Locus 14860

Sequence ID dm3.chrX
Location 15,966,504 – 15,966,628
Length 124
Max. P 0.882283
window20465 window20466 window20467 window20468

overview

Window 5

Location 15,966,504 – 15,966,609
Length 105
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 84.54
Shannon entropy 0.27369
G+C content 0.45256
Mean single sequence MFE -32.92
Consensus MFE -21.74
Energy contribution -20.50
Covariance contribution -1.24
Combinations/Pair 1.33
Mean z-score -2.31
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.05
SVM RNA-class probability 0.882283
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15966504 105 + 22422827
GAGUGUGAAUGCUAGUGCUGGAAAGGGUACGCGAUUUGUGUACCUACAAGGACGGUACCUGG-UAGGUACUCUUAAUGCUAAGUAUGACGGCUUGGAAAAUGAGUA
(((.(((..(((((((((((....((((((((.....)))))))).......))))).))))-))..))).)))....((((((......)))))).......... ( -32.80, z-score =  -2.53, R)
>droSec1.super_47 18971 105 + 216421
GAGUGUGAAUGCCAGUGCUGGAAAGGGUACGCGAUUUGUGUACCUACAAGGACGGUACCUGG-UAGGUACUCCUAAUGAUAACUAUGUCGUCUGGGAAAAAUCGUA
..(((((..(.(((....)))...)..)))))(((((..((((((((.(((......))).)-)))))))(((((((((((....)))))).))))).)))))... ( -36.10, z-score =  -2.98, R)
>droSim1.chrX 12326790 105 + 17042790
GAGUGUGAAUGCCAGUGCUGGAAAGGGUACGCGAUUUGUGUACCUACAAGGACGGUACCUGG-UAGGUACUCCUAAUGAUAACUAUGUCGGCUGGGAAAAAUAGUA
....(((..(((((((((((....((((((((.....)))))))).......))))).))))-))..)))(((((.(((((....)))))..)))))......... ( -35.30, z-score =  -2.81, R)
>droYak2.chrX 10114475 105 + 21770863
GAGUGCGAAUACCAGUGCUGGAAAGGGUACGCGAUUUGUGUACCUACAAGGACGGUACCUAG-CAGGUACUUUUCAAGAUAUGUUGGUCAGCCAAUAAGAAUGGCA
...(((.....(((....)))...((((((((.....)))))))).((.(((.((((((...-..)))))).)))......((((((....))))))....))))) ( -31.50, z-score =  -1.57, R)
>droEre2.scaffold_4690 7637620 106 - 18748788
GAGUGUGAACACCAGUGCUGGAUAGGGUAUGCGAUUUGUAUAACUACAAGGACGGUACCUAGAUAGGUAUAUUUAAUGAUAAGUAUGUCCGCCAGGAUAAAUGGUA
..........((((((.((((...((..((((..((((((....))))))....((((((....))))))............))))..)).)))).))...)))). ( -28.90, z-score =  -1.64, R)
>consensus
GAGUGUGAAUGCCAGUGCUGGAAAGGGUACGCGAUUUGUGUACCUACAAGGACGGUACCUGG_UAGGUACUCUUAAUGAUAAGUAUGUCGGCUAGGAAAAAUAGUA
((((......(((.((.((.....((((((((.....))))))))...)).)))))((((....))))))))..................((((.......)))). (-21.74 = -20.50 +  -1.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,966,504 – 15,966,609
Length 105
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 84.54
Shannon entropy 0.27369
G+C content 0.45256
Mean single sequence MFE -23.04
Consensus MFE -14.66
Energy contribution -14.02
Covariance contribution -0.64
Combinations/Pair 1.29
Mean z-score -2.10
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.51
SVM RNA-class probability 0.725263
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15966504 105 - 22422827
UACUCAUUUUCCAAGCCGUCAUACUUAGCAUUAAGAGUACCUA-CCAGGUACCGUCCUUGUAGGUACACAAAUCGCGUACCCUUUCCAGCACUAGCAUUCACACUC
...........................((.......(((((((-(.(((......))).)))))))).......((............))....)).......... ( -20.40, z-score =  -2.75, R)
>droSec1.super_47 18971 105 - 216421
UACGAUUUUUCCCAGACGACAUAGUUAUCAUUAGGAGUACCUA-CCAGGUACCGUCCUUGUAGGUACACAAAUCGCGUACCCUUUCCAGCACUGGCAUUCACACUC
..((((((.(((..((..((...))..))....)))(((((((-(.(((......))).))))))))..))))))..........(((....)))........... ( -24.70, z-score =  -2.31, R)
>droSim1.chrX 12326790 105 - 17042790
UACUAUUUUUCCCAGCCGACAUAGUUAUCAUUAGGAGUACCUA-CCAGGUACCGUCCUUGUAGGUACACAAAUCGCGUACCCUUUCCAGCACUGGCAUUCACACUC
..............((((..................(((((((-(.(((......))).)))))))).......((............))..)))).......... ( -23.60, z-score =  -2.28, R)
>droYak2.chrX 10114475 105 - 21770863
UGCCAUUCUUAUUGGCUGACCAACAUAUCUUGAAAAGUACCUG-CUAGGUACCGUCCUUGUAGGUACACAAAUCGCGUACCCUUUCCAGCACUGGUAUUCGCACUC
.((((.......))))....................(((((((-(.(((......))).)))))))).......(((........(((....)))....))).... ( -27.60, z-score =  -2.32, R)
>droEre2.scaffold_4690 7637620 106 + 18748788
UACCAUUUAUCCUGGCGGACAUACUUAUCAUUAAAUAUACCUAUCUAGGUACCGUCCUUGUAGUUAUACAAAUCGCAUACCCUAUCCAGCACUGGUGUUCACACUC
(((((......((((.((((....(((....)))...(((((....)))))..))))(((((....)))))..............))))...)))))......... ( -18.90, z-score =  -0.86, R)
>consensus
UACCAUUUUUCCCAGCCGACAUACUUAUCAUUAAGAGUACCUA_CCAGGUACCGUCCUUGUAGGUACACAAAUCGCGUACCCUUUCCAGCACUGGCAUUCACACUC
...........((((.....................(((((((.(.(((......))).)))))))).......((............)).))))........... (-14.66 = -14.02 +  -0.64)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,966,529 – 15,966,628
Length 99
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 79.01
Shannon entropy 0.36254
G+C content 0.41892
Mean single sequence MFE -27.98
Consensus MFE -17.86
Energy contribution -16.78
Covariance contribution -1.08
Combinations/Pair 1.38
Mean z-score -1.93
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.01
SVM RNA-class probability 0.874157
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15966529 99 + 22422827
GGUACGCGAUUUGUGUACCUACAAGGACGGUACCUGG-UAGGUACUCUUAAUGCUAAGUAUGACGGCUUGGAAAAUGAGUAAGCAACAACU----ACUCUGCGU
...(((((....(.((((((((.(((......))).)-))))))).)......((((((......)))))).....(((((.........)----))))))))) ( -29.00, z-score =  -1.55, R)
>droSec1.super_47 18996 99 + 216421
GGUACGCGAUUUGUGUACCUACAAGGACGGUACCUGG-UAGGUACUCCUAAUGAUAACUAUGUCGUCUGGGAAAAAUCGUAAGCAAUAUUU----ACUCUGCAC
.....(((((((..((((((((.(((......))).)-)))))))(((((((((((....)))))).))))).)))))))..(((......----....))).. ( -32.40, z-score =  -3.30, R)
>droSim1.chrX 12326815 99 + 17042790
GGUACGCGAUUUGUGUACCUACAAGGACGGUACCUGG-UAGGUACUCCUAAUGAUAACUAUGUCGGCUGGGAAAAAUAGUAAGCAAUAUCU----ACUCUGCAC
((((.((...((((((((((((.(((......))).)-)))))))(((((.(((((....)))))..)))))...))))...))..)))).----......... ( -27.50, z-score =  -1.37, R)
>droYak2.chrX 10114500 99 + 21770863
GGUACGCGAUUUGUGUACCUACAAGGACGGUACCUAG-CAGGUACUUUUCAAGAUAUGUUGGUCAGCCAAUAAGAAUGGCAAGCAAUAACU----ACUAAGCUC
(((((((.....))))))).....(((.((((((...-..)))))).)))......(((((.(..((((.......)))).).)))))...----......... ( -27.10, z-score =  -1.66, R)
>droEre2.scaffold_4690 7637645 104 - 18748788
GGUAUGCGAUUUGUAUAACUACAAGGACGGUACCUAGAUAGGUAUAUUUAAUGAUAAGUAUGUCCGCCAGGAUAAAUGGUAAGAAAUUAUUUUUUAUUGAGCUU
(((.......(((((....)))))(((((((((((....))))))(((((....))))).))))))))..((((((..((((....))))..))))))...... ( -23.90, z-score =  -1.78, R)
>consensus
GGUACGCGAUUUGUGUACCUACAAGGACGGUACCUGG_UAGGUACUCUUAAUGAUAAGUAUGUCGGCUAGGAAAAAUAGUAAGCAAUAACU____ACUCUGCAC
(((((((.....)))))))....((((..((((((....))))))))))................((((.......))))........................ (-17.86 = -16.78 +  -1.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,966,529 – 15,966,628
Length 99
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 79.01
Shannon entropy 0.36254
G+C content 0.41892
Mean single sequence MFE -24.20
Consensus MFE -13.24
Energy contribution -12.64
Covariance contribution -0.60
Combinations/Pair 1.20
Mean z-score -2.20
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.90
SVM RNA-class probability 0.847590
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15966529 99 - 22422827
ACGCAGAGU----AGUUGUUGCUUACUCAUUUUCCAAGCCGUCAUACUUAGCAUUAAGAGUACCUA-CCAGGUACCGUCCUUGUAGGUACACAAAUCGCGUACC
((((.((((----(((....)).)))))...............................(((((((-(.(((......))).)))))))).......))))... ( -28.40, z-score =  -3.42, R)
>droSec1.super_47 18996 99 - 216421
GUGCAGAGU----AAAUAUUGCUUACGAUUUUUCCCAGACGACAUAGUUAUCAUUAGGAGUACCUA-CCAGGUACCGUCCUUGUAGGUACACAAAUCGCGUACC
((((.((((----(.....))))).((((((.(((..((..((...))..))....)))(((((((-(.(((......))).))))))))..)))))).)))). ( -29.20, z-score =  -3.54, R)
>droSim1.chrX 12326815 99 - 17042790
GUGCAGAGU----AGAUAUUGCUUACUAUUUUUCCCAGCCGACAUAGUUAUCAUUAGGAGUACCUA-CCAGGUACCGUCCUUGUAGGUACACAAAUCGCGUACC
(((((((((----((.((.....))))))))).....((.((........((.....))(((((((-(.(((......))).)))))))).....)))))))). ( -24.00, z-score =  -1.59, R)
>droYak2.chrX 10114500 99 - 21770863
GAGCUUAGU----AGUUAUUGCUUGCCAUUCUUAUUGGCUGACCAACAUAUCUUGAAAAGUACCUG-CUAGGUACCGUCCUUGUAGGUACACAAAUCGCGUACC
.((((....----))))...((..((((.......))))....................(((((((-(.(((......))).)))))))).......))..... ( -25.10, z-score =  -1.38, R)
>droEre2.scaffold_4690 7637645 104 + 18748788
AAGCUCAAUAAAAAAUAAUUUCUUACCAUUUAUCCUGGCGGACAUACUUAUCAUUAAAUAUACCUAUCUAGGUACCGUCCUUGUAGUUAUACAAAUCGCAUACC
..((................................(((((......(((....)))...(((((....)))))))))).(((((....)))))...))..... ( -14.30, z-score =  -1.10, R)
>consensus
GAGCAGAGU____AGUUAUUGCUUACCAUUUUUCCCAGCCGACAUACUUAUCAUUAAGAGUACCUA_CCAGGUACCGUCCUUGUAGGUACACAAAUCGCGUACC
..((....................................((........)).......(((((((.(.(((......))).)))))))).......))..... (-13.24 = -12.64 +  -0.60)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:48:18 2011