Locus 14245

Sequence ID dm3.chrX
Location 12,123,234 – 12,123,467
Length 233
Max. P 0.770254
window19616 window19617 window19618

overview

Window 6

Location 12,123,234 – 12,123,348
Length 114
Sequences 7
Columns 122
Reading direction reverse
Mean pairwise identity 65.23
Shannon entropy 0.68388
G+C content 0.38985
Mean single sequence MFE -21.17
Consensus MFE -6.43
Energy contribution -7.74
Covariance contribution 1.31
Combinations/Pair 1.50
Mean z-score -1.73
Structure conservation index 0.30
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.43
SVM RNA-class probability 0.692086
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12123234 114 - 22422827
AUUCCAACAAUUUCC-CUAAUUUCCCACAUUUGCCAGCGGCC----GGCAAAACACUCUUAAU---ACCGCUUAGCAAAUGUUAAUUGUUUUUCCCCUGGUAAGAACGAUUGCAUUUGCCUA
...............-.............((((((.......----))))))...........---........((((((((.((((((((((((...)).))))))))))))))))))... ( -24.80, z-score =  -2.45, R)
>droEre2.scaffold_4690 4030007 114 + 18748788
AUUCAAACAUUUUCC-CUAAUUUCCCACAUUUGCCAGCGACU----GGCAAAACUCUCCUAAU---ACCGCUUAGCAAAUGUUAAUUGUUUUUCCCCUGAUAACAACGAUUGCAUUUGCGUA
...............-..........((.((((((((...))----))))))...........---........((((((((.(((((((..((....))....))))))))))))))))). ( -23.60, z-score =  -3.83, R)
>droYak2.chrX 20033053 121 + 21770863
AUUCUAACAUUUCCC-CUAAUUUCCCACAUUUUCCAGCGGCCAACUGGCAAAACACUCUUAAUACCACCACUUAGCAAAUGUUAAUUGUUUUUCCCCUGGUAACAACGAUUGCAUUUCCCUA
...............-....................((((((....))).............(((((......(((((.......))))).......)))))........)))......... ( -13.22, z-score =  -0.01, R)
>droSec1.super_45 141359 114 - 245362
AUUCCAACAUUUUCC-CUAAUUUCCCACAUUUGCCAGCGGCU----GGCAAAACACUCUUAAU---ACCGCUUAGCAAAUGUUAAUUGUUUUUCCCCUGGUAACAACGAUUGCAUUUGCCUA
...............-.............((((((((...))----))))))...........---........((((((((.(((((((.((((...)).)).)))))))))))))))... ( -24.10, z-score =  -2.51, R)
>droSim1.chrX 9344972 114 - 17042790
AUUGCAACAUUUUCC-CUAAUUUCCCACAUUUGCCAGCGGCU----GGCAAAACACUCUUAAU---ACCGCUUAGCAAAUGUUAAUUGUUUUUCCCCUGGUAACAACGAUUGCAUUUGCCUA
...............-.............((((((((...))----))))))...........---........((((((((.(((((((.((((...)).)).)))))))))))))))... ( -24.10, z-score =  -1.78, R)
>droPer1.super_12 1956858 110 + 2414086
AUUGCCGCAUUUUCCACCUAUUUUUGAUCAUU--CUGUAACC----CUAAUCCCAGUCUUCGG---AUUUCUCACCGAGCG---AUCGAUCCCGAUUGGUCGAUCACGAUCACGAGUGUCCA
..................(((((.(((((...--........----.............((((---........))))(.(---(((((((......)))))))).)))))).))))).... ( -23.60, z-score =  -0.89, R)
>droGri2.scaffold_14624 3996128 118 + 4233967
UCUAUCGCAAACUUAACCUAAUCUAAGCCAAUAUUAUCGAUA----AUCAUAUCAGUAAAAACAAAAUAAUAUUGUGAGUGUUGGUUGAAUCCAUAAUAUUAAAAUAUAUGCCACAUUUUUA
......(((..((((........))))..((((((((.(((.----.(((.(((((((...((((.......))))...))))))))))))).))))))))........))).......... ( -14.80, z-score =  -0.65, R)
>consensus
AUUCCAACAUUUUCC_CUAAUUUCCCACAUUUGCCAGCGGCC____GGCAAAACACUCUUAAU___ACCGCUUAGCAAAUGUUAAUUGUUUUUCCCCUGGUAACAACGAUUGCAUUUGCCUA
..........................................................................((((((((.(((((((.((.(....).)).)))))))))))))))... ( -6.43 =  -7.74 +   1.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,123,348 – 12,123,467
Length 119
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 97.75
Shannon entropy 0.03087
G+C content 0.26195
Mean single sequence MFE -22.00
Consensus MFE -20.37
Energy contribution -20.15
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.67
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.64
SVM RNA-class probability 0.770254
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12123348 119 + 22422827
UUUUGCUUUUAAUUACACGCUUGAUUAAGUGUUUACUUAAAUUGCGAAUUGAAAAGGUCGAUUUACAUGUUUCGGAAAUCCGCAUUAAUUCGACUUUAAUUAUAAACAAUAGAAUAAAU
.(((((.(((((.((.((((((....)))))).)).)))))..))))).....((((((((.(((.(((...(((....))))))))).))))))))...................... ( -24.70, z-score =  -2.45, R)
>droSec1.super_45 141473 118 + 245362
UUUUGCUUUUAAUUACACGCUUGAUUAAGUGUUUACUUAAAUUGCGAAU-GAAAAGGUCGAUUUACAUGUUUAGCAAAUCCGUAUUAAUUCGACUUUAAUUAUAAACAAUAGAAUAAAU
.(((((.(((((.((.((((((....)))))).)).)))))..))))).-...((((((((.(((.(((..(.....)..)))..))).))))))))...................... ( -19.60, z-score =  -0.96, R)
>droSim1.chrX 9345086 118 + 17042790
UUUUGCUUUUAAUUACACGCUUGAUUAAGUGUUUACUUAAAUUGCGAAU-GAAAAGGUCGAUUUACAUGUUUAGCAAAUCCGCAUUAAUUCGACUUUAAUUAUAAACAAUAGAAUAAAU
.(((((.(((((.((.((((((....)))))).)).)))))..))))).-...((((((((.(((.((((...........))))))).))))))))...................... ( -21.70, z-score =  -1.60, R)
>consensus
UUUUGCUUUUAAUUACACGCUUGAUUAAGUGUUUACUUAAAUUGCGAAU_GAAAAGGUCGAUUUACAUGUUUAGCAAAUCCGCAUUAAUUCGACUUUAAUUAUAAACAAUAGAAUAAAU
.(((((.(((((.((.((((((....)))))).)).)))))..))))).....((((((((.(((.(((.............)))))).))))))))...................... (-20.37 = -20.15 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,123,348 – 12,123,467
Length 119
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 97.75
Shannon entropy 0.03087
G+C content 0.26195
Mean single sequence MFE -21.87
Consensus MFE -18.63
Energy contribution -18.97
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.17
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.58
SVM RNA-class probability 0.750478
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12123348 119 - 22422827
AUUUAUUCUAUUGUUUAUAAUUAAAGUCGAAUUAAUGCGGAUUUCCGAAACAUGUAAAUCGACCUUUUCAAUUCGCAAUUUAAGUAAACACUUAAUCAAGCGUGUAAUUAAAAGCAAAA
..........((((((.((((((..(((((.(((((((((....)))...))).))).)))))..........(((...((((((....))))))....)))..)))))).)))))).. ( -23.40, z-score =  -2.71, R)
>droSec1.super_45 141473 118 - 245362
AUUUAUUCUAUUGUUUAUAAUUAAAGUCGAAUUAAUACGGAUUUGCUAAACAUGUAAAUCGACCUUUUC-AUUCGCAAUUUAAGUAAACACUUAAUCAAGCGUGUAAUUAAAAGCAAAA
..........((((((.((((((..((((........).(((((((.......))))))))))......-...(((...((((((....))))))....)))..)))))).)))))).. ( -20.30, z-score =  -1.89, R)
>droSim1.chrX 9345086 118 - 17042790
AUUUAUUCUAUUGUUUAUAAUUAAAGUCGAAUUAAUGCGGAUUUGCUAAACAUGUAAAUCGACCUUUUC-AUUCGCAAUUUAAGUAAACACUUAAUCAAGCGUGUAAUUAAAAGCAAAA
..........((((((.((((((....((......(((((((((((.......)))))))((.....))-...))))..((((((....)))))).....))..)))))).)))))).. ( -21.90, z-score =  -1.93, R)
>consensus
AUUUAUUCUAUUGUUUAUAAUUAAAGUCGAAUUAAUGCGGAUUUGCUAAACAUGUAAAUCGACCUUUUC_AUUCGCAAUUUAAGUAAACACUUAAUCAAGCGUGUAAUUAAAAGCAAAA
..........((((((.((((((..((((........).(((((((.......))))))))))..........(((...((((((....))))))....)))..)))))).)))))).. (-18.63 = -18.97 +   0.33)

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 01:36:40 2011