Locus 12405

Sequence ID dm3.chr4
Location 733,901 – 734,045
Length 144
Max. P 0.976180
window17045 window17046 window17047

overview

Window 5

Location 733,901 – 733,999
Length 98
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 90.35
Shannon entropy 0.16216
G+C content 0.47271
Mean single sequence MFE -30.50
Consensus MFE -25.00
Energy contribution -25.52
Covariance contribution 0.52
Combinations/Pair 1.12
Mean z-score -1.82
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.51
SVM RNA-class probability 0.725664
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 733901 98 - 1351857
UCCUUUGGGGACAACAAGUGCAUGCGCAAGCUGUACGCCAAAGGAUACCUUU---------AGUAUGUGCAAUCAUCGAAAGUAUCACAAGCUUAGUCGCAUGUAAG
....(((....)))....((((((((((((((((((((.(((((...)))))---------.))..))))......(....).......))))).).)))))))).. ( -27.70, z-score =  -1.78, R)
>droEre2.scaffold_4512 755554 107 + 1286254
UCCUUUGGGGACAACAAGUGCAUGCGCAAGCUUCACGCCAAAGGAAUCCUUUGCCAUGUGCACUAUGUGCACUCAUCGAAAGUAUCGCAAGCUUAGUCGCUUGUAAG
(((((((((.....)..(((...((....))..))).))))))))....((((....((((((...))))))....))))......((((((......))))))... ( -34.50, z-score =  -2.06, R)
>droYak2.chr4 794802 98 - 1374474
UCCUUUGGGGACAACAAGUGCAUGCGCAAGCUUCAAGCCAAAGGAAACCUUU---------ACUUUGUGCACUAAUCGAAAGUAUCGCAAGCAUAGUCGCAUGUAAG
(((((((((.((.....)).)..((....))......)))))))).....((---------((..((((.((((..(....)...(....)..)))))))).)))). ( -26.70, z-score =  -1.54, R)
>droSec1.super_30 450284 98 - 664411
UCCUUUGGGGACAACAAGUGCAUGCGCAAGCUGCACGCCAAAGGAUACCUUU---------AGUAUGUGCACUCAUCGAAAGUAUCGCAAGCUUAGUCGCAUGUGAG
(((((((((.....)..(((((.((....))))))).))))))))...((((---------.(.(((......)))).))))..(((((.((......)).))))). ( -32.40, z-score =  -2.00, R)
>droSim1.chr4 560585 98 - 949497
UCCUUUGGGGACAACAAGUGCAUGCGCAAGCUGCACGCCGAAGGAUACCUUU---------AGUAUGUGCACUCAUCGAAAGUAUCGCAAGCUUAGUCGCAUGUAAG
(((((((((.....)..(((((.((....))))))).)))))))).......---------..((((((((((...(....)...(....)...))).))))))).. ( -31.20, z-score =  -1.74, R)
>consensus
UCCUUUGGGGACAACAAGUGCAUGCGCAAGCUGCACGCCAAAGGAUACCUUU_________AGUAUGUGCACUCAUCGAAAGUAUCGCAAGCUUAGUCGCAUGUAAG
(((((((((.....)..(((((.((....))))))).))))))))..................(((((((......(....)...(....).......))))))).. (-25.00 = -25.52 +   0.52)

alignment

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secondary structure

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dotplot

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Window 6

Location 733,928 – 734,039
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.82
Shannon entropy 0.41390
G+C content 0.48921
Mean single sequence MFE -34.42
Consensus MFE -24.54
Energy contribution -26.06
Covariance contribution 1.52
Combinations/Pair 1.12
Mean z-score -1.99
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.95
SVM RNA-class probability 0.976180
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 733928 111 - 1351857
AAUCCGGCACCAGUUCCCGCUUUCCUGGAUUGCAUUCGUUUCCUUUGGGGACAACAAGUGCAUGCGCAAGCUGUACGCCAAAGGAUACCUUUAGUAUGUGCAAUCAUCGAA---------
....(((...(((...........)))((((((((..((.(((((((((.....)..(((((.((....))))))).)))))))).)).........)))))))).)))..--------- ( -32.80, z-score =  -1.29, R)
>droEre2.scaffold_4512 755581 119 + 1286254
AAUCCGGAAACUGCGUCCGCUUU-CUGGAGAGCAUUCGCUUCCUUUGGGGACAACAAGUGCAUGCGCAAGCUUCACGCCAAAGGAAUCCUUUGCCAUGUGCACUAUGUGCACUCAUCGAA
..((((((((..((....)))))-)))))(.(((...(.((((((((((.....)..(((...((....))..))).))))))))).)...))))..((((((...))))))........ ( -40.70, z-score =  -2.03, R)
>droYak2.chr4 794829 111 - 1374474
AAUCCGGAAACUGAGCCCGCUUUACUGGAGAGCAUUCGUUUCCUUUGGGGACAACAAGUGCAUGCGCAAGCUUCAAGCCAAAGGAAACCUUUACUUUGUGCACUAAUCGAA---------
..((.(....).))((.((((((.....)))))....((((((((((((.((.....)).)..((....))......))))))))))).........).))..........--------- ( -30.70, z-score =  -0.90, R)
>droSec1.super_30 450311 93 - 664411
------------------AAUCCGGUGGAUUGCAUUCGUUUCCUUUGGGGACAACAAGUGCAUGCGCAAGCUGCACGCCAAAGGAUACCUUUAGUAUGUGCACUCAUCGAA---------
------------------....((((((..(((((..((.(((((((((.....)..(((((.((....))))))).)))))))).)).........))))).))))))..--------- ( -34.10, z-score =  -3.03, R)
>droSim1.chr4 560612 93 - 949497
------------------AAUCCGGUGGAUUGCAUUCGUUUCCUUUGGGGACAACAAGUGCAUGCGCAAGCUGCACGCCGAAGGAUACCUUUAGUAUGUGCACUCAUCGAA---------
------------------....((((((..(((((..((.(((((((((.....)..(((((.((....))))))).)))))))).)).........))))).))))))..--------- ( -33.80, z-score =  -2.69, R)
>consensus
AAUCCGG_A_C_G___CCGCUUUGCUGGAUUGCAUUCGUUUCCUUUGGGGACAACAAGUGCAUGCGCAAGCUGCACGCCAAAGGAUACCUUUAGUAUGUGCACUCAUCGAA_________
...........................((((((((..((.(((((((((.....)..(((((.((....))))))).)))))))).)).........))))))))............... (-24.54 = -26.06 +   1.52)

alignment

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secondary structure

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dotplot

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Window 7

Location 733,934 – 734,045
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.69
Shannon entropy 0.35080
G+C content 0.50838
Mean single sequence MFE -34.08
Consensus MFE -24.77
Energy contribution -26.65
Covariance contribution 1.88
Combinations/Pair 1.07
Mean z-score -1.61
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.87
SVM RNA-class probability 0.841396
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 733934 111 - 1351857
UCGACCAAUCCGGCACCAGUUCCCGCUUUCCUGGAUUGCAUUCGUUUCCUUUGGGGACAACAAGUGCAUGCGCAAGCUGUACGCCAAAGGAUACCUUUAGUAUGUGCAAUC---------
..((.((((((((....(((....)))...))))))))...))((.(((((((((.....)..(((((.((....))))))).)))))))).)).................--------- ( -33.20, z-score =  -1.45, R)
>droEre2.scaffold_4512 755587 119 + 1286254
UGGACCAAUCCGGAAACUGCGUCCGCUUU-CUGGAGAGCAUUCGCUUCCUUUGGGGACAACAAGUGCAUGCGCAAGCUUCACGCCAAAGGAAUCCUUUGCCAUGUGCACUAUGUGCACUC
........((((((((..((....)))))-)))))(.(((...(.((((((((((.....)..(((...((....))..))).))))))))).)...))))..((((((...)))))).. ( -40.70, z-score =  -1.77, R)
>droYak2.chr4 794835 111 - 1374474
UGGACCAAUCCGGAAACUGAGCCCGCUUUACUGGAGAGCAUUCGUUUCCUUUGGGGACAACAAGUGCAUGCGCAAGCUUCAAGCCAAAGGAAACCUUUACUUUGUGCACUA---------
((..((.....((((((.(((...(((((.....))))).)))))))))....))..))...(((((((((....))........(((((...))))).....))))))).--------- ( -32.60, z-score =  -1.03, R)
>droSec1.super_30 450317 93 - 664411
UGGACCAAUCCG------------------GUGGAUUGCAUUCGUUUCCUUUGGGGACAACAAGUGCAUGCGCAAGCUGCACGCCAAAGGAUACCUUUAGUAUGUGCACUC---------
.(((....)))(------------------(((.(((((....((.(((((((((.....)..(((((.((....))))))).)))))))).)).....))).)).)))).--------- ( -32.10, z-score =  -2.02, R)
>droSim1.chr4 560618 93 - 949497
UGGACCAAUCCG------------------GUGGAUUGCAUUCGUUUCCUUUGGGGACAACAAGUGCAUGCGCAAGCUGCACGCCGAAGGAUACCUUUAGUAUGUGCACUC---------
.(((....)))(------------------(((.(((((....((.(((((((((.....)..(((((.((....))))))).)))))))).)).....))).)).)))).--------- ( -31.80, z-score =  -1.78, R)
>consensus
UGGACCAAUCCGG_A_C_G___CCGCUUU_CUGGAUUGCAUUCGUUUCCUUUGGGGACAACAAGUGCAUGCGCAAGCUGCACGCCAAAGGAUACCUUUAGUAUGUGCACUC_________
((.((((((((((.................)))))))).....((.(((((((((.....)..(((((.((....))))))).)))))))).)).........)).))............ (-24.77 = -26.65 +   1.88)

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 01:01:29 2011