Locus 10604

Sequence ID dm3.chr3R
Location 14,979,969 – 14,980,127
Length 158
Max. P 0.970013
window14575 window14576 window14577 window14578

overview

Window 5

Location 14,979,969 – 14,980,061
Length 92
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 73.87
Shannon entropy 0.45876
G+C content 0.39875
Mean single sequence MFE -23.28
Consensus MFE -10.51
Energy contribution -11.52
Covariance contribution 1.00
Combinations/Pair 1.33
Mean z-score -2.28
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.18
SVM RNA-class probability 0.905353
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 14979969 92 - 27905053
GUUUAUGGUUGCCCCAUGGA-UCGGGCAUCCGUAAGCGCCACUUGCUACUAAGUGGGCAAAAU--AAAAAAAAUCCAAUACUUUUAC---AUAAUCCA-----
((((((((.(((((......-..))))).))))))))((((((((....))))).))).....--......................---........----- ( -27.30, z-score =  -2.95, R)
>droSim1.chr3R 21019700 90 + 27517382
GUUUAUGGUUGCCCAAUGGA-UCGGGCAUCCGUAAGCGCCACUUGCUACUAAGUGGGCGAAAU----AAAAAAUCCAAUACUUUUAC---AUAAUCCA-----
((((((((.(((((......-..))))).))))))))((((((((....))))).))).....----....................---........----- ( -27.90, z-score =  -3.11, R)
>droSec1.super_25 47156 90 + 827797
GUUUAUGGUUGCCCAAUGGA-UUGGGCAGCCGUAAGCGCUACUUGCUACUAAGUGGGCAAAAU----AAAAAAUCCAAUACUUUUAC---AUAAUCCA-----
((((((((((((((((....-))))))))))))))))((((((((....))))).))).....----....................---........----- ( -31.50, z-score =  -3.98, R)
>droYak2.chr3R 3661579 87 - 28832112
GUUUAUGGUUGCCCGUUGAA-UAGGGCAUCCUUAGGCGCCA--UGCUACUAGGUCUAUAAAAU-----AAAAAUCCAAUACUAUUAC---ACAAUCCA-----
(((((.((.(((((......-..))))).)).)))))(((.--........))).........-----...................---........----- ( -17.30, z-score =  -0.42, R)
>droEre2.scaffold_4770 11097987 87 + 17746568
GCUUGAGGUUGCCCCUUGAA-UCGGGCAGCCGUAGGCGCCA--UGCUACUAAGUGUGUAAAAU-----AAAAAUCCAAUACUAUUAC---ACAAUCCA-----
(((((.((((((((......-..)))))))).)))))....--..........(((((((...-----...............))))---))).....----- ( -25.97, z-score =  -2.56, R)
>droAna3.scaffold_13340 277940 88 + 23697760
-----------UCCUUUGUAUUCGAAAAUCCUCAAGGGC----UCCUAGCACGAGUAGAAAAUAAAAAAAAAACCCAAUACUUUUACGAAAAAAUUCAAAUUG
-----------...(((.((((((.....((....))((----.....)).)))))).))).......................................... (  -9.70, z-score =  -0.67, R)
>consensus
GUUUAUGGUUGCCCAAUGGA_UCGGGCAUCCGUAAGCGCCA__UGCUACUAAGUGGGCAAAAU____AAAAAAUCCAAUACUUUUAC___AUAAUCCA_____
(((((.((.(((((.........))))).)).))))).................................................................. (-10.51 = -11.52 +   1.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,979,999 – 14,980,101
Length 102
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 68.59
Shannon entropy 0.57798
G+C content 0.42686
Mean single sequence MFE -28.02
Consensus MFE -10.65
Energy contribution -10.15
Covariance contribution -0.50
Combinations/Pair 1.50
Mean z-score -1.57
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.583234
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 14979999 102 - 27905053
----AUAAGUGUUAUGUUUCCUUACCCUAAUCACAGACAUCCAAGU--UUAUGGUUGCCCCAUGGAUCGGGCAUCCGUAAGCGCCA-CUUGCUACUAAGUGGGCAAAAU
----....((((((.((......))..))).)))..........((--((((((.(((((........))))).))))))))((((-((((....))))).)))..... ( -28.90, z-score =  -1.74, R)
>droSim1.chr3R 21019728 102 + 27517382
----AUAAGUGUUAUCUUACCUUACCCUAAUCACAGACAUCCAAGU--UUAUGGUUGCCCAAUGGAUCGGGCAUCCGUAAGCGCCA-CUUGCUACUAAGUGGGCGAAAU
----.((((.((......))))))......((.(..........((--((((((.(((((........))))).)))))))).(((-((((....)))))))).))... ( -30.20, z-score =  -2.28, R)
>droSec1.super_25 47184 102 + 827797
----AUAAGUGUUAUCUUACCUUACCCUAAUCACAGACAUCCAAGU--UUAUGGUUGCCCAAUGGAUUGGGCAGCCGUAAGCGCUA-CUUGCUACUAAGUGGGCAAAAU
----.((((.((......))))))....................((--((((((((((((((....))))))))))))))))((((-((((....))))).)))..... ( -33.40, z-score =  -2.94, R)
>droYak2.chr3R 3661606 100 - 28832112
----AUAAGUGUUACGUUGCCUUAUUUUAAUCACAGGCAUCCAAGU--UUAUGGUUGCCCGUUGAAUAGGGCAUCCUUAGGCGCCA---UGCUACUAGGUCUAUAAAAU
----.............((((((((((.....((.((((.(((...--...))).)))).)).))))))))))..(((((..((..---.))..))))).......... ( -25.90, z-score =  -0.99, R)
>droEre2.scaffold_4770 11098014 100 + 17746568
----AUAAGUGUUAUGUUACCUUACCUUAAUCGCAGACAUCCAAGC--UUGAGGUUGCCCCUUGAAUCGGGCAGCCGUAGGCGCCA---UGCUACUAAGUGUGUAAAAU
----.((((.((......))))))........(((.((......((--(((.((((((((........)))))))).)))))((..---.))......)).)))..... ( -27.60, z-score =  -1.27, R)
>droGri2.scaffold_14906 4708661 109 - 14172833
UUCACUGGUUCGCGUCGUGAUUCAAUGUAGUUAUUCAAUUCACAGUGAGAAAAGAAGACUUUUAAGCUGUGUGUUAAUGAGUGCUGCCAUUUUAGCCUUUUUAAAAACU
.....((((((((...))))......(((.(((((.(((.((((((...(((((....)))))..)))))).)))))))).))).)))).................... ( -22.10, z-score =  -0.20, R)
>consensus
____AUAAGUGUUAUCUUACCUUACCCUAAUCACAGACAUCCAAGU__UUAUGGUUGCCCAAUGAAUCGGGCAUCCGUAAGCGCCA_CUUGCUACUAAGUGGGCAAAAU
.......(((..........................................((.(((((........))))).))...((((......)))))))............. (-10.65 = -10.15 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,980,008 – 14,980,127
Length 119
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 73.26
Shannon entropy 0.50808
G+C content 0.43153
Mean single sequence MFE -32.97
Consensus MFE -14.16
Energy contribution -16.50
Covariance contribution 2.34
Combinations/Pair 1.29
Mean z-score -1.98
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.88
SVM RNA-class probability 0.843962
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 14980008 119 + 27905053
ACUUAGUAGCAAGUGGCGCUUACGGAUGCCCGAUCCAUGGGGCAACCAUAAACUUGGAUGUCUGUGAUUAGGGUAAGGAAACAUAACACUUAUUUCACAAGAAUUC-GCCAGCUGCUUAA
....((((((...((((......((.(((((........))))).))........((((.(((((((.((((.((.(....).))...))))..)))).)))))))-))))))))))... ( -38.00, z-score =  -2.61, R)
>droSim1.chr3R 21019737 119 - 27517382
ACUUAGUAGCAAGUGGCGCUUACGGAUGCCCGAUCCAUUGGGCAACCAUAAACUUGGAUGUCUGUGAUUAGGGUAAGGUAAGAUAACACUUAUUUCUCAAGAAUUC-GCCAGCUGCUUAA
....((((((...(((((.((((((((((((((....))))))..(((......)))..))))))))...(((..(((((((......)))))))))).......)-))))))))))... ( -38.60, z-score =  -2.64, R)
>droSec1.super_25 47193 115 - 827797
ACUUAGUAGCAAGUAGCGCUUACGGCUGCCCAAUCCAUUGGGCAACCAUAAACUUGGAUGUCUGUGAUUAGGGUAAGGUAAGAUAACACUUAUUUCUCAAGAAUUC-G----CUGCUUAA
..........(((((((((((((...(((((((((...((((((.(((......))).)))))).)))).)))))..)))))...........(((....)))..)-)----)))))).. ( -33.30, z-score =  -1.85, R)
>droYak2.chr3R 3661615 117 + 28832112
ACCUAGUAGCA--UGGCGCCUAAGGAUGCCCUAUUCAACGGGCAACCAUAAACUUGGAUGCCUGUGAUUAAAAUAAGGCAACGUAACACUUAUUUCUCAAGAACUC-UCCAGCUGCUUCA
....((((((.--(((.((((.(((....)))..(((.((((((.(((......))).)))))))))........))))..............(((....)))...-.)))))))))... ( -34.10, z-score =  -2.71, R)
>droEre2.scaffold_4770 11098023 117 - 17746568
ACUUAGUAGCA--UGGCGCCUACGGCUGCCCGAUUCAAGGGGCAACCUCAAGCUUGGAUGUCUGCGAUUAAGGUAAGGUAACAUAACACUUAUUUCUCAAGAACUC-GCCAGCUGCUUCA
....((((((.--((((((....((.(((((........))))).))....))...((..(((..((...(((((((((......)).))))))).)).)))..))-))))))))))... ( -35.20, z-score =  -1.16, R)
>droGri2.scaffold_14906 4708688 109 + 14172833
ACUCAUUAACA--CACAGCUUAAAAGUCUUCUUUUC------UCACUGUGAA-UUGAAUAACUAC-AUUGAAUCACGACG-CGAACCAGUGAAUUCAAAUGAACCAAGCUAUCAAUGUGA
.....((((..--(((((...(((((....))))).------...)))))..-)))).....(((-(((((.((((....-.......)))).(((....)))........)))))))). ( -18.60, z-score =  -0.93, R)
>consensus
ACUUAGUAGCA__UGGCGCUUACGGAUGCCCGAUCCAUGGGGCAACCAUAAACUUGGAUGUCUGUGAUUAAGGUAAGGUAACAUAACACUUAUUUCUCAAGAACUC_GCCAGCUGCUUAA
....((((((...((((......((.(((((........))))).)).......................(((((((...........)))))))............))))))))))... (-14.16 = -16.50 +   2.34)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,980,008 – 14,980,127
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 73.26
Shannon entropy 0.50808
G+C content 0.43153
Mean single sequence MFE -34.93
Consensus MFE -16.46
Energy contribution -17.30
Covariance contribution 0.84
Combinations/Pair 1.39
Mean z-score -2.28
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.83
SVM RNA-class probability 0.970013
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 14980008 119 - 27905053
UUAAGCAGCUGGC-GAAUUCUUGUGAAAUAAGUGUUAUGUUUCCUUACCCUAAUCACAGACAUCCAAGUUUAUGGUUGCCCCAUGGAUCGGGCAUCCGUAAGCGCCACUUGCUACUAAGU
...(((((.((((-((..(((.((((.....(((...........))).....)))))))..))...((((((((.(((((........))))).)))))))))))).)))))....... ( -37.30, z-score =  -3.03, R)
>droSim1.chr3R 21019737 119 + 27517382
UUAAGCAGCUGGC-GAAUUCUUGAGAAAUAAGUGUUAUCUUACCUUACCCUAAUCACAGACAUCCAAGUUUAUGGUUGCCCAAUGGAUCGGGCAUCCGUAAGCGCCACUUGCUACUAAGU
...(((((.((((-((..((((((....((((.((......))))))......))).)))..))...((((((((.(((((........))))).)))))))))))).)))))....... ( -37.60, z-score =  -3.47, R)
>droSec1.super_25 47193 115 + 827797
UUAAGCAG----C-GAAUUCUUGAGAAAUAAGUGUUAUCUUACCUUACCCUAAUCACAGACAUCCAAGUUUAUGGUUGCCCAAUGGAUUGGGCAGCCGUAAGCGCUACUUGCUACUAAGU
.((((.((----(-((..((((((....((((.((......))))))......))).)))..))...((((((((((((((((....))))))))))))))))))).))))......... ( -36.30, z-score =  -3.56, R)
>droYak2.chr3R 3661615 117 - 28832112
UGAAGCAGCUGGA-GAGUUCUUGAGAAAUAAGUGUUACGUUGCCUUAUUUUAAUCACAGGCAUCCAAGUUUAUGGUUGCCCGUUGAAUAGGGCAUCCUUAGGCGCCA--UGCUACUAGGU
...((((((((((-..(((..(((((((((((.((......))))))))))..)))..))).)))).(((((.((.(((((........))))).)).)))))))..--))))....... ( -35.80, z-score =  -1.48, R)
>droEre2.scaffold_4770 11098023 117 + 17746568
UGAAGCAGCUGGC-GAGUUCUUGAGAAAUAAGUGUUAUGUUACCUUACCUUAAUCGCAGACAUCCAAGCUUGAGGUUGCCCCUUGAAUCGGGCAGCCGUAGGCGCCA--UGCUACUAAGU
...((.(((((((-..((..(((((...((((.((......)))))).)))))..))..........(((((.((((((((........)))))))).)))))))))--.))).)).... ( -38.40, z-score =  -1.92, R)
>droGri2.scaffold_14906 4708688 109 - 14172833
UCACAUUGAUAGCUUGGUUCAUUUGAAUUCACUGGUUCG-CGUCGUGAUUCAAU-GUAGUUAUUCAA-UUCACAGUGA------GAAAAGAAGACUUUUAAGCUGUG--UGUUAAUGAGU
...((((((((...........((((((.((.((..(((-(...))))..)).)-).....))))))-..((((((..------.(((((....)))))..))))))--))))))))... ( -24.20, z-score =  -0.23, R)
>consensus
UUAAGCAGCUGGC_GAAUUCUUGAGAAAUAAGUGUUAUGUUACCUUACCCUAAUCACAGACAUCCAAGUUUAUGGUUGCCCAAUGAAUCGGGCAUCCGUAAGCGCCA__UGCUACUAAGU
...((((..((((....(((....)))........................................(((((.((.(((((........))))).)).)))))))))..))))....... (-16.46 = -17.30 +   0.84)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:27:03 2011