Locus 14813

Sequence ID dm3.chrX
Location 15,656,716 – 15,656,857
Length 141
Max. P 0.979406
window20389 window20390 window20391 window20392

overview

Window 9

Location 15,656,716 – 15,656,819
Length 103
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 65.62
Shannon entropy 0.56191
G+C content 0.27719
Mean single sequence MFE -18.53
Consensus MFE -9.85
Energy contribution -9.17
Covariance contribution -0.69
Combinations/Pair 1.53
Mean z-score -1.00
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.36
SVM RNA-class probability 0.661663
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15656716 103 + 22422827
AGUUGGUUGUAACUUAUUUAAGAGGUUUUAUUCAAACCUAAAUCGAAUAAGACCUCAGAUGGUUAGGUUUC---UUAUUUGUUUCAU-UAUAUUCAUAU-AGGAAUUU
.......(.(((((.((((..((((((((((((...........))))))))))))))))))))).).(((---((((.((......-......)).))-)))))... ( -21.60, z-score =  -1.86, R)
>droSim1.chrX 12139000 96 + 17042790
AGUUGGUUGCAACUUGUUUAAAAGGUUUUAUUCAAAACUAAAUCGAAUAAGACCUCAGAUGGUCAAGUUUC---UUAUUU--------UAUAUUUAUGU-AGGAAUUU
..........((((((......(((((((((((...........)))))))))))........))))))((---((((..--------.........))-)))).... ( -17.74, z-score =  -1.28, R)
>droSec1.super_37 240941 105 + 454039
AGUUGGUUGCAACUUGUUUAAAAGGUUUUAUUCAAAACUAAAUCGAAUAAGACCUCAGAUGGUCAAGUUUC---UUACUCGUCCUAUUUAUAUUUUUUUUAGGAAUUU
....(((.(.((((((......(((((((((((...........)))))))))))........)))))).)---..)))..(((((.............))))).... ( -20.26, z-score =  -1.57, R)
>triCas2.ChLG5 9533398 107 + 18847211
AAUAAAGAUUAAGUUGAU-ACAGAAUUUUGUUUUAAUUGCCUCCGAGUCUGAGUUCUGAUACUUGAACUAUAAAUUACUUAUCGUCGAUUUUUUUAUAUCUUGGGUUU
....(((((.((((((((-.((((.....((.......)).......))))(((((........)))))..............))))))))......)))))...... ( -14.50, z-score =   0.73, R)
>consensus
AGUUGGUUGCAACUUGUUUAAAAGGUUUUAUUCAAAACUAAAUCGAAUAAGACCUCAGAUGGUCAAGUUUC___UUACUUGUC_UAU_UAUAUUUAUAU_AGGAAUUU
..........((((((......(((((((((((...........)))))))))))........))))))....................................... ( -9.85 =  -9.17 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,656,716 – 15,656,819
Length 103
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 65.62
Shannon entropy 0.56191
G+C content 0.27719
Mean single sequence MFE -15.80
Consensus MFE -7.69
Energy contribution -9.50
Covariance contribution 1.81
Combinations/Pair 1.26
Mean z-score -1.77
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.55
SVM RNA-class probability 0.949114
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15656716 103 - 22422827
AAAUUCCU-AUAUGAAUAUA-AUGAAACAAAUAA---GAAACCUAACCAUCUGAGGUCUUAUUCGAUUUAGGUUUGAAUAAAACCUCUUAAAUAAGUUACAACCAACU
..((((..-....))))...-.((.(((.....(---((..........)))(((((.((((((((.......)))))))).)))))........))).))....... ( -15.10, z-score =  -1.62, R)
>droSim1.chrX 12139000 96 - 17042790
AAAUUCCU-ACAUAAAUAUA--------AAAUAA---GAAACUUGACCAUCUGAGGUCUUAUUCGAUUUAGUUUUGAAUAAAACCUUUUAAACAAGUUGCAACCAACU
........-...........--------......---(.((((((.......(((((.((((((((.......)))))))).))))).....)))))).)........ ( -17.00, z-score =  -2.98, R)
>droSec1.super_37 240941 105 - 454039
AAAUUCCUAAAAAAAAUAUAAAUAGGACGAGUAA---GAAACUUGACCAUCUGAGGUCUUAUUCGAUUUAGUUUUGAAUAAAACCUUUUAAACAAGUUGCAACCAACU
....(((((.............)))))(((((..---...))))).......(((((.((((((((.......)))))))).))))).......(((((....))))) ( -20.02, z-score =  -2.55, R)
>triCas2.ChLG5 9533398 107 - 18847211
AAACCCAAGAUAUAAAAAAAUCGACGAUAAGUAAUUUAUAGUUCAAGUAUCAGAACUCAGACUCGGAGGCAAUUAAAACAAAAUUCUGU-AUCAACUUAAUCUUUAUU
........(((........)))...(((((((.......(((((........)))))..((..(((((...............))))).-.)).)))).)))...... ( -11.06, z-score =   0.08, R)
>consensus
AAAUUCCU_AUAUAAAUAUA_AUA_GACAAAUAA___GAAACUUAACCAUCUGAGGUCUUAUUCGAUUUAGUUUUGAAUAAAACCUUUUAAACAAGUUACAACCAACU
.......................................((((((.......(((((.((((((((.......)))))))).))))).....)))))).......... ( -7.69 =  -9.50 +   1.81)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,656,750 – 15,656,857
Length 107
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 64.66
Shannon entropy 0.57854
G+C content 0.29752
Mean single sequence MFE -21.80
Consensus MFE -13.10
Energy contribution -13.22
Covariance contribution 0.12
Combinations/Pair 1.39
Mean z-score -1.52
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.02
SVM RNA-class probability 0.979406
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15656750 107 + 22422827
AACCUAAAUCGAAUAAGACCUCAGAUGGUUAGGUUUC---UUAUUUGUUUCAUU-AUAUUCAUAU-AGGAAUUUUAAUGAGCUUCUUUUUAAGGGGAAGCUCAUUUAAAAUA-
(((((((.((......))((......)))))))))((---((((.((.......-.....)).))-))))((((((((((((((((((....))))))))))).))))))).- ( -27.40, z-score =  -3.23, R)
>droSim1.chrX 12139034 100 + 17042790
AAACUAAAUCGAAUAAGACCUCAGAUGGUCAAGUUUC---UUAUU--UUAUAUUUAUGU-------AGGAAUUUUGACGAGCUUCUUGUUAAAUGGAAUCUCAUUUGAAAUA-
....................((((((.((((((.(((---((((.--..........))-------))))).))))))(((.((((........)))).)))))))))....- ( -20.90, z-score =  -1.69, R)
>droSec1.super_37 240975 109 + 454039
AAACUAAAUCGAAUAAGACCUCAGAUGGUCAAGUUUC---UUACUCGUCCUAUUUAUAUUUUUUUUAGGAAUUUUAAUGAAAUUCUUGUUAAAUGGAAUCUCAUUUGAACUA-
...(((((..(((((.((((......)))).(((...---..)))...........)))))..)))))...(((.(((((.(((((........))))).))))).)))...- ( -19.00, z-score =  -1.01, R)
>triCas2.ChLG5 9533431 110 + 18847211
AAUUGCCUCCGAGUCUGAGUUCUGAUACUUGAACUAUAAAUUACUUAUCGUCGAUUUUUUUAUAUCUUGGGUUUUUAUGCGACUGCUGUUA--UGGCA-CUCAUUUGGGUGAA
..(..((((((((....(((((........)))))..(((((((.....)).)))))........)))))..........((.((((....--.))))-.))....)))..). ( -19.90, z-score =  -0.13, R)
>consensus
AAACUAAAUCGAAUAAGACCUCAGAUGGUCAAGUUUC___UUACUUGUCAUAUUUAUAUUUAUAU_AGGAAUUUUAAUGAGAUUCUUGUUAAAUGGAAUCUCAUUUGAAAUA_
........((((((..((((......))))................................................((((((((........))))))))))))))..... (-13.10 = -13.22 +   0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,656,750 – 15,656,857
Length 107
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 64.66
Shannon entropy 0.57854
G+C content 0.29752
Mean single sequence MFE -17.18
Consensus MFE -7.72
Energy contribution -7.35
Covariance contribution -0.37
Combinations/Pair 1.53
Mean z-score -1.40
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.60
SVM RNA-class probability 0.757007
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15656750 107 - 22422827
-UAUUUUAAAUGAGCUUCCCCUUAAAAAGAAGCUCAUUAAAAUUCCU-AUAUGAAUAU-AAUGAAACAAAUAA---GAAACCUAACCAUCUGAGGUCUUAUUCGAUUUAGGUU
-..(((((((((((((((..........))))))))))...((((..-....))))..-...........)))---))(((((((..(((.(((......))))))))))))) ( -20.70, z-score =  -2.75, R)
>droSim1.chrX 12139034 100 - 17042790
-UAUUUCAAAUGAGAUUCCAUUUAACAAGAAGCUCGUCAAAAUUCCU-------ACAUAAAUAUAA--AAUAA---GAAACUUGACCAUCUGAGGUCUUAUUCGAUUUAGUUU
-((..((.((((((((..((........(.....)(((((..(((..-------............--.....---)))..)))))....))..)))))))).))..)).... ( -12.81, z-score =  -0.25, R)
>droSec1.super_37 240975 109 - 454039
-UAGUUCAAAUGAGAUUCCAUUUAACAAGAAUUUCAUUAAAAUUCCUAAAAAAAAUAUAAAUAGGACGAGUAA---GAAACUUGACCAUCUGAGGUCUUAUUCGAUUUAGUUU
-.......((((((((((..........)))))))))).....(((((.............)))))(((((((---((..(((........))).)))))))))......... ( -21.72, z-score =  -2.31, R)
>triCas2.ChLG5 9533431 110 - 18847211
UUCACCCAAAUGAG-UGCCA--UAACAGCAGUCGCAUAAAAACCCAAGAUAUAAAAAAAUCGACGAUAAGUAAUUUAUAGUUCAAGUAUCAGAACUCAGACUCGGAGGCAAUU
..............-((((.--.....((....))........((..(((........))).................(((((........))))).......)).))))... ( -13.50, z-score =  -0.27, R)
>consensus
_UAUUUCAAAUGAGAUUCCAUUUAACAAGAAGCUCAUUAAAAUUCCU_AUAUAAAUAUAAAUAAAACAAAUAA___GAAACUUAACCAUCUGAGGUCUUAUUCGAUUUAGUUU
.((..((..(((((((((..........)))))))))..............................................((((......))))......))..)).... ( -7.72 =  -7.35 +  -0.37)

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 01:47:14 2011