Locus 5424

Sequence ID dm3.chr2R
Location 20,225,982 – 20,226,189
Length 207
Max. P 0.973128
window7439 window7440 window7441 window7442 window7443

overview

Window 9

Location 20,225,982 – 20,226,091
Length 109
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 90.15
Shannon entropy 0.16369
G+C content 0.52110
Mean single sequence MFE -34.04
Consensus MFE -28.06
Energy contribution -27.75
Covariance contribution -0.31
Combinations/Pair 1.12
Mean z-score -1.66
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.23
SVM RNA-class probability 0.605007
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20225982 109 + 21146708
GGCAAAAGUCAAAGCCGGGCACAAAUUAAAAAUGCCCCACAAUUGCCCGCGAGUUUGAGAUCGGGAACGAGAACGAGAUCGAUCGGGCGAUCGAUCGACAGCUUCUGCA--
.(((.((((.......(((((...........)))))..(.(((((((((((.((((...(((....)))...)))).)))..)))))))).).......)))).))).-- ( -34.80, z-score =  -1.53, R)
>droSec1.super_23 105060 109 + 989336
GGCAAAAGUCAAAGCCGGGCACAAAUUAAAAAUGCCCCACAAUUGCCCGGGAGCUUGAGAUCGGGAACGGGAACGAGAUCGAUCGAGCGAUCGAUCGACAGCUUCUGCA--
(((((..((....)).(((((...........))))).....)))))((((((((((...(((....)))...)))((((((((....))))))))....)))))))..-- ( -36.80, z-score =  -1.95, R)
>droEre2.scaffold_4845 21591871 101 + 22589142
GGCAAAAGUCAAAGCCGGGCACAAAUUAAAAAUGCCCCACAAUUGGCCG------CGAGAUCGAGAACGAGAUCGAGAUCGAUC----GGUCGAUCGACAGCUUCUGCGCU
(((....(((......(((((...........)))))....((((((((------(((..((((........))))..)))..)----))))))).))).((....))))) ( -32.50, z-score =  -1.62, R)
>droSim1.chr2R 18684663 109 + 19596830
GGCAAAAGUCAAAGCCGGGCACAAAUUAAAAAUGCCCCACAAUUGCCCGCGAGUUUGAGAUCGGGAACGAGAACGAGAUCGAUCAAGCGAUCGAUCGACAGCUUCUGCA--
.(((.((((((((.(((((((......................)))))).)..)))))..(((....)))......((((((((....)))))))).....))).))).-- ( -32.05, z-score =  -1.55, R)
>consensus
GGCAAAAGUCAAAGCCGGGCACAAAUUAAAAAUGCCCCACAAUUGCCCGCGAGUUUGAGAUCGGGAACGAGAACGAGAUCGAUCGAGCGAUCGAUCGACAGCUUCUGCA__
.(((.((((.......(((((...........))))).................(((...(((....)))...)))((((((((....))))))))....)))).)))... (-28.06 = -27.75 +  -0.31) 

alignment

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secondary structure

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dotplot

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Window 0

Location 20,225,982 – 20,226,091
Length 109
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 90.15
Shannon entropy 0.16369
G+C content 0.52110
Mean single sequence MFE -37.23
Consensus MFE -33.56
Energy contribution -33.88
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -2.13
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.69
SVM RNA-class probability 0.960842
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20225982 109 - 21146708
--UGCAGAAGCUGUCGAUCGAUCGCCCGAUCGAUCUCGUUCUCGUUCCCGAUCUCAAACUCGCGGGCAAUUGUGGGGCAUUUUUAAUUUGUGCCCGGCUUUGACUUUUGCC
--.((((((((.(((((((((((....))))))))........((((.(((........))).)))).......((((((.........)))))))))...).))))))). ( -37.70, z-score =  -2.11, R)
>droSec1.super_23 105060 109 - 989336
--UGCAGAAGCUGUCGAUCGAUCGCUCGAUCGAUCUCGUUCCCGUUCCCGAUCUCAAGCUCCCGGGCAAUUGUGGGGCAUUUUUAAUUUGUGCCCGGCUUUGACUUUUGCC
--.(((((((.....((((((((....))))))))...........((((............))))(((..((.((((((.........)))))).)).))).))))))). ( -37.20, z-score =  -1.90, R)
>droEre2.scaffold_4845 21591871 101 - 22589142
AGCGCAGAAGCUGUCGAUCGACC----GAUCGAUCUCGAUCUCGUUCUCGAUCUCG------CGGCCAAUUGUGGGGCAUUUUUAAUUUGUGCCCGGCUUUGACUUUUGCC
...(((((((((((.((((((..----(((((....)))))......))))))..)------))))(((..((.((((((.........)))))).)).)))..)))))). ( -37.20, z-score =  -2.35, R)
>droSim1.chr2R 18684663 109 - 19596830
--UGCAGAAGCUGUCGAUCGAUCGCUUGAUCGAUCUCGUUCUCGUUCCCGAUCUCAAACUCGCGGGCAAUUGUGGGGCAUUUUUAAUUUGUGCCCGGCUUUGACUUUUGCC
--.((((((((.(((((((((((....))))))))........((((.(((........))).)))).......((((((.........)))))))))...).))))))). ( -36.80, z-score =  -2.15, R)
>consensus
__UGCAGAAGCUGUCGAUCGAUCGCUCGAUCGAUCUCGUUCUCGUUCCCGAUCUCAAACUCGCGGGCAAUUGUGGGGCAUUUUUAAUUUGUGCCCGGCUUUGACUUUUGCC
...(((((((.....((((((((....))))))))...........((((............))))(((..((.((((((.........)))))).)).))).))))))). (-33.56 = -33.88 +   0.31) 

alignment

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secondary structure

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dotplot

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Window 1

Location 20,226,053 – 20,226,163
Length 110
Sequences 10
Columns 120
Reading direction forward
Mean pairwise identity 80.08
Shannon entropy 0.35870
G+C content 0.40042
Mean single sequence MFE -24.57
Consensus MFE -14.19
Energy contribution -14.29
Covariance contribution 0.10
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.585666
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20226053 110 + 21146708
AACGAGAUCGAUCGGGCGAUCGAUCGACAGCUUCUGC-ACUGCC-------AGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUUGUAAUUUUAAAAUGCUGCCG--
.....((((((((....))))))))(.((((......-...(((-------((((((...))))).)).))(((.(....))))(((((((((....))))))))).....)))).).-- ( -30.10, z-score =  -1.66, R)
>droSec1.super_23 105131 110 + 989336
AACGAGAUCGAUCGAGCGAUCGAUCGACAGCUUCUGC-ACUGCC-------AGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUUGUAAUUUUAAAAUGCUGCCG--
.....((((((((....))))))))(.((((......-...(((-------((((((...))))).)).))(((.(....))))(((((((((....))))))))).....)))).).-- ( -30.10, z-score =  -1.87, R)
>droYak2.chr2R 20193908 97 + 21139217
--------------AUCGAUGGAUCGACAGCACUGGCCUCUGCC-------AGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUUGUAAUUUUAAAAUGCUGCCG--
--------------.((((....))))...(((((((....)))-------)))).............((((((.(....))))(((((((((....))))))))).....)))....-- ( -25.90, z-score =  -1.98, R)
>droEre2.scaffold_4845 21591936 113 + 22589142
----AUCGAGAUCGAUCGGUCGAUCGACAGCUUCUGC-GCUGGCUUCUGCCAGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGAAAAAUUACAUACUUGUAAUUUUAAAAUGCUGCCG--
----.....((((((....))))))(.((((.(((((-((((((....))))))).....(((....)))..........))))(((((((((....))))))))).....)))).).-- ( -34.80, z-score =  -2.56, R)
>droAna3.scaffold_13266 5699931 85 - 19884421
-------------------UCGAUCGACAGCUUC----GCCGG----------UGGAAUUUUCAUAUGAGCGCUUGAUUUCAGUAAAAUUACAUACUUGUAAUUUUAAAAUGCUACCG--
-------------------..((((((..((((.----....(----------((((...)))))..))))..)))))).((.((((((((((....))))))))))...))......-- ( -16.40, z-score =  -0.73, R)
>dp4.chr3 1336135 87 - 19779522
-------------------UCGAUCGACAGC-------UCCGCC-------AGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUUGUAAUUUUAAAAUGCUGCCAAG
-------------------..((((((..((-------((....-------.(((((...)))))..))))..)))))).(((((((((((((....)))))))).....)))))..... ( -19.40, z-score =  -1.54, R)
>droPer1.super_34 526245 87 - 916997
-------------------UCGAUCGACAGC-------UCCGCC-------AGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUUGUAAUUUUAAAAUGCUGCCAAG
-------------------..((((((..((-------((....-------.(((((...)))))..))))..)))))).(((((((((((((....)))))))).....)))))..... ( -19.40, z-score =  -1.54, R)
>droSim1.chr2R 18684734 110 + 19596830
AACGAGAUCGAUCAAGCGAUCGAUCGACAGCUUCUGC-ACUGCC-------AGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUUGUAAUUUUAAAAUGCUGCCG--
.....((((((((....))))))))(.((((......-...(((-------((((((...))))).)).))(((.(....))))(((((((((....))))))))).....)))).).-- ( -29.60, z-score =  -2.01, R)
>droVir3.scaffold_12875 7337733 84 + 20611582
-------------------ACGAUCGACAGCUUC----GCUG-----------UGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUUGUAAUUUUAAAAUGCUGCCG--
-------------------..((((((..(((.(----(.((-----------((((...)))))))))))..)))))).(((((((((((((....)))))))).....)))))...-- ( -20.00, z-score =  -1.73, R)
>droMoj3.scaffold_6496 26132384 83 + 26866924
-------------------UCGAUCGACAGCUUC----GCUG-----------UGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUUGUAAUUUUAAAAUGCUGCC---
-------------------..((((((..(((.(----(.((-----------((((...)))))))))))..)))))).(((((((((((((....)))))))).....)))))..--- ( -20.00, z-score =  -1.81, R)
>consensus
___________________UCGAUCGACAGCUUC____GCUGCC_______AGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUUGUAAUUUUAAAAUGCUGCCG__
.........................(.((((......................((((((((((....))).....)))))))..(((((((((....))))))))).....)))).)... (-14.19 = -14.29 +   0.10) 

alignment

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secondary structure

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dotplot

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Window 2

Location 20,226,053 – 20,226,163
Length 110
Sequences 10
Columns 120
Reading direction reverse
Mean pairwise identity 80.08
Shannon entropy 0.35870
G+C content 0.40042
Mean single sequence MFE -27.32
Consensus MFE -17.98
Energy contribution -18.05
Covariance contribution 0.07
Combinations/Pair 1.11
Mean z-score -2.37
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.88
SVM RNA-class probability 0.973128
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20226053 110 - 21146708
--CGGCAGCAUUUUAAAAUUACAAGUAUGUAAUUUUGCUGAAAUCAAGCGCUCAUAUGAAAAUUCCACU-------GGCAGU-GCAGAAGCUGUCGAUCGAUCGCCCGAUCGAUCUCGUU
--.((((((....((((((((((....))))))))))..........((((((...((.......))..-------.).)))-))....))))))((((((((....))))))))..... ( -35.20, z-score =  -3.28, R)
>droSec1.super_23 105131 110 - 989336
--CGGCAGCAUUUUAAAAUUACAAGUAUGUAAUUUUGCUGAAAUCAAGCGCUCAUAUGAAAAUUCCACU-------GGCAGU-GCAGAAGCUGUCGAUCGAUCGCUCGAUCGAUCUCGUU
--.((((((....((((((((((....))))))))))..........((((((...((.......))..-------.).)))-))....))))))((((((((....))))))))..... ( -35.20, z-score =  -3.09, R)
>droYak2.chr2R 20193908 97 - 21139217
--CGGCAGCAUUUUAAAAUUACAAGUAUGUAAUUUUGCUGAAAUCAAGCGCUCAUAUGAAAAUUCCACU-------GGCAGAGGCCAGUGCUGUCGAUCCAUCGAU--------------
--(((((((((((((((((((((....)))))))))(((.......))).........)))))...(((-------(((....)))))))))))))..........-------------- ( -29.40, z-score =  -2.95, R)
>droEre2.scaffold_4845 21591936 113 - 22589142
--CGGCAGCAUUUUAAAAUUACAAGUAUGUAAUUUUUCUGAAAUCAAGCGCUCAUAUGAAAAUUCCACUGGCAGAAGCCAGC-GCAGAAGCUGUCGAUCGACCGAUCGAUCUCGAU----
--.((((((.(((.(((((((((....)))))))))...))).....((((((....)).........((((....))))))-))....))))))((((((....)))))).....---- ( -34.70, z-score =  -3.18, R)
>droAna3.scaffold_13266 5699931 85 + 19884421
--CGGUAGCAUUUUAAAAUUACAAGUAUGUAAUUUUACUGAAAUCAAGCGCUCAUAUGAAAAUUCCA----------CCGGC----GAAGCUGUCGAUCGA-------------------
--((..(((....((((((((((....))))))))))...........((((...((....))....----------..)))----)..)))..)).....------------------- ( -18.00, z-score =  -1.19, R)
>dp4.chr3 1336135 87 + 19779522
CUUGGCAGCAUUUUAAAAUUACAAGUAUGUAAUUUUGCUGAAAUCAAGCGCUCAUAUGAAAAUUCCACU-------GGCGGA-------GCUGUCGAUCGA-------------------
.((((((((((((((((((((((....)))))))))(((.......))).........)))))(((...-------...)))-------))))))))....------------------- ( -21.90, z-score =  -1.47, R)
>droPer1.super_34 526245 87 + 916997
CUUGGCAGCAUUUUAAAAUUACAAGUAUGUAAUUUUGCUGAAAUCAAGCGCUCAUAUGAAAAUUCCACU-------GGCGGA-------GCUGUCGAUCGA-------------------
.((((((((((((((((((((((....)))))))))(((.......))).........)))))(((...-------...)))-------))))))))....------------------- ( -21.90, z-score =  -1.47, R)
>droSim1.chr2R 18684734 110 - 19596830
--CGGCAGCAUUUUAAAAUUACAAGUAUGUAAUUUUGCUGAAAUCAAGCGCUCAUAUGAAAAUUCCACU-------GGCAGU-GCAGAAGCUGUCGAUCGAUCGCUUGAUCGAUCUCGUU
--.((((((....((((((((((....))))))))))..........((((((...((.......))..-------.).)))-))....))))))((((((((....))))))))..... ( -34.30, z-score =  -2.85, R)
>droVir3.scaffold_12875 7337733 84 - 20611582
--CGGCAGCAUUUUAAAAUUACAAGUAUGUAAUUUUGCUGAAAUCAAGCGCUCAUAUGAAAAUUCCA-----------CAGC----GAAGCUGUCGAUCGU-------------------
--(((((((....((((((((((....))))))))))...........((((...((....))....-----------.)))----)..))))))).....------------------- ( -22.20, z-score =  -2.41, R)
>droMoj3.scaffold_6496 26132384 83 - 26866924
---GGCAGCAUUUUAAAAUUACAAGUAUGUAAUUUUGCUGAAAUCAAGCGCUCAUAUGAAAAUUCCA-----------CAGC----GAAGCUGUCGAUCGA-------------------
---((((((....((((((((((....))))))))))...........((((...((....))....-----------.)))----)..))))))......------------------- ( -20.40, z-score =  -1.79, R)
>consensus
__CGGCAGCAUUUUAAAAUUACAAGUAUGUAAUUUUGCUGAAAUCAAGCGCUCAUAUGAAAAUUCCACU_______GGCAGC____GAAGCUGUCGAUCGA___________________
..(((((((.....(((((((((....)))))))))(((.......)))........................................)))))))........................ (-17.98 = -18.05 +   0.07) 

alignment

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secondary structure

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dotplot

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Window 3

Location 20,226,091 – 20,226,189
Length 98
Sequences 12
Columns 112
Reading direction forward
Mean pairwise identity 83.24
Shannon entropy 0.36773
G+C content 0.38026
Mean single sequence MFE -24.89
Consensus MFE -14.89
Energy contribution -15.96
Covariance contribution 1.07
Combinations/Pair 1.26
Mean z-score -1.98
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.89
SVM RNA-class probability 0.844888
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20226091 98 + 21146708
-----CUGCCAGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUU-GUAAUUUUAAAAUGCUGCC---GAGUGCCGAGAGAGUUGAAAAGCAACA-----
-----.(((...(..(((((((...((.(((((((....(((((((((((((....)-))))))).....))))).)---)))))))).)))))))..)..)))...----- ( -26.00, z-score =  -2.16, R)
>droSec1.super_23 105169 98 + 989336
-----CUGCCAGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUU-GUAAUUUUAAAAUGCUGCC---GAGUGCCGAGAGAGUUGAAAAGCAACA-----
-----.(((...(..(((((((...((.(((((((....(((((((((((((....)-))))))).....))))).)---)))))))).)))))))..)..)))...----- ( -26.00, z-score =  -2.16, R)
>droYak2.chr2R 20193928 103 + 21139217
GGCCUCUGCCAGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUU-GUAAUUUUAAAAUGCUGCC---GAGUGCCGAGAGAGUUGAGCAGCAGCA-----
.....((((..((..(((((((...((.(((((((....(((((((((((((....)-))))))).....))))).)---)))))))).)))))))..)).))))..----- ( -30.50, z-score =  -1.54, R)
>droEre2.scaffold_4845 21591972 103 + 22589142
GGCUUCUGCCAGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGAAAAAUUACAUACUU-GUAAUUUUAAAAUGCUGCC---GAGUGCCGAGAGAGUUGAAAAGCAACA-----
(((....))).((....((((((.....(((((((.(..((..(((((((((....)-))))))))....))..).)---))))))(....)...))))))...)).----- ( -25.40, z-score =  -1.24, R)
>droAna3.scaffold_13266 5699944 97 - 19884421
-----UCGCCGGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGUAAAAUUACAUACUU-GUAAUUUUAAAAUGCUACC---GAGUGCCGAGAGAGUUGAA-AGCAACA-----
-----..((...(..(((((((...((.(((((((.(..((.((((((((((....)-)))))))))...))..).)---)))))))).)))))))..)-.))....----- ( -23.90, z-score =  -1.87, R)
>dp4.chr3 1336148 99 - 19779522
-----CCGCCAGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUU-GUAAUUUUAAAAUGCUGCCAA-GAGUGCCAAGAGAGUUGAA-ACCAACA-----
-----(((....)))(((((((...((.((((((.....(((((((((((((....)-))))))).....)))))....-)))))))).)))))))...-.......----- ( -25.50, z-score =  -2.83, R)
>droPer1.super_34 526258 99 - 916997
-----CCGCCAGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUU-GUAAUUUUAAAAUGCUGCCAA-GAGUGCCAAGAGAGUUGAA-ACCAACA-----
-----(((....)))(((((((...((.((((((.....(((((((((((((....)-))))))).....)))))....-)))))))).)))))))...-.......----- ( -25.50, z-score =  -2.83, R)
>droSim1.chr2R 18684772 98 + 19596830
-----CUGCCAGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUU-GUAAUUUUAAAAUGCUGCC---GAGUGCCGAGAGAGUUGAAAAGCAACA-----
-----.(((...(..(((((((...((.(((((((....(((((((((((((....)-))))))).....))))).)---)))))))).)))))))..)..)))...----- ( -26.00, z-score =  -2.16, R)
>droWil1.scaffold_180745 1289097 98 + 2843958
-----CAGUCUGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGUGAAAUUACAUACUUUGUAAUUUUAAAAUGCUACC---AACUGCCGAGAGAGUUGAA-GCUCACA-----
-----.....((((((...))))))((((((((((....)))((((((((((.....))))))))))....))...(---((((..(....))))))..-)))))..----- ( -21.50, z-score =  -0.94, R)
>droVir3.scaffold_12875 7337746 92 + 20611582
------UCGCUGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUU-GUAAUUUUAAAAUGCUGCC---GAGUGCC--GAGUGCUGAGUUGCA--------
------......((.(((((.(((.((.(((((((....(((((((((((((....)-))))))).....))))).)---)))))))--).)))..))))).))-------- ( -26.00, z-score =  -1.66, R)
>droMoj3.scaffold_6496 26132397 78 + 26866924
------UCGCUGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUU-GUAAUUUUAAAAUGCUGCC---GAGUUGCA------------------------
------(((.((((((...)))))))))(((((((....(((((((((((((....)-))))))).....))))).)---))).))).------------------------ ( -19.30, z-score =  -1.54, R)
>droGri2.scaffold_15245 884712 101 + 18325388
----------GCUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUU-GUAAUUUUAAAAUGCUGACUUCCAGCAACAAGGAAUUAAAUCAAAUAUAUAUCU
----------(((((((..(((....))).........((((((((((((((....)-))))))).....)))))).)))))))............................ ( -23.10, z-score =  -2.87, R)
>consensus
_____CUGCCAGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUU_GUAAUUUUAAAAUGCUGCC___GAGUGCCGAGAGAGUUGAA_AGCAACA_____
...............(((((((...((.((((((.....((((((((((((.......))))))).....))))).....)))))))).)))))))................ (-14.89 = -15.96 +   1.07) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:48:04 2011