Locus 8214

Sequence ID dm3.chr3L
Location 21,054,230 – 21,054,368
Length 138
Max. P 0.601665
window11291 window11292

overview

Window 1

Location 21,054,230 – 21,054,368
Length 138
Sequences 3
Columns 160
Reading direction forward
Mean pairwise identity 53.12
Shannon entropy 0.64115
G+C content 0.36173
Mean single sequence MFE -18.68
Consensus MFE -7.60
Energy contribution -7.60
Covariance contribution 0.00
Combinations/Pair 1.29
Mean z-score -1.06
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.04
SVM RNA-class probability 0.513202
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 21054230 138 + 24543557
---------------CAACAGAGCCCCAAAGCUCUGUCCAUAUA-------CUACACAGUGAUUGCUCCCAAAAUUCAACUUCGGAAUACAAUUAAAAUUUAUAGCGACAGUAAGCCAAAAAUAAGAGAGAACUCUAUUAUCGAUACCCUCGACUACUAG
---------------..(((((((......))))))).......-------........((((((.(((.((........)).)))...))))))..............((((...........((((....))))....((((.....)))).)))).. ( -20.40, z-score =  -1.40, R)
>droEre2.scaffold_4784 20741667 139 + 25762168
---------------CUACAGAGCUCCAAAGCUCUGUCCACAUAGCAAAUACUACACACUGAUUGCUCUCAAAACUCGACUUUUGAAUACAAUUUAAAUUUAUAGCGACAGUAA-CCAAAAA----AGAGAACUCUAU-GUCAAUACCCUCGACUACUAG
---------------..((((((((....))))))))..((((((............((((.(((((.((((((......)))))).................)))))))))..-.(.....----.)......))))-))................... ( -20.87, z-score =  -1.54, R)
>droWil1.scaffold_180949 1034924 159 - 6375548
AGCAACAACACUUCUUGAUAGAGCUUUUGAGCUUAACUAAAAACGAAAUUAACCCAACGUCGAUAUCCACAGAAUAAUGCAAAACAAAAAAACAUAUGCUGAAAAAAAAACCAACCAAAAAUACACAGCAAAACCGAAUAGUGA-ACCUUUGAUUCAUAG
.(((.......((((.(((((((((....))))).........(((..((.....))..))).))))...))))...)))................(((((........................)))))..........((((-(.......))))).. ( -14.76, z-score =  -0.23, R)
>consensus
_______________CAACAGAGCUCCAAAGCUCUGUCCAAAUAG_AA_UACUACACAGUGAUUGCUCACAAAAUUCAACUUAAGAAUACAAUUUAAAUUUAUAGCGACAGUAA_CCAAAAA__A_AGAGAACUCUAUUAUCGAUACCCUCGACUACUAG
.................(((((((......)))))))........................................................................................................................... ( -7.60 =  -7.60 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,054,230 – 21,054,368
Length 138
Sequences 3
Columns 160
Reading direction reverse
Mean pairwise identity 53.12
Shannon entropy 0.64115
G+C content 0.36173
Mean single sequence MFE -34.75
Consensus MFE -13.38
Energy contribution -12.97
Covariance contribution -0.42
Combinations/Pair 1.55
Mean z-score -1.26
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.22
SVM RNA-class probability 0.601665
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 21054230 138 - 24543557
CUAGUAGUCGAGGGUAUCGAUAAUAGAGUUCUCUCUUAUUUUUGGCUUACUGUCGCUAUAAAUUUUAAUUGUAUUCCGAAGUUGAAUUUUGGGAGCAAUCACUGUGUAG-------UAUAUGGACAGAGCUUUGGGGCUCUGUUG---------------
.(((((((((((((((........((((....)))))))))))))).)))))..((((((.......(((((.(((((((((...)))))))))))))).....)))))-------).....(((((((((....))))))))).--------------- ( -39.90, z-score =  -2.56, R)
>droEre2.scaffold_4784 20741667 139 - 25762168
CUAGUAGUCGAGGGUAUUGAC-AUAGAGUUCUCU----UUUUUGG-UUACUGUCGCUAUAAAUUUAAAUUGUAUUCAAAAGUCGAGUUUUGAGAGCAAUCAGUGUGUAGUAUUUGCUAUGUGGACAGAGCUUUGGAGCUCUGUAG---------------
......(((((.....)))))-((((((((((..----.....((-((.(((((.............(((((.(((((((......))))))).)))))....(..((((....))))..).)))))))))..))))))))))..--------------- ( -36.60, z-score =  -1.47, R)
>droWil1.scaffold_180949 1034924 159 + 6375548
CUAUGAAUCAAAGGU-UCACUAUUCGGUUUUGCUGUGUAUUUUUGGUUGGUUUUUUUUUCAGCAUAUGUUUUUUUGUUUUGCAUUAUUCUGUGGAUAUCGACGUUGGGUUAAUUUCGUUUUUAGUUAAGCUCAAAAGCUCUAUCAAGAAGUGUUGUUGCU
..((.((((((((((-.(((..............))).)))))))))).))........((((((((((...........))))..((((...((((..(...(((((((((((........)))).)))))))...)..)))).))))))))))..... ( -27.74, z-score =   0.23, R)
>consensus
CUAGUAGUCGAGGGUAUCGAUAAUAGAGUUCUCU_U__UUUUUGG_UUACUGUCGCUAUAAAUUUAAAUUGUAUUCAAAAGUAGAAUUUUGAGAGCAAUCACUGUGUAGUA_UU_CUAUAUGGACAGAGCUUUGGAGCUCUGUAG_______________
(((...(((((.....)))))..))).((((((.........((((........))))...(((((...........)))))........))))))...........................((((((((....))))))))................. (-13.38 = -12.97 +  -0.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:41:28 2011