Locus 2090

Sequence ID	dm3.chr2L
Location	16,239,786 – 16,239,938
Length	152
Max. P	0.966219

overview

Window 3

Location	16,239,786 – 16,239,938
Length	152
Sequences	12
Columns	172
Reading direction	forward
Mean pairwise identity	75.37
Shannon entropy	0.51143
G+C content	0.44616
Mean single sequence MFE	-40.91
Consensus MFE	-22.43
Energy contribution	-21.68
Covariance contribution	-0.75
Combinations/Pair	1.37
Mean z-score	-1.38
Structure conservation index	0.55
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.79
SVM RNA-class probability	0.817631
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16239786 152 + 23011544
--------------AAUACUAAUAUUUACUUCUUAUUUAGGAGGAACUGUACACCUAUUGCGGCAAUGCCUCGCGGCUGGUUUUGACGCUUCAGCUAAUGCCGCUGACCAUAAUUUUAGUGUUUUACCUGACGCACAGCUUUAUGCGUUAGGU----ACAAUGUACACAG--
--------------..............((((((....))))))...(((((.......((((((..((...))((((((..........))))))..))))))................(((.(((((((((((........))))))))))----).))))))))...-- ( -43.60, z-score =  -2.50, R)
>dp4.chr4_group4 5210815 157 + 6586962
---------------AUACUCAUCUGUCCCUCGUCCUUAGGAGGAACUGUACACCUAUUGCGGCAAUGCCUCGCGGCUGGGUCUGACGCUCCAGCUGCUGCCGCUGACCAUAAUUUUGAUGUUUUACUUGACGCGCUGCUUUAUGCGUUAGAUUAUACUAGUAUAUACACAC
---------------(((((((((.((.((((........)))).))............((((((.......((((((((((.....)).)))))))))))))).............))))......((((((((........))))))))........)))))........ ( -43.31, z-score =  -1.08, R)
>droPer1.super_16 239915 148 - 1990440
------------------------UGUCCCUCGUCCUUAGGAGGAACUGUACACCUAUUGCGGCAAUGCCUCGCGGCUGGGUCUGACGCUCCAGCUGCUGCCGCUGACCAUAAUUUUGAUGUUUUACUUGACGCGCUGCUUUAUGCGUUAGAUUAUACUAGUAUAUACACAC
------------------------.((.((((........)))).))(((((.......((((((.......((((((((((.....)).)))))))))))))).......................((((((((........)))))))).........)))))....... ( -41.71, z-score =  -0.78, R)
>droMoj3.scaffold_6500 9757219 143 + 32352404
------------------UACGAAUGUUUGUUUUUUC-AGGAGGAACUUUUCACCUACUGCGGCAAUGCCUCGCGGCUGGGUCUGACGCUUCAGCUGCUGCCGCUGACCAUAAUUUUGAUGUUUUACUUGACGCGCUGCUUUAUGCGCGU-------CUAGUUUAUACA---
------------------...(((.((((.(((....-.))).))))..))).......((((((.......((((((((((.....)).))))))))))))))...............(((...(((.(((((((........))))))-------).)))....)))--- ( -44.11, z-score =  -1.92, R)
>droGri2.scaffold_15252 8427690 135 - 17193109
---------------------------CUUUUUGUUGUAGGAGGAACUGUUCACCUAUUGCGGCAAUGCCUCGCGGCUGGGUUUGACGCUUCAGCUGCUGCCGCUGACCAUUAUUUUGAUGUUUUACUUGACGCGCUGCUUUAUGCGAGU-------CUAGUUUAUACA---
---------------------------......((((((((.(((....))).))))).((((((.......((((((((((.....)).)))))))))))))).)))...........(((...(((.(((.(((........))).))-------).)))....)))--- ( -38.61, z-score =  -0.66, R)
>droVir3.scaffold_12723 4205310 162 - 5802038
AAUACCGAUAUUUCAUUAUAUUCAUAAAUGUUUUUUUUAGGAGGAACUGUUCACCUAUUGCGGCAACGCCUCACGGCUGGGCCUGACGCUUCAGCUGCUGCCGCUGACCAUACUUUUGAUGUUUUACUUGACGCGUUGCUUUAUGCGCGU-------CUAGUUUAUACA---
......((((((....(((..(((.............((((.(((....))).))))..((((((..((.....((((((((.....)).)))))))))))))))))..))).....))))))..(((.(((((((........))))))-------).))).......--- ( -39.60, z-score =  -0.76, R)
>droWil1.scaffold_180764 1732106 136 - 3949147
----------------UGUAUAUUUGUUUUCUCUCUCUAGGAGGAAUUGUACACCUAUUGCGGCAAUGCGUCGAGGCUGAAUCUAUCGCUAUACCUGAUGCCGUUGACCAUAAUUUUGAUGUUUUACUUAACGCGCUGCUUUAUGCGUUAGA--------------------
----------------((((((.....(((((((.....))))))).)))))).(((.(((((((.(((((((((((...(((.............)))))).)))))............(((......)))))).))))....))).))).-------------------- ( -29.42, z-score =   0.29, R)
>droAna3.scaffold_12916 16028081 163 - 16180835
---AAUAUGCAAUUAUUUAACAUUUUUAUCCAAUUCCCAGGAGGAACUGUACACCUAUUGCGGAAAAGCCUCGCGGCUGGGUUUGACGCUUCAGCUCCUGCCGCUGACCAUGAUUUUGAUGUUUUACUUGACGCGCUGCUUUAUGCGUUAGAG----GAUAUAUACACAC--
---....((((((......(((.((((.(((........))))))).)))......))))))......(((((((((.((..((((....))))..)).)))))........................(((((((........))))))))))----)............-- ( -39.40, z-score =  -0.65, R)
>droEre2.scaffold_4929 7936772 147 + 26641161
------------------ACUCGAUUCAUUU-UUAUUUAGGAGGAACUGUACACCUAUUGCGGCAAUGCCUCGCGGCUGGGUUUGACGCUUCAGCUAAUGCCGCUGACCAUAAUUUUAGUGUUUCACCUGACGUACAGCUUUAUGCGUUAGGU----AUAAUGCACACAA--
------------------.......(((...-.....((((.(........).))))..((((((..((...))((((((((.....)).))))))..)))))))))...........((((...((((((((((........))))))))))----.....))))....-- ( -39.10, z-score =  -0.74, R)
>droYak2.chr2L 3232587 147 - 22324452
------------------UUUUGUUUCCUUUCUUAUUUAGGAGGAACUGUACACCUAUUGCGGCAAUGCCUCGCGGCUGGGUUUGACGCUUCAGCUGAUGCCGCUGACCAUAAUUUUAGUGUUUCACCUGACGUACACCUUUAUGCGUUAGGU----AUAAUGCACAAA---
------------------.((((((((((((........))))))).............((((((........(((((((((.....)).))))))).))))))..............(((((..((((((((((........))))))))))----..))))))))))--- ( -41.70, z-score =  -1.65, R)
>droSec1.super_5 4961648 152 + 5866729
--------------AAUACUAUUAUUUCCUCUUUAUUUAGGAGGAACUGUACACCUAUUGCGGCAAUGCCUCGCGGCUGGUUUUGACGCUUCAGCUAAUGCCGCUGACCAUAAUUUUAGUGUUUUACCUGACGCACAGCUUUAUGCGUUAGGU----ACAAUGUACACAG--
--------------...........((((((((.....)))))))).(((((.......((((((..((...))((((((..........))))))..))))))................(((.(((((((((((........))))))))))----).))))))))...-- ( -48.50, z-score =  -3.93, R)
>droSim1.chr2L 15949233 152 + 22036055
--------------AAUACUAUUAUUUACUUUUUAUUUAGGAGGAACUGUACACCUAUUGCGGCAAUGCCUCGCGGCUGGUUUUGACGCUUCAGCUAAUGCCGCUGACCAUAAUUUUAGUGUUUUACCUGACGCACAGCUUUAUGCGUUAGGU----ACAAUGUACACAG--
--------------(((((((..(((...........((((.(........).))))..((((((..((...))((((((..........))))))..)))))).......)))..))))))).(((((((((((........))))))))))----)............-- ( -41.80, z-score =  -2.17, R)
>consensus
________________U_CUUAUAUUUAUUUUUUAUUUAGGAGGAACUGUACACCUAUUGCGGCAAUGCCUCGCGGCUGGGUUUGACGCUUCAGCUGAUGCCGCUGACCAUAAUUUUGAUGUUUUACUUGACGCGCUGCUUUAUGCGUUAGGU____AUAAUGUACACA___
.....................................((((.(((((............((((((..((...))((((((..........))))))..))))))................))))).)))).((((........))))......................... (-22.43 = -21.68 +  -0.75)

alignment

secondary structure

dotplot

Window 4

Location	16,239,786 – 16,239,938
Length	152
Sequences	12
Columns	172
Reading direction	reverse
Mean pairwise identity	75.37
Shannon entropy	0.51143
G+C content	0.44616
Mean single sequence MFE	-41.62
Consensus MFE	-24.17
Energy contribution	-24.16
Covariance contribution	-0.01
Combinations/Pair	1.17
Mean z-score	-1.78
Structure conservation index	0.58
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.76
SVM RNA-class probability	0.966219
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16239786 152 - 23011544
--CUGUGUACAUUGU----ACCUAACGCAUAAAGCUGUGCGUCAGGUAAAACACUAAAAUUAUGGUCAGCGGCAUUAGCUGAAGCGUCAAAACCAGCCGCGAGGCAUUGCCGCAAUAGGUGUACAGUUCCUCCUAAAUAAGAAGUAAAUAUUAGUAUU--------------
--...((((((((.(----((((.(((((((....))))))).)))))....................((((((...((....))..........(((....)))..))))))....)))))))).................................-------------- ( -44.60, z-score =  -2.49, R)
>dp4.chr4_group4 5210815 157 - 6586962
GUGUGUAUAUACUAGUAUAAUCUAACGCAUAAAGCAGCGCGUCAAGUAAAACAUCAAAAUUAUGGUCAGCGGCAGCAGCUGGAGCGUCAGACCCAGCCGCGAGGCAUUGCCGCAAUAGGUGUACAGUUCCUCCUAAGGACGAGGGACAGAUGAGUAU---------------
((((.(((((....))))).....))))........((.((((..(((...(((((......))))..(((((((....(((..(....)..)))(((....))).)))))))....)...))).(((((((........))))))).)))).))..--------------- ( -45.30, z-score =  -0.90, R)
>droPer1.super_16 239915 148 + 1990440
GUGUGUAUAUACUAGUAUAAUCUAACGCAUAAAGCAGCGCGUCAAGUAAAACAUCAAAAUUAUGGUCAGCGGCAGCAGCUGGAGCGUCAGACCCAGCCGCGAGGCAUUGCCGCAAUAGGUGUACAGUUCCUCCUAAGGACGAGGGACA------------------------
...(((((((.(((..........((((..........))))..........................(((((((....(((..(....)..)))(((....))).)))))))..))))))))))(((((((........))))))).------------------------ ( -43.00, z-score =  -0.77, R)
>droMoj3.scaffold_6500 9757219 143 - 32352404
---UGUAUAAACUAG-------ACGCGCAUAAAGCAGCGCGUCAAGUAAAACAUCAAAAUUAUGGUCAGCGGCAGCAGCUGAAGCGUCAGACCCAGCCGCGAGGCAUUGCCGCAGUAGGUGAAAAGUUCCUCCU-GAAAAAACAAACAUUCGUA------------------
---.......(((.(-------((((((........))))))).))).............(((((...(((((((...((((....)))).....(((....))).)))))))..((((.(........).)))-).............)))))------------------ ( -43.00, z-score =  -2.44, R)
>droGri2.scaffold_15252 8427690 135 + 17193109
---UGUAUAAACUAG-------ACUCGCAUAAAGCAGCGCGUCAAGUAAAACAUCAAAAUAAUGGUCAGCGGCAGCAGCUGAAGCGUCAAACCCAGCCGCGAGGCAUUGCCGCAAUAGGUGAACAGUUCCUCCUACAACAAAAAG---------------------------
---(((....(((.(-------((.(((........))).))).)))...............((....(((((((..((....))..........(((....))).)))))))..((((.(........).))))))))).....--------------------------- ( -35.50, z-score =  -1.80, R)
>droVir3.scaffold_12723 4205310 162 + 5802038
---UGUAUAAACUAG-------ACGCGCAUAAAGCAACGCGUCAAGUAAAACAUCAAAAGUAUGGUCAGCGGCAGCAGCUGAAGCGUCAGGCCCAGCCGUGAGGCGUUGCCGCAAUAGGUGAACAGUUCCUCCUAAAAAAAACAUUUAUGAAUAUAAUGAAAUAUCGGUAUU
---.......(((.(-------(((((..........)))))).)))......(((....((((.(((((((((((..((((....)))).....(((....)))))))))))..((((.(........).)))).............))).)))).)))............ ( -46.30, z-score =  -2.55, R)
>droWil1.scaffold_180764 1732106 136 + 3949147
--------------------UCUAACGCAUAAAGCAGCGCGUUAAGUAAAACAUCAAAAUUAUGGUCAACGGCAUCAGGUAUAGCGAUAGAUUCAGCCUCGACGCAUUGCCGCAAUAGGUGUACAAUUCCUCCUAGAGAGAGAAAACAAAUAUACA----------------
--------------------..((((((..........)))))).(((..(((((...(((.(((.(((..((.((((((....(....).....)))).)).)).)))))).))).)))))....((((((.....))).)))........))).---------------- ( -24.80, z-score =   0.24, R)
>droAna3.scaffold_12916 16028081 163 + 16180835
--GUGUGUAUAUAUC----CUCUAACGCAUAAAGCAGCGCGUCAAGUAAAACAUCAAAAUCAUGGUCAGCGGCAGGAGCUGAAGCGUCAAACCCAGCCGCGAGGCUUUUCCGCAAUAGGUGUACAGUUCCUCCUGGGAAUUGGAUAAAAAUGUUAAAUAAUUGCAUAUU---
--(((((((......----......(((........))).(((.......(((((..........(((((.......))))).(((..((....((((....))))))..)))....))))).(((((((.....))))))))))................))))))).--- ( -40.20, z-score =  -0.35, R)
>droEre2.scaffold_4929 7936772 147 - 26641161
--UUGUGUGCAUUAU----ACCUAACGCAUAAAGCUGUACGUCAGGUGAAACACUAAAAUUAUGGUCAGCGGCAUUAGCUGAAGCGUCAAACCCAGCCGCGAGGCAUUGCCGCAAUAGGUGUACAGUUCCUCCUAAAUAA-AAAUGAAUCGAGU------------------
--...(((((.(((.----...))).))))).((((((((..(.((((...)))).............((((((...((....))..........(((....)))..))))))....)..))))))))............-.............------------------ ( -39.30, z-score =  -1.07, R)
>droYak2.chr2L 3232587 147 + 22324452
---UUUGUGCAUUAU----ACCUAACGCAUAAAGGUGUACGUCAGGUGAAACACUAAAAUUAUGGUCAGCGGCAUCAGCUGAAGCGUCAAACCCAGCCGCGAGGCAUUGCCGCAAUAGGUGUACAGUUCCUCCUAAAUAAGAAAGGAAACAAAA------------------
---(((((....(((----(((((((.(((((.(((((...((....)).)))))....)))))))..((((((...((....))..........(((....)))..))))))..))))))))...(((((.((.....))..)))))))))).------------------ ( -42.00, z-score =  -2.13, R)
>droSec1.super_5 4961648 152 - 5866729
--CUGUGUACAUUGU----ACCUAACGCAUAAAGCUGUGCGUCAGGUAAAACACUAAAAUUAUGGUCAGCGGCAUUAGCUGAAGCGUCAAAACCAGCCGCGAGGCAUUGCCGCAAUAGGUGUACAGUUCCUCCUAAAUAAAGAGGAAAUAAUAGUAUU--------------
--(((((((((((.(----((((.(((((((....))))))).)))))....................((((((...((....))..........(((....)))..))))))....)))))))..((((((.........))))))...))))....-------------- ( -50.90, z-score =  -4.18, R)
>droSim1.chr2L 15949233 152 - 22036055
--CUGUGUACAUUGU----ACCUAACGCAUAAAGCUGUGCGUCAGGUAAAACACUAAAAUUAUGGUCAGCGGCAUUAGCUGAAGCGUCAAAACCAGCCGCGAGGCAUUGCCGCAAUAGGUGUACAGUUCCUCCUAAAUAAAAAGUAAAUAAUAGUAUU--------------
--...((((((((.(----((((.(((((((....))))))).)))))....................((((((...((....))..........(((....)))..))))))....)))))))).................................-------------- ( -44.60, z-score =  -2.88, R)
>consensus
___UGUGUACAUUAG____ACCUAACGCAUAAAGCAGCGCGUCAAGUAAAACAUCAAAAUUAUGGUCAGCGGCAGCAGCUGAAGCGUCAAACCCAGCCGCGAGGCAUUGCCGCAAUAGGUGUACAGUUCCUCCUAAAUAAAAAAGAAAUAAAAA_A________________
........................((((..........))))..........((((......))))..((((((...((....))..........(((....)))..))))))..((((.(........).))))..................................... (-24.17 = -24.16 +  -0.01)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:44:34 2011