Locus 4875

Sequence ID dm3.chr2R
Location 16,117,527 – 16,117,729
Length 202
Max. P 0.997710
window6705 window6706 window6707 window6708 window6709

overview

Window 5

Location 16,117,527 – 16,117,622
Length 95
Sequences 8
Columns 110
Reading direction forward
Mean pairwise identity 71.74
Shannon entropy 0.52823
G+C content 0.57479
Mean single sequence MFE -37.29
Consensus MFE -17.93
Energy contribution -18.16
Covariance contribution 0.24
Combinations/Pair 1.21
Mean z-score -2.74
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.87
SVM RNA-class probability 0.995957
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16117527 95 + 21146708
--------GCCAGAACCAAC---AAUAACAGGACUUGUU----GGCCGGCUCCUGCCGGCUUGGUUAGCCAAGCCAACCAGCCACUUCCUGUUUCCCAGUUUAAGCCGCC
--------((..((((....---...(((((((...(((----((..(((....)))(((((((....)))))))..)))))....))))))).....))))..)).... ( -36.20, z-score =  -3.74, R)
>droSim1.chr2R 14775829 99 + 19596830
--------GCCAGAACCAAC---AAUAACAGGACUUGUUGGCCGGCCGGCUCCUGCCGGCUUGGUUAGCCAAGCCAACCAGCCACUUCCUGUUUCCCAGUUUAAGCCGCC
--------((..((((....---...(((((((...((.(((.((..(((....)))(((((((....)))))))..)).))))).))))))).....))))..)).... ( -38.50, z-score =  -3.31, R)
>droSec1.super_1 13683702 99 + 14215200
--------GCCAGAACCAAC---AAUAACAGGACUUGUUGGCCGGCCGGCUCCUGCCGGCUUGGUUAGCCAAGCCAACCAGCCACUUCCUGUUUCCCAGUUUAAGCCGCC
--------((..((((....---...(((((((...((.(((.((..(((....)))(((((((....)))))))..)).))))).))))))).....))))..)).... ( -38.50, z-score =  -3.31, R)
>droYak2.chr2R 8052795 96 - 21139217
--------GCCAGAACCAAC---AAUAACAGGACUUGUUU---GGCCGCCUCCUGCCGGCUUGGUUAGCCAAGCCAACCAGCCACUUCCUGUUUCCCAGUUUAAGCCGCC
--------((..((((....---...(((((((..((.((---((..((.....)).(((((((....)))))))..)))).))..))))))).....))))..)).... ( -30.50, z-score =  -2.62, R)
>droEre2.scaffold_4845 10267781 95 + 22589142
--------GCCAGAACCAAC---AAUAACAGGACUUGUU----GGCCGGCUCCUGCCGGCUUGGUUAGCCAAGCCAACCAGCCACUUCCUGUUUCCCAGUCUAAGCCGCC
--------((.(((......---...(((((((...(((----((..(((....)))(((((((....)))))))..)))))....)))))))......)))..)).... ( -34.76, z-score =  -3.23, R)
>droAna3.scaffold_13266 10658914 84 - 19884421
--------AGGAGGACUAGC---CGGGACAA-ACUAGGCG---AGCCGGCGGC--CAGGCUUGGCUAACCAAGCCAACCAGCCACUUCCUGUUUUAAAGCC---------
--------((((((....((---(((.....-........---..)))))(((--..(((((((....))))))).....))).))))))...........--------- ( -32.06, z-score =  -1.29, R)
>dp4.chr3 13254389 107 + 19779522
GCGCAACUGCCACAACUGGCGCUCCGAGCAGACAGUGCUAAGAGGUCGGAUGGC-UGGGCUUGGUUAGCCAAGCCAACCAGCCGUUUCCUGUUGCACAAUUUUAAGCU--
(.(((((........(((((.(((..((((.....))))..))))))))(((((-(((((((((....))))))...)))))))).....))))).)...........-- ( -43.90, z-score =  -2.21, R)
>droPer1.super_2 665709 107 - 9036312
GCGCAACUGCCACAACUGGCGCUCCGAGCAGACAGUGCUAAGAGGUCGGAUGGC-UGGGCUUGGUUAGCCAAGCCAACCAGCCGUUUCCUGUUGCACAAUUUUAAGCU--
(.(((((........(((((.(((..((((.....))))..))))))))(((((-(((((((((....))))))...)))))))).....))))).)...........-- ( -43.90, z-score =  -2.21, R)
>consensus
________GCCAGAACCAAC___AAUAACAGGACUUGUUG___GGCCGGCUCCUGCCGGCUUGGUUAGCCAAGCCAACCAGCCACUUCCUGUUUCCCAGUUUAAGCCGCC
..........................(((((.....(((....))).((((......(((((((....)))))))....)))).....)))))................. (-17.93 = -18.16 +   0.24) 

alignment

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secondary structure

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dotplot

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Window 6

Location 16,117,527 – 16,117,622
Length 95
Sequences 8
Columns 110
Reading direction reverse
Mean pairwise identity 71.74
Shannon entropy 0.52823
G+C content 0.57479
Mean single sequence MFE -43.55
Consensus MFE -23.32
Energy contribution -23.95
Covariance contribution 0.63
Combinations/Pair 1.17
Mean z-score -2.68
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.16
SVM RNA-class probability 0.997710
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16117527 95 - 21146708
GGCGGCUUAAACUGGGAAACAGGAAGUGGCUGGUUGGCUUGGCUAACCAAGCCGGCAGGAGCCGGCC----AACAAGUCCUGUUAUU---GUUGGUUCUGGC--------
(((.((((...(((.....))).)))).))).((((((((((....))))))))))....(((((((----(((((.........))---)))))..)))))-------- ( -42.50, z-score =  -2.88, R)
>droSim1.chr2R 14775829 99 - 19596830
GGCGGCUUAAACUGGGAAACAGGAAGUGGCUGGUUGGCUUGGCUAACCAAGCCGGCAGGAGCCGGCCGGCCAACAAGUCCUGUUAUU---GUUGGUUCUGGC--------
....(((..(((..(.((((((((..((((((((((((((((....)))))))(((....)))))))))))).....))))))..))---.)..)))..)))-------- ( -48.70, z-score =  -3.63, R)
>droSec1.super_1 13683702 99 - 14215200
GGCGGCUUAAACUGGGAAACAGGAAGUGGCUGGUUGGCUUGGCUAACCAAGCCGGCAGGAGCCGGCCGGCCAACAAGUCCUGUUAUU---GUUGGUUCUGGC--------
....(((..(((..(.((((((((..((((((((((((((((....)))))))(((....)))))))))))).....))))))..))---.)..)))..)))-------- ( -48.70, z-score =  -3.63, R)
>droYak2.chr2R 8052795 96 + 21139217
GGCGGCUUAAACUGGGAAACAGGAAGUGGCUGGUUGGCUUGGCUAACCAAGCCGGCAGGAGGCGGCC---AAACAAGUCCUGUUAUU---GUUGGUUCUGGC--------
....(((..(((..(.((((((((..((((((((((((((((....))))))))))......)))))---)......))))))..))---.)..)))..)))-------- ( -39.60, z-score =  -2.28, R)
>droEre2.scaffold_4845 10267781 95 - 22589142
GGCGGCUUAGACUGGGAAACAGGAAGUGGCUGGUUGGCUUGGCUAACCAAGCCGGCAGGAGCCGGCC----AACAAGUCCUGUUAUU---GUUGGUUCUGGC--------
(((.((((...(((.....))).)))).))).((((((((((....))))))))))....(((((((----(((((.........))---)))))..)))))-------- ( -42.50, z-score =  -2.68, R)
>droAna3.scaffold_13266 10658914 84 + 19884421
---------GGCUUUAAAACAGGAAGUGGCUGGUUGGCUUGGUUAGCCAAGCCUG--GCCGCCGGCU---CGCCUAGU-UUGUCCCG---GCUAGUCCUCCU--------
---------...........((((.(.(((((((((((((((....))))))).)--)))(((((..---((......-.))..)))---)).)))))))))-------- ( -34.00, z-score =  -0.92, R)
>dp4.chr3 13254389 107 - 19779522
--AGCUUAAAAUUGUGCAACAGGAAACGGCUGGUUGGCUUGGCUAACCAAGCCCA-GCCAUCCGACCUCUUAGCACUGUCUGCUCGGAGCGCCAGUUGUGGCAGUUGCGC
--...........(((((((......(((.((((((((((((....))))).)))-)))).)))..((((.((((.....)))).)))).((((....)))).))))))) ( -46.20, z-score =  -2.71, R)
>droPer1.super_2 665709 107 + 9036312
--AGCUUAAAAUUGUGCAACAGGAAACGGCUGGUUGGCUUGGCUAACCAAGCCCA-GCCAUCCGACCUCUUAGCACUGUCUGCUCGGAGCGCCAGUUGUGGCAGUUGCGC
--...........(((((((......(((.((((((((((((....))))).)))-)))).)))..((((.((((.....)))).)))).((((....)))).))))))) ( -46.20, z-score =  -2.71, R)
>consensus
GGCGGCUUAAACUGGGAAACAGGAAGUGGCUGGUUGGCUUGGCUAACCAAGCCGGCAGGAGCCGGCC___CAACAAGUCCUGUUAUU___GUUGGUUCUGGC________
...................(((((...(((((((((((((((....)))))))......))))))))....((((.....))))...........))))).......... (-23.32 = -23.95 +   0.63) 

alignment

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secondary structure

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dotplot

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Window 7

Location 16,117,527 – 16,117,623
Length 96
Sequences 9
Columns 112
Reading direction forward
Mean pairwise identity 68.35
Shannon entropy 0.61227
G+C content 0.57151
Mean single sequence MFE -36.35
Consensus MFE -12.71
Energy contribution -12.58
Covariance contribution -0.13
Combinations/Pair 1.36
Mean z-score -2.51
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.99
SVM RNA-class probability 0.977938
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 16117527 96 + 21146708
-------GCCAGAACCAACA---AUAACAGGACUUGUU-GGCCG----GCUCCUGCCGGCUUGGUUAGCCAAGCCAACCAGCCACUUCCUGUUUCCCAGUUU-AAGCCGCCG
-------((..((((.....---..(((((((...(((-((..(----((....)))(((((((....)))))))..)))))....))))))).....))))-..))..... ( -36.20, z-score =  -3.76, R)
>droSim1.chr2R 14775829 100 + 19596830
-------GCCAGAACCAACA---AUAACAGGACUUGUU-GGCCGGCCGGCUCCUGCCGGCUUGGUUAGCCAAGCCAACCAGCCACUUCCUGUUUCCCAGUUU-AAGCCGCCG
-------((..((((.....---..(((((((...((.-(((.((..(((....)))(((((((....)))))))..)).))))).))))))).....))))-..))..... ( -38.50, z-score =  -3.31, R)
>droSec1.super_1 13683702 100 + 14215200
-------GCCAGAACCAACA---AUAACAGGACUUGUU-GGCCGGCCGGCUCCUGCCGGCUUGGUUAGCCAAGCCAACCAGCCACUUCCUGUUUCCCAGUUU-AAGCCGCCG
-------((..((((.....---..(((((((...((.-(((.((..(((....)))(((((((....)))))))..)).))))).))))))).....))))-..))..... ( -38.50, z-score =  -3.31, R)
>droYak2.chr2R 8052795 97 - 21139217
-------GCCAGAACCAACA---AUAACAGGACUUGUUUGGCCG----CCUCCUGCCGGCUUGGUUAGCCAAGCCAACCAGCCACUUCCUGUUUCCCAGUUU-AAGCCGCCG
-------((..((((.....---..(((((((..((.((((..(----(.....)).(((((((....)))))))..)))).))..))))))).....))))-..))..... ( -30.50, z-score =  -2.55, R)
>droEre2.scaffold_4845 10267781 96 + 22589142
-------GCCAGAACCAACA---AUAACAGGACUUGUU-GGCCG----GCUCCUGCCGGCUUGGUUAGCCAAGCCAACCAGCCACUUCCUGUUUCCCAGUCU-AAGCCGCCG
-------((.(((.......---..(((((((...(((-((..(----((....)))(((((((....)))))))..)))))....)))))))......)))-..))..... ( -34.76, z-score =  -3.24, R)
>droAna3.scaffold_13266 10658914 85 - 19884421
-------------AGGAGGAC--UAGCCGGGACAAACUAGGCGAGCCGGCGGCCA--GGCUUGGCUAACCAAGCCAACCAGCCACUUCCUGUUUUAAAGCCG----------
-------------((((((..--..(((((...............)))))(((..--(((((((....))))))).....))).))))))............---------- ( -32.06, z-score =  -1.19, R)
>dp4.chr3 13254390 107 + 19779522
CGCAACUGCCACAACUGGCGCUCCGAGCAGACAGUGCUAAGAGGUCGGAUGGCUG--GGCUUGGUUAGCCAAGCCAACCAGCCGUUUCCUGUUGCACAAUUUUAAGCUG---
.(((((........(((((.(((..((((.....))))..))))))))(((((((--(((((((....))))))...)))))))).....)))))..............--- ( -43.80, z-score =  -2.40, R)
>droPer1.super_2 665710 107 - 9036312
CGCAACUGCCACAACUGGCGCUCCGAGCAGACAGUGCUAAGAGGUCGGAUGGCUG--GGCUUGGUUAGCCAAGCCAACCAGCCGUUUCCUGUUGCACAAUUUUAAGCUG---
.(((((........(((((.(((..((((.....))))..))))))))(((((((--(((((((....))))))...)))))))).....)))))..............--- ( -43.80, z-score =  -2.40, R)
>droWil1.scaffold_180701 2619367 106 + 3904529
AGCCAGAGCCAGAGCCAGAGC--AUGGCAAAACAGACU--GCGAGUCCUUGGCUG--AGCUUGACUAACCAAGCCAACGAGCAACUUCCUGUUUUACAGUUUUAAGCUGCCG
((((((.((((..((....))--.))))......(((.--....))).))))))(--.(((((......))))))..((.(((.(((.(((.....)))....))).))))) ( -29.00, z-score =  -0.41, R)
>consensus
_______GCCAGAACCAACA___AUAACAGGACUUGUU_GGCCGGCCGGCUCCUGCCGGCUUGGUUAGCCAAGCCAACCAGCCACUUCCUGUUUCCCAGUUU_AAGCCGCCG
.........................(((((.........((...........))...(((((((....))))))).............)))))................... (-12.71 = -12.58 +  -0.13) 

alignment

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secondary structure

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dotplot

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Window 8

Location 16,117,527 – 16,117,623
Length 96
Sequences 9
Columns 112
Reading direction reverse
Mean pairwise identity 68.35
Shannon entropy 0.61227
G+C content 0.57151
Mean single sequence MFE -42.82
Consensus MFE -18.66
Energy contribution -18.90
Covariance contribution 0.24
Combinations/Pair 1.31
Mean z-score -2.48
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.82
SVM RNA-class probability 0.995596
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 16117527 96 - 21146708
CGGCGGCUU-AAACUGGGAAACAGGAAGUGGCUGGUUGGCUUGGCUAACCAAGCCGGCAGGAGC----CGGCC-AACAAGUCCUGUUAU---UGUUGGUUCUGGC-------
((((.((((-...(((.....))).)))).))))((((((((((....))))))))))....((----(((((-(((((.........)---))))))..)))))------- ( -45.00, z-score =  -3.54, R)
>droSim1.chr2R 14775829 100 - 19596830
CGGCGGCUU-AAACUGGGAAACAGGAAGUGGCUGGUUGGCUUGGCUAACCAAGCCGGCAGGAGCCGGCCGGCC-AACAAGUCCUGUUAU---UGUUGGUUCUGGC-------
.....(((.-.(((..(.((((((((..((((((((((((((((....)))))))(((....)))))))))))-).....))))))..)---).)..)))..)))------- ( -48.70, z-score =  -3.46, R)
>droSec1.super_1 13683702 100 - 14215200
CGGCGGCUU-AAACUGGGAAACAGGAAGUGGCUGGUUGGCUUGGCUAACCAAGCCGGCAGGAGCCGGCCGGCC-AACAAGUCCUGUUAU---UGUUGGUUCUGGC-------
.....(((.-.(((..(.((((((((..((((((((((((((((....)))))))(((....)))))))))))-).....))))))..)---).)..)))..)))------- ( -48.70, z-score =  -3.46, R)
>droYak2.chr2R 8052795 97 + 21139217
CGGCGGCUU-AAACUGGGAAACAGGAAGUGGCUGGUUGGCUUGGCUAACCAAGCCGGCAGGAGG----CGGCCAAACAAGUCCUGUUAU---UGUUGGUUCUGGC-------
.....(((.-.(((..(.((((((((..((((((((((((((((....))))))))))......----))))))......))))))..)---).)..)))..)))------- ( -39.60, z-score =  -2.14, R)
>droEre2.scaffold_4845 10267781 96 - 22589142
CGGCGGCUU-AGACUGGGAAACAGGAAGUGGCUGGUUGGCUUGGCUAACCAAGCCGGCAGGAGC----CGGCC-AACAAGUCCUGUUAU---UGUUGGUUCUGGC-------
((((.((((-...(((.....))).)))).))))((((((((((....))))))))))....((----(((((-(((((.........)---))))))..)))))------- ( -45.00, z-score =  -3.34, R)
>droAna3.scaffold_13266 10658914 85 + 19884421
----------CGGCUUUAAAACAGGAAGUGGCUGGUUGGCUUGGUUAGCCAAGCC--UGGCCGCCGGCUCGCCUAGUUUGUCCCGGCUA--GUCCUCCU-------------
----------............((((.(.(((((((((((((((....)))))))--.))))(((((..((.......))..))))).)--))))))))------------- ( -34.00, z-score =  -0.85, R)
>dp4.chr3 13254390 107 - 19779522
---CAGCUUAAAAUUGUGCAACAGGAAACGGCUGGUUGGCUUGGCUAACCAAGCC--CAGCCAUCCGACCUCUUAGCACUGUCUGCUCGGAGCGCCAGUUGUGGCAGUUGCG
---..............(((((......(((.((((((((((((....))))).)--)))))).)))..((((.((((.....)))).)))).((((....)))).))))). ( -44.00, z-score =  -2.33, R)
>droPer1.super_2 665710 107 + 9036312
---CAGCUUAAAAUUGUGCAACAGGAAACGGCUGGUUGGCUUGGCUAACCAAGCC--CAGCCAUCCGACCUCUUAGCACUGUCUGCUCGGAGCGCCAGUUGUGGCAGUUGCG
---..............(((((......(((.((((((((((((....))))).)--)))))).)))..((((.((((.....)))).)))).((((....)))).))))). ( -44.00, z-score =  -2.33, R)
>droWil1.scaffold_180701 2619367 106 - 3904529
CGGCAGCUUAAAACUGUAAAACAGGAAGUUGCUCGUUGGCUUGGUUAGUCAAGCU--CAGCCAAGGACUCGC--AGUCUGUUUUGCCAU--GCUCUGGCUCUGGCUCUGGCU
(((((((((....(((.....))).))))))).))..(((((((....)))))))--.(((((.((((....--.)))).....((((.--((....))..))))..))))) ( -36.40, z-score =  -0.82, R)
>consensus
CGGCGGCUU_AAACUGGGAAACAGGAAGUGGCUGGUUGGCUUGGCUAACCAAGCCGGCAGGAGCCGGCCGGCC_AACAAGUCCUGUUAU___UGUUGGUUCUGGC_______
...(((((.....(((.....))).....)))))(..(((((((....)))))))..)...................................................... (-18.66 = -18.90 +   0.24) 

alignment

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secondary structure

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dotplot

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Window 9

Location 16,117,623 – 16,117,729
Length 106
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 73.01
Shannon entropy 0.52007
G+C content 0.49441
Mean single sequence MFE -32.96
Consensus MFE -22.41
Energy contribution -22.92
Covariance contribution 0.51
Combinations/Pair 1.48
Mean z-score -1.25
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.43
SVM RNA-class probability 0.939463
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16117623 106 - 21146708
-UCCCCUAUU-UUUUCGCACCACUAGCA-CGCGUUUGUGAAAAUCAUGGGUGAGACUAGCCGGUCGAAAUAUGCAUAUGGAUAUUCCACUCUGCGUGCCGGUGGGUCGG
-(((((....-((((((((..((.....-...)).))))))))....))).))((((.((((((......(((((..(((.....)))...))))))))))).)))).. ( -34.60, z-score =  -1.50, R)
>droSim1.chr2R 14775929 108 - 19596830
AUCCCCUAUUGUUUUCGCACCACUAGCA-CGCGUUUGUGCAAAUCAUGGGUCAGACUAGCCGGUGGAAAUAUGCAUAUGGAUAUUCCUCUCUGCGUGCCGGUGGGUCGG
...............((..((((..(((-(((...((((((..((((.(((.......))).)))).....)))))).((.....)).....))))))..))))..)). ( -35.50, z-score =  -1.14, R)
>droSec1.super_1 13683802 108 - 14215200
UUCCCCUAUUGUUUUCGCACCACUAGAA-CGCGUUUGCGAAAAUCAUGGGUCAGACUAGCCGGUGGAAAUAUGCAUAUGGAUAUUCCUCUCUGCGUGCCGGUGGGUCGG
....(((((.(((((((((..((.....-...)).))))))))).)))))...((((.((((((......(((((...((.....))....))))))))))).)))).. ( -36.30, z-score =  -1.78, R)
>droYak2.chr2R 8052892 109 + 21139217
UUUCCCCAUUGUUCUCGCACCUCUGGCACCGCAUUUGUGGAAAUCAUGGGUCAGGCUAGCCGGUCGAAAUAUGCAUAUGGAUAUUCCGCUCUACGUGCCGGUGGGUCGA
....(((((.(((..((((....((....))....))))..))).)))))...((((.((((((((.(((((.(....).))))).))........)))))).)))).. ( -31.40, z-score =   0.60, R)
>droEre2.scaffold_4845 10267877 108 - 22589142
UGCCCUCAUUGUUUUCGCACCUCUAGCA-CGCAUUUGUGAAAAUCAUGGGUCAGGCUAGCCGGUCGAAAUAUGCAUAUGGAUAUACCUCUCUGCGUGCCGGUGGGUCGG
((.((.(((.(((((((((.........-......))))))))).))))).))((((.((((((......(((((...((.....))....))))))))))).)))).. ( -31.36, z-score =  -0.00, R)
>droWil1.scaffold_180701 2619473 103 - 3904529
----UUUGCU-UUUUCGUGUGCAUAUUU-UGAAUCUGCACAUACACCUUCCCCCACAUAGUCACACUAAUAUAUGUUCACAUAUGUAUUAAUGUGUGUUUGUGUGCCGG
----......-.....(((((((.((..-...)).))))))).......((..(((((((.(((((((((((((((....))))))))))..))))).)))))))..)) ( -28.60, z-score =  -3.65, R)
>consensus
UUCCCCUAUUGUUUUCGCACCACUAGCA_CGCAUUUGUGAAAAUCAUGGGUCAGACUAGCCGGUCGAAAUAUGCAUAUGGAUAUUCCUCUCUGCGUGCCGGUGGGUCGG
....(((((.(((((((((................))))))))).)))))...((((.((((((......(((((...((.....))....))))))))))).)))).. (-22.41 = -22.92 +   0.51) 

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 22:37:47 2011