCGCAGCCAUAAUUAAUAACUCAACUGAUCGCAGACAUCUCAUCACCCCGGAUUUGAGUUGGAAACAUUCU-----
.((((..((((((((((......)))))))((((.((((.......))))..................(((....)))...))))........)))...))))((....))....----- ( -26.60, z-score =  -2.71, R)
>consensus
______UGCCAU__UUCCACUCACGCCGGCUGCAAAUGCAAUCUUCGCAGCCAUAAUUUGUAACUC_____AUCGCAGACAUGGCAUCACCCCGGAUUUGAGUUGGAAACAUCAU_____
..............(((((((((..((((.......(((.......)))(((((..(((((.............))))).)))))......))))...)))).)))))............ ( -8.79 = -11.59 +   2.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:39:45 2011