Locus 10294

Sequence ID dm3.chr3R
Location 12,762,986 – 12,763,121
Length 135
Max. P 0.917317
window14156 window14157

overview

Window 6

Location 12,762,986 – 12,763,095
Length 109
Sequences 11
Columns 117
Reading direction forward
Mean pairwise identity 84.39
Shannon entropy 0.32155
G+C content 0.27536
Mean single sequence MFE -22.14
Consensus MFE -13.47
Energy contribution -13.24
Covariance contribution -0.24
Combinations/Pair 1.24
Mean z-score -2.37
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.26
SVM RNA-class probability 0.917317
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12762986 109 + 27905053
GGAAGAAAUAGAGCUAUAGCUAUAAAAAGAAUUUCUUCC-AUUUUUAACGAUUCACC-------AAUUUGAAUAAGUUAAUUAACAAAAUUAAUAUUCAAAUGGGUUUAUGGCCGAA
(((((((((..(((....))).........)))))))))-........(.((..(((-------.((((((((..(((((((.....))))))))))))))).)))..)).)..... ( -23.90, z-score =  -3.19, R)
>droPer1.super_0 11615571 105 + 11822988
----AGGAAAAACGCAGAGCCAUAAAAAGAAUUUCUUCA-AUUUUUAACGAUUCCCA-------AAUUUGAAUAAGUUAAUUAACAAAAUUAAUAUUCAAAUAGGUUUAUGGUCGCG
----........(((.((.((((((((((((((.....)-))))))........((.-------.((((((((..(((((((.....))))))))))))))).)))))))))))))) ( -19.90, z-score =  -2.63, R)
>droAna3.scaffold_13340 16561566 109 - 23697760
GGAGGGAAUAGAGCGAUAGCCAUAAAAAGAAUUUCUUCC-AUUUUUAACGAUUCUUG-------AAUUUGAAUAAGUUAAUUAACAAAAUUAAUAUUCAAAUGGGUUUAUGGCCGAA
..................(((((((((((((((......-.........))))))).-------.((((((((..(((((((.....)))))))))))))))...)))))))).... ( -19.76, z-score =  -0.75, R)
>droEre2.scaffold_4770 8876787 109 - 17746568
GGAAGAAAUAGAGCUAUAGCUAUAAAAAGAAUUUCUUCC-AUUUUUAACGAUUCCCC-------AAUUUGAAUAAGUUAAUUAACAAAAUUAAUAUUCAAAUGGGUUUAUGGCCGAA
(((((((((..(((....))).........)))))))))-..............(((-------(.(((((((..(((((((.....))))))))))))))))))............ ( -24.20, z-score =  -2.88, R)
>droYak2.chr3R 17206937 109 - 28832112
GGAAGAAAUAGAGCUAUAGCUAUAAAAAGAAUUUCUUCC-AUUUUUAACGAUUCCCC-------AAUUUGAAUAAGUUAAUUAACAAAAUUAAUAUUCAAAUGGGUUUAUGGCCGAA
(((((((((..(((....))).........)))))))))-..............(((-------(.(((((((..(((((((.....))))))))))))))))))............ ( -24.20, z-score =  -2.88, R)
>droSec1.super_12 730893 109 - 2123299
AAAAGAAAUAGAGCUAUAGCUAUAAAAAGAAUUUCUUCC-AUUUUUAACGAUUCCCC-------AAUUUGAAUAAGUUAAUUAACAAAAUUAAUAUUCAAAUGGGUUUAUGGCCGAA
..................((((((((..(((((......-.........)))))(((-------(.(((((((..(((((((.....)))))))))))))))))))))))))).... ( -20.26, z-score =  -2.11, R)
>droSim1.chr3R 18807145 109 - 27517382
GGAAGAAAUAGAGCUAUAGCUAUAAAAAGAAUUUCUUCC-AUUUUUAACGAUUCCCC-------AAUUUGAAUAAGUUAAUUAACAAAAUUAAUAUUCAAAUGGGUUUAUGGCCGAA
(((((((((..(((....))).........)))))))))-..............(((-------(.(((((((..(((((((.....))))))))))))))))))............ ( -24.20, z-score =  -2.88, R)
>droWil1.scaffold_181130 11856329 113 - 16660200
---CGGUGAAUUUCGGAGGUAAUAAAAAGAAUUUCUUCC-AUUUUUAACGACUAUCCCAAACAAAAUUUGAAUAAGUUAAUUAACAAAAUUAAUAUUCAAAUAGGUUUAUGGACGAA
---((.((((..(.(((((.(((.......))).)))))-)..)))).))....(((.((((...((((((((..(((((((.....)))))))))))))))..))))..))).... ( -19.30, z-score =  -1.00, R)
>dp4.chr2 17760254 105 + 30794189
----AGGAAAAACGCAGAGCCAUAAAAAGAAUUUCUUCA-AUUUUUAACGAUUCCCA-------AAUUUGAAUAAGUUAAUUAACAAAAUUAAUAUUCAAAUAGGUUUAUGGUCGCG
----........(((.((.((((((((((((((.....)-))))))........((.-------.((((((((..(((((((.....))))))))))))))).)))))))))))))) ( -19.90, z-score =  -2.63, R)
>droVir3.scaffold_12855 9851446 108 - 10161210
AAAAAGAAUGAAGGGAAAGCAAUAAAAGA-GUUUCUUUC-AUAUUUAACGAUGCUCC-------UAUUUGAAUAAGUUAAUUAACAGAAUUAAUAUUCAAAUGGGUUUAUGGCCGCA
.......((((((((((..(.......).-.))))))))-))......(.(((..((-------(((((((((..(((((((.....))))))))))))))))))..))).)..... ( -26.20, z-score =  -3.33, R)
>droMoj3.scaffold_6540 2046352 110 + 34148556
GAAAAGAAUGAAGGGAAAACAAUAAAAAGUGUUUCUUUCCAUAUUUAACGAUGCCUC-------UAUUUGAAUAAGUUAAUUAACAAAAUUAAUAUUCAAAUGGGUUUAUGGCCGCA
.........((((((((.((........)).))))))))..........(..(((((-------(((((((((..(((((((.....)))))))))))))))))).....)))..). ( -21.70, z-score =  -1.81, R)
>consensus
GGAAGGAAUAGAGCUAUAGCUAUAAAAAGAAUUUCUUCC_AUUUUUAACGAUUCCCC_______AAUUUGAAUAAGUUAAUUAACAAAAUUAAUAUUCAAAUGGGUUUAUGGCCGAA
..................((((((((((((((........))))))...................((((((((..(((((((.....)))))))))))))))...)))))))).... (-13.47 = -13.24 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,763,025 – 12,763,121
Length 96
Sequences 12
Columns 120
Reading direction reverse
Mean pairwise identity 88.07
Shannon entropy 0.23201
G+C content 0.30709
Mean single sequence MFE -21.06
Consensus MFE -11.09
Energy contribution -10.95
Covariance contribution -0.14
Combinations/Pair 1.04
Mean z-score -2.83
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.73
SVM RNA-class probability 0.801993
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12763025 96 - 27905053
--------------CACAUAAUGAAGCCAUAAGCCGCCAU---UUCGGCCAUAAACCCAUUUGAAUAUUAAUUUUGUUAAUUAACUUAUUCAAAUU-------GGUGAAUCGUUAAAAAU
--------------....((((((........((((....---..)))).....(((.(((((((((((((((.....))))))..))))))))).-------)))...))))))..... ( -21.30, z-score =  -3.28, R)
>droPer1.super_0 11615606 99 - 11822988
-----------UUUCACAUGAUGAAGCCAUAAGCCGCCAU---CGCGACCAUAAACCUAUUUGAAUAUUAAUUUUGUUAAUUAACUUAUUCAAAUUU-------GGGAAUCGUUAAAAAU
-----------.......((((((..((......(((...---.)))........(..(((((((((((((((.....))))))..)))))))))..-------)))..))))))..... ( -18.10, z-score =  -1.92, R)
>droAna3.scaffold_13340 16561605 94 + 23697760
----------------CAUAAUGAAGCCAUAAGCCACCAU---UUCGGCCAUAAACCCAUUUGAAUAUUAAUUUUGUUAAUUAACUUAUUCAAAUU-------CAAGAAUCGUUAAAAAU
----------------..((((((........(((.....---...))).........(((((((((((((((.....))))))..))))))))).-------......))))))..... ( -14.70, z-score =  -2.69, R)
>droEre2.scaffold_4770 8876826 96 + 17746568
--------------CACAUAAUGAAGCCAUAAGCCGCCAU---UUCGGCCAUAAACCCAUUUGAAUAUUAAUUUUGUUAAUUAACUUAUUCAAAUU-------GGGGAAUCGUUAAAAAU
--------------....((((((..((....((((....---..))))......((.(((((((((((((((.....))))))..))))))))).-------))))..))))))..... ( -24.10, z-score =  -3.52, R)
>droYak2.chr3R 17206976 96 + 28832112
--------------CACAUAAUGAAGCCAUAAGCCGCCAU---UUCGGCCAUAAACCCAUUUGAAUAUUAAUUUUGUUAAUUAACUUAUUCAAAUU-------GGGGAAUCGUUAAAAAU
--------------....((((((..((....((((....---..))))......((.(((((((((((((((.....))))))..))))))))).-------))))..))))))..... ( -24.10, z-score =  -3.52, R)
>droSec1.super_12 730932 96 + 2123299
--------------CACAUAAUGAAGCCAUAAGCCGCCCU---UUCGGCCAUAAACCCAUUUGAAUAUUAAUUUUGUUAAUUAACUUAUUCAAAUU-------GGGGAAUCGUUAAAAAU
--------------....((((((..((....((((....---..))))......((.(((((((((((((((.....))))))..))))))))).-------))))..))))))..... ( -24.10, z-score =  -3.50, R)
>droSim1.chr3R 18807184 96 + 27517382
--------------CACAUAAUGAAGCCAUAAGCCGCCAU---UUCGGCCAUAAACCCAUUUGAAUAUUAAUUUUGUUAAUUAACUUAUUCAAAUU-------GGGGAAUCGUUAAAAAU
--------------....((((((..((....((((....---..))))......((.(((((((((((((((.....))))))..))))))))).-------))))..))))))..... ( -24.10, z-score =  -3.52, R)
>droWil1.scaffold_181130 11856365 103 + 16660200
--------------CACAUAAUGAAGCCAUAAGCCGCCAU---UUCGUCCAUAAACCUAUUUGAAUAUUAAUUUUGUUAAUUAACUUAUUCAAAUUUUGUUUGGGAUAGUCGUUAAAAAU
--------------....((((((.((.....))......---...((((.(((((..(((((((((((((((.....))))))..)))))))))...)))))))))..))))))..... ( -19.50, z-score =  -2.31, R)
>dp4.chr2 17760289 99 - 30794189
-----------UUUCACAUGAUGAAGCCAUAAGCCGCCAU---CGCGACCAUAAACCUAUUUGAAUAUUAAUUUUGUUAAUUAACUUAUUCAAAUUU-------GGGAAUCGUUAAAAAU
-----------.......((((((..((......(((...---.)))........(..(((((((((((((((.....))))))..)))))))))..-------)))..))))))..... ( -18.10, z-score =  -1.92, R)
>droVir3.scaffold_12855 9851484 98 + 10161210
------------CAUACAUAAUGAAGCCAUAAGCCUCCAU---UGCGGCCAUAAACCCAUUUGAAUAUUAAUUCUGUUAAUUAACUUAUUCAAAUA-------GGAGCAUCGUUAAAUAU
------------......((((((.((.....(((.....---...)))......((.(((((((((((((((.....))))))..))))))))).-------)).)).))))))..... ( -20.40, z-score =  -2.93, R)
>droMoj3.scaffold_6540 2046392 110 - 34148556
AAGCUAGCGCGGCUCACAUAAUGAAGCCAUAAGCCGCCAU---UGCGGCCAUAAACCCAUUUGAAUAUUAAUUUUGUUAAUUAACUUAUUCAAAUA-------GAGGCAUCGUUAAAUAU
.((((.....))))....((((((.(((....(((((...---.))))).........(((((((((((((((.....))))))..))))))))).-------..))).))))))..... ( -29.50, z-score =  -3.18, R)
>droGri2.scaffold_14906 12938793 97 - 14172833
----------------CAUAAUGAAGCCAUAAGCUGCCAUUGCUGCGACCAUAAACCCAUUUGAAUAUUAAUUUUGUUAAUUAACUUAUUCAAAUU-------UUAACAUCGUUAAAUAU
----------------..(((((.(((.....)))..)))))..((((...((((...(((((((((((((((.....))))))..))))))))))-------)))...))))....... ( -14.70, z-score =  -1.70, R)
>consensus
______________CACAUAAUGAAGCCAUAAGCCGCCAU___UUCGGCCAUAAACCCAUUUGAAUAUUAAUUUUGUUAAUUAACUUAUUCAAAUU_______GGGGAAUCGUUAAAAAU
..................((((((.((.....))........................(((((((((((((((.....))))))..)))))))))..............))))))..... (-11.09 = -10.95 +  -0.14)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:21:12 2011