Locus 1831

Sequence ID dm3.chr2L
Location 14,220,323 – 14,220,499
Length 176
Max. P 0.935947
window2517 window2518 window2519

overview

Window 7

Location 14,220,323 – 14,220,419
Length 96
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 73.41
Shannon entropy 0.48932
G+C content 0.48616
Mean single sequence MFE -35.90
Consensus MFE -17.87
Energy contribution -18.32
Covariance contribution 0.45
Combinations/Pair 1.36
Mean z-score -1.39
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.16
SVM RNA-class probability 0.570293
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14220323 96 - 23011544
CCUCCAGUGCCAAGGCGACUG--UUUGGCAUUCGCCAGGCAUUUGCA----------------UUUUCUUUUUUGGCCCCUC---UCGGAAAAAUUCCAAGCCAUAAGGGGGAAAAU-
(((((...((((((((((.((--((((((....)))))))).)))).----------------........)))))).....---..(((.....))).........))))).....- ( -31.60, z-score =  -1.20, R)
>droEre2.scaffold_4929 15395276 110 + 26641161
CCUCCAGAGCCAAGGCGACUG--UUUGGCAUUCGCCAGGCAUUUGCAUUUGUACGCGCUGCA-UUUUCUUUUUUGGCCUCC---GUCGGAAAAAUUCCGAGCCAUAAGGGGAAAAU--
....(((.((((((((((.((--((((((....)))))))).)))).))))...)).)))..-(((((((((.((((....---.(((((.....))))))))).)))))))))..-- ( -39.20, z-score =  -2.19, R)
>droYak2.chr2L 14318763 112 - 22324452
CCUCCAGUGCCAAGGCGACUG--UUUGGCAUUCGCCAGGCAUUUGCAUUUGUACGCGCUGCAUUUUCUUUUUUUGGCCCCC---GUCGGAAAAAUUCCGAGCCAUAGGGGGGAAAAU-
....((((((((((((((.((--((((((....)))))))).)))).))))...))))))..((((((((((.((((....---.(((((.....))))))))).))))))))))..- ( -43.10, z-score =  -2.35, R)
>droSec1.super_3 477953 115 - 7220098
CCUCCAGUGCCAAGGCGACUG--UUUGGCAUUCGCCAGGCAUUUGCAUUUGUACGCGCUGCAUUUUCUUUUUUUGGCCCCCCCCAUCGGAAAAAUUCCAAGCCAUGAGGGGGAAAAU-
....((((((((((((((.((--((((((....)))))))).)))).))))...)))))).................(((((.(((.((............))))).))))).....- ( -39.40, z-score =  -1.38, R)
>droSim1.chr2L 13963658 115 - 22036055
CCUCCAGUGCCAAGGAGACUG--UUUGGCAUUCGCCAGGCAUUUGCAUGUGUACGCGCUGCAUUUUCUUUUUUUGGCCCCCCCCAUCGGAAAAAUUCCAAGCCAUAAGGGGGAAAAU-
(((((...((((((((((.((--((((((....))))))))..((((.(((....))))))).....))))))))))..........(((.....))).........))))).....- ( -38.60, z-score =  -1.39, R)
>droGri2.scaffold_15252 4763889 102 - 17193109
----CAAUUGAAAAGCACUUGCACUUGGCGCUGGCUUGGUAUUUGCAUU---------UGCAUUAACAAAGUGUGACCAAC---AUUGAAAAUGCAUCUCGCAAUGCAAAUGAACAUU
----(((.((..((((...(((.....)))...))))..)).)))((((---------((((((.....(((((.....))---)))......((.....))))))))))))...... ( -23.50, z-score =   0.17, R)
>consensus
CCUCCAGUGCCAAGGCGACUG__UUUGGCAUUCGCCAGGCAUUUGCAUUUGUACGCGCUGCAUUUUCUUUUUUUGGCCCCC___AUCGGAAAAAUUCCAAGCCAUAAGGGGGAAAAU_
.....((((((.((....)).....((((....))))))))))....................(((((((((.((((..........(((.....)))..)))).))))))))).... (-17.87 = -18.32 +   0.45)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,220,352 – 14,220,446
Length 94
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 77.18
Shannon entropy 0.42184
G+C content 0.47686
Mean single sequence MFE -31.63
Consensus MFE -17.73
Energy contribution -19.07
Covariance contribution 1.34
Combinations/Pair 1.16
Mean z-score -2.12
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.40
SVM RNA-class probability 0.935947
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14220352 94 - 23011544
GCAUUUUAAUCAAGUGCCAAGAAAACACCUCCAGUGCCAAGGCGACUG--UUUGGCAUUCGCCAGGCAUUUGCA----------------UUUUCUUUUUUGGCCCCUCUCG---
...............(((((((((.(((.....))).....((((.((--((((((....)))))))).)))).----------------.....)))))))))........--- ( -27.10, z-score =  -2.28, R)
>droEre2.scaffold_4929 15395304 109 + 26641161
GCAUUUUAAUCAAGUGCCAAGAAAACACCUCCAGAGCCAAGGCGACUG--UUUGGCAUUCGCCAGGCAUUUGCAUUUGUACGCGCUGCAUUUUC-UUUUUUGGCCUCCGUCG---
............((.(((((((((.......(((.((((((((((.((--((((((....)))))))).)))).))))...)).))).......-)))))))))))......--- ( -32.54, z-score =  -1.95, R)
>droYak2.chr2L 14318792 110 - 22324452
GCAUUUUAAUCAAGUGCCAAGAAAACACCUCCAGUGCCAAGGCGACUG--UUUGGCAUUCGCCAGGCAUUUGCAUUUGUACGCGCUGCAUUUUCUUUUUUUGGCCCCCGUCG---
...............((((((((((......((((((((((((((.((--((((((....)))))))).)))).))))...)))))).......))))))))))........--- ( -36.12, z-score =  -3.01, R)
>droSec1.super_3 477982 113 - 7220098
GCAUUUUAAUCAAGUGCCAAGAAAACACCUCCAGUGCCAAGGCGACUG--UUUGGCAUUCGCCAGGCAUUUGCAUUUGUACGCGCUGCAUUUUCUUUUUUUGGCCCCCCCCAUCG
...............((((((((((......((((((((((((((.((--((((((....)))))))).)))).))))...)))))).......))))))))))........... ( -36.12, z-score =  -3.35, R)
>droSim1.chr2L 13963687 113 - 22036055
GCAUUUUAAUCAAGUGCCAAGAAAACACCUCCAGUGCCAAGGAGACUG--UUUGGCAUUCGCCAGGCAUUUGCAUGUGUACGCGCUGCAUUUUCUUUUUUUGGCCCCCCCCAUCG
...............((((((((((.......((((((.((....)).--..((((....))))))))))((((.(((....))))))).....))))))))))........... ( -32.90, z-score =  -2.05, R)
>droGri2.scaffold_15252 4763919 99 - 17193109
GCAUUUUAAGCACAUGCCAAGCAA----CAACAAUUGAAAAGCACUUGCACUUGGCGCUGGCUUGGUAUUUGCAUU---------UGCAUUAACAAAGUGUGACCAACAUUG---
(((......(((.(((((((((..----((.....))...(((.((.......)).))).))))))))).)))...---------)))........(((((.....))))).--- ( -25.00, z-score =  -0.06, R)
>consensus
GCAUUUUAAUCAAGUGCCAAGAAAACACCUCCAGUGCCAAGGCGACUG__UUUGGCAUUCGCCAGGCAUUUGCAUUUGUACGCGCUGCAUUUUCUUUUUUUGGCCCCCCUCG___
...............(((((((((........((((((.((....)).....((((....))))))))))((((...........))))......)))))))))........... (-17.73 = -19.07 +   1.34)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,220,446 – 14,220,499
Length 53
Sequences 5
Columns 54
Reading direction reverse
Mean pairwise identity 81.94
Shannon entropy 0.32412
G+C content 0.55306
Mean single sequence MFE -17.50
Consensus MFE -8.90
Energy contribution -10.06
Covariance contribution 1.16
Combinations/Pair 1.27
Mean z-score -2.30
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.679241
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14220446 53 - 23011544
GCCCAUAGAUUGCAG-UUCCCAAUGGCACUUAUGGCCAUCGAAACGCAGUCGCU
.......((((((..-(((...(((((.(....)))))).)))..))))))... ( -16.40, z-score =  -2.35, R)
>droAna3.scaffold_12916 4613910 52 + 16180835
GCCCCUGAACCUCGG--UUGCAGGCGCACUUGUAGCCACCGCACUGCACAAGCU
((.(((((((....)--)).)))).)).(((((.((.........))))))).. ( -15.40, z-score =  -0.38, R)
>droEre2.scaffold_4929 15395413 53 + 26641161
GCCCAUAGAUUGCAG-UUCACAGUGGCACUUAUGGCCAUCGAAACGCAGUCGCU
.......((((((..-(((...(((((.(....)))))).)))..))))))... ( -16.70, z-score =  -2.12, R)
>droSec1.super_3 478095 54 - 7220098
GCCCAUAGAUUGCAGUUUCCCAGUGGCACUUAUGGCCAUCGAAACGCAGUCGCU
.......((((((.(((((...(((((.(....)))))).)))))))))))... ( -19.50, z-score =  -3.32, R)
>droSim1.chr2L 13963800 54 - 22036055
GCCCAUAGAUUGCAGUUUCCCAGUGGCACUUAUGGCCAUCGAAACGCAGUCGCU
.......((((((.(((((...(((((.(....)))))).)))))))))))... ( -19.50, z-score =  -3.32, R)
>consensus
GCCCAUAGAUUGCAG_UUCCCAGUGGCACUUAUGGCCAUCGAAACGCAGUCGCU
.......((((((.(.(((...(((((.......))))).))).)))))))... ( -8.90 = -10.06 +   1.16)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:39:40 2011