Locus 4168

Sequence ID dm3.chr2R
Location 10,945,857 – 10,946,013
Length 156
Max. P 0.986847
window5714 window5715 window5716

overview

Window 4

Location 10,945,857 – 10,945,955
Length 98
Sequences 8
Columns 104
Reading direction reverse
Mean pairwise identity 58.82
Shannon entropy 0.82112
G+C content 0.46335
Mean single sequence MFE -27.14
Consensus MFE -7.36
Energy contribution -9.25
Covariance contribution 1.89
Combinations/Pair 1.40
Mean z-score -2.38
Structure conservation index 0.27
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.25
SVM RNA-class probability 0.986847
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10945857 98 - 21146708
CAAAACCGAUCCAUAAGCC-AUGGAUA-AACCACAUGCUGCCACAUAGU-UGGUAGCA--AAUCGAGUUUACGAGGAAACUGUUGCUCAGAUGUGGCAAAAAU-
........((((((.....-)))))).-..(((((((((((((......-))))))).--....((((..((.((....)))).))))..)))))).......- ( -32.60, z-score =  -4.34, R)
>droSim1.chr2R 9698217 97 - 19596830
CAAAACCGAUCCAUAAGCC-AUGGAUA-AACCACAUGCUGCCACAUAGU-UGGUAGCA--AAUCGAGUUUACGAGGAAACUGUUGCUCAGAUGUGGCAAAAU--
........((((((.....-)))))).-..(((((((((((((......-))))))).--....((((..((.((....)))).))))..))))))......-- ( -32.60, z-score =  -4.27, R)
>droSec1.super_1 8455667 97 - 14215200
CAAAACCGAUCCAUAAGCC-AUGGAUA-AACCACAUGCUGCCACAUAGU-UGGUAGCA--AAUCGAGUUUACGAGGAAACUGUUGCUCAGAUAUGGCAAAAU--
................(((-(((....-.......((((((((......-))))))))--....((((..((.((....)))).))))...)))))).....-- ( -29.40, z-score =  -3.65, R)
>droYak2.chr2R 10879454 97 - 21139217
CAAAACCGAUCCAUAAGCC-AUGGAUA-AACCACAUGCUGCCACAUAGU-UGGUAGCA--AAUCGAGUUUAUGCGAAAACUGUUGCUCAGAUGUGGCAAAAU--
........((((((.....-)))))).-..(((((((((((((......-))))))).--....((((....(((.....))).))))..))))))......-- ( -28.40, z-score =  -2.94, R)
>droEre2.scaffold_4845 7675327 95 + 22589142
-CGAACCGAUCCGUAAGCC-AUGGAUA-AACCACAUGCUGCCACAUAGU-UGGUAGCA--AAUCGAGUUUAUGCGGAAACUGUUGCUCAGAUGUGGCAAAU---
-.......((((((.....-)))))).-..(((((((((((((......-))))))).--....((((....(((....).)).))))..)))))).....--- ( -30.10, z-score =  -2.55, R)
>droAna3.scaffold_13266 17495885 78 + 19884421
-------------CAUGCCGAUCCAUU-UGCCACAUGCUGCCAGCUAGU-UGGGGG-------AGAGCUCCCAUAGCAGCAGCAACUUGG----GGCGAAGACU
-------------............((-((((.((((((((..((((..-((((((-------....)))))))))).))))))...)).----)))))).... ( -30.40, z-score =  -1.47, R)
>droWil1.scaffold_180699 2363259 87 - 2593675
-------------UGGGGAGGCCAAUA-ACACACUUA-UGUCACACAGUGUGGCCACAUUAGCCAAAUUCCAACCAUGUCUACAGCCGAAAU--GGCCUAAAUU
-------------((((..(((.(((.-.((((((..-........)))))).....))).))).........((((.((.......)).))--)))))).... ( -17.70, z-score =   0.64, R)
>droVir3.scaffold_12875 9812646 80 - 20611582
---------UUUAAAGACAUCUCGAGGCAGCCACAUGUUGCCAGCAGGGUCAACAGCAUACCACACGCUAACAAACAGAACAGAGCUGC---------------
---------........((.(((..((((((.....))))))(((..(((.........)))....))).............))).)).--------------- ( -15.90, z-score =  -0.42, R)
>consensus
_AAAACCGAUCCAUAAGCC_AUGGAUA_AACCACAUGCUGCCACAUAGU_UGGUAGCA__AAUCGAGUUUACGAGGAAACUGUUGCUCAGAUGUGGCAAAAA__
................(((................((((((((.......))))))))......((((................))))......)))....... ( -7.36 =  -9.25 +   1.89)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,945,894 – 10,945,990
Length 96
Sequences 8
Columns 100
Reading direction reverse
Mean pairwise identity 55.86
Shannon entropy 0.87959
G+C content 0.49408
Mean single sequence MFE -28.50
Consensus MFE -7.43
Energy contribution -8.34
Covariance contribution 0.91
Combinations/Pair 1.94
Mean z-score -1.68
Structure conservation index 0.26
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.876873
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10945894 96 - 21146708
ACACAGCCAGUGGAAGUGGAAGUGGUUGUGGGUGGCAAAACCGAUCCAUAAGC--CAUGGAUAAACCACA-UGCUGCCA-CAUAGUUGGUAGCAAAUCGA
.((((((((.(.........).)))))))).((((........((((((....--.))))))...)))).-((((((((-......))))))))...... ( -33.30, z-score =  -2.10, R)
>droSim1.chr2R 9698253 96 - 19596830
ACACAGCCAGUGGAAGUGGAAGUGGUUGUGGGUGGCAAAACCGAUCCAUAAGC--CAUGGAUAAACCACA-UGCUGCCA-CAUAGUUGGUAGCAAAUCGA
.((((((((.(.........).)))))))).((((........((((((....--.))))))...)))).-((((((((-......))))))))...... ( -33.30, z-score =  -2.10, R)
>droSec1.super_1 8455703 90 - 14215200
ACACAGCCAGUG------GAAGUGGUUGUGGGUGGCAAAACCGAUCCAUAAGC--CAUGGAUAAACCACA-UGCUGCCA-CAUAGUUGGUAGCAAAUCGA
.((((((((...------....)))))))).((((........((((((....--.))))))...)))).-((((((((-......))))))))...... ( -32.20, z-score =  -2.36, R)
>droYak2.chr2R 10879490 93 - 21139217
ACACAGUCCACA---GCAGAAGUGGAUGUGGGUGGCAAAACCGAUCCAUAAGC--CAUGGAUAAACCACA-UGCUGCCA-CAUAGUUGGUAGCAAAUCGA
.((((.(((((.---......))))))))).((((........((((((....--.))))))...)))).-((((((((-......))))))))...... ( -32.30, z-score =  -2.91, R)
>droEre2.scaffold_4845 7675362 80 + 22589142
---------------ACAGAAGUGGAUGUGGGUGGC-GAACCGAUCCGUAAGC--CAUGGAUAAACCACA-UGCUGCCA-CAUAGUUGGUAGCAAAUCGA
---------------...((.((((.....(((...-..))).((((((....--.))))))...)))).-((((((((-......))))))))..)).. ( -26.60, z-score =  -2.02, R)
>droAna3.scaffold_13266 17495919 73 + 19884421
-------------------ACACAACGGCAAAUAGUCAAAGCUGGUGGCAUGC-CGAUCCAUUUGCCACA-UGCUGCCAGC-UAGUUGGGGGAGA-----
-------------------...(((((((.....)))..((((((..(((((.-(((.....)))...))-)))..)))))-).)))).......----- ( -28.30, z-score =  -2.02, R)
>droWil1.scaffold_180699 2363284 91 - 2593675
---------AUCAAGCAUGCAGCACUUGCUGUCAGUUGUGGGGAGGCCAAUAACACACUUAUGUCACACAGUGUGGCCACAUUAGCCAAAUUCCAACCAU
---------....(((..(((((....)))))..)))((((((((((.(((..((((((..........)))))).....))).)))....)))..)))) ( -21.50, z-score =   0.64, R)
>droVir3.scaffold_12875 9812674 83 - 20611582
-------------AACUACAACCGAUGGAGGGAGUUAAGCCUUGUUUAAAGACAUCUCGAGGCAGCCACA-UGUUGCCAGCAGGGUCAACAGCAUAC---
-------------((((....((......)).))))..((((((((....((....))..((((((....-.))))))))))))))...........--- ( -20.50, z-score =  -0.58, R)
>consensus
__________U____GUAGAAGUGGUUGUGGGUGGCAAAACCGAUCCAUAAGC__CAUGGAUAAACCACA_UGCUGCCA_CAUAGUUGGUAGCAAAUCGA
..............................(((......))).((((((.......)))))).........((((((((.......))))))))...... ( -7.43 =  -8.34 +   0.91)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,945,916 – 10,946,013
Length 97
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 74.38
Shannon entropy 0.45152
G+C content 0.49511
Mean single sequence MFE -29.58
Consensus MFE -16.26
Energy contribution -16.78
Covariance contribution 0.52
Combinations/Pair 1.36
Mean z-score -1.39
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.584145
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10945916 97 - 21146708
CAUGACACAGAAGUGAUGUUGCCACACAGCCAGUGGAAGUGGAAGUGGUUGUGGGUGGCAAAACCGAUCCAUAAGCCAUGGAUAAACCACA-UGCUGC
.......(((..(((.(((..((.((((((((.(.........).))))))))))..)))......((((((.....))))))....))).-..))). ( -32.50, z-score =  -1.74, R)
>droSim1.chr2R 9698275 97 - 19596830
CAUGACACAGAAGUGAUGUUGCCACACAGCCAGUGGAAGUGGAAGUGGUUGUGGGUGGCAAAACCGAUCCAUAAGCCAUGGAUAAACCACA-UGCUGC
.......(((..(((.(((..((.((((((((.(.........).))))))))))..)))......((((((.....))))))....))).-..))). ( -32.50, z-score =  -1.74, R)
>droSec1.super_1 8455725 91 - 14215200
CAUGACACAGAAGUGAUGUUGCCACACAGC---C---AGUGGAAGUGGUUGUGGGUGGCAAAACCGAUCCAUAAGCCAUGGAUAAACCACA-UGCUGC
.......(((..(((.(((..((.((((((---(---(.......))))))))))..)))......((((((.....))))))....))).-..))). ( -31.40, z-score =  -1.88, R)
>droYak2.chr2R 10879512 94 - 21139217
CAUGACACAGAAGUGAUGUUGCCACACAGUCCAC---AGCAGAAGUGGAUGUGGGUGGCAAAACCGAUCCAUAAGCCAUGGAUAAACCACA-UGCUGC
.......(((..(((.(((..((.((((.(((((---.......)))))))))))..)))......((((((.....))))))....))).-..))). ( -31.50, z-score =  -2.20, R)
>droWil1.scaffold_180699 2363307 87 - 2593675
--UUAGUCAAAGAAGA--UUACCAUCAAGC------AUGCAGCACUUGCUGUCAGUUGUGGGG-AGGCCAAUAACACACUUAUGUCACACAGUGUGGC
--.(((((......))--)))((((..(((------..(((((....)))))..)))))))..-..........((((((..........)))))).. ( -20.00, z-score =   0.60, R)
>consensus
CAUGACACAGAAGUGAUGUUGCCACACAGCC__C__AAGUGGAAGUGGUUGUGGGUGGCAAAACCGAUCCAUAAGCCAUGGAUAAACCACA_UGCUGC
.......(((..(((...(((((((((((((...............))))))..))))))).....((((((.....))))))....)))....))). (-16.26 = -16.78 +   0.52)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:24:03 2011