Locus 449

Sequence ID	dm3.chr2L
Location	3,139,947 – 3,140,080
Length	133
Max. P	0.796368

overview

Window 0

Location	3,139,947 – 3,140,051
Length	104
Sequences	7
Columns	116
Reading direction	forward
Mean pairwise identity	63.16
Shannon entropy	0.71026
G+C content	0.35650
Mean single sequence MFE	-23.17
Consensus MFE	-7.31
Energy contribution	-6.79
Covariance contribution	-0.52
Combinations/Pair	1.74
Mean z-score	-1.57
Structure conservation index	0.32
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.56
SVM RNA-class probability	0.742104
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 3139947 104 + 23011544
ACAAACA-AGGCAAGAAAUUGUAAAAUUCUA-AAUGAGGAGACAAAAAACUCCAUAAAUUUGUGGAGUCCACAGUGCUGAAAAAGUGGAAAACAUGGCAUGACCAU----------
.......-..((((....)))).........-.....(....)......(((((((....)))))))(((((..(......)..)))))....((((.....))))---------- ( -20.90, z-score =  -1.42, R)
>droSim1.chr2L 3081074 113 + 22036055
ACAAACA-AGGCAAGAAAUUGUAAAAUUCUA-AAUGGGGAGACAAAAA-CUCCAUAAAUUUGUGGAGCUCACAGUGCUGCGAAAGUGGAAAACAUCUAAGCACUCUGAAUGACCAU
.......-..((((....)))).........-.(((((....).....-(((((((....))))))).(((.((((((((....))(((.....))).)))))).)))....)))) ( -29.20, z-score =  -2.96, R)
>droSec1.super_5 1291682 113 + 5866729
ACAAACA-AGGCAAGAAAUUGUAAAAUUCUA-AAUGGGGAGACAAAAA-CUCCAUAAAUUUGUGGAGCCCGUAGUGCUGCGAAAGUGGAAAACAUUUAAGCACUCUGAAUGACCAU
.......-..((((....))))...((((..-.(((((....).....-(((((((....))))))).))))((((((....(((((.....))))).))))))..))))...... ( -28.00, z-score =  -2.32, R)
>droYak2.chr2L 3132700 113 + 22324452
ACAAACA-AGGCAAGAAAUUGUAAAAUUCUA-AAUGGUGAGGCAAAAA-CUCCAUAAAUUUGUGGAGUCCACAGUGCUGCGAAAAUGGAAAUUAUCUAAGCACUCUGCAUGACCAA
.......-..((((....)))).........-..((((.(.(((...(-(((((((....))))))))....((((((..((.(((....))).))..)))))).))).).)))). ( -31.30, z-score =  -3.27, R)
>droEre2.scaffold_4929 3183779 113 + 26641161
ACAAACA-AGGAAAGAAAUUGUAAAAUUCUA-AAUGGGGAGGCAAAAA-CUCCAUAAAUUUGUGGAGUCCACAGUGCUGCGAAAAUGGAAAUUAUCUCAGCACUCUGCAUGACCAA
....(((-(.........)))).........-..(((....(((...(-(((((((....))))))))....(((((((.((.(((....))).)).))))))).)))....))). ( -30.60, z-score =  -2.92, R)
>droAna3.scaffold_12913 360318 93 + 441482
ACAAGCACAGGAAAGAAAUUGUAAAAUCCAACGAAUGGGAAGCAAAAAGGCUAGCAAAUUUAUGAACCCUACGGUUUUACAGAAAUUGUUUUU-----------------------
..................((((((((((........(((.(((......)))..((......))..)))...))))))))))...........----------------------- ( -11.90, z-score =   0.81, R)
>droVir3.scaffold_12963 20090601 85 + 20206255
------UCGAGCGGGAUCGAAUGUAAUUCAUUAAAUUUGAAUUUGAAGAGCUAAGAAAAUUAUUUUUCUCAGAAUAU-----AAACGGAUAAUCUA--------------------
------((((((....((((((..((((.....))))...))))))...))).((((((....))))))........-----...)))........-------------------- ( -10.30, z-score =   1.09, R)
>consensus
ACAAACA_AGGCAAGAAAUUGUAAAAUUCUA_AAUGGGGAGACAAAAA_CUCCAUAAAUUUGUGGAGCCCACAGUGCUGCGAAAAUGGAAAAUAUCUAAGCACUCUG_AUGACCA_
.........((((.....((((....((((......)))).))))....(((((((....))))))).......))))...................................... ( -7.31 =  -6.79 +  -0.52)

alignment

secondary structure

dotplot

Window 1

Location	3,139,983 – 3,140,080
Length	97
Sequences	7
Columns	108
Reading direction	forward
Mean pairwise identity	59.27
Shannon entropy	0.80385
G+C content	0.36195
Mean single sequence MFE	-21.94
Consensus MFE	-4.26
Energy contribution	-4.16
Covariance contribution	-0.10
Combinations/Pair	1.71
Mean z-score	-2.19
Structure conservation index	0.19
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.72
SVM RNA-class probability	0.796368
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 3139983 97 + 23011544
GAGACAAAAAACUCCAUAAAUUUGUGGAGUCCACAGUGCUGAAAAAGUGGAAAACAUG----------GCAUGACC-AUAAGUUGCCCUAUAAAAUGCUCAAAAUAAA
(((.((.....(((((((....)))))))(((((..(......)..)))))......(----------(((.....-......))))........)))))........ ( -21.40, z-score =  -2.40, R)
>droSim1.chr2L 3081110 106 + 22036055
GAGACAAAAA-CUCCAUAAAUUUGUGGAGCUCACAGUGCUGCGAAAGUGGAAAACAUCUAAGCACUCUGAAUGACC-AUAAGUUGCCCUAUAAAAUGCUCUAAAUAAA
(((.((....-.......(((((((((...(((.((((((((....))(((.....))).)))))).)))....))-)))))))...........)))))........ ( -24.65, z-score =  -2.80, R)
>droSec1.super_5 1291718 106 + 5866729
GAGACAAAAA-CUCCAUAAAUUUGUGGAGCCCGUAGUGCUGCGAAAGUGGAAAACAUUUAAGCACUCUGAAUGACC-AUAAGUUGCCCUAUAAAAUGCUUAAAAUUAA
(((.((....-(((((((....)))))))...((((.((.((....((((....((((((.......)))))).))-))..)).)).))))....)))))........ ( -20.70, z-score =  -1.64, R)
>droYak2.chr2L 3132736 106 + 22324452
GAGGCAAAAA-CUCCAUAAAUUUGUGGAGUCCACAGUGCUGCGAAAAUGGAAAUUAUCUAAGCACUCUGCAUGACC-AAGAAUUGCCCUAUAAAAUUCUCAAAAUAAA
..(((((..(-(((((((....)))))))).((.((((((..((.(((....))).))..)))))).)).......-.....)))))..................... ( -26.80, z-score =  -3.42, R)
>droEre2.scaffold_4929 3183815 106 + 26641161
GAGGCAAAAA-CUCCAUAAAUUUGUGGAGUCCACAGUGCUGCGAAAAUGGAAAUUAUCUCAGCACUCUGCAUGACC-AACAAUUGCCCUGUAAAAUGCUCAAAAUAAA
..(((((..(-(((((((....)))))))).((.(((((((.((.(((....))).)).))))))).)).......-.....)))))..................... ( -30.90, z-score =  -4.05, R)
>droAna3.scaffold_12913 360357 85 + 441482
-AAGCAAAAAGGCUAGCAAAUUUAUGAACCCUACGGUUUUACAGAAAUUGUUUUUAAGU------------UGUCCGAUCUAUUCGACUUCAAUACAC----------
-.(((......)))(((((.(((..(((((....)))))....))).))))).....((------------((..(((.....)))....))))....---------- ( -10.60, z-score =   0.41, R)
>droVir3.scaffold_12963 20090634 90 + 20206255
-AAUUUGAAGAGCUAAGAAAAUUAUUUUUCUCAGAAUA-UAAACGGAUAAUCUAAAGCAGUGCCAUAGGGUAAUCUGAAUCAAGGCAUUGCA----------------
-.(((((.....((.((((((....)))))).))....-....)))))........((((((((....(((.......)))..)))))))).---------------- ( -18.52, z-score =  -1.39, R)
>consensus
GAGACAAAAA_CUCCAUAAAUUUGUGGAGCCCACAGUGCUGCGAAAAUGGAAAACAUCUAAGCACUCUGCAUGACC_AUAAAUUGCCCUAUAAAAUGCUCAAAAUAAA
...........(((((((....)))))))............................................................................... ( -4.26 =  -4.16 +  -0.10)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:13:08 2011