Locus 13833

Sequence ID dm3.chrX
Location 9,452,191 – 9,452,328
Length 137
Max. P 0.995205
window19031 window19032 window19033 window19034

overview

Window 1

Location 9,452,191 – 9,452,288
Length 97
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 64.48
Shannon entropy 0.56361
G+C content 0.47020
Mean single sequence MFE -25.88
Consensus MFE -16.06
Energy contribution -19.00
Covariance contribution 2.94
Combinations/Pair 1.20
Mean z-score -1.26
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.53
SVM RNA-class probability 0.947479
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9452191 97 + 22422827
-----UGAGUAUUAUUGUCGAAUCAUUAUCAAAGUCGUUUCCUGGUUUGGAUUCCUCGGAUUUGGUUGAGGAACCAAGCCAUGUGCCGACAUUUCGUCGGCA
-----.....................................((((((((.((((((((......))))))))))))))))..(((((((.....))))))) ( -32.70, z-score =  -2.89, R)
>droSim1.chrX 9470300 96 - 17042790
-----UGAGUAAUAUUAUCGAAUCAUUAUCAAAUUCGUUUCCUAGUUUGGAUUCCUCGGAAUCGGGCGAGGACCCAAGCC-UGUGCCGACAUUUCGUCGGCA
-----.............(((((.........))))).......((((((..((((((........)))))).)))))).-..(((((((.....))))))) ( -28.50, z-score =  -1.57, R)
>droSec1.super_15 218224 96 + 1954846
-----UGAGUAACAUUAUCGAAUCAUUAUCAAAUUCGUUUCCUGGUUUGGAUUCCUCGGAUUCGGGCGACGACCCAAGCC-UGUGCCGACAUUUCGUCGGCA
-----......(((....(((((.........)))))......(((((((..((((((....)))).))....)))))))-)))((((((.....)))))). ( -26.70, z-score =  -0.72, R)
>droEre2.scaffold_4784 23198909 90 - 25762168
CGAAUUAAAUCCCCUCCACUGGCAAAUCCACGCCUCGUCAUCUGGAAAAGAUUCCUCCCUCUCAAGCAAGGAAUUAGGCU-CAUCGCGACA-----------
....................(((........)))..(((..........(((((((..((....))..)))))))..((.-....))))).----------- ( -15.60, z-score =   0.14, R)
>consensus
_____UGAGUAACAUUAUCGAAUCAUUAUCAAAUUCGUUUCCUGGUUUGGAUUCCUCGGAUUCGGGCGAGGAACCAAGCC_UGUGCCGACAUUUCGUCGGCA
...........................................(((((((.(((((((........))))))))))))))....((((((.....)))))). (-16.06 = -19.00 +   2.94)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,452,191 – 9,452,288
Length 97
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 64.48
Shannon entropy 0.56361
G+C content 0.47020
Mean single sequence MFE -28.45
Consensus MFE -13.34
Energy contribution -16.40
Covariance contribution 3.06
Combinations/Pair 1.20
Mean z-score -1.92
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.67
SVM RNA-class probability 0.959849
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9452191 97 - 22422827
UGCCGACGAAAUGUCGGCACAUGGCUUGGUUCCUCAACCAAAUCCGAGGAAUCCAAACCAGGAAACGACUUUGAUAAUGAUUCGACAAUAAUACUCA-----
(((((((.....)))))))..(((.((((((((((..........)))))).)))).)))(....)....((((.......))))............----- ( -29.20, z-score =  -3.49, R)
>droSim1.chrX 9470300 96 + 17042790
UGCCGACGAAAUGUCGGCACA-GGCUUGGGUCCUCGCCCGAUUCCGAGGAAUCCAAACUAGGAAACGAAUUUGAUAAUGAUUCGAUAAUAUUACUCA-----
(((((((.....)))))))(.-((.(((((((((((........))))).)))))).)).)....((((((.......)))))).............----- ( -30.70, z-score =  -2.75, R)
>droSec1.super_15 218224 96 - 1954846
UGCCGACGAAAUGUCGGCACA-GGCUUGGGUCGUCGCCCGAAUCCGAGGAAUCCAAACCAGGAAACGAAUUUGAUAAUGAUUCGAUAAUGUUACUCA-----
(((((((.....)))))))..-((.((((((....))))))..))(((...(((......)))..((((((.......)))))).........))).----- ( -30.50, z-score =  -2.01, R)
>droEre2.scaffold_4784 23198909 90 + 25762168
-----------UGUCGCGAUG-AGCCUAAUUCCUUGCUUGAGAGGGAGGAAUCUUUUCCAGAUGACGAGGCGUGGAUUUGCCAGUGGAGGGGAUUUAAUUCG
-----------....((....-.))....((((((......)))))).(((((((((((((....)..((((......))))..))))))))))))...... ( -23.40, z-score =   0.58, R)
>consensus
UGCCGACGAAAUGUCGGCACA_GGCUUGGGUCCUCGCCCGAAUCCGAGGAAUCCAAACCAGGAAACGAAUUUGAUAAUGAUUCGAUAAUAUUACUCA_____
(((((((.....)))))))...((.(((((((((((........))))).)))))).)).(....)....((((.......))))................. (-13.34 = -16.40 +   3.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,452,222 – 9,452,328
Length 106
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 70.77
Shannon entropy 0.47399
G+C content 0.50274
Mean single sequence MFE -34.38
Consensus MFE -20.02
Energy contribution -23.90
Covariance contribution 3.88
Combinations/Pair 1.24
Mean z-score -1.86
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.56
SVM RNA-class probability 0.949962
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9452222 106 + 22422827
GUUUCCUGGUUUGGAUUCCUCGGAUUUGGUUGAGGAACCAAGCCAUGUGCCGACAUUUCGUCGGCAAUGUAGCUGUAACGAUGUGUACGCGCUUUGAGGUGACUGU
(((.((((((((((.((((((((......)))))))))))))))..((((..((((.((((((((......))))..)))).))))..))))....))).)))... ( -42.70, z-score =  -3.86, R)
>droSim1.chrX 9470331 105 - 17042790
GUUUCCUAGUUUGGAUUCCUCGGAAUCGGGCGAGGACCCAAGCC-UGUGCCGACAUUUCGUCGGCACUGUAGCUGUAACGAUGUGUACGCGCUUUGAGGUGACUGU
(((.(((.((((((..((((((........)))))).)))))).-.((((((((.....))))))))...........(((.(((....))).)))))).)))... ( -39.20, z-score =  -2.00, R)
>droSec1.super_15 218255 105 + 1954846
GUUUCCUGGUUUGGAUUCCUCGGAUUCGGGCGACGACCCAAGCC-UGUGCCGACAUUUCGUCGGCACUGUAGCUGUAACGAUGUGUACGCGCUUUGAGGUGACUGU
(((.((((((((((..((((((....)))).))....)))))))-.((((((((.....))))))))...........(((.(((....))).)))))).)))... ( -37.10, z-score =  -1.25, R)
>droEre2.scaffold_4784 23198945 89 - 25762168
GUCAUCUGGAAAAGAUUCCUCCCUCUCAAGCAAGGAAUUAGGCU---------CAUCGC---GACAGUGUUGCUGUAUUUAAGAGCAAAUGUCUUAAA-UGU----
..(((..(((...(((((((..((....))..)))))))..(((---------(.....---.((((.....))))......)))).....)))...)-)).---- ( -18.50, z-score =  -0.30, R)
>consensus
GUUUCCUGGUUUGGAUUCCUCGGAUUCGGGCGAGGAACCAAGCC_UGUGCCGACAUUUCGUCGGCACUGUAGCUGUAACGAUGUGUACGCGCUUUGAGGUGACUGU
(((.((((((((((.(((((((........))))))))))))))..((((((((.....))))))))...........(((.(((....))).)))))).)))... (-20.02 = -23.90 +   3.88)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,452,222 – 9,452,328
Length 106
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 70.77
Shannon entropy 0.47399
G+C content 0.50274
Mean single sequence MFE -31.28
Consensus MFE -18.11
Energy contribution -19.55
Covariance contribution 1.44
Combinations/Pair 1.33
Mean z-score -2.58
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.78
SVM RNA-class probability 0.995205
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9452222 106 - 22422827
ACAGUCACCUCAAAGCGCGUACACAUCGUUACAGCUACAUUGCCGACGAAAUGUCGGCACAUGGCUUGGUUCCUCAACCAAAUCCGAGGAAUCCAAACCAGGAAAC
.......((....(((..(((........))).)))....(((((((.....)))))))..(((.((((((((((..........)))))).)))).))))).... ( -32.00, z-score =  -3.30, R)
>droSim1.chrX 9470331 105 + 17042790
ACAGUCACCUCAAAGCGCGUACACAUCGUUACAGCUACAGUGCCGACGAAAUGUCGGCACA-GGCUUGGGUCCUCGCCCGAUUCCGAGGAAUCCAAACUAGGAAAC
.......((((..(((..(((........))).)))...((((((((.....)))))))).-((.((((((....))))))..))))))..(((......)))... ( -36.20, z-score =  -2.97, R)
>droSec1.super_15 218255 105 - 1954846
ACAGUCACCUCAAAGCGCGUACACAUCGUUACAGCUACAGUGCCGACGAAAUGUCGGCACA-GGCUUGGGUCGUCGCCCGAAUCCGAGGAAUCCAAACCAGGAAAC
.......((((..(((..(((........))).)))...((((((((.....)))))))).-((.((((((....))))))..))))))..(((......)))... ( -36.20, z-score =  -2.78, R)
>droEre2.scaffold_4784 23198945 89 + 25762168
----ACA-UUUAAGACAUUUGCUCUUAAAUACAGCAACACUGUC---GCGAUG---------AGCCUAAUUCCUUGCUUGAGAGGGAGGAAUCUUUUCCAGAUGAC
----.((-(((.......((.(((((((..((((.....)))).---((((.(---------((.....))).))))))))))).))((((....))))))))).. ( -20.70, z-score =  -1.29, R)
>consensus
ACAGUCACCUCAAAGCGCGUACACAUCGUUACAGCUACAGUGCCGACGAAAUGUCGGCACA_GGCUUGGGUCCUCGCCCGAAUCCGAGGAAUCCAAACCAGGAAAC
.......((((......................(((...((((((((.....))))))))..)))((((((....))))))....))))..(((......)))... (-18.11 = -19.55 +   1.44)

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 01:28:40 2011