Locus 15346

Sequence ID dm3.chrX
Location 18,535,019 – 18,535,126
Length 107
Max. P 0.974313
window21140 window21141 window21142

overview

Window 0

Location 18,535,019 – 18,535,119
Length 100
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 80.90
Shannon entropy 0.32270
G+C content 0.48248
Mean single sequence MFE -37.14
Consensus MFE -26.61
Energy contribution -28.29
Covariance contribution 1.68
Combinations/Pair 1.12
Mean z-score -2.37
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.91
SVM RNA-class probability 0.974313
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18535019 100 + 22422827
ACGGAGCAUCGGCAACAU-UAUUU-GGCUAGUGAUUCACUCGAGCGAGUGGCGACAAUCGCUGGCUCAGAUU-------------GGUUGUCUGUGGUGUUUCUUUUCUGUUAUU
..((((((((((((((..-.((((-((((((((((((((((....)))))).....))))))))).))))).-------------.))))))...))))))))............ ( -39.50, z-score =  -4.18, R)
>droSim1.chrX 14305943 113 + 17042790
ACGGAGCAUCGGCAACAU-UAUUU-GGCUAGUGAUUCACUCGAGCGAGUGGCGACAAUCGCUGGCUCAGAUUCGCAUUUUGCGUUGGUUGCCUGUGGUGUUUGUUUUCUGCUCCU
..((((((..((((((..-.((((-((((((((((((((((....)))))).....))))))))).))))).(((.....)))...))))))...((.........)))))))). ( -43.10, z-score =  -2.72, R)
>droSec1.super_8 838766 113 + 3762037
ACGGAGCAUCGGCAACAU-UAUUU-AGCUAGUGAUUCACUCGAGCGAGUGGCGACAAUCGCUGGCUCAGAUUCGCAUUUUGCGUUGGUUGCCUGUGGUGUUUGUUUUCUGCUCCU
..((((((..((((((..-.((((-((((((((((((((((....)))))).....)))))))))).)))).(((.....)))...))))))...((.........)))))))). ( -41.10, z-score =  -2.30, R)
>droYak2.chrX 17161137 103 + 21770863
ACGGAGCAGCGGCAUCAU-UUUUU-GACUAGUGAUUCACUCGAGCGAGUGGCGACAAUCGCUGGCUUAGAUUC---------GCAUUUUGCGC-UGGUUUUUCUACUCGGUUUUU
((.(((.((((((.....-..(((-((((((((((((((((....)))))).....)))))))).)))))...---------((.....))))-))......)).))).)).... ( -27.40, z-score =  -0.17, R)
>droEre2.scaffold_4690 8844592 105 + 18748788
ACGGAGCAUCGGCAACAUAUAUUUUGGCUAGUGAUUCACUCGAGCGAUUGACGACAAUCGCUGGCUUGGAUU----------GCCUGUGGUGUUGGGUGUUUCUUUUCUGGUUUU
..((((((((..((((((.(((...(((....((((((..(.((((((((....)))))))).)..))))))----------))).)))))))))))))))))............ ( -34.60, z-score =  -2.46, R)
>consensus
ACGGAGCAUCGGCAACAU_UAUUU_GGCUAGUGAUUCACUCGAGCGAGUGGCGACAAUCGCUGGCUCAGAUUC_________GCUGGUUGCCUGUGGUGUUUCUUUUCUGCUCUU
..((((((((((((((....((((.((((((((((((((((....)))))).....)))))))))).))))...............))))))...))))))))............ (-26.61 = -28.29 +   1.68)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,535,034 – 18,535,126
Length 92
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 76.57
Shannon entropy 0.36703
G+C content 0.42347
Mean single sequence MFE -25.25
Consensus MFE -17.25
Energy contribution -17.38
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -1.40
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.30
SVM RNA-class probability 0.634252
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18535034 92 + 22422827
--CAUUAUUUGGCUAGUGAUUCACUCGAGCGAGUGGCGACAAUCGCUGGCUCAGAUU-------------GGUUGUCUGUGGUGUUUCUUUUCUGUUAUUAUUUUUU
--(((((...((((((((((((((((....)))))).....))))))))))(((((.-------------....))))))))))....................... ( -24.80, z-score =  -1.92, R)
>droSec1.super_8 838781 105 + 3762037
--CAUUAUUUAGCUAGUGAUUCACUCGAGCGAGUGGCGACAAUCGCUGGCUCAGAUUCGCAUUUUGCGUUGGUUGCCUGUGGUGUUUGUUUUCUGCUCCUAUUUUUU
--........((((((((((((((((....)))))).....))))))))))((((((((((....(((.....))).))))).)))))................... ( -26.20, z-score =  -0.08, R)
>droYak2.chrX 17161152 95 + 21770863
--CAUUUUUUGACUAGUGAUUCACUCGAGCGAGUGGCGACAAUCGCUGGCUUAGAUUCGC----------AUUUUGCGCUGGUUUUUCUACUCGGUUUUUAUUUUUU
--.....(((((((((((((((((((....)))))).....)))))))).)))))...((----------.....))((((((......)).))))........... ( -21.80, z-score =  -0.90, R)
>droEre2.scaffold_4690 8844607 97 + 18748788
CAUAUAUUUUGGCUAGUGAUUCACUCGAGCGAUUGACGACAAUCGCUGGCUUGGAUUGCC----------UGUGGUGUUGGGUGUUUCUUUUCUGGUUUUAUUUCUU
..........((((((.((..((((((((((((((....))))))).(((.......)))----------.......)))))))..))....))))))......... ( -28.20, z-score =  -2.70, R)
>consensus
__CAUUAUUUGGCUAGUGAUUCACUCGAGCGAGUGGCGACAAUCGCUGGCUCAGAUUCGC__________GGUUGUCUGUGGUGUUUCUUUUCUGUUUUUAUUUUUU
..........((((((((((((((((....)))))).....))))))))))........................................................ (-17.25 = -17.38 +   0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,535,034 – 18,535,126
Length 92
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 76.57
Shannon entropy 0.36703
G+C content 0.42347
Mean single sequence MFE -18.05
Consensus MFE -9.36
Energy contribution -9.42
Covariance contribution 0.06
Combinations/Pair 1.08
Mean z-score -2.04
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.39
SVM RNA-class probability 0.670487
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18535034 92 - 22422827
AAAAAAUAAUAACAGAAAAGAAACACCACAGACAACC-------------AAUCUGAGCCAGCGAUUGUCGCCACUCGCUCGAGUGAAUCACUAGCCAAAUAAUG--
............................((((.....-------------..)))).((.((.((((.....(((((....))))))))).)).)).........-- ( -13.30, z-score =  -1.52, R)
>droSec1.super_8 838781 105 - 3762037
AAAAAAUAGGAGCAGAAAACAAACACCACAGGCAACCAACGCAAAAUGCGAAUCUGAGCCAGCGAUUGUCGCCACUCGCUCGAGUGAAUCACUAGCUAAAUAAUG--
........((..((((..............(....)...(((.....)))..))))..)).(((.....)))(((((....)))))...................-- ( -22.90, z-score =  -1.66, R)
>droYak2.chrX 17161152 95 - 21770863
AAAAAAUAAAAACCGAGUAGAAAAACCAGCGCAAAAU----------GCGAAUCUAAGCCAGCGAUUGUCGCCACUCGCUCGAGUGAAUCACUAGUCAAAAAAUG--
..............((.(((.........(((.....----------)))...........(((.....)))(((((....))))).....))).))........-- ( -18.00, z-score =  -1.78, R)
>droEre2.scaffold_4690 8844607 97 - 18748788
AAGAAAUAAAACCAGAAAAGAAACACCCAACACCACA----------GGCAAUCCAAGCCAGCGAUUGUCGUCAAUCGCUCGAGUGAAUCACUAGCCAAAAUAUAUG
...................((..(((.(.........----------(((.......)))((((((((....)))))))).).)))..))................. ( -18.00, z-score =  -3.22, R)
>consensus
AAAAAAUAAAAACAGAAAAGAAACACCACAGACAACC__________GCGAAUCUAAGCCAGCGAUUGUCGCCACUCGCUCGAGUGAAUCACUAGCCAAAAAAUG__
.........................................................((.((.((((.....(((((....))))))))).)).))........... ( -9.36 =  -9.42 +   0.06)

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 01:57:33 2011