Locus 1846

Sequence ID dm3.chr2L
Location 14,398,065 – 14,398,170
Length 105
Max. P 0.744398
window2540 window2541

overview

Window 0

Location 14,398,065 – 14,398,170
Length 105
Sequences 11
Columns 115
Reading direction forward
Mean pairwise identity 80.77
Shannon entropy 0.38247
G+C content 0.46083
Mean single sequence MFE -26.03
Consensus MFE -15.51
Energy contribution -15.28
Covariance contribution -0.23
Combinations/Pair 1.11
Mean z-score -1.74
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.56
SVM RNA-class probability 0.744398
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14398065 105 + 23011544
---GAGAGAAACACAAAACCCUGUCACAUUAACUGUCAACUGCCGCACA--ACUGACACUUGUCAUAUUGACAACCGACAGCGUCAUUUGACUGUCA-----AACGCGGGCCAAC
---...............(((((((........(((((..((.....))--..))))).(((((.....)))))..))))((((...(((.....))-----))))))))..... ( -22.00, z-score =  -0.79, R)
>droWil1.scaffold_180764 2647244 98 + 3949147
----------ACACAAAACGCUGUCACAUUAACUGUCAACUGCUGCAAA--ACUGACACUUGUCAUAUUGACAAGUGACAGCGUCAUUUGACUGUCA-----AACUCAGACCAAA
----------...((((((((((((((......(((((...........--..))))).(((((.....)))))))))))))))..)))).(((...-----....)))...... ( -28.32, z-score =  -3.30, R)
>dp4.chr4_group1 1759914 115 - 5278887
AGAGAGAGAAACACAAAACGCUGUCACAUUAACUGUCAACUGCUGCAAAGCACUGACACUUGUCAUAUUGACAAGUGACAGCGUCAUUUGACUGUCAGAAAGAACAGAGACAGAC
.............((((((((((((((......(((((..((((....)))).))))).(((((.....)))))))))))))))..)))).(((((............))))).. ( -38.10, z-score =  -3.65, R)
>droAna3.scaffold_12916 14761000 105 - 16180835
---AAGAGAAACACAAAACGCUGUCACAUUAACUGUCAACUACUGCAGA--ACUGACACUUGUCAUAUUGACAAGUGACAGCGUCAUUUGACUGUCA-----AACCCGGGCCAAG
---....((....((((((((((((((.....((((........)))).--........(((((.....)))))))))))))))..))))....)).-----............. ( -27.80, z-score =  -2.15, R)
>droEre2.scaffold_4929 6151316 105 + 26641161
---GGGAGAAACACAAAACCCUGUCACAUUAACUGUCAACUGCCGCACA--ACUGACACUUGUCAUAUUGACAACCGACAGCGUCAUUUGACUGUCA-----AACGCGGGCCAAC
---...............(((((((........(((((..((.....))--..))))).(((((.....)))))..))))((((...(((.....))-----))))))))..... ( -22.00, z-score =  -0.26, R)
>droYak2.chr2L 14502452 105 + 22324452
---GGGAGAAACACAAAACCCUGUCACAUUAACUGUCAACUGCCGCACA--ACUGACACUUGUCAUAUUGACAACCGACAGCGUCAUUUGACUGUCA-----AACGCGGGCCAAC
---...............(((((((........(((((..((.....))--..))))).(((((.....)))))..))))((((...(((.....))-----))))))))..... ( -22.00, z-score =  -0.26, R)
>droSec1.super_3 657686 104 + 7220098
---GAGAGAA-CACAAAACCCUGUCACAUUAACUGUCAACUGCCGCACA--ACUGACACUUGUCAUAUUGACAACCGACAGCGUCAUUUGACUGUCA-----AACGCGGGCCAAC
---.......-.......(((((((........(((((..((.....))--..))))).(((((.....)))))..))))((((...(((.....))-----))))))))..... ( -22.00, z-score =  -0.74, R)
>droSim1.chr2L 14145870 105 + 22036055
---GAGAGAAACACAAAACCCUGUCACAUUAACUGUCAACUGCCGCACA--ACUGACACUUGUCAUAUUGACAACCGACAGCGUCAUUUGACUGUCA-----AACGCGGGCCAAC
---...............(((((((........(((((..((.....))--..))))).(((((.....)))))..))))((((...(((.....))-----))))))))..... ( -22.00, z-score =  -0.79, R)
>droGri2.scaffold_15126 703369 87 + 8399593
------------------CGCUGUCACAUUAACUGUCAACUGCUGCAAA--ACUGACACUUGUCAUAUUGACAGCUGACAGCGUCAUUUGACUGUCAAACUUGGCCC--------
------------------.(((((((((.....))).....(((((((.--..((((....))))..))).)))).))))))(((....))).((((....))))..-------- ( -24.70, z-score =  -2.44, R)
>droVir3.scaffold_12723 3007746 87 - 5802038
------------------CGCUGUCACAUUAACUGUCAACUGCUGCAAA--AGUGACACUUGUCAUAUUGACAACUGACAGCGUCAUUUGACUGUCAAACUCGGCUC--------
------------------.(((((((.......(((((.((........--))))))).(((((.....))))).)))))))(((....))).(((......)))..-------- ( -24.50, z-score =  -2.18, R)
>droMoj3.scaffold_6500 16298224 95 - 32352404
------------------CGCUGUCACAUUAACUGUCAACUGCUGCAAA--AGUGACACUUGUCAUAUUGACAGCUGACAGCGUCAUUUGGCUGUCAAAGGCAGCUCGGCUCUAC
------------------.((((((................(((((((.--.(((((....))))).))).))))(((((((........)))))))..)))))).......... ( -32.90, z-score =  -2.59, R)
>consensus
___GAGAGAAACACAAAACGCUGUCACAUUAACUGUCAACUGCUGCAAA__ACUGACACUUGUCAUAUUGACAACUGACAGCGUCAUUUGACUGUCA_____AACGCGGGCCAAC
....................(((((........(((((...............))))).(((((.....)))))..))))).(((....)))....................... (-15.51 = -15.28 +  -0.23)

alignment

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secondary structure

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dotplot

Postscript

Window 1

Location 14,398,065 – 14,398,170
Length 105
Sequences 11
Columns 115
Reading direction reverse
Mean pairwise identity 80.77
Shannon entropy 0.38247
G+C content 0.46083
Mean single sequence MFE -31.25
Consensus MFE -19.71
Energy contribution -19.41
Covariance contribution -0.30
Combinations/Pair 1.13
Mean z-score -1.40
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.542586
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14398065 105 - 23011544
GUUGGCCCGCGUU-----UGACAGUCAAAUGACGCUGUCGGUUGUCAAUAUGACAAGUGUCAGU--UGUGCGGCAGUUGACAGUUAAUGUGACAGGGUUUUGUGUUUCUCUC---
...(((((..(((-----..((((((....)))((((((..(((((.(((((((....))))..--)))..)))))..))))))...)))))).))))).............--- ( -31.10, z-score =  -0.82, R)
>droWil1.scaffold_180764 2647244 98 - 3949147
UUUGGUCUGAGUU-----UGACAGUCAAAUGACGCUGUCACUUGUCAAUAUGACAAGUGUCAGU--UUUGCAGCAGUUGACAGUUAAUGUGACAGCGUUUUGUGU----------
....(((......-----.)))...((...(((((((((((((((((((.((((....))))((--......)).)))))))).....)))))))))))...)).---------- ( -32.20, z-score =  -2.02, R)
>dp4.chr4_group1 1759914 115 + 5278887
GUCUGUCUCUGUUCUUUCUGACAGUCAAAUGACGCUGUCACUUGUCAAUAUGACAAGUGUCAGUGCUUUGCAGCAGUUGACAGUUAAUGUGACAGCGUUUUGUGUUUCUCUCUCU
(.(((((............))))).)....((((((((((((((((.....))))).((((((((((....)))).))))))......)))))))))))................ ( -39.10, z-score =  -3.25, R)
>droAna3.scaffold_12916 14761000 105 + 16180835
CUUGGCCCGGGUU-----UGACAGUCAAAUGACGCUGUCACUUGUCAAUAUGACAAGUGUCAGU--UCUGCAGUAGUUGACAGUUAAUGUGACAGCGUUUUGUGUUUCUCUU---
........(((..-----.((((..(((..(((((((((((((((((((.((((....))))(.--....)....)))))))).....)))))))))))))))))).)))..--- ( -32.10, z-score =  -1.70, R)
>droEre2.scaffold_4929 6151316 105 - 26641161
GUUGGCCCGCGUU-----UGACAGUCAAAUGACGCUGUCGGUUGUCAAUAUGACAAGUGUCAGU--UGUGCGGCAGUUGACAGUUAAUGUGACAGGGUUUUGUGUUUCUCCC---
...(((((..(((-----..((((((....)))((((((..(((((.(((((((....))))..--)))..)))))..))))))...)))))).))))).............--- ( -31.10, z-score =  -0.79, R)
>droYak2.chr2L 14502452 105 - 22324452
GUUGGCCCGCGUU-----UGACAGUCAAAUGACGCUGUCGGUUGUCAAUAUGACAAGUGUCAGU--UGUGCGGCAGUUGACAGUUAAUGUGACAGGGUUUUGUGUUUCUCCC---
...(((((..(((-----..((((((....)))((((((..(((((.(((((((....))))..--)))..)))))..))))))...)))))).))))).............--- ( -31.10, z-score =  -0.79, R)
>droSec1.super_3 657686 104 - 7220098
GUUGGCCCGCGUU-----UGACAGUCAAAUGACGCUGUCGGUUGUCAAUAUGACAAGUGUCAGU--UGUGCGGCAGUUGACAGUUAAUGUGACAGGGUUUUGUG-UUCUCUC---
...(((((..(((-----..((((((....)))((((((..(((((.(((((((....))))..--)))..)))))..))))))...)))))).))))).....-.......--- ( -31.10, z-score =  -0.79, R)
>droSim1.chr2L 14145870 105 - 22036055
GUUGGCCCGCGUU-----UGACAGUCAAAUGACGCUGUCGGUUGUCAAUAUGACAAGUGUCAGU--UGUGCGGCAGUUGACAGUUAAUGUGACAGGGUUUUGUGUUUCUCUC---
...(((((..(((-----..((((((....)))((((((..(((((.(((((((....))))..--)))..)))))..))))))...)))))).))))).............--- ( -31.10, z-score =  -0.82, R)
>droGri2.scaffold_15126 703369 87 - 8399593
--------GGGCCAAGUUUGACAGUCAAAUGACGCUGUCAGCUGUCAAUAUGACAAGUGUCAGU--UUUGCAGCAGUUGACAGUUAAUGUGACAGCG------------------
--------...............((((.((...(((((((((((((((..((((....))))..--.)))..))))))))))))..)).))))....------------------ ( -29.30, z-score =  -2.13, R)
>droVir3.scaffold_12723 3007746 87 + 5802038
--------GAGCCGAGUUUGACAGUCAAAUGACGCUGUCAGUUGUCAAUAUGACAAGUGUCACU--UUUGCAGCAGUUGACAGUUAAUGUGACAGCG------------------
--------.......(((((.....)))))..(((((((.(((((.((..((((....))))..--)).))))).....(((.....))))))))))------------------ ( -25.20, z-score =  -0.91, R)
>droMoj3.scaffold_6500 16298224 95 + 32352404
GUAGAGCCGAGCUGCCUUUGACAGCCAAAUGACGCUGUCAGCUGUCAAUAUGACAAGUGUCACU--UUUGCAGCAGUUGACAGUUAAUGUGACAGCG------------------
((((.......))))...(((((((........)))))))(((((((...((((...(((((((--........)).)))))))))...))))))).------------------ ( -30.40, z-score =  -1.38, R)
>consensus
GUUGGCCCGCGUU_____UGACAGUCAAAUGACGCUGUCAGUUGUCAAUAUGACAAGUGUCAGU__UGUGCAGCAGUUGACAGUUAAUGUGACAGCGUUUUGUGUUUCUCUC___
..................(((((((........))))))).((((((...((((...((((((.............))))))))))...)))))).................... (-19.71 = -19.41 +  -0.30)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:39:58 2011