Locus 15027

Sequence ID	dm3.chrX
Location	17,040,609 – 17,040,718
Length	109
Max. P	0.997672

overview

Window 8

Location	17,040,609 – 17,040,718
Length	109
Sequences	11
Columns	114
Reading direction	forward
Mean pairwise identity	61.91
Shannon entropy	0.75938
G+C content	0.37023
Mean single sequence MFE	-19.79
Consensus MFE	-9.67
Energy contribution	-8.92
Covariance contribution	-0.75
Combinations/Pair	1.39
Mean z-score	-0.42
Structure conservation index	0.49
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.47
SVM RNA-class probability	0.710006
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 17040609 109 + 22422827
AACCAAGGUACCGCAUAUGCUUUAUAAUGGUUUUG-UAAUGUGGUUUUAAGUUCCCGGAGAACAAGAAGAGGCUUUGAU-AUCUUCAAGCACUAGGACA---UUAAAACCUUGU
...(((((((((((((.(((..............)-)))))))))(((((..(((..(.(.....(((((.........-.)))))...).)..)))..---))))))))))). ( -24.84, z-score =  -0.76, R)
>droSec1.super_17 881707 109 + 1527944
CACCAAGGUACCGCAUAUGCUUUAUAAUGGUUUUG-UAGUGUGGUUUUAAAUUCCAGGAAAACAAGAAGAGGAUUUUAU-AUCUUCAGGCACUAGGACA---UUAAAACCUUGG
..(((((((...((....))....(((((...((.-((((((.(((((..........))))).....((((((.....-))))))..)))))).))))---)))..))))))) ( -28.00, z-score =  -2.16, R)
>droYak2.chrX 15650330 109 + 21770863
CACCAAGGUACCGCAUAUGCUUUAUAAUGGUUUUG-UCGUGUGGUUUUAAGUUCCAGGAGAACGAGAAGAGGCUUUGUG-AUCUUCAGGCACUAGGAUA---UUAAAACCUUGG
..((((((((((((((..(((.......)))....-..)))))))((..(((.((.(((((.((.((((...)))).))-.))))).)).)))..))..---.....))))))) ( -28.00, z-score =  -0.91, R)
>droEre2.scaffold_4690 7387317 101 + 18748788
-------GUACCGCA-AUGCUUUAUAGUGGUUUUG-UCGUGUGGUUUUAAGUUCCAGGAGAACGAGAAGAGGCUUUGUU-AUCUUCAGGCACUAGGAUA---UUAAAACCUUGG
-------.(((.(((-(.(((.......))).)))-).))).((((((((..(((.((.(.....(((((.........-.)))))...).)).)))..---)))))))).... ( -21.60, z-score =   0.39, R)
>droVir3.scaffold_12970 9771805 93 + 11907090
-----------AACUAAAUAACUGGAGUUGAAUUGCGGUUGUAGUUUCAAGUUCCAAGAGAGUAGGAAGAGUAG---UG---CUUCGAACACUAGGAUA---UUGAAACAGAA-
-----------......(((((((.(((...))).))))))).(((((((..(((...((.((..((((.....---..---))))..)).)).)))..---)))))))....- ( -21.70, z-score =  -1.56, R)
>droMoj3.scaffold_6473 5146052 89 - 16943266
-----------AGCCAAAAUACUCGAUUUGUUUU-CAUUUGUAGUUUCAAGUUCCAAGAGAGUAAGAAGAGUUG---CG---CUUCAGACACUAGGAUA---UUGAAACA----
-----------.......................-........(((((((..(((...((.((..((((.....---..---))))..)).)).)))..---))))))).---- ( -16.20, z-score =  -0.33, R)
>droGri2.scaffold_14853 7080832 90 - 10151454
----------------AUUAAUUAUGAUUAAUGUGCAAUUGUCGUUUCAAGUUCCAAGAGAGUAGGAAGAGGAG---UGUCGCUUCAAACACUAGGAUA---UUGAAACCAA--
----------------.........(((.(((.....))))))(((((((..(((...((.((..((((.((..---..)).))))..)).)).)))..---)))))))...-- ( -16.80, z-score =  -0.47, R)
>droSim1.chrX 13221348 85 + 17042790
---------------------GAAUGCUUUCUUUC-UAAUGUAGUCUUAAAUUCCAGGAGAGCGGGAAGUGGUUUAAU----CUUCAAGCACUAAUAUAA--UUAACACUUAU-
---------------------...(((((((((..-.(((..........)))..)))))))))...((((.((....----....)).)))).......--...........- ( -11.00, z-score =   0.96, R)
>droAna3.scaffold_13248 2278755 97 + 4840945
--------------UUAAACAUUAUAAUAUUGAAGCUAUUGUGGCUUUAGUUUCCAUGAGAGCAAGAAGAGGCUAUAU---CUUUCAAGCACAAGGAUAAUAUUAAAACCUAUU
--------------..........(((((((((((((.....))))))....(((.((...((..(((((.......)---))))...)).)).))).)))))))......... ( -14.70, z-score =   0.33, R)
>dp4.chrXL_group1e 8801468 92 - 12523060
------------------AUAUCCGAAUUGG-UUGCAGGUGUAGUUUUAAGUUCCAAGAGAGCAAGAUGAGGGGAUAUGUAUCGUCAAGCACUAGGAUA---UUAAAACUUGUG
------------------((((((....((.-...))(((((........((((.....))))..(((((...........)))))..))))).)))))---)........... ( -16.60, z-score =   0.32, R)
>droPer1.super_17 1272345 92 - 1930428
------------------AUAUCCGAAUUUG-UUGCAGGUGUAGUUUUAAGUUCCAAGAGAGCAAGAUGAGGGGAUAUGUAUCGUCAAGCACUAGGAUA---UUAAAACUUGUG
------------------(((((((((((((-..((.......))..)))))))....((.((..(((((...........)))))..)).)).)))))---)........... ( -18.20, z-score =  -0.39, R)
>consensus
_____________C__AUACAUUAUAAUUGUUUUGCUAGUGUAGUUUUAAGUUCCAAGAGAGCAAGAAGAGGCUUUAUG_AUCUUCAAGCACUAGGAUA___UUAAAACCUAGG
..........................................((((((((..(((.((.(.....((((.............))))...).)).))).....)))))))).... ( -9.67 =  -8.92 +  -0.75)

alignment

secondary structure

dotplot

Window 9

Location	17,040,609 – 17,040,718
Length	109
Sequences	11
Columns	114
Reading direction	reverse
Mean pairwise identity	61.91
Shannon entropy	0.75938
G+C content	0.37023
Mean single sequence MFE	-17.01
Consensus MFE	-11.95
Energy contribution	-11.35
Covariance contribution	-0.61
Combinations/Pair	1.37
Mean z-score	-1.24
Structure conservation index	0.70
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.15
SVM RNA-class probability	0.997672
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 17040609 109 - 22422827
ACAAGGUUUUAA---UGUCCUAGUGCUUGAAGAU-AUCAAAGCCUCUUCUUGUUCUCCGGGAACUUAAAACCACAUUA-CAAAACCAUUAUAAAGCAUAUGCGGUACCUUGGUU
....((((((((---..(((..(.((..(((((.-.........)))))..))...)..)))..))))))))......-...(((((...((..((....))..))...))))) ( -26.50, z-score =  -2.35, R)
>droSec1.super_17 881707 109 - 1527944
CCAAGGUUUUAA---UGUCCUAGUGCCUGAAGAU-AUAAAAUCCUCUUCUUGUUUUCCUGGAAUUUAAAACCACACUA-CAAAACCAUUAUAAAGCAUAUGCGGUACCUUGGUG
....((((((((---..(((..(.((..(((((.-.........)))))..))...)..)))..))))))))......-....((((...((..((....))..))...)))). ( -23.60, z-score =  -2.13, R)
>droYak2.chrX 15650330 109 - 21770863
CCAAGGUUUUAA---UAUCCUAGUGCCUGAAGAU-CACAAAGCCUCUUCUCGUUCUCCUGGAACUUAAAACCACACGA-CAAAACCAUUAUAAAGCAUAUGCGGUACCUUGGUG
....((((((((---..(((.((.((..(((((.-.........)))))..)).))...)))..))))))))......-....((((...((..((....))..))...)))). ( -23.20, z-score =  -1.77, R)
>droEre2.scaffold_4690 7387317 101 - 18748788
CCAAGGUUUUAA---UAUCCUAGUGCCUGAAGAU-AACAAAGCCUCUUCUCGUUCUCCUGGAACUUAAAACCACACGA-CAAAACCACUAUAAAGCAU-UGCGGUAC-------
....((((((((---..(((.((.((..(((((.-.........)))))..)).))...)))..))))))))......-....(((.(..........-.).)))..------- ( -18.50, z-score =  -1.32, R)
>droVir3.scaffold_12970 9771805 93 - 11907090
-UUCUGUUUCAA---UAUCCUAGUGUUCGAAG---CA---CUACUCUUCCUACUCUCUUGGAACUUGAAACUACAACCGCAAUUCAACUCCAGUUAUUUAGUU-----------
-....(((((((---.....((((((.....)---))---)))...((((.........)))).)))))))................................----------- ( -13.80, z-score =  -1.24, R)
>droMoj3.scaffold_6473 5146052 89 + 16943266
----UGUUUCAA---UAUCCUAGUGUCUGAAG---CG---CAACUCUUCUUACUCUCUUGGAACUUGAAACUACAAAUG-AAAACAAAUCGAGUAUUUUGGCU-----------
----.(((((((---..(((.((.((..((((---..---.....))))..))...)).)))..)))))))........-....((((........))))...----------- ( -15.40, z-score =  -1.04, R)
>droGri2.scaffold_14853 7080832 90 + 10151454
--UUGGUUUCAA---UAUCCUAGUGUUUGAAGCGACA---CUCCUCUUCCUACUCUCUUGGAACUUGAAACGACAAUUGCACAUUAAUCAUAAUUAAU----------------
--...(((((((---..(((.((.((..((((.(...---...).))))..))...)).)))..)))))))...........................---------------- ( -15.90, z-score =  -1.87, R)
>droSim1.chrX 13221348 85 - 17042790
-AUAAGUGUUAA--UUAUAUUAGUGCUUGAAG----AUUAAACCACUUCCCGCUCUCCUGGAAUUUAAGACUACAUUA-GAAAGAAAGCAUUC---------------------
-...(((.((((--...((..((.((..((((----.........))))..)).))..))....)))).)))......-..............--------------------- (  -9.30, z-score =   0.80, R)
>droAna3.scaffold_13248 2278755 97 - 4840945
AAUAGGUUUUAAUAUUAUCCUUGUGCUUGAAAG---AUAUAGCCUCUUCUUGCUCUCAUGGAAACUAAAGCCACAAUAGCUUCAAUAUUAUAAUGUUUAA--------------
....(((((((......(((.((.((..(((.(---(.......)))))..))...)).)))...)))))))............................-------------- ( -13.70, z-score =   0.35, R)
>dp4.chrXL_group1e 8801468 92 + 12523060
CACAAGUUUUAA---UAUCCUAGUGCUUGACGAUACAUAUCCCCUCAUCUUGCUCUCUUGGAACUUAAAACUACACCUGCAA-CCAAUUCGGAUAU------------------
....((((((((---..(((.((.((..((.((...........)).))..))...)).)))..))))))))..........-((.....))....------------------ ( -14.00, z-score =  -1.70, R)
>droPer1.super_17 1272345 92 + 1930428
CACAAGUUUUAA---UAUCCUAGUGCUUGACGAUACAUAUCCCCUCAUCUUGCUCUCUUGGAACUUAAAACUACACCUGCAA-CAAAUUCGGAUAU------------------
....((((((((---..(((.((.((..((.((...........)).))..))...)).)))..))))))))..........-.............------------------ ( -13.20, z-score =  -1.40, R)
>consensus
CAAAGGUUUUAA___UAUCCUAGUGCUUGAAGAU_CAUAAAGCCUCUUCUUGCUCUCCUGGAACUUAAAACCACACUAGCAAAACAAUUAUAAUGCAU__G_____________
....((((((((.....(((.((.((..((((.............))))..)).))...)))..)))))))).......................................... (-11.95 = -11.35 +  -0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:51:38 2011