Locus 11078

Sequence ID dm3.chr3R
Location 18,576,499 – 18,576,629
Length 130
Max. P 0.992153
window15214 window15215 window15216

overview

Window 4

Location 18,576,499 – 18,576,615
Length 116
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 76.32
Shannon entropy 0.46149
G+C content 0.47416
Mean single sequence MFE -35.75
Consensus MFE -16.69
Energy contribution -17.89
Covariance contribution 1.20
Combinations/Pair 1.34
Mean z-score -2.69
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.13
SVM RNA-class probability 0.983147
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18576499 116 + 27905053
ACUGUUACUUUCUUAGGCAGACCAUGUCACUGCAUUUGCAGGCAAAGCCCUGCAGUAGUAACCAUUAUUUUGUAUGACCAUCCAUGUGAUGGUCACCCUAUGCGAGUAACUGUUCG
((.(((((((.(.((((..(((((.((.(((((...((((((......))))))))))).)).......(..((((......))))..))))))..)))).).))))))).))... ( -36.80, z-score =  -3.15, R)
>droEre2.scaffold_4820 972150 116 - 10470090
ACUGUUACUCUCUUAGGAAGACCAUGCCACUGCAUUCUCAAGCAAAGGCCUACUGAAGUAACCAUCAUUCGGCAUGCCCAACCAUGGGAUGGUCACCCUAAGCGAGUAACUGUUCG
((.(((((((.((((((..((((((.(((.(((........)))..(((...(((((..........)))))...)))......))).))))))..)))))).))))))).))... ( -43.20, z-score =  -5.00, R)
>droYak2.chr3R 19425756 116 + 28832112
ACUGUUACUUUCUUAGGAAGACCAUGCCACUUCAUUCGCAAGCAAAGCCCUACGGUAGUAACCAUCAUUUCGCAUGACCAGUCAUGUGAUGGUCACCCUAAGCGCGUAACUGUUCG
((.(((((...((((((..((((((((..........))).............(((....)))......((((((((....)))))))))))))..))))))...))))).))... ( -33.10, z-score =  -2.97, R)
>droSec1.super_0 18932977 116 + 21120651
ACUGUUACUUUAUUAGGCAUACCAUGUCACUGUAUUGCCAGGCAAAGCCCUGCAGUAGUAACCAUCAUUUUGCAUGACCAACCAUGUGAUGGCCACCCUAAGCGAGUAACUGUUCG
((.(((((((..(((((...............((((((..(((...)))..))))))((..(((((.....(((((......))))))))))..)))))))..))))))).))... ( -31.30, z-score =  -1.52, R)
>droSim1.chr3R 18387408 116 + 27517382
ACUGUUACUUUUGUAGGCAGACCAUGCCACUGCAUUUGCAGGCAAAGCCCUGCAGUAGUAACCAUCAUUUUGCAUGACCAACCAUGUGAUGGUCACCCUAAGCGAGUAACUGUUCA
((.(((((((...((((..((((((...(((((...((((((......)))))))))))............(((((......))))).))))))..))))...))))))).))... ( -38.40, z-score =  -2.82, R)
>droMoj3.scaffold_6540 1086513 114 - 34148556
ACUGCGACGCCGACUGAGAGACCGUUUCUCUG-AGUUGCGUGAACUCGCGUACUGAAAUCAACUACACUCU-CAGCAGCUAUCUCGCUCUGGUCACACUCACAUUGUAACAGUUGG
...((((((((((((.(((((.....))))).-))))).)))...))))..........(((((.......-(((.(((......))))))((.(((.......))).))))))). ( -31.70, z-score =  -0.67, R)
>consensus
ACUGUUACUUUCUUAGGCAGACCAUGCCACUGCAUUUGCAGGCAAAGCCCUACAGUAGUAACCAUCAUUUUGCAUGACCAACCAUGUGAUGGUCACCCUAAGCGAGUAACUGUUCG
((.(((((((.(.((((..((((((((..............))).........................(((((((......))))))))))))..)))).).))))))).))... (-16.69 = -17.89 +   1.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,576,499 – 18,576,615
Length 116
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 76.32
Shannon entropy 0.46149
G+C content 0.47416
Mean single sequence MFE -41.53
Consensus MFE -21.76
Energy contribution -23.27
Covariance contribution 1.50
Combinations/Pair 1.28
Mean z-score -2.71
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.52
SVM RNA-class probability 0.992153
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18576499 116 - 27905053
CGAACAGUUACUCGCAUAGGGUGACCAUCACAUGGAUGGUCAUACAAAAUAAUGGUUACUACUGCAGGGCUUUGCCUGCAAAUGCAGUGACAUGGUCUGCCUAAGAAAGUAACAGU
......((((((..(.(((((((((((((.....)))))))))...........((((((.(((((((......))))))...).))))))........)))).)..))))))... ( -40.90, z-score =  -3.39, R)
>droEre2.scaffold_4820 972150 116 + 10470090
CGAACAGUUACUCGCUUAGGGUGACCAUCCCAUGGUUGGGCAUGCCGAAUGAUGGUUACUUCAGUAGGCCUUUGCUUGAGAAUGCAGUGGCAUGGUCUUCCUAAGAGAGUAACAGU
......(((((((.(((((((.((((((.((((.(((.((....)).))).))))((((....))))(((.((((........)))).))))))))).))))))).)))))))... ( -50.90, z-score =  -4.95, R)
>droYak2.chr3R 19425756 116 - 28832112
CGAACAGUUACGCGCUUAGGGUGACCAUCACAUGACUGGUCAUGCGAAAUGAUGGUUACUACCGUAGGGCUUUGCUUGCGAAUGAAGUGGCAUGGUCUUCCUAAGAAAGUAACAGU
......(((((...(((((((((((((((((((((....))))).....))))))))))......((((((.((((.((.......)))))).))))))))))))...)))))... ( -42.40, z-score =  -3.55, R)
>droSec1.super_0 18932977 116 - 21120651
CGAACAGUUACUCGCUUAGGGUGGCCAUCACAUGGUUGGUCAUGCAAAAUGAUGGUUACUACUGCAGGGCUUUGCCUGGCAAUACAGUGACAUGGUAUGCCUAAUAAAGUAACAGU
......((((((.((....((((((((((((((((....))))).....)))))))))))...)).((((..((((((.((......)).)).)))).)))).....))))))... ( -37.20, z-score =  -1.44, R)
>droSim1.chr3R 18387408 116 - 27517382
UGAACAGUUACUCGCUUAGGGUGACCAUCACAUGGUUGGUCAUGCAAAAUGAUGGUUACUACUGCAGGGCUUUGCCUGCAAAUGCAGUGGCAUGGUCUGCCUACAAAAGUAACAGU
......((((((....(((((((((((((((((((....))))).....)))))))))))...(((((.((.(((((((....)))..)))).))))))))))....))))))... ( -41.00, z-score =  -2.14, R)
>droMoj3.scaffold_6540 1086513 114 + 34148556
CCAACUGUUACAAUGUGAGUGUGACCAGAGCGAGAUAGCUGCUG-AGAGUGUAGUUGAUUUCAGUACGCGAGUUCACGCAACU-CAGAGAAACGGUCUCUCAGUCGGCGUCGCAGU
....((((((((.......))))).))).((((....(((((((-((((....(((..(((.(((..(((......))).)))-.)))..)))...))))))).)))).))))... ( -36.80, z-score =  -0.77, R)
>consensus
CGAACAGUUACUCGCUUAGGGUGACCAUCACAUGGUUGGUCAUGCAAAAUGAUGGUUACUACUGCAGGGCUUUGCCUGCAAAUGCAGUGACAUGGUCUGCCUAAGAAAGUAACAGU
......((((((....((((..((((((..(((((....)))))..........((((((...(((((......)))))......))))))))))))..))))....))))))... (-21.76 = -23.27 +   1.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,576,516 – 18,576,629
Length 113
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 75.63
Shannon entropy 0.46554
G+C content 0.46322
Mean single sequence MFE -34.47
Consensus MFE -18.25
Energy contribution -19.17
Covariance contribution 0.92
Combinations/Pair 1.36
Mean z-score -1.44
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.27
SVM RNA-class probability 0.622570
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18576516 113 - 27905053
-AAAGUAAAACUCG---GCGAACAGUUACUCGCAUAGGGUGACCAUCACAUGGAUGGUCAUACAAAAUAAUGGUUACUACUGCAGGGCUUUGCCUGCAAAUGCAGUGACAUGGUCUG
-...(((..((((.---((((........))))...))))(((((((.....))))))).))).........((((((.(((((((......))))))...).))))))........ ( -36.00, z-score =  -2.63, R)
>droEre2.scaffold_4820 972167 114 + 10470090
AAAAGUAAAACUCU---GCGAACAGUUACUCGCUUAGGGUGACCAUCCCAUGGUUGGGCAUGCCGAAUGAUGGUUACUUCAGUAGGCCUUUGCUUGAGAAUGCAGUGGCAUGGUCUU
.........(((((---((((........))))..)))))((((((.((((.(((.((....)).))).))))((((....))))(((.((((........)))).))))))))).. ( -37.10, z-score =  -1.47, R)
>droYak2.chr3R 19425773 114 - 28832112
AAAAGUAAAACUCU---GCGAACAGUUACGCGCUUAGGGUGACCAUCACAUGACUGGUCAUGCGAAAUGAUGGUUACUACCGUAGGGCUUUGCUUGCGAAUGAAGUGGCAUGGUCUU
..(((((((.((((---(((...(((.....)))...((((((((((((((((....))))).....)))))))))))..))))))).)))))))((.(......).))........ ( -35.60, z-score =  -1.87, R)
>droSec1.super_0 18932994 113 - 21120651
-AAAGUAAAACUCA---GCGAACAGUUACUCGCUUAGGGUGGCCAUCACAUGGUUGGUCAUGCAAAAUGAUGGUUACUACUGCAGGGCUUUGCCUGGCAAUACAGUGACAUGGUAUG
-...(((...((.(---((((........))))).))((((((((((((((((....))))).....)))))))))))..(((.((((...)))).))).))).............. ( -33.30, z-score =  -0.94, R)
>droSim1.chr3R 18387425 113 - 27517382
-AAAGUAAAACUCG---GUGAACAGUUACUCGCUUAGGGUGACCAUCACAUGGUUGGUCAUGCAAAAUGAUGGUUACUACUGCAGGGCUUUGCCUGCAAAUGCAGUGGCAUGGUCUG
-...(((...((.(---((((........))))).))((((((((((((((((....))))).....)))))))))))..))).(((((.(((((((....)))..)))).))))). ( -38.40, z-score =  -2.24, R)
>droMoj3.scaffold_6540 1086530 113 + 34148556
--AAAUAAACUCCAACUGCCAACUGUUACAAUGUGAGUGUGACCAGAGCGAGA-UAGCUGCUGAGAGUGUAGUUGAUUUCAGUACGCGAGUUCACGCAACU-CAGAGAAACGGUCUC
--...................((((((....(.((((((((..((((((....-..))).)))...(((((.(((....)))))))).......))).)))-)).)..))))))... ( -26.40, z-score =   0.49, R)
>consensus
_AAAGUAAAACUCA___GCGAACAGUUACUCGCUUAGGGUGACCAUCACAUGGUUGGUCAUGCAAAAUGAUGGUUACUACUGCAGGGCUUUGCCUGCAAAUGCAGUGACAUGGUCUG
........................(((((........(((((((((((((((......)))).....)))))))))))...(((((......))))).......)))))........ (-18.25 = -19.17 +   0.92)

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 00:35:55 2011