Locus 2722

Sequence ID dm3.chr2L
Location 21,522,584 – 21,522,674
Length 90
Max. P 0.998597
window3738 window3739

overview

Window 8

Location 21,522,584 – 21,522,674
Length 90
Sequences 12
Columns 110
Reading direction forward
Mean pairwise identity 56.59
Shannon entropy 0.83482
G+C content 0.30464
Mean single sequence MFE -18.64
Consensus MFE -5.65
Energy contribution -5.65
Covariance contribution -0.00
Combinations/Pair 1.40
Mean z-score -2.78
Structure conservation index 0.30
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.39
SVM RNA-class probability 0.998537
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 21522584 90 + 23011544
------AAAAUUUUAGAUUU-AUGUUUUAUAGAUCUGAAAUUU--GUUUAAACAA--GUCCUUUUCAGGGCUACAACGUUCCGUUGCAAGAGAAAAAAACU---------
------.(((((((((((((-(((...))))))))))))))))--((((.....(--(((((....)))))).(((((...)))))..........)))).--------- ( -22.60, z-score =  -3.49, R)
>droSim1.chrU 36846 90 + 15797150
------AAAAAUUUAGAUUU-AUGAUUUAUAGAUCUGAAAUUU--GUUUAUACAA--GUCCUUUUCAGGGCUACAACGUUCUUUUGCAAGAGAAAAAAACU---------
------.....(((((((((-(((...))))))))))))....--((((.....(--(((((....))))))......((((((....))))))..)))).--------- ( -18.60, z-score =  -2.25, R)
>droSec1.super_402 2902 90 + 12115
------AAAACUUUAGAUUU-AUGAUUUAUAGAUCUGAAAUUU--GUUUAUACAA--GUCCUUUUCAGGGCUACAACGUUCUGUUGCAAGAGAAAAAAACU---------
------.(((.(((((((((-(((...)))))))))))).)))--((((.....(--(((((....)))))).((((.....))))..........)))).--------- ( -17.70, z-score =  -1.60, R)
>droYak2.chrU 21897419 82 + 28119190
-------------AAAAUUU-UAGAUUUCAACAUCUGAAAUUU--GUUUAUACAA--GCCCUUUUCAGGGCUACAACGAUUCGUUGCAAGAGAAAAAACU----------
-------------.((((((-(((((......)))))))))))--((((.....(--(((((....)))))).(((((...))))).........)))).---------- ( -20.90, z-score =  -3.89, R)
>droEre2.scaffold_4583 7495 81 - 11978
-------------AAAAUUU-UAGAUUUCUAGAUCUGAAAUUU--GUCUAAACAA--GCCCUUUUCAGGGCUACAACAUUCACUUGCAAGAGAAAAAAA-----------
-------------.((((((-((((((....))))))))))))--.........(--(((((....))))))......(((.((....)).))).....----------- ( -18.90, z-score =  -2.85, R)
>droAna3.scaffold_13030 44327 84 - 47400
-------------GAAAUUU-UAGAUUUCGAAAUCUAAAAUUA--AAUUAAACAA--GCCCUUUUCAGGGCUACAAGA-UAUGUUUUAAAGAGAAAGAAAUUA-------
-------------..(((((-((((((....))))))))))).--.........(--(((((....))))))......-........................------- ( -16.90, z-score =  -2.74, R)
>dp4.Unknown_singleton_1517 10427 92 + 24252
-------------GAAAUUU-UAGAUGUAUCCGUCUGAAAUUG--AUUUAAACAA--GCCCUUUUCAGGGCUACAAAACUAUAUUCAAAAGAGAUACAAAUUAUCGAGCC
-------------..(((((-((((((....))))))))))).--.........(--(((((....))))))....................((((.....))))..... ( -19.80, z-score =  -2.98, R)
>droPer1.super_0 3279948 92 + 11822988
-------------GAAAUUU-UAGAUGUAUCCGUCUGAAAUUG--AUUUAAACAA--GCCCUUUUCAGGGCUACAAAACUAUAUUCAAAAGAGAUACAAAUUAUCGAGCC
-------------..(((((-((((((....))))))))))).--.........(--(((((....))))))....................((((.....))))..... ( -19.80, z-score =  -2.98, R)
>droWil1.scaffold_181036 31123 89 + 110856
AUUGAAAAAAUUUUAGAUAU-CGAAUACGAAAAUCUAAAAUUUU-ACUUAAACAC--AGCCAGGUCGGCGCGUUAAGUUUCAGCGUUAAGCGU-----------------
..((((((((((((((((.(-((....)))..))))))))))))-((((((....--.(((.....)))...))))))))))((.....))..----------------- ( -22.00, z-score =  -2.86, R)
>droVir3.scaffold_13047 1623303 86 + 19223366
--------------GCAUAUGCAAAUUUCUAAUAAUGAAAUUUGUUUUCCUACAAA-GCCCUUUUAAGGGCUACAAAUACGAUUUUCUAAGAGAAAGAAUU---------
--------------......(((((((((.......)))))))))..........(-(((((....))))))..........(((((.....)))))....--------- ( -18.50, z-score =  -2.77, R)
>droMoj3.scaffold_6540 26892971 79 - 34148556
---------------------GAAUUUCAAAACUAUGAAAUUCGCAAUUAAUCAAA-GUCCUUUUCAGGACUACUAUUACAUAUUUCUUAGAGAAAAAAUA---------
---------------------((((((((......))))))))............(-(((((....))))))...........((((.....)))).....--------- ( -15.30, z-score =  -3.66, R)
>anoGam1.chr2L 35944003 82 - 48795086
--------------------CAGCAUUGCAAUAACGCUCUCUUGGUUCCAAGCAACAGUCCUUUUCAGGACUACAAAUCGAAUCAUUCAAGAACUUCAUCAU--------
--------------------.......((......))(((..((((((........((((((....)))))).......))))))....)))..........-------- ( -12.66, z-score =  -1.27, R)
>consensus
_____________UAAAUUU_UAGAUUUAUAAAUCUGAAAUUU__AUUUAAACAA__GCCCUUUUCAGGGCUACAACAUUAUGUUGCAAAGAAAAAAAACU_________
.........................................................(((((....)))))....................................... ( -5.65 =  -5.65 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,522,584 – 21,522,674
Length 90
Sequences 12
Columns 110
Reading direction reverse
Mean pairwise identity 56.59
Shannon entropy 0.83482
G+C content 0.30464
Mean single sequence MFE -20.14
Consensus MFE -5.92
Energy contribution -6.18
Covariance contribution 0.26
Combinations/Pair 1.40
Mean z-score -2.86
Structure conservation index 0.29
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.41
SVM RNA-class probability 0.998597
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 21522584 90 - 23011544
---------AGUUUUUUUCUCUUGCAACGGAACGUUGUAGCCCUGAAAAGGAC--UUGUUUAAAC--AAAUUUCAGAUCUAUAAAACAU-AAAUCUAAAAUUUU------
---------((((((((((..((((((((...))))))))....)))))))))--).........--((((((.((((.(((.....))-).)))).)))))).------ ( -18.30, z-score =  -2.46, R)
>droSim1.chrU 36846 90 - 15797150
---------AGUUUUUUUCUCUUGCAAAAGAACGUUGUAGCCCUGAAAAGGAC--UUGUAUAAAC--AAAUUUCAGAUCUAUAAAUCAU-AAAUCUAAAUUUUU------
---------.(((((((((....).)))))))).((((((..((((((.....--((((....))--)).))))))..)))))).....-..............------ ( -13.90, z-score =  -1.20, R)
>droSec1.super_402 2902 90 - 12115
---------AGUUUUUUUCUCUUGCAACAGAACGUUGUAGCCCUGAAAAGGAC--UUGUAUAAAC--AAAUUUCAGAUCUAUAAAUCAU-AAAUCUAAAGUUUU------
---------((((((((((..(((((((.....)))))))....)))))))))--).........--((((((.((((.(((.....))-).)))).)))))).------ ( -17.50, z-score =  -2.23, R)
>droYak2.chrU 21897419 82 - 28119190
----------AGUUUUUUCUCUUGCAACGAAUCGUUGUAGCCCUGAAAAGGGC--UUGUAUAAAC--AAAUUUCAGAUGUUGAAAUCUA-AAAUUUU-------------
----------.((((...(...(((((((...)))))))(((((....)))))--..)...))))--((((((.((((......)))).-)))))).------------- ( -22.40, z-score =  -3.82, R)
>droEre2.scaffold_4583 7495 81 + 11978
-----------UUUUUUUCUCUUGCAAGUGAAUGUUGUAGCCCUGAAAAGGGC--UUGUUUAGAC--AAAUUUCAGAUCUAGAAAUCUA-AAAUUUU-------------
-----------.....(((.((....)).)))((((..((((((....)))))--)......)))--)(((((.((((......)))).-)))))..------------- ( -16.90, z-score =  -1.15, R)
>droAna3.scaffold_13030 44327 84 + 47400
-------UAAUUUCUUUCUCUUUAAAACAUA-UCUUGUAGCCCUGAAAAGGGC--UUGUUUAAUU--UAAUUUUAGAUUUCGAAAUCUA-AAAUUUC-------------
-------.................(((((..-......((((((....)))))--))))))....--.(((((((((((....))))))-)))))..------------- ( -19.40, z-score =  -4.06, R)
>dp4.Unknown_singleton_1517 10427 92 - 24252
GGCUCGAUAAUUUGUAUCUCUUUUGAAUAUAGUUUUGUAGCCCUGAAAAGGGC--UUGUUUAAAU--CAAUUUCAGACGGAUACAUCUA-AAAUUUC-------------
............(((((((..((((((....((((...((((((....)))))--).....))))--....)))))).)))))))....-.......------------- ( -23.50, z-score =  -3.17, R)
>droPer1.super_0 3279948 92 - 11822988
GGCUCGAUAAUUUGUAUCUCUUUUGAAUAUAGUUUUGUAGCCCUGAAAAGGGC--UUGUUUAAAU--CAAUUUCAGACGGAUACAUCUA-AAAUUUC-------------
............(((((((..((((((....((((...((((((....)))))--).....))))--....)))))).)))))))....-.......------------- ( -23.50, z-score =  -3.17, R)
>droWil1.scaffold_181036 31123 89 - 110856
-----------------ACGCUUAACGCUGAAACUUAACGCGCCGACCUGGCU--GUGUUUAAGU-AAAAUUUUAGAUUUUCGUAUUCG-AUAUCUAAAAUUUUUUCAAU
-----------------..((.....))((((((((((((((((.....))).--))).))))))-((((((((((((..(((....))-).)))))))))))))))).. ( -24.60, z-score =  -4.16, R)
>droVir3.scaffold_13047 1623303 86 - 19223366
---------AAUUCUUUCUCUUAGAAAAUCGUAUUUGUAGCCCUUAAAAGGGC-UUUGUAGGAAAACAAAUUUCAUUAUUAGAAAUUUGCAUAUGC--------------
---------..((((.......))))..((.(((....((((((....)))))-)..))).))...((((((((.......)))))))).......-------------- ( -19.20, z-score =  -2.42, R)
>droMoj3.scaffold_6540 26892971 79 + 34148556
---------UAUUUUUUCUCUAAGAAAUAUGUAAUAGUAGUCCUGAAAAGGAC-UUUGAUUAAUUGCGAAUUUCAUAGUUUUGAAAUUC---------------------
---------.....((((.(((.(((((.(((((((((((((((....)))))-)...))).)))))).))))).)))....))))...--------------------- ( -20.10, z-score =  -3.80, R)
>anoGam1.chr2L 35944003 82 + 48795086
--------AUGAUGAAGUUCUUGAAUGAUUCGAUUUGUAGUCCUGAAAAGGACUGUUGCUUGGAACCAAGAGAGCGUUAUUGCAAUGCUG--------------------
--------..(((((.((((((....(.(((((.(..(((((((....)))))))..).))))).)...)))))).))))).........-------------------- ( -22.40, z-score =  -2.70, R)
>consensus
_________AGUUUUUUUCCCUUGAAACAGAAAGUUGUAGCCCUGAAAAGGGC__UUGUUUAAAC__AAAUUUCAGAUCUAUAAAUCUA_AAAUUUA_____________
.......................................(((((....)))))......................................................... ( -5.92 =  -6.18 +   0.26)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:56:37 2011