Locus 2848

Sequence ID dm3.chr2RHet
Location 545,132 – 545,244
Length 112
Max. P 0.993970
window3928 window3929

overview

Window 8

Location 545,132 – 545,244
Length 112
Sequences 4
Columns 128
Reading direction forward
Mean pairwise identity 55.05
Shannon entropy 0.71299
G+C content 0.46430
Mean single sequence MFE -33.44
Consensus MFE -17.71
Energy contribution -18.15
Covariance contribution 0.44
Combinations/Pair 1.20
Mean z-score -0.66
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.01
SVM RNA-class probability 0.872217
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 545132 112 + 3288761
----------CUUCUCCACAGUGUCUGUGUUGUGAGUCUUAAAUAAAUUUCGUCUUAGGCUAAGCCGCGUAACUGCGCUGCCGGAUACGCCAGCGGCGUAGCGGCUUCCUUAUGUAUAUCUU------
----------...((((((((...)))))....)))..............(((...(((..(((((((.....((((((((.((.....)).)))))))))))))))))).)))........------ ( -32.40, z-score =  -0.95, R)
>droYak2.chrX_random 539130 108 + 1802292
----------UUUCUACA-AGUGUCUGUUUUGUGAUUCUUAAUUAUAUUUCGUCGAAGGCUAAGCCGCGUAGCUGCGCUGCCGGAUACGACAGCAGCGGAGCGGCUCUCUUA---AUAUCUU------
----------((((.(((-(((((..(((..(.....)..))).)))))).)).))))....((((((....((((((((.((....)).)))).)))).))))))......---.......------ ( -29.30, z-score =  -0.04, R)
>droEre2.scaffold_4929 25605958 117 + 26641161
---UUUCUGUGGUCUUUAUUAUAUUCAUCUUCCAAAAAGUACUUAUCUUUAAAUUAGCCUAGAGCUGCGCAACUUCGCUGCCAGAGAGACCGGCAGGGGAGGGGCUGUCUUAU--CUAUUUU------
---.(((((.(((.((((..........(((.....)))..........))))...))))))))....((..((((.(((((.........))))).))))..))........--.......------ ( -23.55, z-score =   1.56, R)
>droPer1.super_1295 3240 128 - 6930
CUGUUUUAUGGUGAUUUCUCUUCUAUAUUUUACAAUUGUGGUUUGGGCUUUUGUAAGCCCAAAGCCGCGGAGCUGCGCUGCCAGUGACGCCGGCAGCGGAGCGGCAGAACUAUGUGUUCUUAUCUCUU
.(((..(((((.((....))..)))))....))).(((((((((((((((....)))))).))))))))).(((.(((((((.(.....).))))))).)))...(((((.....)))))........ ( -48.50, z-score =  -3.23, R)
>consensus
__________GUUCUUCAUAGUGUCUAUUUUGCAAUUCUUAAUUAUAUUUCGUCUAACCCAAAGCCGCGUAACUGCGCUGCCAGAGACGCCAGCAGCGGAGCGGCUGUCUUAU__AUAUCUU______
...............................................................(((((....((((((((.((....)).)))).)))).)))))....................... (-17.71 = -18.15 +   0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 545,132 – 545,244
Length 112
Sequences 4
Columns 128
Reading direction reverse
Mean pairwise identity 55.05
Shannon entropy 0.71299
G+C content 0.46430
Mean single sequence MFE -30.43
Consensus MFE -18.09
Energy contribution -19.52
Covariance contribution 1.44
Combinations/Pair 1.19
Mean z-score -1.32
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.66
SVM RNA-class probability 0.993970
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 545132 112 - 3288761
------AAGAUAUACAUAAGGAAGCCGCUACGCCGCUGGCGUAUCCGGCAGCGCAGUUACGCGGCUUAGCCUAAGACGAAAUUUAUUUAAGACUCACAACACAGACACUGUGGAGAAG----------
------............(((.((((((.((..(((((.((....)).)))))..))...))))))...)))....................(((....(((((...))))))))...---------- ( -31.80, z-score =  -1.85, R)
>droYak2.chrX_random 539130 108 - 1802292
------AAGAUAU---UAAGAGAGCCGCUCCGCUGCUGUCGUAUCCGGCAGCGCAGCUACGCGGCUUAGCCUUCGACGAAAUAUAAUUAAGAAUCACAAAACAGACACU-UGUAGAAA----------
------.......---.....(((((((...((((((((((....)))))..)))))...)))))))....................((((..((........))..))-))......---------- ( -26.70, z-score =  -0.50, R)
>droEre2.scaffold_4929 25605958 117 - 26641161
------AAAAUAG--AUAAGACAGCCCCUCCCCUGCCGGUCUCUCUGGCAGCGAAGUUGCGCAGCUCUAGGCUAAUUUAAAGAUAAGUACUUUUUGGAAGAUGAAUAUAAUAAAGACCACAGAAA---
------.......--.......((((.......((((((.....))))))(((......))).......))))..((((((((.......))))))))...........................--- ( -19.40, z-score =   1.51, R)
>droPer1.super_1295 3240 128 + 6930
AAGAGAUAAGAACACAUAGUUCUGCCGCUCCGCUGCCGGCGUCACUGGCAGCGCAGCUCCGCGGCUUUGGGCUUACAAAAGCCCAAACCACAAUUGUAAAAUAUAGAAGAGAAAUCACCAUAAAACAG
........(((((.....)))))((.(((.(((((((((.....))))))))).)))...))((.(((((((((....)))))))))))...................((....))............ ( -43.80, z-score =  -4.46, R)
>consensus
______AAAAUAU__AUAAGACAGCCGCUCCGCUGCCGGCGUAUCCGGCAGCGCAGCUACGCGGCUUAGCCCUAAACGAAAUAUAAUUAAGAAUCACAAAACAGACACUAUAAAGAAC__________
.....................(((((((..(((((((((.....))))))))).......)))))))............................................................. (-18.09 = -19.52 +   1.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:59:12 2011