Locus 14030

Sequence ID dm3.chrX
Location 10,706,805 – 10,706,964
Length 159
Max. P 0.724194
window19297 window19298

overview

Window 7

Location 10,706,805 – 10,706,964
Length 159
Sequences 3
Columns 162
Reading direction forward
Mean pairwise identity 69.43
Shannon entropy 0.39679
G+C content 0.45759
Mean single sequence MFE -44.97
Consensus MFE -23.18
Energy contribution -24.30
Covariance contribution 1.12
Combinations/Pair 1.12
Mean z-score -1.95
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.51
SVM RNA-class probability 0.724194
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10706805 159 + 22422827
UUUUGAUGCCCAAAACCUUGGAGGGGCGCAUCGAAUCGCGGCCAAGGCGUAUAUA--AGGACCAUUGGUCGCCAUUUUCGCCCAAC-UUGGAUAAAUAGUAGUUACCCAACUAACUGAUCUAAACUGGUCUGGAUUUAUUUGAUUCGAUUUGAUGCAGGGGU
.......((((....(((....)))..(((((((((((((((((((((.(.....--).).)).)))))))).......(.(((..-((((((...((((((((....)))).))))))))))..))).).(((((.....)))))))))))))))..)))) ( -49.60, z-score =  -1.48, R)
>droSec1.super_11789 1094 135 + 1231
UUGAGAUGCCCAAAGCCUUGGAGGGGCGCAUCGAAUCGCGGCCAAGGCGUAUAUA--AAGACCAUUGGGCGCCAUUUUCGCCCAACAUUGGAUAAAUAGUAGCUACCCAACUAACUGAUCUAAACUGGUCUGGAUUU-------------------------
.........((...(((((((....(((........)))..))))))).......--.(((((((((((((.......)))))))..((((((...((((.........))))....))))))..))))))))....------------------------- ( -40.90, z-score =  -1.06, R)
>droEre2.scaffold_4690 14325285 130 - 18748788
UUUUGAUGCCCAAAACCUUGGAGGGGCGCAUCGAAUCGCGUCCAAAGCGUAUAUAUAAAAAGCAUUGGGCGCCAUUUUCGCC-AAC---GAACUGAUCUAAACUG--AAUUUAUUUGAUUCGAUUCGAUGCAGGGU--------------------------
.......((((....(((....)))..((((((((((((((((((.((.............)).))))))))....((((..-..)---)))............(--((((.....))))))))))))))).))))-------------------------- ( -44.42, z-score =  -3.29, R)
>consensus
UUUUGAUGCCCAAAACCUUGGAGGGGCGCAUCGAAUCGCGGCCAAGGCGUAUAUA__AAGACCAUUGGGCGCCAUUUUCGCCCAAC_UUGGAUAAAUAGUAGCUACCCAACUAACUGAUCUAAACUGGUCUGGAUUU_________________________
.....((((((((....))))..((.(((........))).))...))))........(((((.(((((((.......)))))))....((((......(((........)))....)))).....)))))............................... (-23.18 = -24.30 +   1.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,706,805 – 10,706,964
Length 159
Sequences 3
Columns 162
Reading direction reverse
Mean pairwise identity 69.43
Shannon entropy 0.39679
G+C content 0.45759
Mean single sequence MFE -40.77
Consensus MFE -27.53
Energy contribution -28.10
Covariance contribution 0.57
Combinations/Pair 1.26
Mean z-score -1.25
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.29
SVM RNA-class probability 0.629731
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10706805 159 - 22422827
ACCCCUGCAUCAAAUCGAAUCAAAUAAAUCCAGACCAGUUUAGAUCAGUUAGUUGGGUAACUACUAUUUAUCCAA-GUUGGGCGAAAAUGGCGACCAAUGGUCCU--UAUAUACGCCUUGGCCGCGAUUCGAUGCGCCCCUCCAAGGUUUUGGGCAUCAAAA
......(((((.(((((...............((((................((((((((.......))))))))-(((((.((.......)).)))))))))..--.......((....))..))))).)))))((((..(....)....))))....... ( -39.70, z-score =  -0.05, R)
>droSec1.super_11789 1094 135 - 1231
-------------------------AAAUCCAGACCAGUUUAGAUCAGUUAGUUGGGUAGCUACUAUUUAUCCAAUGUUGGGCGAAAAUGGCGCCCAAUGGUCUU--UAUAUACGCCUUGGCCGCGAUUCGAUGCGCCCCUCCAAGGCUUUGGGCAUCUCAA
-------------------------...((((((...((..(((((.....(((((((((.......)))))))))((((((((.......))))))))))))).--.))....(((((((..(((........)))....)))))))))))))........ ( -44.90, z-score =  -1.88, R)
>droEre2.scaffold_4690 14325285 130 + 18748788
--------------------------ACCCUGCAUCGAAUCGAAUCAAAUAAAUU--CAGUUUAGAUCAGUUC---GUU-GGCGAAAAUGGCGCCCAAUGCUUUUUAUAUAUACGCUUUGGACGCGAUUCGAUGCGCCCCUCCAAGGUUUUGGGCAUCAAAA
--------------------------.....((((((((((((((.......)))--)............(((---(..-..))))....(((.((((.((.............)).)))).)))))))))))))((((..(....)....))))....... ( -37.72, z-score =  -1.82, R)
>consensus
_________________________AAAUCCAGACCAGUUUAGAUCAGUUAGUUGGGUAGCUACUAUUUAUCCAA_GUUGGGCGAAAAUGGCGCCCAAUGGUCUU__UAUAUACGCCUUGGCCGCGAUUCGAUGCGCCCCUCCAAGGUUUUGGGCAUCAAAA
............................((((((........((((.......(((((((.......)))))))..((((((((.......))))))))))))...........(((((((..(((........)))....)))))))))))))........ (-27.53 = -28.10 +   0.57)

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 01:32:20 2011