Locus 12252

Sequence ID	dm3.chr3R
Location	26,787,049 – 26,787,202
Length	153
Max. P	0.833677

overview

Window 0

Location	26,787,049 – 26,787,202
Length	153
Sequences	10
Columns	168
Reading direction	forward
Mean pairwise identity	51.97
Shannon entropy	1.00040
G+C content	0.51591
Mean single sequence MFE	-58.38
Consensus MFE	-0.63
Energy contribution	-0.83
Covariance contribution	0.20
Combinations/Pair	1.33
Mean z-score	-2.72
Structure conservation index	0.01
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.73
SVM RNA-class probability	0.800579
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26787049 153 + 27905053
CGGCCUAGUAGCCUAAUGCAGUUCCUACAAAAUUGCCCCUCUGAAGGGAAUGAGGAGGAGGAUUCUCACAACGAAAUGGCUGCUAAUCCUUCCGCCCAUUCC--GUUCAGGAACCCAAGCUUUUCGAUCUGGGACUCUUAGGAAGGAAUUGCGCG-------------
.(((......)))....(((((((((.(...........((((((.((((((.((.((((((((..((((......))..))..))))).))).))))))))--.))))))..((((..(.....)...))))........).)))))))))...------------- ( -50.90, z-score =  -1.36, R)
>droSim1.chr3R 26431359 153 + 27517382
CGGCCUAGUAGUCUAAUGCAGUUCCUACAAAAUUGCGCCUCUGAAGGGAAUGAGGAGGAGGAUUCCCACCACGAAAUGGCUGCUAUUCCUUCCGCCCAUUCC--GUUCAGGAACCAAAGCUUUUCGAUCUGGGACUUUUAGGAAGGAAUUGCGCG-------------
..((.(((....)))..(((((((((.............((((((.((((((.((.((((((....(((((.....))).))....))).))).))))))))--.))))))..(((((((((........))).))))..)).))))))))))).------------- ( -48.90, z-score =  -0.95, R)
>droSec1.super_4 5612108 153 + 6179234
CGGCCUAGUAGUCUAAUGCAGUUCCUACAAAAUUGCGCCUCUGAAGGGAAUGAGGAGGAGGAUUCCCACCACGAAAUGGCUGCUAAUCCUUCCGCCCAUUCC--GUUCAGGAACCAAAGCUUUUCGAUCUGGGACUUUUAGGAAGGAAUUGCGCG-------------
..((.(((....)))..(((((((((.............((((((.((((((.((.((((((((..(((((.....))).))..))))).))).))))))))--.))))))..(((((((((........))).))))..)).))))))))))).------------- ( -51.60, z-score =  -1.68, R)
>droYak2.chr3R 27714254 153 + 28832112
CGACCUAGCAGCCUAAUGCAGUUCCUCGAAACUUGCGUCUCCGAAGGGAAUGAAAGGGAGGAUUCAGAUCUCGAAAUGGAUACAAAUUCUUGCGCUCAUUCU--GCUCGGGAACCCAAGCUUUUCGAUCUGGGACUUUUGGGCAGUAAUUGCGCG-------------
.......((.((((((...((((((((((((((((.((..((((..(((((((..(.(((((((...((((......))))...))))))).)..)))))))--..))))..)).))))..))))))...)))))).)))))).((....)))).------------- ( -54.80, z-score =  -2.53, R)
>droEre2.scaffold_4820 9268760 153 - 10470090
CGACCUAGUAGCCUAAUGCAGUUCCUCGAAAACUGCGUCUCUGAAGGGAAUGGAAAGGAGGAUGAGGAUCUCGAAAUGGAUACACAUCCUUCCGCCCAUCCU--GUUCAGGAACCCAAGCUUUUCGAUCUGGGACUUUUAGGAAGAAAUUGCCCG-------------
...........(((((...(((((((((((((((..((..(((((.((.((((...((((((((.(.((((......)))).).))))))))...)))).))--.)))))..))...)).)))))))...)))))).))))).............------------- ( -49.90, z-score =  -1.72, R)
>droAna3.scaffold_12911 1208923 147 - 5364042
CGUCCCAGUAGCUUGAUGCAGUUCCUCAAUCGUUGCGGAAGUGAACAGGACGAGGAGAUGGA--AGUGCCACAGAAUGGC----ACUCCUUGUGCUCGUGCU--GCACAAUCCCGCAAGAUUUUCGAACUGGGACCCGGGGGUACGAGUGUCGUA-------------
.((((((((.((.....))...((...((((.((((((...((..(((.(((((.(.(.(((--.((((((.....))))----))))).).).))))).))--)..))...))))))))))...)))))))))).......((((.....))))------------- ( -58.90, z-score =  -2.51, R)
>dp4.chr2 30417707 168 - 30794189
CGCCCCAGCAGCUUGAUGCAGUUUCUGAAGCUUGGCGACGAGGAUGAGAAGCUGAGCAAUGAUGGGGACAAGGAGAAUACUCCUUCUGCUCCUUCUCCUCCUCAGUCGCAAAGCUGCAGCGACAGCAUGAAGGUGUUUGAGGUGGGAACACAAAAAGCUGCGGAAUUC
...((((((..(((.((((.(((.(((.(((((.((((((((((.((((((..(((((....((....))(((((....)))))..))))))))))).))))).))))).))))).))).))).)))).)))((((((.......)))))).....)))).))..... ( -76.00, z-score =  -4.58, R)
>droPer1.super_7 1284675 168 - 4445127
CGCCCCAGCAGCUUGAUGCAGUUUCUGAAGCUUGGCGACGAGGAUGAGAAGCUGAGCAAUGAUGGGGACAAGGAGAAUGCUCCUUCUGCUCCUUCUCCUCCUCAGUCGCAAAGCUGCAGCGACAGCAUGAAGGUGUUUGAGGUGGGAACACAAAAAGCUGCGGAAUUC
...((((((..(((.((((.(((.(((.(((((.((((((((((.((((((..(((((....((....))(((((....)))))..))))))))))).))))).))))).))))).))).))).)))).)))((((((.......)))))).....)))).))..... ( -76.20, z-score =  -4.17, R)
>droWil1.scaffold_181130 10386413 138 + 16660200
CGUCCUAGCAGCGUAAGGCUGUUUCUGCAACUAUGCGGUGAGUUAAAGAGAGAAAAGGAUAGCUCUCAAACUCAGUUGCCUAGUCACAGCAAUAGCCAUAGG--UUUUUUCAGCUAGGAUGUCUUGGCCCUGCUGAUUAC----------------------------
((((((((((((.((.(((((((.(((..((((.((((((((((...(((((..........))))).)))))).)))).))))..))).))))))).)).)--))......)))))))))..(..((...))..)....---------------------------- ( -50.10, z-score =  -3.03, R)
>droVir3.scaffold_12855 8564047 139 - 10161210
----CAGGCAGAGCGAAA-GAUCCAGCCUGCAACUGGGUGACACUAACAUGGAGGAGGACAGGGCUCAGACCCAGGAGCCUUCUCCAUGUCAGUGUACCAGUCAGAGCAAUUACUUUGA--GCUGGGCCCGGAUGCUCGGCCCUAC----------------------
----.(((..((.(....-).))..(((.(((.((((((.(((((.((((((((((((.(.(((......))).)...)))))))))))).))))).((((((((((......))))))--.)))))))))).)))..))))))..---------------------- ( -66.50, z-score =  -4.65, R)
>consensus
CGGCCUAGCAGCCUAAUGCAGUUCCUCCAAAAUUGCGCCUCUGAAGAGAAUGAGAAGGAGGAUUCGCACAACGAAAUGGCUACUAAUCCUUCCGCCCAUUCU__GUUCAGGAACCCAAGCUUUUCGAUCUGGGACUUUUAGGAAGGAAUUGCGCG_____________
.......(((......)))..................................................................................................................................................... ( -0.63 =  -0.83 +   0.20)

alignment

secondary structure

dotplot

Window 1

Location	26,787,049 – 26,787,202
Length	153
Sequences	10
Columns	168
Reading direction	reverse
Mean pairwise identity	51.97
Shannon entropy	1.00040
G+C content	0.51591
Mean single sequence MFE	-56.56
Consensus MFE	0.00
Energy contribution	0.00
Covariance contribution	0.00
Combinations/Pair	0.00
Mean z-score	-2.83
Structure conservation index	-0.00
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.85
SVM RNA-class probability	0.833677
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26787049 153 - 27905053
-------------CGCGCAAUUCCUUCCUAAGAGUCCCAGAUCGAAAAGCUUGGGUUCCUGAAC--GGAAUGGGCGGAAGGAUUAGCAGCCAUUUCGUUGUGAGAAUCCUCCUCCUCAUUCCCUUCAGAGGGGCAAUUUUGUAGGAACUGCAUUAGGCUACUAGGCCG
-------------...(((.(((((.(..((..(((((.((((.((....)).)))).(((((.--((((((((.(((.(((((.(((((......)))))...)))))))).)).)))))).))))).)))))..))..).))))).)))....((((....)))). ( -60.10, z-score =  -3.12, R)
>droSim1.chr3R 26431359 153 - 27517382
-------------CGCGCAAUUCCUUCCUAAAAGUCCCAGAUCGAAAAGCUUUGGUUCCUGAAC--GGAAUGGGCGGAAGGAAUAGCAGCCAUUUCGUGGUGGGAAUCCUCCUCCUCAUUCCCUUCAGAGGCGCAAUUUUGUAGGAACUGCAUUAGACUACUAGGCCG
-------------.(((((.(((((...(((((((.((.(((((((....))))))).(((((.--((((((((.(((.(((......(((((...))))).....)))))).)).)))))).))))).)).))..))))).))))).))).((((....)))))).. ( -47.60, z-score =  -0.68, R)
>droSec1.super_4 5612108 153 - 6179234
-------------CGCGCAAUUCCUUCCUAAAAGUCCCAGAUCGAAAAGCUUUGGUUCCUGAAC--GGAAUGGGCGGAAGGAUUAGCAGCCAUUUCGUGGUGGGAAUCCUCCUCCUCAUUCCCUUCAGAGGCGCAAUUUUGUAGGAACUGCAUUAGACUACUAGGCCG
-------------.(((((.(((((...(((((((.((.(((((((....))))))).(((((.--((((((((.(((.(((((....(((((...)))))...)))))))).)).)))))).))))).)).))..))))).))))).))).((((....)))))).. ( -51.10, z-score =  -1.55, R)
>droYak2.chr3R 27714254 153 - 28832112
-------------CGCGCAAUUACUGCCCAAAAGUCCCAGAUCGAAAAGCUUGGGUUCCCGAGC--AGAAUGAGCGCAAGAAUUUGUAUCCAUUUCGAGAUCUGAAUCCUCCCUUUCAUUCCCUUCGGAGACGCAAGUUUCGAGGAACUGCAUUAGGCUGCUAGGUCG
-------------.(((((.....))).....(((.((...(((((..(((((.((..(((((.--.(((((((.(..((.((((..(((........)))..)))).))..).)))))))..)))))..)).)))))))))))).)))))....((((....)))). ( -42.70, z-score =  -0.48, R)
>droEre2.scaffold_4820 9268760 153 + 10470090
-------------CGGGCAAUUUCUUCCUAAAAGUCCCAGAUCGAAAAGCUUGGGUUCCUGAAC--AGGAUGGGCGGAAGGAUGUGUAUCCAUUUCGAGAUCCUCAUCCUCCUUUCCAUUCCCUUCAGAGACGCAGUUUUCGAGGAACUGCAUUAGGCUACUAGGUCG
-------------.((((...............))))..((((....(((((((((..(((((.--.(((((((.((.((((((.(.(((........))).).)))))).)).)))))))..)))))..))(((((((.....))))))).)))))))....)))). ( -52.96, z-score =  -2.16, R)
>droAna3.scaffold_12911 1208923 147 + 5364042
-------------UACGACACUCGUACCCCCGGGUCCCAGUUCGAAAAUCUUGCGGGAUUGUGC--AGCACGAGCACAAGGAGU----GCCAUUCUGUGGCACU--UCCAUCUCCUCGUCCUGUUCACUUCCGCAACGAUUGAGGAACUGCAUCAAGCUACUGGGACG
-------------((((.....)))).......((((((((((...((((((((((((.((.((--((.(((((.....(((((----(((((...))))))))--))......))))).)))).)).)))))))).))))...)))))((.....))....))))). ( -61.10, z-score =  -4.70, R)
>dp4.chr2 30417707 168 + 30794189
GAAUUCCGCAGCUUUUUGUGUUCCCACCUCAAACACCUUCAUGCUGUCGCUGCAGCUUUGCGACUGAGGAGGAGAAGGAGCAGAAGGAGUAUUCUCCUUGUCCCCAUCAUUGCUCAGCUUCUCAUCCUCGUCGCCAAGCUUCAGAAACUGCAUCAAGCUGCUGGGGCG
...(((((((((((...(((((.........)))))....((((.((..(((.(((((.(((((.(((((.((((((((((((((((((....))))))..........))))))..)))))).)))))))))).))))).)))..)).)))).))))))).)))).. ( -70.60, z-score =  -4.59, R)
>droPer1.super_7 1284675 168 + 4445127
GAAUUCCGCAGCUUUUUGUGUUCCCACCUCAAACACCUUCAUGCUGUCGCUGCAGCUUUGCGACUGAGGAGGAGAAGGAGCAGAAGGAGCAUUCUCCUUGUCCCCAUCAUUGCUCAGCUUCUCAUCCUCGUCGCCAAGCUUCAGAAACUGCAUCAAGCUGCUGGGGCG
...(((((((((((...(((((.........)))))....((((.((..(((.(((((.(((((.(((((.((((((((((((((((((....))))))..........))))))..)))))).)))))))))).))))).)))..)).)))).))))))).)))).. ( -69.60, z-score =  -4.06, R)
>droWil1.scaffold_181130 10386413 138 - 16660200
----------------------------GUAAUCAGCAGGGCCAAGACAUCCUAGCUGAAAAAA--CCUAUGGCUAUUGCUGUGACUAGGCAACUGAGUUUGAGAGCUAUCCUUUUCUCUCUUUAACUCACCGCAUAGUUGCAGAAACAGCCUUACGCUGCUAGGACG
----------------------------(((((((((((((........)))).))))).....--.....((((.((.(((..((((.((...((((((.(((((..(....)..)))))...))))))..)).))))..))).)).))))))))............ ( -44.20, z-score =  -2.62, R)
>droVir3.scaffold_12855 8564047 139 + 10161210
----------------------GUAGGGCCGAGCAUCCGGGCCCAGC--UCAAAGUAAUUGCUCUGACUGGUACACUGACAUGGAGAAGGCUCCUGGGUCUGAGCCCUGUCCUCCUCCAUGUUAGUGUCACCCAGUUGCAGGCUGGAUC-UUUCGCUCUGCCUG----
----------------------...((((.((((....((..(((((--(.........(((...((((((.((((((((((((((.((((....((((....)))).).))).))))))))))))))...)))))))))))))))..)-)...)))).)))).---- ( -65.60, z-score =  -4.33, R)
>consensus
_____________CGCGCAAUUCCUUCCUAAAAGUCCCAGAUCGAAAAGCUUGGGUUCCUGAAC__AGAAUGAGCGGAAGGAUUAGCAGCCAUUUCGUGGUGCGAAUCCUCCUCCUCAUUCCCUUCAGAGCCGCAAUGUUGGAGGAACUGCAUUAGGCUACUAGGCCG
........................................................................................................................................................................ (  0.00 =   0.00 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:58:41 2011