Locus 948

Sequence ID dm3.chr2L
Location 6,956,300 – 6,956,480
Length 180
Max. P 0.911529
window1287 window1288 window1289 window1290

overview

Window 7

Location 6,956,300 – 6,956,405
Length 105
Sequences 3
Columns 105
Reading direction forward
Mean pairwise identity 85.58
Shannon entropy 0.19875
G+C content 0.37218
Mean single sequence MFE -17.87
Consensus MFE -10.40
Energy contribution -12.73
Covariance contribution 2.33
Combinations/Pair 1.00
Mean z-score -2.82
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.79
SVM RNA-class probability 0.817822
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 6956300 105 + 23011544
ACAGUACAUUUUUAAAACCUCCUUAACUACACUUUAUAAACACAACACAUGUUUGCCGAUCUAGCCAAACGCGGAUAAAAAUCCGCAUCCGCUGUUGCUAUAUUA
(((((.............................................(((((.(......).)))))((((((....))))))....))))).......... ( -18.10, z-score =  -2.75, R)
>droSim1.chr2L 6753211 102 + 22036055
AUAGUACAUUUACAAAACCUCCUUAACACAACACAAUAAACCUAUGUCAAUUGUG---AUCUAGCCCAACGCGGAUAAAAAUCCGCAUCCGCUGUUGCUAUAUUA
((((((.........................((((((..((....))..))))))---...((((.....((((((....))))))....)))).)))))).... ( -20.20, z-score =  -3.56, R)
>droSec1.super_3 2488995 102 + 7220098
AUAGUACAUUUUCAAAACCUCCUUAACACAACACAAUAAACCUAUGCCAAUUGUG---AUCUAGCCCAACACGGAUAAAAAUCCGCAUCCGCUGUUGCUAUAUUA
((((((.........................((((((............))))))---...((((......(((((....))))).....)))).)))))).... ( -15.30, z-score =  -2.15, R)
>consensus
AUAGUACAUUUUCAAAACCUCCUUAACACAACACAAUAAACCUAUGACAAUUGUG___AUCUAGCCCAACGCGGAUAAAAAUCCGCAUCCGCUGUUGCUAUAUUA
((((((.........................((((((............))))))......((((.....((((((....))))))....)))).)))))).... (-10.40 = -12.73 +   2.33)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,956,340 – 6,956,445
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 70.16
Shannon entropy 0.51940
G+C content 0.33826
Mean single sequence MFE -21.62
Consensus MFE -10.10
Energy contribution -10.42
Covariance contribution 0.32
Combinations/Pair 1.24
Mean z-score -1.47
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.35
SVM RNA-class probability 0.657561
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 6956340 105 + 23011544
------CACAACACAU--GUUUGCC------GAUCUAGCCAAACGCGGAUAAAAAUCCGCAUCCGCUGUUGCUAUAU-UAGUAAAAAGUUUUAAAUAAGAGAAGGCAUAAAUUACUUUAU
------..........--...((((------..((((((.....((((((....))))))....))).((((((...-)))))).............)))...))))............. ( -21.30, z-score =  -1.81, R)
>droSim1.chr2L 6753242 111 + 22036055
------CACAAUAAAC--CUAUGUCAAUUGUGAUCUAGCCCAACGCGGAUAAAAAUCCGCAUCCGCUGUUGCUAUAU-UAGUAAAAAGUAUUAAAUAAGAGAAGGAUUAAAUUACUUUUG
------..........--......(((..(((((.((..((...((((((....))))))....(((.((((((...-))))))..)))..............))..)).)))))..))) ( -21.40, z-score =  -2.07, R)
>droSec1.super_3 2489026 111 + 7220098
------CACAAUAAAC--CUAUGCCAAUUGUGAUCUAGCCCAACACGGAUAAAAAUCCGCAUCCGCUGUUGCUAUAU-UAGUAAAAAGUAUUAAAUAGGAGAAUGAUUAAAUUACUAUUG
------..........--......((((.(((((.(((..((((((((((..........))))).)))))((((.(-(((((.....))))))))))........))).))))).)))) ( -17.50, z-score =  -0.96, R)
>droYak2.chr2L 16371265 119 - 22324452
CGUUAAUAAGGUU-UUUGGUUAAACACCUACAUUUACGACCCAUGCGGAUAAAAAUCCGCAUCCGCUGUAUCUAUAUAUAGUGAUAAGUAUUAGAUAAGAAAAUGUACAAAUCACUUUUG
.........((((-(..(((.....)))(((((((.(.....((((((((....)))))))).((((((((....))))))))...............).))))))).)))))....... ( -25.10, z-score =  -2.21, R)
>droEre2.scaffold_4929 15872346 119 + 26641161
AGGUAUUUGGGUAGUUUGGUUAAUCAUCUACUUUCUUGACCCAUGCGAAUAAAAAUCCGCAUCCGCUGUAGCUAU-UUUAGUUAUAGGUAUUAAAUAAGAAGAUGUUUCGAUCACUUUUG
................(((((...(((((.(((..((((..((((((..........)))))...(((((((((.-..))))))))))..))))..))).)))))....)))))...... ( -22.80, z-score =  -0.28, R)
>consensus
______CACAAUAAAU__GUUUGCCAACUACGAUCUAGCCCAACGCGGAUAAAAAUCCGCAUCCGCUGUUGCUAUAU_UAGUAAAAAGUAUUAAAUAAGAGAAUGAUUAAAUUACUUUUG
.................................(((........((((((....))))))....(((..(((((....)))))...)))........))).................... (-10.10 = -10.42 +   0.32)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,956,340 – 6,956,445
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 70.16
Shannon entropy 0.51940
G+C content 0.33826
Mean single sequence MFE -23.96
Consensus MFE -11.81
Energy contribution -11.61
Covariance contribution -0.20
Combinations/Pair 1.27
Mean z-score -1.81
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.22
SVM RNA-class probability 0.911529
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 6956340 105 - 23011544
AUAAAGUAAUUUAUGCCUUCUCUUAUUUAAAACUUUUUACUA-AUAUAGCAACAGCGGAUGCGGAUUUUUAUCCGCGUUUGGCUAGAUC------GGCAAAC--AUGUGUUGUG------
(((((....)))))............................-.....((((((.(((((((((((....)))))))))))(((.....------)))....--...)))))).------ ( -24.80, z-score =  -1.87, R)
>droSim1.chr2L 6753242 111 - 22036055
CAAAAGUAAUUUAAUCCUUCUCUUAUUUAAUACUUUUUACUA-AUAUAGCAACAGCGGAUGCGGAUUUUUAUCCGCGUUGGGCUAGAUCACAAUUGACAUAG--GUUUAUUGUG------
........(((((..((.........................-.....((....)).(((((((((....)))))))))))..)))))((((((.(((....--))).))))))------ ( -24.70, z-score =  -2.43, R)
>droSec1.super_3 2489026 111 - 7220098
CAAUAGUAAUUUAAUCAUUCUCCUAUUUAAUACUUUUUACUA-AUAUAGCAACAGCGGAUGCGGAUUUUUAUCCGUGUUGGGCUAGAUCACAAUUGGCAUAG--GUUUAUUGUG------
...((((((...........................))))))-...((((..((((....((((((....)))))))))).))))...((((((..((....--))..))))))------ ( -21.53, z-score =  -0.89, R)
>droYak2.chr2L 16371265 119 + 22324452
CAAAAGUGAUUUGUACAUUUUCUUAUCUAAUACUUAUCACUAUAUAUAGAUACAGCGGAUGCGGAUUUUUAUCCGCAUGGGUCGUAAAUGUAGGUGUUUAACCAAA-AACCUUAUUAACG
....((((((..(((...............)))..))))))...((((..(((.((..((((((((....))))))))..)).)))..))))(((.....)))...-............. ( -27.56, z-score =  -2.53, R)
>droEre2.scaffold_4929 15872346 119 - 26641161
CAAAAGUGAUCGAAACAUCUUCUUAUUUAAUACCUAUAACUAAA-AUAGCUACAGCGGAUGCGGAUUUUUAUUCGCAUGGGUCAAGAAAGUAGAUGAUUAACCAAACUACCCAAAUACCU
....(((.....((.(((((.(((.(((...((((((.......-...((....))....((((((....)))))))))))).))).))).))))).))......)))............ ( -21.20, z-score =  -1.35, R)
>consensus
CAAAAGUAAUUUAAACAUUCUCUUAUUUAAUACUUUUUACUA_AUAUAGCAACAGCGGAUGCGGAUUUUUAUCCGCGUUGGGCUAGAUCACAAUUGACAAAC__AUUUAUUGUG______
....(((((...........................)))))..............(.(((((((((....))))))))).)....................................... (-11.81 = -11.61 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,956,366 – 6,956,480
Length 114
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 75.44
Shannon entropy 0.43542
G+C content 0.30660
Mean single sequence MFE -18.30
Consensus MFE -11.69
Energy contribution -11.49
Covariance contribution -0.20
Combinations/Pair 1.24
Mean z-score -1.25
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.681483
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 6956366 114 - 23011544
AAGUUUCCAUUCAAAUAUAGUUUCUUUGGUAGUUCAUAAAGUAAUUUAUGCCUUCUCUUAUUUAAAACUUUUUACUA-AUAUAGCAACAGCGGAUGCGGAUUUUUAUCCGCGUUU
...................(((...(((((((..((((((....)))))).....................))))))-)...)))......((((((((((....)))))))))) ( -20.20, z-score =  -1.53, R)
>droSim1.chr2L 6753274 103 - 22036055
-------AACUUAACUUUCCAUUCUUU----GUUCCAAAAGUAAUUUAAUCCUUCUCUUAUUUAAUACUUUUUACUA-AUAUAGCAACAGCGGAUGCGGAUUUUUAUCCGCGUUG
-------....((((..(((.......----((...(((((((..((((............))))))))))).))..-.....((....))))).((((((....)))))))))) ( -16.80, z-score =  -2.54, R)
>droSec1.super_3 2489058 102 - 7220098
------------AAGUUUUCAUUCUUUGGUAGUUCCAAUAGUAAUUUAAUCAUUCUCCUAUUUAAUACUUUUUACUA-AUAUAGCAACAGCGGAUGCGGAUUUUUAUCCGUGUUG
------------.............((((.....))))((((((...........................))))))-.....((....)).(((((((((....))))))))). ( -15.53, z-score =  -0.93, R)
>droYak2.chr2L 16371304 115 + 22324452
AAAUUUAAAUUGAAAUAUAAUUUCAGUGGGCGUUCCAAAAGUGAUUUGUACAUUUUCUUAUCUAAUACUUAUCACUAUAUAUAGAUACAGCGGAUGCGGAUUUUUAUCCGCAUGG
..(((((.((((((((...))))))))((.....))...((((((..(((...............)))..)))))).....))))).......((((((((....)))))))).. ( -23.06, z-score =  -1.52, R)
>droEre2.scaffold_4929 15872386 114 - 26641161
AAAUUUCAAUUCAAAUAUAAUUUCAGUGGGAGUUCCAAAAGUGAUCGAAACAUCUUCUUAUUUAAUACCUAUAACUAAA-AUAGCUACAGCGGAUGCGGAUUUUUAUUCGCAUGG
.........................(((((.(((....(((.(((......)))..)))....))).))))).......-...((....))..((((((((....)))))))).. ( -15.90, z-score =   0.29, R)
>consensus
AA_UUU_AAUUCAAAUAUAAUUUCUUUGGGAGUUCCAAAAGUAAUUUAAACAUUCUCUUAUUUAAUACUUUUUACUA_AUAUAGCAACAGCGGAUGCGGAUUUUUAUCCGCGUUG
.................................(((...(((((...........................))))).......((....)))))(((((((....)))))))... (-11.69 = -11.49 +  -0.20)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:22:40 2011