Locus 4121

Sequence ID dm3.chr2R
Location 10,620,495 – 10,620,595
Length 100
Max. P 0.912619
window5654 window5655

overview

Window 4

Location 10,620,495 – 10,620,595
Length 100
Sequences 7
Columns 118
Reading direction forward
Mean pairwise identity 78.56
Shannon entropy 0.40564
G+C content 0.42415
Mean single sequence MFE -26.82
Consensus MFE -15.74
Energy contribution -16.38
Covariance contribution 0.63
Combinations/Pair 1.10
Mean z-score -2.00
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.23
SVM RNA-class probability 0.912619
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10620495 100 + 21146708
-AGUCCGAGACAUCGUCGAAACUUUUGCCAUAGCUC--GAACAUAAUUAUAAAAGUUUCGACAAGUAUUUGCCCAGGUGGGCCA------------GUGUUCGUGCAAAAAAUAA---
-.(..((((.(((.(((((((((((((.........--...........)))))))))))))........((((....))))..------------)))))))..).........--- ( -27.75, z-score =  -3.01, R)
>droYak2.chr2R 10554366 112 + 21139217
-AGUCCGAGACAUCGUCGAAACUUUUGCCAUAGCUC--GAACAUAAUUAUAAAAGUUUCGACAAGUAUUUGCCCAGGUGGGCCAGCAACGCAGCCAGUGUUCGUGCAAAAAAUAA---
-.(..((((.(((.(((((((((((((.........--...........)))))))))))))........((((....))))..((......))..)))))))..).........--- ( -27.85, z-score =  -1.63, R)
>droEre2.scaffold_4845 7361930 109 - 22589142
-AGUCCGAGACAUCGUCGAAACUUUUGCCAUAGCUC--GAACAUAAUUAUAAAAGUUUCGACAAGUAUUUGCCCAGGUGGGCCAACA---CAGCCAGUGUUCGGGCAAAAAACAG---
-.(((((((.(((.(((((((((((((.........--...........)))))))))))))..((.((.((((....)))).)).)---).....)))))))))).........--- ( -34.55, z-score =  -4.15, R)
>droAna3.scaffold_13266 5100056 102 - 19884421
GAGUCCGAGACAUCGUCGGAACUUUUGCCAUAGCUC--GAACAUAAUUAUAAAAGUUUCGACAAGUAUUUGCCCAGGUGGGCUA--------------GCUCUUGCAAAAAACAAAAA
..((..(((.(...(((((((((((((.........--...........)))))))))))))........((((....))))..--------------))))..))............ ( -24.95, z-score =  -1.65, R)
>dp4.chr3 5280668 104 + 19779522
-AGUCCGAGACGUGGCUAAAACUUUUGCCAUUGCUC--GAACAUAAUUAUAAAAGUUUCGACAAGUAUUUGGCCAGGUGGGCAAGGA--------GCAGUUCCACACAGAAACAA---
-.((.((((..(((((..........)))))..)))--).))............(((((.........(((.((....)).)))(((--------(...)))).....)))))..--- ( -26.60, z-score =  -1.35, R)
>droPer1.super_2 5485945 104 + 9036312
-AGUCCGAGACGUGGCUAAAACUUUUGCCAUUGCUC--GAACAUAAUUAUAAAAGUUUCGACAAGUAUUUGGCCAGGUGGGCAAGGA--------GCAGUUCCAUACAGAAACAA---
-.((.((((..(((((..........)))))..)))--).))............(((((.........(((.((....)).)))(((--------(...)))).....)))))..--- ( -26.60, z-score =  -1.43, R)
>droWil1.scaffold_180699 1345704 89 + 2593675
-GGUCCGAGACAUCGUUGAAACUUUUGCCAUAGCUCCUGAACAUAAUUAUAAAAGUUUCGACAAGUAUUUGCC-AGGUGGGCAAAAAGCAA---------------------------
-.(((...)))...(((((((((((((......................))))))))))))).....((((((-.....))))))......--------------------------- ( -19.45, z-score =  -0.79, R)
>consensus
_AGUCCGAGACAUCGUCGAAACUUUUGCCAUAGCUC__GAACAUAAUUAUAAAAGUUUCGACAAGUAUUUGCCCAGGUGGGCAAG_A_________GUGUUCGUGCAAAAAACAA___
..(((...)))...(((((((((((((......................)))))))))))))........((((....)))).................................... (-15.74 = -16.38 +   0.63)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,620,495 – 10,620,595
Length 100
Sequences 7
Columns 118
Reading direction reverse
Mean pairwise identity 78.56
Shannon entropy 0.40564
G+C content 0.42415
Mean single sequence MFE -26.10
Consensus MFE -14.37
Energy contribution -15.03
Covariance contribution 0.65
Combinations/Pair 1.04
Mean z-score -1.64
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.22
SVM RNA-class probability 0.597308
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10620495 100 - 21146708
---UUAUUUUUUGCACGAACAC------------UGGCCCACCUGGGCAAAUACUUGUCGAAACUUUUAUAAUUAUGUUC--GAGCUAUGGCAAAAGUUUCGACGAUGUCUCGGACU-
---.........(..((((((.------------..((((....))))......((((((((((((((...((...((..--..)).))...))))))))))))))))).)))..).- ( -27.20, z-score =  -2.79, R)
>droYak2.chr2R 10554366 112 - 21139217
---UUAUUUUUUGCACGAACACUGGCUGCGUUGCUGGCCCACCUGGGCAAAUACUUGUCGAAACUUUUAUAAUUAUGUUC--GAGCUAUGGCAAAAGUUUCGACGAUGUCUCGGACU-
---.........(..((((((..(((......))).((((....))))......((((((((((((((...((...((..--..)).))...))))))))))))))))).)))..).- ( -29.30, z-score =  -1.42, R)
>droEre2.scaffold_4845 7361930 109 + 22589142
---CUGUUUUUUGCCCGAACACUGGCUG---UGUUGGCCCACCUGGGCAAAUACUUGUCGAAACUUUUAUAAUUAUGUUC--GAGCUAUGGCAAAAGUUUCGACGAUGUCUCGGACU-
---...........(((((((......(---((((.((((....)))).)))))((((((((((((((...((...((..--..)).))...))))))))))))))))).))))...- ( -33.80, z-score =  -2.89, R)
>droAna3.scaffold_13266 5100056 102 + 19884421
UUUUUGUUUUUUGCAAGAGC--------------UAGCCCACCUGGGCAAAUACUUGUCGAAACUUUUAUAAUUAUGUUC--GAGCUAUGGCAAAAGUUCCGACGAUGUCUCGGACUC
.......(((((((...(((--------------..((((....)))).........(((((.(............))))--)))))...))))))).(((((.(....))))))... ( -26.80, z-score =  -1.88, R)
>dp4.chr3 5280668 104 - 19779522
---UUGUUUCUGUGUGGAACUGC--------UCCUUGCCCACCUGGCCAAAUACUUGUCGAAACUUUUAUAAUUAUGUUC--GAGCAAUGGCAAAAGUUUUAGCCACGUCUCGGACU-
---..(((((.(((((((.....--------)))..(((.....)))...)))).....)))))............((((--(((...((((..........))))...))))))).- ( -23.50, z-score =  -0.74, R)
>droPer1.super_2 5485945 104 - 9036312
---UUGUUUCUGUAUGGAACUGC--------UCCUUGCCCACCUGGCCAAAUACUUGUCGAAACUUUUAUAAUUAUGUUC--GAGCAAUGGCAAAAGUUUUAGCCACGUCUCGGACU-
---..(((((.(((((((.....--------)))..(((.....)))...)))).....)))))............((((--(((...((((..........))))...))))))).- ( -23.50, z-score =  -1.04, R)
>droWil1.scaffold_180699 1345704 89 - 2593675
---------------------------UUGCUUUUUGCCCACCU-GGCAAAUACUUGUCGAAACUUUUAUAAUUAUGUUCAGGAGCUAUGGCAAAAGUUUCAACGAUGUCUCGGACC-
---------------------------......((((((.....-)))))).....((((((((((((...((...(((....))).))...)))))))))..(((....)))))).- ( -18.60, z-score =  -0.73, R)
>consensus
___UUGUUUUUUGCACGAACAC_________U_CUGGCCCACCUGGGCAAAUACUUGUCGAAACUUUUAUAAUUAUGUUC__GAGCUAUGGCAAAAGUUUCGACGAUGUCUCGGACU_
....................................((((....))))........((((((((((((...((...(((....))).))...)))))))))..(((....)))))).. (-14.37 = -15.03 +   0.65)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:23:13 2011