Locus 3264

Sequence ID dm3.chr2R
Location 3,905,992 – 3,906,126
Length 134
Max. P 0.999228
window4494 window4495 window4496 window4497

overview

Window 4

Location 3,905,992 – 3,906,102
Length 110
Sequences 8
Columns 112
Reading direction forward
Mean pairwise identity 65.95
Shannon entropy 0.62997
G+C content 0.47316
Mean single sequence MFE -22.65
Consensus MFE -12.76
Energy contribution -13.16
Covariance contribution 0.41
Combinations/Pair 1.18
Mean z-score -2.46
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.72
SVM RNA-class probability 0.999228
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3905992 110 + 21146708
AGAUUUAACAGCAGCUAACAAACCGAAUUCGUCGGCUGCUGUAAUUAAAACAAAGAGUGCGUUCAGCACA--CAGGACCCCAUCCCACGCACUUCCUUCCUCCCCUCCUCUU
.......((((((((..((...........))..))))))))............((((((((........--..(((.....))).)))))))).................. ( -25.60, z-score =  -3.32, R)
>droPer1.super_2 5732082 88 + 9036312
AGACCUAACAGCAGCUAACCAAACCAAGAAACUGGCUGCUGUAAUUAAA-CAGAUGCUAAGAGUAGCACA--CAGACUCCCGCCUCAGCCC---------------------
.......((((((((((...............)))))))))).......-..((.((...((((......--...))))..)).)).....--------------------- ( -19.76, z-score =  -1.82, R)
>dp4.chr3 5537866 88 + 19779522
AGACCUAACAGCAGCUAACCAAACCAAGAAACUGGCUGCUGUAAUUAAA-CAGAUGCUAAGAGUAGCACA--CAGACUCCCGCCUCAGCCC---------------------
.......((((((((((...............)))))))))).......-..((.((...((((......--...))))..)).)).....--------------------- ( -19.76, z-score =  -1.82, R)
>droAna3.scaffold_13266 16223715 90 + 19884421
GGAUUUAACAGCAGUUAACAAACCAAGCCCGUCGGUGGCUGUAAUUAAAACAAAAAAAACAGAGAUAGCAGCCUUAUCUUCUUUCUCUAU----------------------
.......(((((.(((....)))...(((....))).)))))..................(((((.((.((......)).)).)))))..---------------------- ( -14.20, z-score =  -0.30, R)
>droSim1.chr2R_random 1107514 110 + 2996586
AGAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUGUAAUUAAAACAAAGAGUGCGUUCAGCACA--CAGGACCCCAUCCCUCGCACUUCCUUCCUCCCCUCCUCUU
.......((((((((..((...........))..))))))))............(((((((.........--.(((........)))))))))).................. ( -25.40, z-score =  -3.18, R)
>droSec1.super_1 1542138 110 + 14215200
AGAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUGUAAUUAAAACAAAGAGUGCGUUCAGCACA--CAGGACCCCAUCCCUCGCACUUCCUUCCUCCCCUCCUCUU
.......((((((((..((...........))..))))))))............(((((((.........--.(((........)))))))))).................. ( -25.40, z-score =  -3.18, R)
>droYak2.chr2L 16561376 90 + 22324452
AGAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUGUAAUUAAAACAAAGAGUGCGUUCAGCACA--CAGGACCUCAUCCUUCUCAA--------------------
.......((((((((..((...........))..))))))))...........(((((((.....)))).--.((((.....)))))))...-------------------- ( -24.80, z-score =  -3.45, R)
>droEre2.scaffold_4929 7919336 97 - 26641161
AGAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUGUAAUUAAAACAAAGAGUGCGUUCCGCACAUCCUGUGUGCAUCCCCAGCUUCCUCGG---------------
.......((((((((..((...........))..))))))))............(((.((.....((((((...)))))).......))...)))..--------------- ( -26.30, z-score =  -2.60, R)
>consensus
AGAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUGUAAUUAAAACAAAGAGUGCGUUCAGCACA__CAGGACCCCAUCCCACCCAC____________________
.......(((((((((.((...........)).)))))))))...................................................................... (-12.76 = -13.16 +   0.41)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,905,992 – 3,906,102
Length 110
Sequences 8
Columns 112
Reading direction reverse
Mean pairwise identity 65.95
Shannon entropy 0.62997
G+C content 0.47316
Mean single sequence MFE -30.75
Consensus MFE -15.62
Energy contribution -15.19
Covariance contribution -0.43
Combinations/Pair 1.55
Mean z-score -1.47
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.75
SVM RNA-class probability 0.965685
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3905992 110 - 21146708
AAGAGGAGGGGAGGAAGGAAGUGCGUGGGAUGGGGUCCUG--UGUGCUGAACGCACUCUUUGUUUUAAUUACAGCAGCCGACGAAUUCGGUUUGUUAGCUGCUGUUAAAUCU
..((((..(((((...(..((..((..((((...))))..--))..))...)...)))))..))))....((((((((..((((((...))))))..))))))))....... ( -40.40, z-score =  -3.24, R)
>droPer1.super_2 5732082 88 - 9036312
---------------------GGGCUGAGGCGGGAGUCUG--UGUGCUACUCUUAGCAUCUG-UUUAAUUACAGCAGCCAGUUUCUUGGUUUGGUUAGCUGCUGUUAGGUCU
---------------------(((((.((((....)))).--.((((((....))))))...-..((((..((((((((((.........)))))).))))..))))))))) ( -25.50, z-score =   0.24, R)
>dp4.chr3 5537866 88 - 19779522
---------------------GGGCUGAGGCGGGAGUCUG--UGUGCUACUCUUAGCAUCUG-UUUAAUUACAGCAGCCAGUUUCUUGGUUUGGUUAGCUGCUGUUAGGUCU
---------------------(((((.((((....)))).--.((((((....))))))...-..((((..((((((((((.........)))))).))))..))))))))) ( -25.50, z-score =   0.24, R)
>droAna3.scaffold_13266 16223715 90 - 19884421
----------------------AUAGAGAAAGAAGAUAAGGCUGCUAUCUCUGUUUUUUUUGUUUUAAUUACAGCCACCGACGGGCUUGGUUUGUUAACUGCUGUUAAAUCC
----------------------(((((((.((.((......)).)).)))))))................(((((....(((((((...)))))))....)))))....... ( -17.60, z-score =   0.05, R)
>droSim1.chr2R_random 1107514 110 - 2996586
AAGAGGAGGGGAGGAAGGAAGUGCGAGGGAUGGGGUCCUG--UGUGCUGAACGCACUCUUUGUUUUAAUUACAGCAGCCGACGGAUUCGGUUUGUUAGCUGCUGUUAAAUCU
..((((..(((((...(..((..((.(((((...))))).--))..))...)...)))))..))))....((((((((..((((((...))))))..))))))))....... ( -37.30, z-score =  -2.11, R)
>droSec1.super_1 1542138 110 - 14215200
AAGAGGAGGGGAGGAAGGAAGUGCGAGGGAUGGGGUCCUG--UGUGCUGAACGCACUCUUUGUUUUAAUUACAGCAGCCGACGGAUUCGGUUUGUUAGCUGCUGUUAAAUCU
..((((..(((((...(..((..((.(((((...))))).--))..))...)...)))))..))))....((((((((..((((((...))))))..))))))))....... ( -37.30, z-score =  -2.11, R)
>droYak2.chr2L 16561376 90 - 22324452
--------------------UUGAGAAGGAUGAGGUCCUG--UGUGCUGAACGCACUCUUUGUUUUAAUUACAGCAGCCGACGGAUUCGGUUUGUUAGCUGCUGUUAAAUCU
--------------------...(((((((..(((....(--((((.....))))).)))..))))....((((((((..((((((...))))))..))))))))....))) ( -29.00, z-score =  -2.37, R)
>droEre2.scaffold_4929 7919336 97 + 26641161
---------------CCGAGGAAGCUGGGGAUGCACACAGGAUGUGCGGAACGCACUCUUUGUUUUAAUUACAGCAGCCGACGGAUUCGGUUUGUUAGCUGCUGUUAAAUCU
---------------((.((....)).))(((..(((.((((.(((((...)))))))))))).......((((((((..((((((...))))))..))))))))...))). ( -33.40, z-score =  -2.46, R)
>consensus
____________________GUGCGUGGGAUGGGGUCCUG__UGUGCUGAACGCACUCUUUGUUUUAAUUACAGCAGCCGACGGAUUCGGUUUGUUAGCUGCUGUUAAAUCU
...........................((((...........((((.....))))...............((((((((.((((((.....)))))).))))))))...)))) (-15.62 = -15.19 +  -0.43)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,906,029 – 3,906,126
Length 97
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 61.92
Shannon entropy 0.59441
G+C content 0.47289
Mean single sequence MFE -13.57
Consensus MFE -4.82
Energy contribution -4.26
Covariance contribution -0.56
Combinations/Pair 1.57
Mean z-score -1.78
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.53
SVM RNA-class probability 0.733649
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3906029 97 + 21146708
GCUGUAAUUAAAACAAAGAGUGCGUUCAGCACACAGGACCCCAUCCCACGCACUUCCUUCCUCCCCUCCUCUUUGUCCCCACAAAAGCAACGCAUAU-----
(((.........(((((((((((.....))))...(((.....))).......................))))))).........))).........----- ( -17.57, z-score =  -3.26, R)
>droAna3.scaffold_13266 16223752 79 + 19884421
GCUGUAAUUAAAACAAAAAAAACAGAGAUAGCA----GCCUUAUCUUCUUUCUCUAUUUUCUUCAAAGAACCGUAGCAC-AUGU------------------
((((...................(((((.((.(----(......)).)).)))))...((((....))))...))))..-....------------------ ( -10.40, z-score =  -0.83, R)
>droSim1.chr2R_random 1107551 102 + 2996586
GCUGUAAUUAAAACAAAGAGUGCGUUCAGCACACAGGACCCCAUCCCUCGCACUUCCUUCCUCCCCUCCUCUUCGUCCCCACGUAGUCCGUGCAACGCAUAU
...................(((((((..((((...(((.....)))........................((.(((....))).))...))))))))))).. ( -16.70, z-score =  -1.86, R)
>droSec1.super_1 1542175 83 + 14215200
GCUGUAAUUAAAACAAAGAGUGCGUUCAGCACACAGGACCCCAUCCCUCGCACUUCCUUCCUCCCCUCCUCUUCGUCCC-AUAU------------------
............((.((((((((.....))))...(((.....))).......................)))).))...-....------------------ (  -9.60, z-score =  -1.15, R)
>consensus
GCUGUAAUUAAAACAAAGAGUGCGUUCAGCACACAGGACCCCAUCCCUCGCACUUCCUUCCUCCCCUCCUCUUCGUCCC_ACAU__________________
.................(((((((........................)))))))............................................... ( -4.82 =  -4.26 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,906,029 – 3,906,126
Length 97
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 61.92
Shannon entropy 0.59441
G+C content 0.47289
Mean single sequence MFE -24.15
Consensus MFE -10.71
Energy contribution -11.53
Covariance contribution 0.81
Combinations/Pair 1.38
Mean z-score -1.46
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.77
SVM RNA-class probability 0.812048
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3906029 97 - 21146708
-----AUAUGCGUUGCUUUUGUGGGGACAAAGAGGAGGGGAGGAAGGAAGUGCGUGGGAUGGGGUCCUGUGUGCUGAACGCACUCUUUGUUUUAAUUACAGC
-----......(((((((((.((....)).))))).((((((...(..((..((..((((...))))..))..))...)...))))))..........)))) ( -27.80, z-score =  -1.51, R)
>droAna3.scaffold_13266 16223752 79 - 19884421
------------------ACAU-GUGCUACGGUUCUUUGAAGAAAAUAGAGAAAGAAGAUAAGGC----UGCUAUCUCUGUUUUUUUUGUUUUAAUUACAGC
------------------...(-((((....)).....((((((((((((((.((.((......)----).)).)))))))))))))).........))).. ( -17.60, z-score =  -1.28, R)
>droSim1.chr2R_random 1107551 102 - 2996586
AUAUGCGUUGCACGGACUACGUGGGGACGAAGAGGAGGGGAGGAAGGAAGUGCGAGGGAUGGGGUCCUGUGUGCUGAACGCACUCUUUGUUUUAAUUACAGC
......((((((((.....))))(((((((((((..(.(.........((..((.(((((...))))).))..))...).).))))))))))).....)))) ( -28.50, z-score =  -1.04, R)
>droSec1.super_1 1542175 83 - 14215200
------------------AUAU-GGGACGAAGAGGAGGGGAGGAAGGAAGUGCGAGGGAUGGGGUCCUGUGUGCUGAACGCACUCUUUGUUUUAAUUACAGC
------------------...(-(((((((((((..(.(.........((..((.(((((...))))).))..))...).).))))))))))))........ ( -22.70, z-score =  -1.99, R)
>consensus
__________________ACAU_GGGACAAAGAGGAGGGGAGGAAGGAAGUGCGAGGGAUGGGGUCCUGUGUGCUGAACGCACUCUUUGUUUUAAUUACAGC
.......................(((((((((((........(.....((((((..(((.....)))..)))))).....).)))))))))))......... (-10.71 = -11.53 +   0.81)

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 22:07:00 2011