Locus 3387

Sequence ID dm3.chr2R
Location 4,773,697 – 4,773,816
Length 119
Max. P 0.964267
window4657 window4658

overview

Window 7

Location 4,773,697 – 4,773,816
Length 119
Sequences 7
Columns 119
Reading direction forward
Mean pairwise identity 80.31
Shannon entropy 0.40037
G+C content 0.59755
Mean single sequence MFE -49.33
Consensus MFE -29.49
Energy contribution -31.86
Covariance contribution 2.37
Combinations/Pair 1.26
Mean z-score -2.27
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.73
SVM RNA-class probability 0.964267
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 4773697 119 + 21146708
AAGAAGGCGGCACAGGAGCGGCAGGAGGCGCAAAAGGCUCAGGAGGCCGCUAUGGCCUCCAUCGAGGCGGAAGCCAAGAAGUCGUCAUCUGCGCCUCAGGAGACUCCAGCUGUUCACCA
........((.....(((((((..((((((((...(((...(((((((.....))))))).((..(((....)))..))....)))...))))))))((....))...))))))).)). ( -57.10, z-score =  -3.35, R)
>droSim1.chr2R 3446648 119 + 19596830
AAGAAGGCGGCACAGGAGCGGCAGGAGGCGCAAAAGGCUCAGGAGGCCGCUAUGGCCUCCAUCGAGGCGGAAGCCAAGAAGUCGUCAUCUGCGCCUCAGGAGACUCCAGCCGUCCACCA
.....((((((...(((((..(..((((((((...(((...(((((((.....))))))).((..(((....)))..))....)))...))))))))..).).)))).))))))..... ( -60.60, z-score =  -4.15, R)
>droSec1.super_1 2411549 119 + 14215200
AAGAAGGCGGCACAAGAGCGGCAGGAGGCGCAAAAGGCUCAGGAGGCCGCUAUGGCCUCCAUCGAGGCGGAAGCCAAGAAGUCGUCAUCUGCGCCUCAGGAGACUCCAGCCGUCCACCA
.....((.((.......(((((..((((((((...(((...(((((((.....))))))).((..(((....)))..))....)))...))))))))((....))...))))))).)). ( -57.71, z-score =  -3.70, R)
>droYak2.chr2L 17432178 119 + 22324452
AAGAAGGCGGCACAGGAGCGGCAGGAAGCACAAAAGGCUCAGGAGGCCGCGAUGGCCUCCAUCGAGGCGGAAGCCAAGAAGUCGUCAUCUGCGCCUCAGGAGACUCCAGCCGUCCACCA
..((.((((((.((((.(((((..((.((.......)))).(((((((.....))))))).((..(((....)))..)).)))))..)))).)))..((....))...))).))..... ( -50.10, z-score =  -2.02, R)
>droEre2.scaffold_4929 8763395 119 - 26641161
AAGAAGGCGGCACAGGAGCGGCAGGAGGCGCAAAAGGCUCAGGAGGCCGCAAUGGCCUCCAUCGAGGCGGAAGCCAAGAAGUCCUCAUCUGCGCCUCAGGAGACUCCAGCCGUCCACCA
.....((((((...(((((..(..((((((((..(((((..(((((((.....))))))).((..(((....)))..)))).)))....))))))))..).).)))).))))))..... ( -60.40, z-score =  -4.05, R)
>droWil1.scaffold_180697 1453561 119 - 4168966
AAAAAGGCUGCCCAAGAGCGUCAGGAGGCUCAGAAGGCACAAGAAGCGGCUAUGGCAUCGAUUGAAGCGGAGGCCAAGAAAUCCUCUGCUGCCCCCCAGGAGACUCCAGCUGUUCAUCA
........((((...((((.(....).))))....))))...(((.(((((..(((.((....))((((((((.........)))))))))))....((....))..)))))))).... ( -35.50, z-score =   1.17, R)
>triCas2.ChLG3 11743028 113 - 32080666
AAACGAGCAGCUCAAGAAAAAGUCGAAGCUCAAGCGGCUCAACAAGCGGUAAUGCAAGCAAUUGAGUCCGAAUCCAAACA------ACCUGUUGUUACUGAACCUUCUGCCGUUUCACA
(((((.((((...(((......(((..((((((((.(((.....))).))..((....)).)))))).))).....((((------(....))))).......)))))))))))).... ( -23.90, z-score =   0.24, R)
>consensus
AAGAAGGCGGCACAGGAGCGGCAGGAGGCGCAAAAGGCUCAGGAGGCCGCUAUGGCCUCCAUCGAGGCGGAAGCCAAGAAGUCGUCAUCUGCGCCUCAGGAGACUCCAGCCGUCCACCA
.....((((((....(((..(((((((.(......).))).(((((((.....))))))).((..(((....)))..)).........))))..))).((.....)).))))))..... (-29.49 = -31.86 +   2.37)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,773,697 – 4,773,816
Length 119
Sequences 7
Columns 119
Reading direction reverse
Mean pairwise identity 80.31
Shannon entropy 0.40037
G+C content 0.59755
Mean single sequence MFE -48.36
Consensus MFE -36.05
Energy contribution -36.29
Covariance contribution 0.23
Combinations/Pair 1.41
Mean z-score -1.67
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.48
SVM RNA-class probability 0.942714
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 4773697 119 - 21146708
UGGUGAACAGCUGGAGUCUCCUGAGGCGCAGAUGACGACUUCUUGGCUUCCGCCUCGAUGGAGGCCAUAGCGGCCUCCUGAGCCUUUUGCGCCUCCUGCCGCUCCUGUGCCGCCUUCUU
.((((....((.(((((.....((((((((((.(.(....((..(((....)))..)).(((((((.....)))))))...).).)))))))))).....))))).))..))))..... ( -51.40, z-score =  -2.53, R)
>droSim1.chr2R 3446648 119 - 19596830
UGGUGGACGGCUGGAGUCUCCUGAGGCGCAGAUGACGACUUCUUGGCUUCCGCCUCGAUGGAGGCCAUAGCGGCCUCCUGAGCCUUUUGCGCCUCCUGCCGCUCCUGUGCCGCCUUCUU
.((.((.((((.(((((.....((((((((((.(.(....((..(((....)))..)).(((((((.....)))))))...).).)))))))))).....)))))...)))))).)).. ( -55.80, z-score =  -2.99, R)
>droSec1.super_1 2411549 119 - 14215200
UGGUGGACGGCUGGAGUCUCCUGAGGCGCAGAUGACGACUUCUUGGCUUCCGCCUCGAUGGAGGCCAUAGCGGCCUCCUGAGCCUUUUGCGCCUCCUGCCGCUCUUGUGCCGCCUUCUU
.((.((.((((.(((((.....((((((((((.(.(....((..(((....)))..)).(((((((.....)))))))...).).)))))))))).....)))))...)))))).)).. ( -53.90, z-score =  -2.52, R)
>droYak2.chr2L 17432178 119 - 22324452
UGGUGGACGGCUGGAGUCUCCUGAGGCGCAGAUGACGACUUCUUGGCUUCCGCCUCGAUGGAGGCCAUCGCGGCCUCCUGAGCCUUUUGUGCUUCCUGCCGCUCCUGUGCCGCCUUCUU
.((.((.((((.(((((.....((((((((((.(.(....((..(((....)))..)).(((((((.....)))))))...).).)))))))))).....)))))...)))))).)).. ( -51.20, z-score =  -2.04, R)
>droEre2.scaffold_4929 8763395 119 + 26641161
UGGUGGACGGCUGGAGUCUCCUGAGGCGCAGAUGAGGACUUCUUGGCUUCCGCCUCGAUGGAGGCCAUUGCGGCCUCCUGAGCCUUUUGCGCCUCCUGCCGCUCCUGUGCCGCCUUCUU
.((.((.((((.(((((.....((((((((((..(((.(((...(((....))).....(((((((.....))))))).)))))))))))))))).....)))))...)))))).)).. ( -58.80, z-score =  -3.37, R)
>droWil1.scaffold_180697 1453561 119 + 4168966
UGAUGAACAGCUGGAGUCUCCUGGGGGGCAGCAGAGGAUUUCUUGGCCUCCGCUUCAAUCGAUGCCAUAGCCGCUUCUUGUGCCUUCUGAGCCUCCUGACGCUCUUGGGCAGCCUUUUU
.........(((((((.(((..((((((((..(((((......((((.((..........)).))))......)))))..))))))))))).))))....(((....))))))...... ( -38.20, z-score =   1.30, R)
>triCas2.ChLG3 11743028 113 + 32080666
UGUGAAACGGCAGAAGGUUCAGUAACAACAGGU------UGUUUGGAUUCGGACUCAAUUGCUUGCAUUACCGCUUGUUGAGCCGCUUGAGCUUCGACUUUUUCUUGAGCUGCUCGUUU
....(((((((((.((((((((.(((((....)------))))......(((.((((((.....((......))..))))))))).))))))))...(((......))))))).))))) ( -29.20, z-score =   0.47, R)
>consensus
UGGUGGACGGCUGGAGUCUCCUGAGGCGCAGAUGACGACUUCUUGGCUUCCGCCUCGAUGGAGGCCAUAGCGGCCUCCUGAGCCUUUUGCGCCUCCUGCCGCUCCUGUGCCGCCUUCUU
.......((((.(((((.....((((((((((...........(((((((((......)))))))))....((((....).))).)))))))))).....)))))...))))....... (-36.05 = -36.29 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:09:16 2011