Locus 13469

Sequence ID dm3.chrX
Location 6,736,886 – 6,737,059
Length 173
Max. P 0.889818
window18552 window18553 window18554 window18555

overview

Window 2

Location 6,736,886 – 6,736,991
Length 105
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 68.19
Shannon entropy 0.57282
G+C content 0.64250
Mean single sequence MFE -38.98
Consensus MFE -23.76
Energy contribution -23.72
Covariance contribution -0.04
Combinations/Pair 1.41
Mean z-score -0.96
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.99
SVM RNA-class probability 0.868249
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6736886 105 + 22422827
UGAAACCCUGACCGGUGGUAUCAUUGCCGCCACCGCCGCCGCCGUUACCGCCACGAUUCUGGCCGGGAUUCGAGUGCUGGUGUUGCUGCUGCUGCAGCGCAGAAU--
.......(((...(((((((....)))))))..(((((.(((((...((((((......))).)))....)).))).)))))..(((((....))))).)))...-- ( -41.30, z-score =  -1.13, R)
>droSim1.chrX_random 2160843 105 + 5698898
UGAAACCCUGACCGGCGGAAUCAUUGCCGCCAGCGCCGCCGCCGUUACCGCCACGAUUCUGGCCGGGAUUCGAGUGCUGGUGCUGCUGCUGCUGCAGCGCAGAAU--
.......(((...(((((........)))))(((((((.(((((...((((((......))).)))....)).))).)))))))(((((....))))).)))...-- ( -45.00, z-score =  -1.55, R)
>droSec1.super_4 6120154 105 - 6179234
UGAAACCCUGACCGGCGGAAUCAUUGCCGCCACCGCCGCCGCCGUUACCGCCACGAUUCUGGCCGGGAUUCGAGUGCUGGUGCUGCUGCUGCUGCAGCGCAGAAU--
.......(((...(((((........)))))..(((((.(((((...((((((......))).)))....)).))).)))))..(((((....))))).)))...-- ( -39.70, z-score =  -0.49, R)
>droYak2.chrX 2703782 81 + 21770863
UGAAACCCUGACCGCUGGAGUCAUUGCCGGC------------------GUUACGAUUUUGGCCGGGAUUC---UGUUGGUGCUGCUGCUGCAGCGCCGCAU-----
.(((.(((.....(((((........)))))------------------((((......)))).))).)))---(((.((((((((....))))))))))).----- ( -31.70, z-score =  -1.41, R)
>droWil1.scaffold_180777 2851743 102 - 4753960
UGAAACCCUGGCCAGUGGCAUCGCCACCACCGCCGACGGCGCCG-----ACGAUGCCUGUCGCUGAUGCUCCUCCUCCAGUGCGACCGCCACCGGCCGGCGAUGUGU
.....(.((((((.(((((.((((..........(((((.((..-----.....)))))))((((..(......)..))))))))..))))).)))))).)...... ( -37.20, z-score =  -0.22, R)
>consensus
UGAAACCCUGACCGGUGGAAUCAUUGCCGCCACCGCCGCCGCCGUUACCGCCACGAUUCUGGCCGGGAUUCGAGUGCUGGUGCUGCUGCUGCUGCAGCGCAGAAU__
.(((.(((.....(((((........)))))..................((((......)))).))).)))........(((((((.......)))))))....... (-23.76 = -23.72 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,736,886 – 6,736,991
Length 105
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 68.19
Shannon entropy 0.57282
G+C content 0.64250
Mean single sequence MFE -41.41
Consensus MFE -22.54
Energy contribution -23.26
Covariance contribution 0.72
Combinations/Pair 1.44
Mean z-score -0.78
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.11
SVM RNA-class probability 0.546468
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6736886 105 - 22422827
--AUUCUGCGCUGCAGCAGCAGCAACACCAGCACUCGAAUCCCGGCCAGAAUCGUGGCGGUAACGGCGGCGGCGGUGGCGGCAAUGAUACCACCGGUCAGGGUUUCA
--.......(((((....))))).............(((.(((((((...(((((.((.((....)).)).)))))((.((........)).)))))).))).))). ( -38.90, z-score =   0.15, R)
>droSim1.chrX_random 2160843 105 - 5698898
--AUUCUGCGCUGCAGCAGCAGCAGCACCAGCACUCGAAUCCCGGCCAGAAUCGUGGCGGUAACGGCGGCGGCGCUGGCGGCAAUGAUUCCGCCGGUCAGGGUUUCA
--....((((((((....))))).))).........(((.(((((((.....(((.((.((....)).)).)))..(((((........))))))))).))).))). ( -43.00, z-score =  -0.05, R)
>droSec1.super_4 6120154 105 + 6179234
--AUUCUGCGCUGCAGCAGCAGCAGCACCAGCACUCGAAUCCCGGCCAGAAUCGUGGCGGUAACGGCGGCGGCGGUGGCGGCAAUGAUUCCGCCGGUCAGGGUUUCA
--....((((((((....))))).))).........(((.(((((((...(((((.((.((....)).)).)))))(((((........))))))))).))).))). ( -45.90, z-score =  -0.98, R)
>droYak2.chrX 2703782 81 - 21770863
-----AUGCGGCGCUGCAGCAGCAGCACCAACA---GAAUCCCGGCCAAAAUCGUAAC------------------GCCGGCAAUGACUCCAGCGGUCAGGGUUUCA
-----....((.(((((....))))).))....---(((.(((.(((...........------------------...)))..(((((.....)))))))).))). ( -27.64, z-score =  -1.03, R)
>droWil1.scaffold_180777 2851743 102 + 4753960
ACACAUCGCCGGCCGGUGGCGGUCGCACUGGAGGAGGAGCAUCAGCGACAGGCAUCGU-----CGGCGCCGUCGGCGGUGGUGGCGAUGCCACUGGCCAGGGUUUCA
........(((((((((....(((((..((..(......)..))))))).((((((((-----((.(((((....))))).))))))))))))))))).))...... ( -51.60, z-score =  -2.00, R)
>consensus
__AUUCUGCGCUGCAGCAGCAGCAGCACCAGCACUCGAAUCCCGGCCAGAAUCGUGGCGGUAACGGCGGCGGCGGUGGCGGCAAUGAUUCCACCGGUCAGGGUUUCA
.....((((......)))).................(((.(((((((....((((.((.......)).))))....(((((........))))))))).))).))). (-22.54 = -23.26 +   0.72)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,736,954 – 6,737,059
Length 105
Sequences 10
Columns 115
Reading direction forward
Mean pairwise identity 63.05
Shannon entropy 0.75578
G+C content 0.65051
Mean single sequence MFE -45.68
Consensus MFE -13.59
Energy contribution -13.81
Covariance contribution 0.22
Combinations/Pair 1.50
Mean z-score -1.54
Structure conservation index 0.30
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.55
SVM RNA-class probability 0.740083
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6736954 105 + 22422827
UUCGAGUGCUGGUGUUGCUGCUGCUG--CAGCGCAGAAUC---GGCGGCUCCUGUUGAACUGCUCGAGAAUGUCCUGGAGCGUGGGCUCUGUUGGCCACUGGUCGCCGGA-----
(((..((((((.....((....))..--)))))).)))((---(((((((...........((((.((......)).))))((((.(......).)))).))))))))).----- ( -42.20, z-score =  -0.30, R)
>droSim1.chrX_random 2160911 105 + 5698898
UUCGAGUGCUGGUGCUGCUGCUGCUG--CAGCGCAGAAUC---GGCGGCUCCUGUCGAACUGCUCGAGAAUGUCCUGGAGCGUGGGCUCUGUUGGCCACUGGUCGCCGGG-----
...((((((((((.((((.((((...--)))))))).)))---))).))))(((.(((.((((((.((......)).))))((((.(......).)))).))))).))).----- ( -44.90, z-score =  -0.49, R)
>droSec1.super_4 6120222 105 - 6179234
UUCGAGUGCUGGUGCUGCUGCUGCUG--CAGCGCAGAAUC---GGCGGCUCCUGUCGAACUGCUCGAGAAUGUCCUGGAGCGUGGGCUCUGUUGGCCACUGGUCGCCGGG-----
...((((((((((.((((.((((...--)))))))).)))---))).))))(((.(((.((((((.((......)).))))((((.(......).)))).))))).))).----- ( -44.90, z-score =  -0.49, R)
>droYak2.chrX 2703832 99 + 21770863
------UUCUGUUGGUGCUGCUGCUG--CAGCGCCGCAUC---AGCGGCUCCUGUCGAACUGCUCGAGAAUGUCCUGGAGCGUGGGCUCUGUUGGCCACUGGUAGCCGGA-----
------..(((.(((((((((....)--))))))))...)---))(((((((.........((((.((......)).))))((((.(......).)))).)).)))))..----- ( -45.80, z-score =  -1.83, R)
>droEre2.scaffold_4690 15664504 102 + 18748788
UUUGAAUGCUGGUGCUGCUGCUG-----CAGCGCAGAAUC---GGCGGCUCCUGUCGAACUGCUCGAGAAUGUCCUGGAGCGUGGGCUCUGUUGGCCACUGGUCGCCGGA-----
...........(((((((....)-----))))))....((---(((((((...........((((.((......)).))))((((.(......).)))).))))))))).----- ( -44.50, z-score =  -1.65, R)
>droAna3.scaffold_13117 536319 101 + 5790199
------UGCGACUGGUGGUCACAUUGGGAGCAGUCGGCUC---CGCCGCUCCCGUUGAGCUGCUGGAAAAGGUCCUGGAGCGUGGGCUCUGCUGGCCGCUAGUGGCUGGC-----
------.((.((((((((((.((.(((((((.(.((....---))).))))))).))(((....(((.....))).(((((....)))))))))))))))))).))....----- ( -48.80, z-score =  -1.44, R)
>droWil1.scaffold_180777 2851806 110 - 4753960
CUCCUCCUCCAGUGCGACCGCCACCGGCCGGCGAUGUGUCCACAGCGGCUCCAGUUGAGCUGCUGCUAAAUGUACGAGAGCGUGGGCUCUGUUGGCCACUGGUCGCUGGA-----
.......((((..(((((((.....((((((((..(.((((((((((((((.....))))))))(((...........))))))))).)))))))))..)))))))))))----- ( -50.40, z-score =  -1.98, R)
>dp4.chrXL_group1a 8722516 84 + 9151740
-----------------------CCCGGUGGCGAUGUGUC---AGCGGCUCCCGUGGAGCUGCUCGAGAAUGUCCUGGAGCGCGGGCUCUGCUGGCCACUGGUCGCCGGU-----
-----------------------.((((((((.(((.(((---(((((..(((((......((((.((......)).)))))))))..)))))))))).).)))))))).----- ( -45.40, z-score =  -2.46, R)
>droPer1.super_15 1118956 84 + 2181545
-----------------------CCCGGUGGCGAUGUGUC---AGGGGCUCCCGUGGAGCUGCUCGAGAAUGUCCUGGAGCGCGGGCUCUGCUGGCCACUGGUCGCCGGU-----
-----------------------.((((((((.(((.(((---((((...)))(..(((((((((.((......)).))))...)))))..))))))).).)))))))).----- ( -41.70, z-score =  -1.26, R)
>anoGam1.chrX 6810202 90 + 22145176
------------------------UCAGUCAGGUAGGUUU-GCUGCGCUGGCAGCGAUUCGGCCCAAAGCCGAUGGUGGUGGUAGCCACCCAUGCCAUGCGGCAGGUGGGCCGAA
------------------------...(((((((((....-.)))).))))).....(((((((((..((((((((((((((...)))))...))))).))))...))))))))) ( -48.20, z-score =  -3.46, R)
>consensus
______UGCUGGUGCUGCUGCUGCUG__CAGCGCAGAAUC___AGCGGCUCCUGUCGAACUGCUCGAGAAUGUCCUGGAGCGUGGGCUCUGUUGGCCACUGGUCGCCGGA_____
.............................................((((..(((....((.((((.(........).)))))).((((.....))))..)))..))))....... (-13.59 = -13.81 +   0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 6,736,954 – 6,737,059
Length 105
Sequences 10
Columns 115
Reading direction reverse
Mean pairwise identity 63.05
Shannon entropy 0.75578
G+C content 0.65051
Mean single sequence MFE -37.20
Consensus MFE -13.08
Energy contribution -14.17
Covariance contribution 1.09
Combinations/Pair 1.37
Mean z-score -1.49
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.09
SVM RNA-class probability 0.889818
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6736954 105 - 22422827
-----UCCGGCGACCAGUGGCCAACAGAGCCCACGCUCCAGGACAUUCUCGAGCAGUUCAACAGGAGCCGCC---GAUUCUGCGCUG--CAGCAGCAGCAACACCAGCACUCGAA
-----..(((((....((((.(......).))))((((.(((....))).)))).((((.....))))))))---).......((((--(....)))))................ ( -32.80, z-score =  -0.64, R)
>droSim1.chrX_random 2160911 105 - 5698898
-----CCCGGCGACCAGUGGCCAACAGAGCCCACGCUCCAGGACAUUCUCGAGCAGUUCGACAGGAGCCGCC---GAUUCUGCGCUG--CAGCAGCAGCAGCACCAGCACUCGAA
-----..(((((....((((.(......).))))(((((.((((...........))))....)))))))))---)....(((((((--(....))))).)))............ ( -36.00, z-score =  -0.79, R)
>droSec1.super_4 6120222 105 + 6179234
-----CCCGGCGACCAGUGGCCAACAGAGCCCACGCUCCAGGACAUUCUCGAGCAGUUCGACAGGAGCCGCC---GAUUCUGCGCUG--CAGCAGCAGCAGCACCAGCACUCGAA
-----..(((((....((((.(......).))))(((((.((((...........))))....)))))))))---)....(((((((--(....))))).)))............ ( -36.00, z-score =  -0.79, R)
>droYak2.chrX 2703832 99 - 21770863
-----UCCGGCUACCAGUGGCCAACAGAGCCCACGCUCCAGGACAUUCUCGAGCAGUUCGACAGGAGCCGCU---GAUGCGGCGCUG--CAGCAGCAGCACCAACAGAA------
-----((((((((....)))))....((((....((((.(((....))).)))).))))....)))(((((.---...)))))((((--(....)))))..........------ ( -39.90, z-score =  -2.36, R)
>droEre2.scaffold_4690 15664504 102 - 18748788
-----UCCGGCGACCAGUGGCCAACAGAGCCCACGCUCCAGGACAUUCUCGAGCAGUUCGACAGGAGCCGCC---GAUUCUGCGCUG-----CAGCAGCAGCACCAGCAUUCAAA
-----..(((((....((((.(......).))))(((((.((((...........))))....)))))))))---)...(((.((((-----(....)))))..)))........ ( -34.30, z-score =  -1.24, R)
>droAna3.scaffold_13117 536319 101 - 5790199
-----GCCAGCCACUAGCGGCCAGCAGAGCCCACGCUCCAGGACCUUUUCCAGCAGCUCAACGGGAGCGGCG---GAGCCGACUGCUCCCAAUGUGACCACCAGUCGCA------
-----((..(((......)))..)).((((....(((...(((.....)))))).))))...((((((((((---....)).))))))))..((((((.....))))))------ ( -40.50, z-score =  -2.14, R)
>droWil1.scaffold_180777 2851806 110 + 4753960
-----UCCAGCGACCAGUGGCCAACAGAGCCCACGCUCUCGUACAUUUAGCAGCAGCUCAACUGGAGCCGCUGUGGACACAUCGCCGGCCGGUGGCGGUCGCACUGGAGGAGGAG
-----((((((((((.(((.((.(((((((....))))).)).......(((((.((((.....)))).))))))).))).(((((....))))).))))))..))))....... ( -47.70, z-score =  -1.67, R)
>dp4.chrXL_group1a 8722516 84 - 9151740
-----ACCGGCGACCAGUGGCCAGCAGAGCCCGCGCUCCAGGACAUUCUCGAGCAGCUCCACGGGAGCCGCU---GACACAUCGCCACCGGG-----------------------
-----...(((((...(((..((((.........((((.(((....))).)))).(((((...))))).)))---).))).)))))......----------------------- ( -32.40, z-score =  -0.94, R)
>droPer1.super_15 1118956 84 - 2181545
-----ACCGGCGACCAGUGGCCAGCAGAGCCCGCGCUCCAGGACAUUCUCGAGCAGCUCCACGGGAGCCCCU---GACACAUCGCCACCGGG-----------------------
-----...(((((...(((..(((..(..(((((((((.(((....))).)))).)).....)))..)..))---).))).)))))......----------------------- ( -28.00, z-score =   0.11, R)
>anoGam1.chrX 6810202 90 - 22145176
UUCGGCCCACCUGCCGCAUGGCAUGGGUGGCUACCACCACCAUCGGCUUUGGGCCGAAUCGCUGCCAGCGCAGC-AAACCUACCUGACUGA------------------------
(((((((((...((((.((((....(((((...))))).))))))))..)))))))))..(((((....)))))-................------------------------ ( -44.40, z-score =  -4.46, R)
>consensus
_____UCCGGCGACCAGUGGCCAACAGAGCCCACGCUCCAGGACAUUCUCGAGCAGUUCGACAGGAGCCGCC___GAUUCUGCGCUG__CAGCAGCAGCAGCACCAGCA______
........((((....((((.(......).))))((((.((......)).)))).((((.....))))))))........................................... (-13.08 = -14.17 +   1.09)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:22:05 2011