Locus 13081

Sequence ID dm3.chrX
Location 4,218,693 – 4,218,866
Length 173
Max. P 0.949005
window17976 window17977 window17978 window17979 window17980

overview

Window 6

Location 4,218,693 – 4,218,803
Length 110
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 93.51
Shannon entropy 0.11207
G+C content 0.42196
Mean single sequence MFE -25.66
Consensus MFE -21.70
Energy contribution -22.34
Covariance contribution 0.64
Combinations/Pair 1.05
Mean z-score -1.79
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.43
SVM RNA-class probability 0.690540
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4218693 110 + 22422827
GAUUGUGCAAUAAAGCUAUAAUAAUAAAAUAACAAACAAACCGUUAAAGCGAACGCCGUCGCACACUCAUCGCACCCACACAAACGCACCAUAGGUAUUGGUGUGUGGCU
((.(((((......(((.((((....................)))).)))((......))))))).))...((..........((((((((.......)))))))).)). ( -23.05, z-score =  -0.56, R)
>droSim1.chrX 3246765 110 + 17042790
GAUUGUGCAAUAAAGCUAUAAUAAUAAAAUAACAAACAAACCGUUAAGGCGAACGCCGUCGCACACUCAUCGCACCAACACAAACGCACCAAAGGUAUAGGUGUGUUGGU
((.(((((.....................((((.........)))).(((....)))...))))).)).....(((((((((.....(((...))).....))))))))) ( -28.60, z-score =  -2.53, R)
>droSec1.super_4 3671092 110 - 6179234
GAUUGUGCAAUAAAGCUAUAAUAAUAAAAUAACAAACAAACCGUUAAGGCGAACGCCGUCGCACACUCAUCGCACCAACACAAACGCACCAAAGGUAUAGGUGUGUUGGU
((.(((((.....................((((.........)))).(((....)))...))))).)).....(((((((((.....(((...))).....))))))))) ( -28.60, z-score =  -2.53, R)
>droYak2.chrX 17547589 104 - 21770863
GAUUGUGCAAUAAAGCUAUAAUAAUAAAAUAACAAACAAACCGUUAAGGCGAACGCCGUCGCACACUCAUCGCACCAACACAAACGCACCA------UAGGUGUGUUGUU
((.(((((.....................((((.........)))).(((....)))...))))).))..............((((((((.------..))))))))... ( -24.10, z-score =  -1.94, R)
>droEre2.scaffold_4690 1588930 104 + 18748788
GAUUGUGCAAUAAAGCUAUAAUAAUAAAAUAACAAACAAACCGUUAAGGCGAACGCCGUCGCACACUCAUCGCACCAACACAAGCUCACCA------UAGGUGUGUGGGU
....((((.....................((((.........)))).(((....)))...))))(((((.((((((...............------..))))))))))) ( -23.93, z-score =  -1.39, R)
>consensus
GAUUGUGCAAUAAAGCUAUAAUAAUAAAAUAACAAACAAACCGUUAAGGCGAACGCCGUCGCACACUCAUCGCACCAACACAAACGCACCA_AGGUAUAGGUGUGUUGGU
((.(((((.....................((((.........)))).(((....)))...))))).))..............((((((((.........))))))))... (-21.70 = -22.34 +   0.64)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,218,732 – 4,218,828
Length 96
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 83.78
Shannon entropy 0.28340
G+C content 0.55939
Mean single sequence MFE -35.08
Consensus MFE -24.70
Energy contribution -26.94
Covariance contribution 2.24
Combinations/Pair 1.07
Mean z-score -2.40
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.55
SVM RNA-class probability 0.949005
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4218732 96 + 22422827
ACCGUUAAAGCGAACGCCGUCGCACACUCAUCGCACCCACACAAACGCACCAUAGGUAUUGGUGUGUGGCUGCAUGAUGGGGCGGAAGAAAUGGAG--
.((((....((((......))))...(((((((((.(((((((.....(((...))).....))))))).)))..))))))))))...........-- ( -33.80, z-score =  -1.56, R)
>droSim1.chrX 3246804 98 + 17042790
ACCGUUAAGGCGAACGCCGUCGCACACUCAUCGCACCAACACAAACGCACCAAAGGUAUAGGUGUGUUGGUGCAUGAGGGGGUGGAAGAUAUAGGGAG
.((.....(((....)))(((.(((.(((((.(((((((((((.....(((...))).....))))))))))))))))...)))...)))...))... ( -39.50, z-score =  -4.02, R)
>droSec1.super_4 3671131 98 - 6179234
ACCGUUAAGGCGAACGCCGUCGCACACUCAUCGCACCAACACAAACGCACCAAAGGUAUAGGUGUGUUGGUGCAUGAGGGGGUGGAAGAUAUAGGGAG
.((.....(((....)))(((.(((.(((((.(((((((((((.....(((...))).....))))))))))))))))...)))...)))...))... ( -39.50, z-score =  -4.02, R)
>droYak2.chrX 17547628 87 - 21770863
ACCGUUAAGGCGAACGCCGUCGCACACUCAUCGCACCAACACAAACGCACCA------UAGGUGUGUUGUUGCACGAGGGG-UGGUGGAAAGAG----
........(((....))).((((.(((((.(((...(((((...(((((((.------..))))))))))))..))).)))-))))))......---- ( -30.80, z-score =  -1.36, R)
>droEre2.scaffold_4690 1588969 90 + 18748788
ACCGUUAAGGCGAACGCCGUCGCACACUCAUCGCACCAACACAAGCUCACCA------UAGGUGUGUGGGUGCACGAUGCGGGGGAAGCGGAAGAG--
.(((((..(((....))).((.(...(.(((((((((.(((((..((.....------.)).))))).)))))..)))).).).))))))).....-- ( -31.80, z-score =  -1.07, R)
>consensus
ACCGUUAAGGCGAACGCCGUCGCACACUCAUCGCACCAACACAAACGCACCA_AGGUAUAGGUGUGUUGGUGCAUGAGGGGGUGGAAGAAAUAGAG__
.(((((...((((......))))...(((((.(((((((((((.....((.....)).....))))))))))))))))..)))))............. (-24.70 = -26.94 +   2.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,218,732 – 4,218,828
Length 96
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 83.78
Shannon entropy 0.28340
G+C content 0.55939
Mean single sequence MFE -30.68
Consensus MFE -24.66
Energy contribution -25.02
Covariance contribution 0.36
Combinations/Pair 1.13
Mean z-score -1.54
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.782535
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4218732 96 - 22422827
--CUCCAUUUCUUCCGCCCCAUCAUGCAGCCACACACCAAUACCUAUGGUGCGUUUGUGUGGGUGCGAUGAGUGUGCGACGGCGUUCGCUUUAACGGU
--...........(((...((((..(((.(((((((....((((...))))....))))))).)))))))((((.(((....))).))))....))). ( -30.00, z-score =  -0.39, R)
>droSim1.chrX 3246804 98 - 17042790
CUCCCUAUAUCUUCCACCCCCUCAUGCACCAACACACCUAUACCUUUGGUGCGUUUGUGUUGGUGCGAUGAGUGUGCGACGGCGUUCGCCUUAACGGU
...((.......(((((...((((((((((((((((....((((...))))....))))))))))).))))).))).)).(((....))).....)). ( -35.10, z-score =  -3.74, R)
>droSec1.super_4 3671131 98 + 6179234
CUCCCUAUAUCUUCCACCCCCUCAUGCACCAACACACCUAUACCUUUGGUGCGUUUGUGUUGGUGCGAUGAGUGUGCGACGGCGUUCGCCUUAACGGU
...((.......(((((...((((((((((((((((....((((...))))....))))))))))).))))).))).)).(((....))).....)). ( -35.10, z-score =  -3.74, R)
>droYak2.chrX 17547628 87 + 21770863
----CUCUUUCCACCA-CCCCUCGUGCAACAACACACCUA------UGGUGCGUUUGUGUUGGUGCGAUGAGUGUGCGACGGCGUUCGCCUUAACGGU
----......((.(((-(..((((((((.(((((((...(------((...))).))))))).))).))))).))).)..(((....))).....)). ( -24.50, z-score =   0.44, R)
>droEre2.scaffold_4690 1588969 90 - 18748788
--CUCUUCCGCUUCCCCCGCAUCGUGCACCCACACACCUA------UGGUGAGCUUGUGUUGGUGCGAUGAGUGUGCGACGGCGUUCGCCUUAACGGU
--.....(((.......(((((((((((((.(((((.((.------.....))..))))).))))).))))...))))..(((....)))....))). ( -28.70, z-score =  -0.26, R)
>consensus
__CCCUAUAUCUUCCACCCCCUCAUGCACCAACACACCUAUACCU_UGGUGCGUUUGUGUUGGUGCGAUGAGUGUGCGACGGCGUUCGCCUUAACGGU
.............((.....((((((((((((((((((.........)))......)))))))))).)))))........(((....))).....)). (-24.66 = -25.02 +   0.36)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,218,764 – 4,218,866
Length 102
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 81.07
Shannon entropy 0.32737
G+C content 0.50381
Mean single sequence MFE -22.13
Consensus MFE -18.74
Energy contribution -19.58
Covariance contribution 0.84
Combinations/Pair 1.10
Mean z-score -0.90
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.15
SVM RNA-class probability 0.567026
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4218764 102 + 22422827
GCACCCACACAAACGCACCAUAGGUAUUGGUGUGUGGCUGCAUGAUGGGGCGGAAGAAAU--GGAGAG-GAGAACGGCAGGCGAAGGAACAAUAAUCAUAUUUGC
((.((((((((.((((((((.......))))))))...))..)).)))).(....)....--......-.......))..(((((.((.......))...))))) ( -23.50, z-score =   0.03, R)
>droSim1.chrX 3246836 104 + 17042790
GCACCAACACAAACGCACCAAAGGUAUAGGUGUGUUGGUGCAUGAGGGGGUGGAAGAUAUAGGGAGAG-GAGAAAGGCAGGCGAAGGAACAAUAAUCAUAUUUGC
(((((((((((.....(((...))).....)))))))))))...........................-...........(((((.((.......))...))))) ( -23.90, z-score =  -2.50, R)
>droSec1.super_4 3671163 104 - 6179234
GCACCAACACAAACGCACCAAAGGUAUAGGUGUGUUGGUGCAUGAGGGGGUGGAAGAUAUAGGGAGAG-GAGAAAGGCAGGCGAAGGAACAAUAAUCAUAUUUGC
(((((((((((.....(((...))).....)))))))))))...........................-...........(((((.((.......))...))))) ( -23.90, z-score =  -2.50, R)
>droYak2.chrX 17547660 92 - 21770863
GCACCAACACAAACGCACCAUAGGU------GUGUUGUUGCACGA-GGGGUGGUGGAAA----GAGAG-GGGAAGGG-AGGCUAACGAACAAGAAUCAUAUUUGC
(((((..........((((((...(------((((....))))).-...))))))....----.....-.))....(-(..((........))..)).....))) ( -18.05, z-score =   0.52, R)
>droEre2.scaffold_4690 1589001 95 + 18748788
GCACCAACACAAGCUCACCAUAGGU------GUGUGGGUGCACGAUGCGGGGGAAGCGG----AAGAGCGGGGAGAACAGGCAAAGGAACAAUAAUCAUAUUUGC
(((((.(((((..((......)).)------)))).))))).....(((((.((..(..----..).((..(.....)..)).............))...))))) ( -21.30, z-score =  -0.03, R)
>consensus
GCACCAACACAAACGCACCAUAGGUAU_GGUGUGUUGGUGCAUGAGGGGGUGGAAGAAAU__GGAGAG_GAGAAAGGCAGGCGAAGGAACAAUAAUCAUAUUUGC
(((((((((((.....(((...))).....))))))))))).......................................(((((.((.......))...))))) (-18.74 = -19.58 +   0.84)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,218,764 – 4,218,866
Length 102
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 81.07
Shannon entropy 0.32737
G+C content 0.50381
Mean single sequence MFE -17.54
Consensus MFE -14.82
Energy contribution -15.98
Covariance contribution 1.16
Combinations/Pair 1.07
Mean z-score -1.14
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.52
SVM RNA-class probability 0.727710
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4218764 102 - 22422827
GCAAAUAUGAUUAUUGUUCCUUCGCCUGCCGUUCUC-CUCUCC--AUUUCUUCCGCCCCAUCAUGCAGCCACACACCAAUACCUAUGGUGCGUUUGUGUGGGUGC
(((....(((...........)))..))).......-......--...................(((.(((((((....((((...))))....))))))).))) ( -17.80, z-score =   0.51, R)
>droSim1.chrX 3246836 104 - 17042790
GCAAAUAUGAUUAUUGUUCCUUCGCCUGCCUUUCUC-CUCUCCCUAUAUCUUCCACCCCCUCAUGCACCAACACACCUAUACCUUUGGUGCGUUUGUGUUGGUGC
(((....(((...........)))..))).......-...........................(((((((((((....((((...))))....))))))))))) ( -19.90, z-score =  -3.25, R)
>droSec1.super_4 3671163 104 + 6179234
GCAAAUAUGAUUAUUGUUCCUUCGCCUGCCUUUCUC-CUCUCCCUAUAUCUUCCACCCCCUCAUGCACCAACACACCUAUACCUUUGGUGCGUUUGUGUUGGUGC
(((....(((...........)))..))).......-...........................(((((((((((....((((...))))....))))))))))) ( -19.90, z-score =  -3.25, R)
>droYak2.chrX 17547660 92 + 21770863
GCAAAUAUGAUUCUUGUUCGUUAGCCU-CCCUUCCC-CUCUC----UUUCCACCACCCC-UCGUGCAACAACAC------ACCUAUGGUGCGUUUGUGUUGGUGC
((....((((.......))))..))..-........-.....----....(((((....-..(..(((..((.(------(((...)))).)))))..)))))). ( -13.80, z-score =   0.02, R)
>droEre2.scaffold_4690 1589001 95 - 18748788
GCAAAUAUGAUUAUUGUUCCUUUGCCUGUUCUCCCCGCUCUU----CCGCUUCCCCCGCAUCGUGCACCCACAC------ACCUAUGGUGAGCUUGUGUUGGUGC
(((((...((.......)).)))))...........((....----..)).......((((((.((((...(.(------(((...)))).)...)))))))))) ( -16.30, z-score =   0.24, R)
>consensus
GCAAAUAUGAUUAUUGUUCCUUCGCCUGCCCUUCUC_CUCUCC__AUAUCUUCCACCCCAUCAUGCACCAACACACC_AUACCUAUGGUGCGUUUGUGUUGGUGC
................................................................(((((((((((....((((...))))....))))))))))) (-14.82 = -15.98 +   1.16)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:14:15 2011