Locus 2791

Sequence ID dm3.chr2L
Location 22,407,571 – 22,407,688
Length 117
Max. P 0.942748
window3838 window3839 window3840

overview

Window 8

Location 22,407,571 – 22,407,673
Length 102
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 78.56
Shannon entropy 0.37196
G+C content 0.41668
Mean single sequence MFE -23.12
Consensus MFE -14.70
Energy contribution -14.78
Covariance contribution 0.08
Combinations/Pair 1.27
Mean z-score -1.70
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.66
SVM RNA-class probability 0.779063
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22407571 102 + 23011544
-AAAAUCAUAAAUUUGGCGGGACGAACGCACAAACUUU-CUGAUCUAGCCGC-UGCAAUCCGUAGCGAGCUAAAUAA-GAAAAUCAGUUCGUUACAGAUUGAUAAA
-...((((...(((((....(((((((........(((-((.((.(((((((-(((.....)))))).)))).)).)-))))....))))))).)))))))))... ( -29.90, z-score =  -3.62, R)
>droSec1.super_69 23438 93 + 174750
-CAAAUCAUAAAUUUGGUGGGACGAACGCACAAACUCU-CUGAGCUAGCCGC-UGCAACCAGUAGCGAGCGAAAUAAAGAAAAUCAGUUCGUUACA----------
-...((((......))))(..((((((((.((......-.)).))..(((((-(((.....)))))).))................))))))..).---------- ( -24.50, z-score =  -2.08, R)
>droYak2.chr2h_random 792673 105 - 3774259
UUAUUCUAUAAAUUUGGUGGGACGAACGCACAAACUCUACUGAGCUAGCCGCACGUAUUCCGUAGCGAGC-AGACAAACAAAAUCAGUUCGUUACAAGAAUAUGAA
.((((((..........((..((((((.......(((....)))...((((((((.....))).))).))-...............))))))..)))))))).... ( -23.30, z-score =  -1.20, R)
>droEre2.scaffold_4784 23980780 90 + 25762168
-CAAAUCAUAAAUUUGGUGGAACGAACAAACAAACUCU-CUGAGCUAGCCGU-UGAAAUUCGUAGCGAGCAGAACCAAGAAAAACAGUUCGUU-------------
-...((((......))))..(((((((..........(-(((.((((..((.-.......))))))...)))).....(.....).)))))))------------- ( -15.10, z-score =   0.08, R)
>droSim1.chrU 8921692 93 - 15797150
-CAAAUCAUAAAUUUGGUGGGACGAACACACAAACUCU-CUGAGCUAGCCGC-UGCAACCAGUAGCGAGCGAAAUAAAGAAAAUCGGUUCGUUACA----------
-...((((......))))(..((((((.......(((.-..)))...(((((-(((.....)))))).))................))))))..).---------- ( -22.80, z-score =  -1.69, R)
>consensus
_CAAAUCAUAAAUUUGGUGGGACGAACGCACAAACUCU_CUGAGCUAGCCGC_UGCAAUCCGUAGCGAGCGAAAUAAAGAAAAUCAGUUCGUUACA__________
....((((......))))..(((((((.......(((....)))...(((((.(((.....)))))).))................)))))))............. (-14.70 = -14.78 +   0.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 22,407,584 – 22,407,688
Length 104
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 72.18
Shannon entropy 0.44260
G+C content 0.44844
Mean single sequence MFE -24.05
Consensus MFE -15.98
Energy contribution -16.10
Covariance contribution 0.12
Combinations/Pair 1.11
Mean z-score -1.72
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.48
SVM RNA-class probability 0.942748
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22407584 104 + 23011544
UGGCGGGACGAACGCACAAACUUU-CUGAUCUAGCCGC-UGCAAUCCGUAGCGAGCUAAAUAA-GAAAAUCAGUUCGUUACAGAUUGAUAAAAUAAAAUGUGUAUAU
......(((((((........(((-((.((.(((((((-(((.....)))))).)))).)).)-))))....)))))))(((.(((..........))).))).... ( -27.30, z-score =  -2.38, R)
>droSec1.super_69 23451 80 + 174750
UGGUGGGACGAACGCACAAACUCU-CUGAGCUAGCCGC-UGCAACCAGUAGCGAGCGAAAUAAAGAAAAUCAGUUCGUUACA-------------------------
...((..((((((((.((......-.)).))..(((((-(((.....)))))).))................))))))..))------------------------- ( -23.40, z-score =  -1.66, R)
>droYak2.chr2h_random 792687 106 - 3774259
UGGUGGGACGAACGCACAAACUCUACUGAGCUAGCCGCACGUAUUCCGUAGCGAGC-AGACAAACAAAAUCAGUUCGUUACAAGAAUAUGAAGCAAAGAAAUAAAAU
..(((.(.....).)))...(((....)))......((.(((((((.(((((((((-.((.........)).)))))))))..)))))))..))............. ( -23.80, z-score =  -1.58, R)
>droSim1.chrU 8921705 80 - 15797150
UGGUGGGACGAACACACAAACUCU-CUGAGCUAGCCGC-UGCAACCAGUAGCGAGCGAAAUAAAGAAAAUCGGUUCGUUACA-------------------------
...((..((((((.......(((.-..)))...(((((-(((.....)))))).))................))))))..))------------------------- ( -21.70, z-score =  -1.28, R)
>consensus
UGGUGGGACGAACGCACAAACUCU_CUGAGCUAGCCGC_UGCAACCAGUAGCGAGCGAAAUAAAGAAAAUCAGUUCGUUACA_________________________
....(..((((((.......(((....)))...(((((.(((.....)))))).))................))))))..).......................... (-15.98 = -16.10 +   0.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 22,407,584 – 22,407,688
Length 104
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 72.18
Shannon entropy 0.44260
G+C content 0.44844
Mean single sequence MFE -23.38
Consensus MFE -14.52
Energy contribution -14.40
Covariance contribution -0.12
Combinations/Pair 1.11
Mean z-score -1.25
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.34
SVM RNA-class probability 0.651363
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22407584 104 - 23011544
AUAUACACAUUUUAUUUUAUCAAUCUGUAACGAACUGAUUUUC-UUAUUUAGCUCGCUACGGAUUGCA-GCGGCUAGAUCAG-AAAGUUUGUGCGUUCGUCCCGCCA
..........................(..((((((.(((((((-(.(((((((.((((.(.....).)-)))))))))).))-)))))).....))))))..).... ( -26.90, z-score =  -2.50, R)
>droSec1.super_69 23451 80 - 174750
-------------------------UGUAACGAACUGAUUUUCUUUAUUUCGCUCGCUACUGGUUGCA-GCGGCUAGCUCAG-AGAGUUUGUGCGUUCGUCCCACCA
-------------------------((..((((((.((((((((.......(((.((..(((....))-)..)).)))..))-)))))).....))))))..))... ( -21.30, z-score =  -0.66, R)
>droYak2.chr2h_random 792687 106 + 3774259
AUUUUAUUUCUUUGCUUCAUAUUCUUGUAACGAACUGAUUUUGUUUGUCU-GCUCGCUACGGAAUACGUGCGGCUAGCUCAGUAGAGUUUGUGCGUUCGUCCCACCA
.........................((..((((((.(((.......))).-((.(((.(((.....))))))((.(((((....))))).))))))))))..))... ( -22.90, z-score =  -0.47, R)
>droSim1.chrU 8921705 80 + 15797150
-------------------------UGUAACGAACCGAUUUUCUUUAUUUCGCUCGCUACUGGUUGCA-GCGGCUAGCUCAG-AGAGUUUGUGUGUUCGUCCCACCA
-------------------------((..((((((((...((((((.....(((.((..(((....))-)..)).)))..))-))))....)).))))))..))... ( -22.40, z-score =  -1.36, R)
>consensus
_________________________UGUAACGAACUGAUUUUCUUUAUUUCGCUCGCUACGGAUUGCA_GCGGCUAGCUCAG_AGAGUUUGUGCGUUCGUCCCACCA
.........................((..((((((................((.(((............)))))..((.(((......))).))))))))..))... (-14.52 = -14.40 +  -0.12)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:58:00 2011