Locus 14925

Sequence ID	dm3.chrX
Location	16,375,989 – 16,376,089
Length	100
Max. P	0.999920

overview

Window 3

Location	16,375,989 – 16,376,089
Length	100
Sequences	11
Columns	103
Reading direction	forward
Mean pairwise identity	61.55
Shannon entropy	0.85023
G+C content	0.46320
Mean single sequence MFE	-25.67
Consensus MFE	-9.70
Energy contribution	-9.40
Covariance contribution	-0.30
Combinations/Pair	1.30
Mean z-score	-1.43
Structure conservation index	0.38
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.86
SVM RNA-class probability	0.972205
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16375989 100 + 22422827
CACUAGCCGAUCUACAAGAUAAUCCAGUAGAUCGCUGAACAAGAUUUGCGAUCUC-ACGCAGAGACACAAGCCGUUUGACAGGAAUGUGCCUAGGCAUAAG--
.....((((((((((..(.....)..)))))))...........((((((.....-.))))))(.((((..((........))..)))).)..))).....-- ( -27.00, z-score =  -2.34, R)
>droSim1.chrX 12587498 100 + 17042790
CACUAGCCGAUCUACAAGAUAAUCCAGUAGAUCGCUGAACAAGGUUUGCGAUCUC-ACGCGGAGACACAAGCCGUUUGACAGGAAUGUGCCUAGGCGUAGG--
..(((((((((((((..(.....)..)))))))(..((((..((((((.(.((((-.....))))).))))))))))..)(((......))).))).))).-- ( -31.90, z-score =  -2.24, R)
>droSec1.super_17 195526 100 + 1527944
CACUAGCCGAUCUACAAAAUAAUCCAGUAGAUCGCUGAACAAGGUUUGCGAUCUC-ACGCGGAGACACAAGCCGUUUGACAGGAAUGUGCCUAGGCAUAAG--
...((((.(((((((...........))))))))))).....((((((.(.((((-.....))))).))))))............(((((....)))))..-- ( -30.50, z-score =  -2.90, R)
>droYak2.chrX 10494941 100 + 21770863
CACUAGCCGAUCUACAAGAUAAUCCAGUAGAUCUCUGACCAGGGUUUGCGAUCUC-ACGCGGAGACACAAGCCGUUUGACAGGAAUGUGCCUAGGCAUAAG--
.....((((((((((..(.....)..)))))))((((...(.((((((.(.((((-.....))))).)))))).)....))))..........))).....-- ( -28.80, z-score =  -1.58, R)
>droEre2.scaffold_4690 8026642 100 - 18748788
CACUAGCCGAUCUACAAGAUAAUCUCGUAGAUCUCGGACUAAGGUUUGCGAUCCC-ACGCGGAGACACAAGCCGUUUGACAGGAAUGUGCCUAGGCAUAGG--
..(((((((((((((.((.....)).)))))))((((((...((((((.(.((((-....)).))).)))))))))))).(((......))).))).))).-- ( -33.40, z-score =  -2.73, R)
>droAna3.scaffold_13335 1773120 96 - 3335858
CAAUUAACGAUCUACAAUGGAA--CAGAGAAUUAC-GUUUAGAA--UGCGAUCUCUACGCGAAGACACAAGCUGUUUGACUAGAAUGUGCCUGGGCAUAGA--
..........((((...(.(((--(((.......(-((.((((.--.......)))).)))..........)))))).).)))).(((((....)))))..-- ( -17.53, z-score =   0.08, R)
>dp4.chrXL_group1e 9478425 85 - 12523060
------------CACAAAGUGUUCUACGCUGUAACUG---GAGUUUUGCCAGCUU-AGGCAGAGACACAGGCCGUUUGACUGGAGUGUGCCUAGGCCUAAG--
------------.....((((.....))))....(((---(.......))))(((-((((..((.((((..(((......)))..)))).))..)))))))-- ( -27.60, z-score =  -0.74, R)
>droWil1.scaffold_181096 5794900 95 + 12416693
--------UACUAAAAAAUGGAUAUACCCUAAACUAAACUGGGCCAACAUACAUUAGGCCCUAGACACAAAUCGUUUGACUGAAAUGUGCCUAGGCCUAAAUG
--------..........(((.....(((...........)))))).......(((((((.(((.((((..(((......)))..)))).))))))))))... ( -22.50, z-score =  -3.19, R)
>droMoj3.scaffold_6359 3297206 95 + 4525533
-UUGAAAUUGUUUUGCAAUU--UUUACAGGGU-AUUCCAUGUGCUUUUGCG-CAU-AGGCAAAGACACAAACCGUUUGACUGGAAUGUGCCUAAGCUUAGG--
-..(((((((.....)))))--)).....((.-...)).(((((....)))-))(-((((..((.((((..(((......)))..)))).))..)))))..-- ( -22.30, z-score =  -0.33, R)
>droGri2.scaffold_14853 3232060 89 - 10151454
-------UGAUUCC--AAUUGAUCUGCA-AAU-AUAGCGAGUGCACUUCUGACUU-AAGCAAAGACACACACCGUUUGACUGAAGUGUGCCUGAGCUUAGG--
-------.......--....((..((((-...-........))))..))...(((-((((..((.(((((..((......))..))))).))..)))))))-- ( -18.90, z-score =  -0.24, R)
>droVir3.scaffold_12970 2083277 95 + 11907090
----UGCCAAUUGUUGGACUCUUAUACACAAU-ACAGGGAGUGCCCUUUUGCCAU-AAGCAAGGACACAAACCGUUUGACUGGAGUGUGCCCAAGCUUAGU--
----((.(((..(..((((((((.........-...)))))).)))..))).))(-((((..((.((((..(((......)))..)))).))..)))))..-- ( -21.90, z-score =   0.49, R)
>consensus
CACUAGCCGAUCUACAAAAUAAUCUAGUAGAUCACUGAACAAGCUUUGCGAUCUC_ACGCAGAGACACAAGCCGUUUGACUGGAAUGUGCCUAGGCAUAGG__
..........................................................((..((.((((..((........))..)))).))..))....... ( -9.70 =  -9.40 +  -0.30)

alignment

secondary structure

dotplot

Window 4

Location	16,375,989 – 16,376,089
Length	100
Sequences	11
Columns	103
Reading direction	reverse
Mean pairwise identity	61.55
Shannon entropy	0.85023
G+C content	0.46320
Mean single sequence MFE	-30.25
Consensus MFE	-15.26
Energy contribution	-14.47
Covariance contribution	-0.79
Combinations/Pair	1.54
Mean z-score	-2.65
Structure conservation index	0.50
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	4.90
SVM RNA-class probability	0.999920
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16375989 100 - 22422827
--CUUAUGCCUAGGCACAUUCCUGUCAAACGGCUUGUGUCUCUGCGU-GAGAUCGCAAAUCUUGUUCAGCGAUCUACUGGAUUAUCUUGUAGAUCGGCUAGUG
--(((((((..(((((((..((........))..)))))))..))))-)))................((((((((((.((.....)).))))))).))).... ( -34.30, z-score =  -3.29, R)
>droSim1.chrX 12587498 100 - 17042790
--CCUACGCCUAGGCACAUUCCUGUCAAACGGCUUGUGUCUCCGCGU-GAGAUCGCAAACCUUGUUCAGCGAUCUACUGGAUUAUCUUGUAGAUCGGCUAGUG
--..(((((..(((((((..((........))..)))))))..))))-)(((((((............)))))))(((((...(((.....)))...))))). ( -33.30, z-score =  -2.73, R)
>droSec1.super_17 195526 100 - 1527944
--CUUAUGCCUAGGCACAUUCCUGUCAAACGGCUUGUGUCUCCGCGU-GAGAUCGCAAACCUUGUUCAGCGAUCUACUGGAUUAUUUUGUAGAUCGGCUAGUG
--(((((((..(((((((..((........))..)))))))..))))-)))................((((((((((...........))))))).))).... ( -32.10, z-score =  -2.60, R)
>droYak2.chrX 10494941 100 - 21770863
--CUUAUGCCUAGGCACAUUCCUGUCAAACGGCUUGUGUCUCCGCGU-GAGAUCGCAAACCCUGGUCAGAGAUCUACUGGAUUAUCUUGUAGAUCGGCUAGUG
--(((((((..(((((((..((........))..)))))))..))))-)))..........((((((...(((((((.((.....)).))))))))))))).. ( -36.50, z-score =  -3.32, R)
>droEre2.scaffold_4690 8026642 100 + 18748788
--CCUAUGCCUAGGCACAUUCCUGUCAAACGGCUUGUGUCUCCGCGU-GGGAUCGCAAACCUUAGUCCGAGAUCUACGAGAUUAUCUUGUAGAUCGGCUAGUG
--(((((((..(((((((..((........))..)))))))..))))-)))..........((((((...((((((((((.....)))))))))))))))).. ( -40.40, z-score =  -4.55, R)
>droAna3.scaffold_13335 1773120 96 + 3335858
--UCUAUGCCCAGGCACAUUCUAGUCAAACAGCUUGUGUCUUCGCGUAGAGAUCGCA--UUCUAAAC-GUAAUUCUCUG--UUCCAUUGUAGAUCGUUAAUUG
--(((((((..(((((((..((........))..)))))))..)))))))(((((((--.....(((-(........))--))....))).))))........ ( -24.20, z-score =  -3.00, R)
>dp4.chrXL_group1e 9478425 85 + 12523060
--CUUAGGCCUAGGCACACUCCAGUCAAACGGCCUGUGUCUCUGCCU-AAGCUGGCAAAACUC---CAGUUACAGCGUAGAACACUUUGUG------------
--(((((((..(((((((..((........))..)))))))..))))-)))((((.......)---))).(((((.((.....)).)))))------------ ( -26.10, z-score =  -1.53, R)
>droWil1.scaffold_181096 5794900 95 - 12416693
CAUUUAGGCCUAGGCACAUUUCAGUCAAACGAUUUGUGUCUAGGGCCUAAUGUAUGUUGGCCCAGUUUAGUUUAGGGUAUAUCCAUUUUUUAGUA--------
...(((((((((((((((..((........))..)))))))).)))))))((.((((..((((...........)))))))).))..........-------- ( -29.50, z-score =  -3.51, R)
>droMoj3.scaffold_6359 3297206 95 - 4525533
--CCUAAGCUUAGGCACAUUCCAGUCAAACGGUUUGUGUCUUUGCCU-AUG-CGCAAAAGCACAUGGAAU-ACCCUGUAAA--AAUUGCAAAACAAUUUCAA-
--.....((..(((((((..((........))..)))))))..))((-(((-.((....)).)))))...-.........(--(((((.....))))))...- ( -24.50, z-score =  -2.34, R)
>droGri2.scaffold_14853 3232060 89 + 10151454
--CCUAAGCUCAGGCACACUUCAGUCAAACGGUGUGUGUCUUUGCUU-AAGUCAGAAGUGCACUCGCUAU-AUU-UGCAGAUCAAUU--GGAAUCA-------
--(((((((..((((((((.((........)).))))))))..))))-).....((..((((........-...-))))..))....--)).....------- ( -22.30, z-score =  -0.78, R)
>droVir3.scaffold_12970 2083277 95 - 11907090
--ACUAAGCUUGGGCACACUCCAGUCAAACGGUUUGUGUCCUUGCUU-AUGGCAAAAGGGCACUCCCUGU-AUUGUGUAUAAGAGUCCAACAAUUGGCA----
--..(((((..(((((((..((........))..)))))))..))))-)((.(((...((.((((..(((-((...))))).)))))).....))).))---- ( -29.50, z-score =  -1.44, R)
>consensus
__CCUAUGCCUAGGCACAUUCCAGUCAAACGGCUUGUGUCUCCGCGU_GAGAUCGCAAACCUUAUUCAGUGAUCUACUAGAUUAUUUUGUAGAUCGGCUAGUG
.....((((..(((((((..((........))..)))))))..))))........................................................ (-15.26 = -14.47 +  -0.79)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:49:38 2011