Locus 8756

Sequence ID	dm3.chr3R
Location	1,394,176 – 1,394,273
Length	97
Max. P	0.745583

overview

Window 8

Location	1,394,176 – 1,394,273
Length	97
Sequences	11
Columns	114
Reading direction	forward
Mean pairwise identity	64.73
Shannon entropy	0.76304
G+C content	0.46002
Mean single sequence MFE	-27.48
Consensus MFE	-10.67
Energy contribution	-10.03
Covariance contribution	-0.64
Combinations/Pair	1.24
Mean z-score	-0.98
Structure conservation index	0.39
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.57
SVM RNA-class probability	0.745583
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1394176 97 + 27905053
GGGGCUUCGAGAUCUCCGCCUCGAAGCGUGAGAGCUCAUCCUCGAUGUUGCGACGCUUUGUACCCAUUUGAAGUGGGGUUUUCUCUUUUAAAAAAUC-----------------
...((((((((........))))))))(.((((((((....(((......)))(((((((........))))))))))))))).)............----------------- ( -29.20, z-score =  -0.96, R)
>droSim1.chr3R 1429676 97 + 27517382
GAGGCUUCGAGAUCUCCGCCUCGAAGCGUGAGAGCUCAUCCUCGAUGUUGCGACGCUUUGUACCCAUUUUAAAUGGGUUUGGCUCUUUUAAAAAAUC-----------------
(((((((((((........))))))))((....)).....)))........((.(((....((((((.....))))))..)))))............----------------- ( -29.60, z-score =  -1.82, R)
>droYak2.chr3R 17357865 108 + 28832112
GAGGCUUCGAGAUCUCCGCCUCGAAGCGUGAGAGCUCAUCCUCGAUGUUCCGACGCUUUGUACCCAUUUAAAGUGGGUUUGGGGCUACUAGAAAACUUGAAGAUUCUC------
(((.(((((((.(((..((((((((((((..((((((......)).))))..)))))))..((((((.....))))))..)))))....)))...))))))).)))..------ ( -39.00, z-score =  -2.54, R)
>droEre2.scaffold_4770 1663827 108 + 17746568
GAGGCUUCGAGAUCUCCGCCUCGAAGCGAGAGAGCUCAUCCUCGAUGUUGCGACGCUUUGUACCCAUUUAACAUAGGUUUGGGGCUAUGAGAAAACUGGAAGAUUCUC------
(((.((((.((.((((.((((((((.((((.((.....)))))((((.(((((....)))))..)))).......).))))))))...))))...)).)))).)))..------ ( -30.70, z-score =  -0.02, R)
>droAna3.scaffold_13250 3507089 90 - 3535662
GAGGCUUUGAUAUCUCCGCCUCAAAGCGGGACAACUCGUCCUCGAUAUUUCGACGUUUUGUGCCCAUCGAU-GUUUUUUUUAAGGAUGCUC-----------------------
(((((...(....)...)))))..((((((((((..((((...((....))))))..)))).)))......-(((((.....)))))))).----------------------- ( -22.80, z-score =  -0.91, R)
>dp4.chr2 9588925 105 - 30794189
GGGGCUUGGAGAUCUCAGCUUCGAAGCGAGACAGCUCGUCCUCGAUAUUGCGACGUUUCGUACCCAUUUAUUGAUAUCUUAAUGGAUAAAUAAUUUUU-AACUCUC--------
.(((..(((((.((.(((..((((.(((((....)))))..))))..))).))..)))))..)))(((((((.((......)).))))))).......-.......-------- ( -25.70, z-score =  -0.95, R)
>droPer1.super_3 3394483 106 - 7375914
GGGGCUUGGAGAUCUCAGCUUCGAAGCGAGACAGCUCGUCCUCGAUAUUGCGACGUUUCGUACCCAUUUAUUGAUAUCUUAAUGGAUAAAUAAUUUUUUAACUCUC--------
.(((..(((((.((.(((..((((.(((((....)))))..))))..))).))..)))))..)))(((((((.((......)).)))))))...............-------- ( -25.70, z-score =  -0.91, R)
>droWil1.scaffold_181130 13222044 84 + 16660200
GCGGCUUGGAAAUUUCUGCUUCAAAGCGCGACAAUUCGUCCUCUAUGUGACGACGUUUUGUACCCAUUUUUUAA-AUAUCAACUC-----------------------------
(((.(((.(((........))).)))))).((((..((((.((.....)).))))..)))).............-..........----------------------------- ( -17.70, z-score =  -1.57, R)
>droVir3.scaffold_13047 16652971 112 + 19223366
GCGGCUUAGAGAUCUCCGCUUCGAAGCGCGAGAGCUCAUCUUCGAUAUUGCGACGUUUUGUGCCCAUUUCGAA-AGGCGUA-CGCUAUUGUUGAGAUGUCAACAAUAAAAAUUC
..(((...(((.((((((((....)))).)))).)))((((.(((((..((((((((((.............)-)))))).-)))...)))))))))))).............. ( -33.22, z-score =  -1.16, R)
>droMoj3.scaffold_6540 12960547 112 + 34148556
GCGGCUUUGAGAUCUCUGCUUCAAAGCGUGAGAGCUCAUCUUCGAUGUUACGACGUUUUGUCCCCAUUUCAGA-GGCUAAACUUCUAAUCAAACGAUUUCAAGUAAAAUAGUC-
..(.(((((((((........((((((((...(((((......)).)))...)))))))).....))))))))-).)...((((..((((....))))..)))).........- ( -24.12, z-score =  -0.18, R)
>droGri2.scaffold_15116 1618133 98 + 1808639
GCGGCUUGGAGAUCUCCGCCUCAAAUCGAGAGAGCUCGUCUUCGAUAUUGCGACGUUUUGUGCCCAUUUC-AA-AGGCGUAACGUUAUUUUCGUU-UGCCU-------------
..(((((((((((....(((((.......))).))..))))))))......((((((...((((......-..-.)))).)))))).........-.))).------------- ( -24.50, z-score =   0.23, R)
>consensus
GAGGCUUCGAGAUCUCCGCCUCGAAGCGAGAGAGCUCAUCCUCGAUGUUGCGACGUUUUGUACCCAUUUAAAAUGGGUUUAACGCUAUUAUAAAAUU___A_____________
..(((...((....)).))).(((((((.((....))....(((......))))))))))...................................................... (-10.67 = -10.03 +  -0.64)

alignment

secondary structure

dotplot

Window 9

Location	1,394,176 – 1,394,273
Length	97
Sequences	11
Columns	114
Reading direction	reverse
Mean pairwise identity	64.73
Shannon entropy	0.76304
G+C content	0.46002
Mean single sequence MFE	-25.71
Consensus MFE	-10.14
Energy contribution	-9.66
Covariance contribution	-0.49
Combinations/Pair	1.29
Mean z-score	-0.85
Structure conservation index	0.39
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.29
SVM RNA-class probability	0.631422
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1394176 97 - 27905053
-----------------GAUUUUUUAAAAGAGAAAACCCCACUUCAAAUGGGUACAAAGCGUCGCAACAUCGAGGAUGAGCUCUCACGCUUCGAGGCGGAGAUCUCGAAGCCCC
-----------------............((((....((((.......))))..((...(.(((......))).).))...))))..(((((((((......)))))))))... ( -23.70, z-score =  -0.28, R)
>droSim1.chr3R 1429676 97 - 27517382
-----------------GAUUUUUUAAAAGAGCCAAACCCAUUUAAAAUGGGUACAAAGCGUCGCAACAUCGAGGAUGAGCUCUCACGCUUCGAGGCGGAGAUCUCGAAGCCUC
-----------------...........(((((((.((((((.....))))))......(.(((......))).).)).)))))...(((((((((......)))))))))... ( -29.90, z-score =  -2.32, R)
>droYak2.chr3R 17357865 108 - 28832112
------GAGAAUCUUCAAGUUUUCUAGUAGCCCCAAACCCACUUUAAAUGGGUACAAAGCGUCGGAACAUCGAGGAUGAGCUCUCACGCUUCGAGGCGGAGAUCUCGAAGCCUC
------(((.((((((..((.((((....((.....(((((.......))))).....))...)))).)).))))))...)))....(((((((((......)))))))))... ( -31.10, z-score =  -0.92, R)
>droEre2.scaffold_4770 1663827 108 - 17746568
------GAGAAUCUUCCAGUUUUCUCAUAGCCCCAAACCUAUGUUAAAUGGGUACAAAGCGUCGCAACAUCGAGGAUGAGCUCUCUCGCUUCGAGGCGGAGAUCUCGAAGCCUC
------(((...((((.((...((((...((.....((((((.....)))))).....))..(((....((((((.((((....)))))))))).))))))).)).)))).))) ( -32.60, z-score =  -1.44, R)
>droAna3.scaffold_13250 3507089 90 + 3535662
-----------------------GAGCAUCCUUAAAAAAAAC-AUCGAUGGGCACAAAACGUCGAAAUAUCGAGGACGAGUUGUCCCGCUUUGAGGCGGAGAUAUCAAAGCCUC
-----------------------((((...............-.((((((.........))))))......(.((((.....))))))))).(((((.((....))...))))) ( -23.90, z-score =  -1.56, R)
>dp4.chr2 9588925 105 + 30794189
--------GAGAGUU-AAAAAUUAUUUAUCCAUUAAGAUAUCAAUAAAUGGGUACGAAACGUCGCAAUAUCGAGGACGAGCUGUCUCGCUUCGAAGCUGAGAUCUCCAAGCCCC
--------((((...-..........((((((((............)))))))).......((.((.(.((((((.((((....)))))))))).).)).))))))........ ( -22.10, z-score =  -0.51, R)
>droPer1.super_3 3394483 106 + 7375914
--------GAGAGUUAAAAAAUUAUUUAUCCAUUAAGAUAUCAAUAAAUGGGUACGAAACGUCGCAAUAUCGAGGACGAGCUGUCUCGCUUCGAAGCUGAGAUCUCCAAGCCCC
--------((((..............((((((((............)))))))).......((.((.(.((((((.((((....)))))))))).).)).))))))........ ( -22.10, z-score =  -0.51, R)
>droWil1.scaffold_181130 13222044 84 - 16660200
-----------------------------GAGUUGAUAU-UUAAAAAAUGGGUACAAAACGUCGUCACAUAGAGGACGAAUUGUCGCGCUUUGAAGCAGAAAUUUCCAAGCCGC
-----------------------------..........-.........(.(.((((..((((.((.....)).))))..))))).)((((.((((......)))).))))... ( -16.40, z-score =  -0.19, R)
>droVir3.scaffold_13047 16652971 112 - 19223366
GAAUUUUUAUUGUUGACAUCUCAACAAUAGCG-UACGCCU-UUCGAAAUGGGCACAAAACGUCGCAAUAUCGAAGAUGAGCUCUCGCGCUUCGAAGCGGAGAUCUCUAAGCCGC
.......(((((((((....)))))))))(((-...((.(-(((((.((..((((.....)).)).)).))))))..(((.((((.((((....)))))))).)))...))))) ( -31.40, z-score =  -1.23, R)
>droMoj3.scaffold_6540 12960547 112 - 34148556
-GACUAUUUUACUUGAAAUCGUUUGAUUAGAAGUUUAGCC-UCUGAAAUGGGGACAAAACGUCGUAACAUCGAAGAUGAGCUCUCACGCUUUGAAGCAGAGAUCUCAAAGCCGC
-(((..(((((.(..((....))..).)))))((((.(((-((......)))).).))))))).............((((.((((..(((....))).)))).))))....... ( -23.60, z-score =   0.41, R)
>droGri2.scaffold_15116 1618133 98 - 1808639
-------------AGGCA-AACGAAAAUAACGUUACGCCU-UU-GAAAUGGGCACAAAACGUCGCAAUAUCGAAGACGAGCUCUCUCGAUUUGAGGCGGAGAUCUCCAAGCCGC
-------------.(((.-((((.......))))..((((-..-.....)))).......(((.(((.((((((((.....))).)))))))).)))(((....)))..))).. ( -26.00, z-score =  -0.77, R)
>consensus
_____________U___AAUUUUAUAAAAGCGUUAAACCCAUUUUAAAUGGGUACAAAACGUCGCAACAUCGAGGAUGAGCUCUCACGCUUCGAGGCGGAGAUCUCCAAGCCGC
..................................................(((.......(((......((((((.((........))))))))......)))......))).. (-10.14 =  -9.66 +  -0.49)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:51:33 2011