Locus 15526

Sequence ID dm3.chrX
Location 19,395,943 – 19,396,051
Length 108
Max. P 0.878162
window21411 window21412 window21413 window21414

overview

Window 1

Location 19,395,943 – 19,396,038
Length 95
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 71.60
Shannon entropy 0.40872
G+C content 0.32969
Mean single sequence MFE -12.60
Consensus MFE -7.93
Energy contribution -7.55
Covariance contribution -0.38
Combinations/Pair 1.17
Mean z-score -1.31
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.583041
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19395943 95 + 22422827
GAUAGUCGAAAAACAUGAACAAAUUACGAAUUUUACAUCCUCUGUUCCUCAACAAGGAACUACUAUGUACAUAUACAUACAUAUAUGUUCGUUAU
..............(((((((......................((((((.....))))))...((((((........))))))..)))))))... ( -15.70, z-score =  -1.70, R)
>droYak2.chrX 9830486 74 - 21770863
UACAGUCAUAAAAUAUGAACUAAUGACGAAUCUUAGAUUCCCCGUUCCCAAACAGGGAACUAC-AUGUUAGUCUU--------------------
.....(((((...)))))((((((...(((((...)))))...((((((.....))))))...-..))))))...-------------------- ( -16.50, z-score =  -2.61, R)
>droSec1.super_8 1678893 74 + 3762037
GAUAGAUAUAGAACAUGAACAAAUGACGAAUUUUACAUCCCCCGUUCCUCAACAAGGAACUAA-AUGUUAGUUUU--------------------
(((.(((((....(((......)))..................((((((.....))))))...-))))).)))..-------------------- (  -9.10, z-score =  -0.57, R)
>droSim1.chrX_random 5047668 74 + 5698898
GAUAGAUAUAGAACAUGAACAAAUGACGAAUUUUACAUACUCCGUUCCUCAACAAGGAACUAA-AUGUUAGUUUU--------------------
(((.(((((....(((......)))..................((((((.....))))))...-))))).)))..-------------------- (  -9.10, z-score =  -0.37, R)
>consensus
GAUAGACAUAAAACAUGAACAAAUGACGAAUUUUACAUCCCCCGUUCCUCAACAAGGAACUAA_AUGUUAGUUUU____________________
...........................................((((((.....))))))................................... ( -7.93 =  -7.55 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,395,943 – 19,396,038
Length 95
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 71.60
Shannon entropy 0.40872
G+C content 0.32969
Mean single sequence MFE -16.91
Consensus MFE -10.65
Energy contribution -9.90
Covariance contribution -0.75
Combinations/Pair 1.29
Mean z-score -1.42
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.41
SVM RNA-class probability 0.682041
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19395943 95 - 22422827
AUAACGAACAUAUAUGUAUGUAUAUGUACAUAGUAGUUCCUUGUUGAGGAACAGAGGAUGUAAAAUUCGUAAUUUGUUCAUGUUUUUCGACUAUC
.....((((...(((((((......)))))))...))))...(((((((((((..(((((..............))))).))))))))))).... ( -22.14, z-score =  -1.82, R)
>droYak2.chrX 9830486 74 + 21770863
--------------------AAGACUAACAU-GUAGUUCCCUGUUUGGGAACGGGGAAUCUAAGAUUCGUCAUUAGUUCAUAUUUUAUGACUGUA
--------------------..((((((...-...((((((.....))))))((.(((((...))))).)).))))))................. ( -19.40, z-score =  -1.88, R)
>droSec1.super_8 1678893 74 - 3762037
--------------------AAAACUAACAU-UUAGUUCCUUGUUGAGGAACGGGGGAUGUAAAAUUCGUCAUUUGUUCAUGUUCUAUAUCUAUC
--------------------......(((((-...(((((((...)))))))((.((((.....)))).))........)))))........... ( -13.50, z-score =  -0.85, R)
>droSim1.chrX_random 5047668 74 - 5698898
--------------------AAAACUAACAU-UUAGUUCCUUGUUGAGGAACGGAGUAUGUAAAAUUCGUCAUUUGUUCAUGUUCUAUAUCUAUC
--------------------...........-...(((((((...)))))))((((((((..((((.....))))...))))))))......... ( -12.60, z-score =  -1.13, R)
>consensus
____________________AAAACUAACAU_GUAGUUCCUUGUUGAGGAACGGAGGAUGUAAAAUUCGUCAUUUGUUCAUGUUCUAUAACUAUC
...................................((((((.....))))))((((.(((..((((.....))))...))).))))......... (-10.65 =  -9.90 +  -0.75)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,395,950 – 19,396,051
Length 101
Sequences 3
Columns 101
Reading direction forward
Mean pairwise identity 70.92
Shannon entropy 0.37688
G+C content 0.33148
Mean single sequence MFE -14.30
Consensus MFE -9.01
Energy contribution -8.57
Covariance contribution -0.44
Combinations/Pair 1.10
Mean z-score -1.48
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.20
SVM RNA-class probability 0.592117
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19395950 101 + 22422827
GAAAAACAUGAACAAAUUACGAAUUUUACAUCCUCUGUUCCUCAACAAGGAACUACUAUGUACAUAUACAUACAUAUAUGUUCGUUAUGACACUUACUGAU
......((((........(((((...(((((.....((((((.....))))))....)))))((((((......)))))))))))))))............ ( -15.90, z-score =  -1.90, R)
>droYak2.chrX 9830493 80 - 21770863
AUAAAAUAUGAACUAAUGACGAAUCUUAGAUUCCCCGUUCCCAAACAGGGAACU---------------------ACAUGUUAGUCUUGACACUUUCUGAU
....((((((..........(((((...)))))...((((((.....)))))).---------------------.))))))................... ( -15.70, z-score =  -1.75, R)
>droSim1.chrX_random 5047675 80 + 5698898
AUAGAACAUGAACAAAUGACGAAUUUUACAUACUCCGUUCCUCAACAAGGAACU---------------------AAAUGUUAGUUUUGACACUUACUGAU
.(((..(((......))).((((....((((.....((((((.....)))))).---------------------..))))....)))).......))).. ( -11.30, z-score =  -0.78, R)
>consensus
AUAAAACAUGAACAAAUGACGAAUUUUACAUACUCCGUUCCUCAACAAGGAACU_____________________AAAUGUUAGUUUUGACACUUACUGAU
....................................((((((.....)))))).........................((((......))))......... ( -9.01 =  -8.57 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,395,950 – 19,396,051
Length 101
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 70.92
Shannon entropy 0.37688
G+C content 0.33148
Mean single sequence MFE -20.13
Consensus MFE -11.39
Energy contribution -11.07
Covariance contribution -0.33
Combinations/Pair 1.21
Mean z-score -2.12
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.878162
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19395950 101 - 22422827
AUCAGUAAGUGUCAUAACGAACAUAUAUGUAUGUAUAUGUACAUAGUAGUUCCUUGUUGAGGAACAGAGGAUGUAAAAUUCGUAAUUUGUUCAUGUUUUUC
.((((((((.((....))((((...(((((((......)))))))...)))))))))))).(((((((..(((.......)))..)))))))......... ( -22.00, z-score =  -1.67, R)
>droYak2.chrX 9830493 80 + 21770863
AUCAGAAAGUGUCAAGACUAACAUGU---------------------AGUUCCCUGUUUGGGAACGGGGAAUCUAAGAUUCGUCAUUAGUUCAUAUUUUAU
.....(((((((...((((((.....---------------------.((((((.....))))))((.(((((...))))).)).)))))).))))))).. ( -22.20, z-score =  -2.81, R)
>droSim1.chrX_random 5047675 80 - 5698898
AUCAGUAAGUGUCAAAACUAACAUUU---------------------AGUUCCUUGUUGAGGAACGGAGUAUGUAAAAUUCGUCAUUUGUUCAUGUUCUAU
.....(((((((........))))))---------------------)(((((((...)))))))((((((((..((((.....))))...)))))))).. ( -16.20, z-score =  -1.87, R)
>consensus
AUCAGUAAGUGUCAAAACUAACAUAU_____________________AGUUCCUUGUUGAGGAACGGAGAAUGUAAAAUUCGUCAUUUGUUCAUGUUUUAU
........(((....((((((...........................((((((.....))))))...((((.....))))....)))))))))....... (-11.39 = -11.07 +  -0.33)

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 02:01:11 2011