Locus 4729

Sequence ID dm3.chr2R
Location 15,329,738 – 15,329,876
Length 138
Max. P 0.989153
window6490 window6491

overview

Window 0

Location 15,329,738 – 15,329,876
Length 138
Sequences 6
Columns 139
Reading direction forward
Mean pairwise identity 73.88
Shannon entropy 0.50717
G+C content 0.50432
Mean single sequence MFE -40.95
Consensus MFE -23.82
Energy contribution -25.13
Covariance contribution 1.32
Combinations/Pair 1.38
Mean z-score -2.14
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.35
SVM RNA-class probability 0.989153
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15329738 138 + 21146708
-CCGUUAGUGAUGGAACGACGUGCGCACAACAGCACGAUAGUUGGAUAACAGCACGACAACAGCACGUGUCGUGCGUUUUUUAGGUCCAUUUGUGCGCCUCAGCGCGGCCACACUAUCCUUUCCUUCUUUUCUUACAAG
-..((.((.((.((((.(..((((........))))((((((((((((((.((((((((........)))))))))))......)))))...(((.(((.......))))))))))))).)))).))....)).))... ( -43.00, z-score =  -1.99, R)
>droSim1.chr2R 14042184 138 + 19596830
-CCGUUAGUGAUGGAAGGCCGUGCGCACAACAGCACGAUAGUUCGAUAACAGCACGACAACAGCACGUGUCGUGCGUUUUUUAGGUCCAUUUGUGCGCUUCAGCGCGGUCACACUAACCUUUCCUUCUUUUCUUACAAG
-..(((((((.(((..(((.(.((((((((.....(((....)))......((((((((........))))))))...............))))))))..).)).)..))))))))))..................... ( -42.80, z-score =  -2.11, R)
>droSec1.super_1 12845753 139 + 14215200
CCUGUUAGUGAUGGAAGGCCGUGCGCACAACAGCACGAUAGUUCGAUAACAGCACGACAACAGCACGUGUCGUGCGUUUUUUAGGUUCAUUUGUGCGCUUCAGCGCGGCCACACUAACCUUUCCUUCUUUUCUUACAAG
...(((((((.(((..(((.(.((((((((.(((.(((....)))......((((((((........)))))))).........)))...))))))))..).)).)..))))))))))..................... ( -45.10, z-score =  -2.55, R)
>droYak2.chr2R 7292471 138 - 21139217
-GCGUUAGUGAUGGAACGGCGAGCGCACAACAGCACGAUAGUCCGAUAACAGCACGACAACAGCACGUGUCGUGCGUUAUUUAGGCCCAUUCGUGCGCUUCGGCGCGGCCACACUAACCUUUCCUUCUUUUCUUACAAG
-..(((((((..(((....((.((........)).))....)))((((((.((((((((........))))))))))))))..((((.......((((....)))))))).)))))))..................... ( -49.61, z-score =  -3.24, R)
>droEre2.scaffold_4845 9528374 138 + 22589142
-CCGCUAGUGAUGGAACAGCGUGCGCACAACAGCACGAUAGUCCGAUAACAGCACGACAACAGCACGUGUCGAGCGUUUUUUAGGCCCAUUCGUGCGCUUCAGUGCGGCCACACUAACCUUUCCUUCUUUUCUUACAAG
-....(((((.((((....(((((........)))))....))))......((.(((((........))))).))........((((.......((((....)))))))).)))))....................... ( -37.71, z-score =  -0.79, R)
>droAna3.scaffold_13266 17949152 112 - 19884421
------------------CCAUUUG---AAUUUGAGAAAACCCAGACAAAAACGCGUUAGUACCACA--AUAAGUGGUAUUUGGCCAGACUGCCCUCCUCCCAUCUGGCAGCACUGGUUCCCUCUUUUCUUUUCG----
------------------......(---((...(((..((((.((........((...((((((((.--....))))))))..))..(.(((((............)))))).))))))..)))..)))......---- ( -27.50, z-score =  -2.15, R)
>consensus
_CCGUUAGUGAUGGAACGCCGUGCGCACAACAGCACGAUAGUCCGAUAACAGCACGACAACAGCACGUGUCGUGCGUUUUUUAGGCCCAUUUGUGCGCUUCAGCGCGGCCACACUAACCUUUCCUUCUUUUCUUACAAG
.....(((((.(((.....(((((........((((((....((.......((((((((........))))))))........)).....))))))......))))).))))))))....................... (-23.82 = -25.13 +   1.32)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,329,738 – 15,329,876
Length 138
Sequences 6
Columns 139
Reading direction reverse
Mean pairwise identity 73.88
Shannon entropy 0.50717
G+C content 0.50432
Mean single sequence MFE -42.97
Consensus MFE -27.50
Energy contribution -28.73
Covariance contribution 1.23
Combinations/Pair 1.37
Mean z-score -0.97
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.57
SVM RNA-class probability 0.744914
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15329738 138 - 21146708
CUUGUAAGAAAAGAAGGAAAGGAUAGUGUGGCCGCGCUGAGGCGCACAAAUGGACCUAAAAAACGCACGACACGUGCUGUUGUCGUGCUGUUAUCCAACUAUCGUGCUGUUGUGCGCACGUCGUUCCAUCACUAACGG-
............((.((((..((((((.(((..((((....))))................(((((((((((........)))))))).)))..)))))))))((((......))))......)))).))........- ( -41.80, z-score =  -0.29, R)
>droSim1.chr2R 14042184 138 - 19596830
CUUGUAAGAAAAGAAGGAAAGGUUAGUGUGACCGCGCUGAAGCGCACAAAUGGACCUAAAAAACGCACGACACGUGCUGUUGUCGUGCUGUUAUCGAACUAUCGUGCUGUUGUGCGCACGGCCUUCCAUCACUAACGG-
............((.((((.(((((((((....))))))..((((((((..(.((......(((((((((((........)))))))).)))...((....)))).)..))))))))...))))))).))........- ( -43.90, z-score =  -1.33, R)
>droSec1.super_1 12845753 139 - 14215200
CUUGUAAGAAAAGAAGGAAAGGUUAGUGUGGCCGCGCUGAAGCGCACAAAUGAACCUAAAAAACGCACGACACGUGCUGUUGUCGUGCUGUUAUCGAACUAUCGUGCUGUUGUGCGCACGGCCUUCCAUCACUAACAGG
.....................((((((((((..(.((((..((((((((...............((((((((........)))))))).((...(((....))).))..)))))))).)))))..))).)))))))... ( -45.70, z-score =  -1.59, R)
>droYak2.chr2R 7292471 138 + 21139217
CUUGUAAGAAAAGAAGGAAAGGUUAGUGUGGCCGCGCCGAAGCGCACGAAUGGGCCUAAAUAACGCACGACACGUGCUGUUGUCGUGCUGUUAUCGGACUAUCGUGCUGUUGUGCGCUCGCCGUUCCAUCACUAACGC-
.....................(((((((((((.(((((((...((((((.(((.((...(((((((((((((........)))))))).))))).)).)))))))))..))).))))..))))......)))))))..- ( -51.20, z-score =  -1.78, R)
>droEre2.scaffold_4845 9528374 138 - 22589142
CUUGUAAGAAAAGAAGGAAAGGUUAGUGUGGCCGCACUGAAGCGCACGAAUGGGCCUAAAAAACGCUCGACACGUGCUGUUGUCGUGCUGUUAUCGGACUAUCGUGCUGUUGUGCGCACGCUGUUCCAUCACUAGCGG-
............((.((((....(((((((..(((((...(((((((((.(((.((.....(((((.(((((........))))).)).)))...)).))))))))).))))))))))))))))))).))........- ( -42.70, z-score =   0.28, R)
>droAna3.scaffold_13266 17949152 112 + 19884421
----CGAAAAGAAAAGAGGGAACCAGUGCUGCCAGAUGGGAGGAGGGCAGUCUGGCCAAAUACCACUUAU--UGUGGUACUAACGCGUUUUUGUCUGGGUUUUCUCAAAUU---CAAAUGG------------------
----......(((..(((..((((.(.....)(((((..(((...(((......)))...((((((....--.))))))........)))..)))))))))..)))...))---)......------------------ ( -32.50, z-score =  -1.13, R)
>consensus
CUUGUAAGAAAAGAAGGAAAGGUUAGUGUGGCCGCGCUGAAGCGCACAAAUGGACCUAAAAAACGCACGACACGUGCUGUUGUCGUGCUGUUAUCGAACUAUCGUGCUGUUGUGCGCACGGCGUUCCAUCACUAACGG_
............((.((((...(((((((....))))))).((((((((..(.((.........((((((((........)))))))).(((....)))....)).)..))))))))......)))).))......... (-27.50 = -28.73 +   1.23)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:34:51 2011