Locus 5750

Sequence ID dm3.chr3L
Location 816,614 – 816,707
Length 93
Max. P 0.999772
window7903 window7904

overview

Window 3

Location 816,614 – 816,707
Length 93
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 50.67
Shannon entropy 0.82504
G+C content 0.35286
Mean single sequence MFE -20.55
Consensus MFE -7.60
Energy contribution -9.22
Covariance contribution 1.63
Combinations/Pair 1.45
Mean z-score -2.99
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.36
SVM RNA-class probability 0.999772
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 816614 93 + 24543557
--------------AAAAAACUACACAGAAAAAAAA-----AGAAUUAAUUUUAA--CUUGCCGCAUAUCACAAACACUAUUUGCGGCGAAUUAAACAUCAUUGCCAUCACACU
--------------......................-----.........(((((--.((((((((................)))))))).))))).................. ( -13.89, z-score =  -3.33, R)
>droEre2.scaffold_4784 832074 114 + 25762168
AAAAAAAGGAACAUAAAAGAUCGCGUUGAAUUAAACGAUUUAAAUUGGAUAUCAAAACUCGCCGCAGACCACAAACACUAUUUGCGGCGAGUUUUGCAUCAUUGCCAACACACC
.......((..((....((((((..(......)..))))))....))(((..((((((((((((((((............)))))))))))))))).)))....))........ ( -31.40, z-score =  -4.62, R)
>droYak2.chr3L 811957 103 + 24197627
AAAUAAUGGAACAGAAAAAAAAG-----AAAUAAA------AAAUGGGAUAUCAAAACUCGCCGCAAACCAUAACCACUAUUUGCGGCGAAUUUAACAUCAUUGCCAACACACU
......(((....((........-----.......------...(((....)))(((.((((((((((............)))))))))).)))....))....)))....... ( -17.90, z-score =  -2.83, R)
>droMoj3.scaffold_6496 17934691 107 + 26866924
AAACUCGUAUUCUGAUAAAAUGAAGUCUUAUUUUGA-----UUAGCAAGCAAUACAGCUCGCACCACUGUGCGAAUAAAUACCGAGCUACACUCAACAC--UCAUCUGCAUAUU
......(((((((((((((((((....))))))).)-----)))).....))))).((((((((....)))))).........(((.....))).....--......))..... ( -19.00, z-score =  -1.19, R)
>consensus
AAA_AA_GGAACAGAAAAAAUAACGU_GAAAUAAAA_____AAAUUGAAUAUCAAAACUCGCCGCAAACCACAAACACUAUUUGCGGCGAAUUUAACAUCAUUGCCAACACACU
..........................................................(((((((((((..........)))))))))))........................ ( -7.60 =  -9.22 +   1.63)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 816,614 – 816,707
Length 93
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 50.67
Shannon entropy 0.82504
G+C content 0.35286
Mean single sequence MFE -25.59
Consensus MFE -12.41
Energy contribution -12.60
Covariance contribution 0.19
Combinations/Pair 1.65
Mean z-score -1.75
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.39
SVM RNA-class probability 0.998541
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 816614 93 - 24543557
AGUGUGAUGGCAAUGAUGUUUAAUUCGCCGCAAAUAGUGUUUGUGAUAUGCGGCAAG--UUAAAAUUAAUUCU-----UUUUUUUUCUGUGUAGUUUUUU--------------
.............((((.(((((((.((((((.((..........)).)))))).))--))))))))).....-----......................-------------- ( -14.10, z-score =   0.63, R)
>droEre2.scaffold_4784 832074 114 - 25762168
GGUGUGUUGGCAAUGAUGCAAAACUCGCCGCAAAUAGUGUUUGUGGUCUGCGGCGAGUUUUGAUAUCCAAUUUAAAUCGUUUAAUUCAACGCGAUCUUUUAUGUUCCUUUUUUU
((((((((((.((((((.((((((((((((((.((..........)).)))))))))))))).............))))))....))))))).))).................. ( -33.44, z-score =  -3.09, R)
>droYak2.chr3L 811957 103 - 24197627
AGUGUGUUGGCAAUGAUGUUAAAUUCGCCGCAAAUAGUGGUUAUGGUUUGCGGCGAGUUUUGAUAUCCCAUUU------UUUAUUU-----CUUUUUUUUCUGUUCCAUUAUUU
.......(((....(((((((((((((((((((((.((....)).)))))))))))).))))))))))))...------.......-----....................... ( -27.20, z-score =  -3.59, R)
>droMoj3.scaffold_6496 17934691 107 - 26866924
AAUAUGCAGAUGA--GUGUUGAGUGUAGCUCGGUAUUUAUUCGCACAGUGGUGCGAGCUGUAUUGCUUGCUAA-----UCAAAAUAAGACUUCAUUUUAUCAGAAUACGAGUUU
....(((..((((--(((..(((.....)))..)))))))..)))...((((((((((......))))))..)-----))).....((((((.((((.....))))..)))))) ( -27.60, z-score =  -0.97, R)
>consensus
AGUGUGUUGGCAAUGAUGUUAAAUUCGCCGCAAAUAGUGUUUGUGGUAUGCGGCGAGUUUUAAUAUCCAAUUU_____UUUUAAUUC_ACGCAAUUUUUUCUGUUCC_UU_UUU
..(((....)))..((((((((((((((((((.((..........)).))))))))))).)))))))............................................... (-12.41 = -12.60 +   0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:54:25 2011