Locus 8514

Sequence ID dm3.chr3L
Location 24,276,560 – 24,276,664
Length 104
Max. P 0.999868
window11695 window11696 window11697 window11698

overview

Window 5

Location 24,276,560 – 24,276,662
Length 102
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 61.95
Shannon entropy 0.58658
G+C content 0.55172
Mean single sequence MFE -34.91
Consensus MFE -17.15
Energy contribution -17.65
Covariance contribution 0.50
Combinations/Pair 1.10
Mean z-score -3.71
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.58
SVM RNA-class probability 0.999853
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 24276560 102 + 24543557
------GCACCGAAGAUCUAC-ACACAAUUAAUUUGUGUCACUCACUUCUUCUCCGUGCUAUCCUU--------CGAACCACACUCGGCGACAGCGACCACACGCUGCCGCCGCGCU
------((((.(((((.....-((((((.....))))))........)))))...)))).......--------.........(.(((((.(((((......))))).))))).).. ( -31.72, z-score =  -5.05, R)
>droYak2.chrU 20653638 109 - 28119190
-------GACUGAAGUUCUAC-GCACAACUGCCGUGUGUCGCACACCUCUUCUACGUGCUUACCACAUGUGCAGCGAAACACACUCGGCAUCAGCAACAACACGCUGGCGCCGCGCU
-------.............(-((....((((((((((..((((...........))))....)))))).))))............(((..((((........))))..)))))).. ( -33.70, z-score =  -1.12, R)
>droAna3.scaffold_13260 592172 109 + 2125536
UGUACACUGUUCCAGUUCUGGUACGCAACUGCCGGCGUCCAACUGUGUACCUACUGUGCAUACUAC--------CAAACCUCGAUCGGCGACAGCGACACAACGCUGUCGCCUCGCU
((((((..((.(((((..(((.((((........))))))))))).).))....))))))......--------.......(((..((((((((((......))))))))))))).. ( -38.70, z-score =  -3.06, R)
>droMoj3.scaffold_6498 3063543 102 + 3408170
------GCACUUGAAUUCUGG-ACGCAACUAACUUGUGUCUCUCAAUUAUUCUUUGUGCCUACCAU--------CGAACCUCACUCGGCGACAGCGACACGACGCUGUCGCCCCGCU
------((((..((((...((-((((((.....)))))))).......))))...)))).......--------............((((((((((......))))))))))..... ( -35.50, z-score =  -5.60, R)
>consensus
______GCACUGAAGUUCUAC_ACACAACUAACGUGUGUCACUCACUUAUUCUCCGUGCUUACCAC________CGAACCACACUCGGCGACAGCGACAACACGCUGUCGCCGCGCU
......................................................................................((((((((((......))))))))))..... (-17.15 = -17.65 +   0.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 24,276,560 – 24,276,662
Length 102
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 61.95
Shannon entropy 0.58658
G+C content 0.55172
Mean single sequence MFE -39.23
Consensus MFE -21.67
Energy contribution -22.43
Covariance contribution 0.75
Combinations/Pair 1.38
Mean z-score -1.67
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.05
SVM RNA-class probability 0.980464
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 24276560 102 - 24543557
AGCGCGGCGGCAGCGUGUGGUCGCUGUCGCCGAGUGUGGUUCG--------AAGGAUAGCACGGAGAAGAAGUGAGUGACACAAAUUAAUUGUGU-GUAGAUCUUCGGUGC------
.((((((((((((((......))))))))))..((((...((.--------...))..))))...(((((..((....((((((.....))))))-.))..))))).))))------ ( -42.30, z-score =  -3.81, R)
>droYak2.chrU 20653638 109 + 28119190
AGCGCGGCGCCAGCGUGUUGUUGCUGAUGCCGAGUGUGUUUCGCUGCACAUGUGGUAAGCACGUAGAAGAGGUGUGCGACACACGGCAGUUGUGC-GUAGAACUUCAGUC-------
.((((((((((...((((.(((((...(((((.((((((......)))))).))))).((((.(.....).)))))))))))))))).)))))))-..............------- ( -41.50, z-score =  -0.32, R)
>droAna3.scaffold_13260 592172 109 - 2125536
AGCGAGGCGACAGCGUUGUGUCGCUGUCGCCGAUCGAGGUUUG--------GUAGUAUGCACAGUAGGUACACAGUUGGACGCCGGCAGUUGCGUACCAGAACUGGAACAGUGUACA
..(((((((((((((......))))))))))..))).......--------...((((((.((((.(((((.(((((((...)))))...)).)))))...)))).....)))))). ( -41.50, z-score =  -1.45, R)
>droMoj3.scaffold_6498 3063543 102 - 3408170
AGCGGGGCGACAGCGUCGUGUCGCUGUCGCCGAGUGAGGUUCG--------AUGGUAGGCACAAAGAAUAAUUGAGAGACACAAGUUAGUUGCGU-CCAGAAUUCAAGUGC------
.(((.((((((((((......))))))))))((((...((((.--------.((.......))..))))......(.(((.(((.....))).))-))...))))...)))------ ( -31.60, z-score =  -1.09, R)
>consensus
AGCGCGGCGACAGCGUGGUGUCGCUGUCGCCGAGUGAGGUUCG________AUGGUAAGCACAGAGAAGAAGUGAGUGACACAAGGCAGUUGCGU_CCAGAACUUCAGUGC______
.((((((((((((((......))))))))))..((((.(((((...........(....)............))))).)))).........))))...................... (-21.67 = -22.43 +   0.75)

alignment

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secondary structure

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dotplot

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Window 7

Location 24,276,560 – 24,276,664
Length 104
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 61.99
Shannon entropy 0.59247
G+C content 0.54637
Mean single sequence MFE -35.08
Consensus MFE -17.15
Energy contribution -17.65
Covariance contribution 0.50
Combinations/Pair 1.10
Mean z-score -3.73
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.64
SVM RNA-class probability 0.999868
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 24276560 104 + 24543557
----GCACCGAAGAUCUAC-ACACAAUUAAUUUGUGUCACUCACUUCUUCUCCGUGCUAUCCUU--------CGAACCACACUCGGCGACAGCGACCACACGCUGCCGCCGCGCUGU
----((((.(((((.....-((((((.....))))))........)))))...)))).......--------......((((.(((((.(((((......))))).))))).).))) ( -33.32, z-score =  -4.86, R)
>droYak2.chrU 20653638 111 - 28119190
-----GACUGAAGUUCUAC-GCACAACUGCCGUGUGUCGCACACCUCUUCUACGUGCUUACCACAUGUGCAGCGAAACACACUCGGCAUCAGCAACAACACGCUGGCGCCGCGCUAU
-----.............(-((....((((((((((..((((...........))))....)))))).))))............(((..((((........))))..)))))).... ( -33.70, z-score =  -1.12, R)
>droAna3.scaffold_13260 592174 109 + 2125536
UACACUGUUCCAGUUCUGGUACGCAACUGCCGGCGUCCAACUGUGUACCUACUGUGCAUACUAC--------CAAACCUCGAUCGGCGACAGCGACACAACGCUGUCGCCUCGCUAC
.....(((..((((...((((((((..((........))..)))))))).)))).)))......--------.......(((..((((((((((......))))))))))))).... ( -37.80, z-score =  -3.29, R)
>droMoj3.scaffold_6498 3063543 104 + 3408170
----GCACUUGAAUUCUGG-ACGCAACUAACUUGUGUCUCUCAAUUAUUCUUUGUGCCUACCAU--------CGAACCUCACUCGGCGACAGCGACACGACGCUGUCGCCCCGCUAA
----((((..((((...((-((((((.....)))))))).......))))...)))).......--------............((((((((((......))))))))))....... ( -35.50, z-score =  -5.67, R)
>consensus
____GCACUGAAGUUCUAC_ACACAACUAACGUGUGUCACUCACUUAUUCUCCGUGCUUACCAC________CGAACCACACUCGGCGACAGCGACAACACGCUGUCGCCGCGCUAU
....................................................................................((((((((((......))))))))))....... (-17.15 = -17.65 +   0.50)

alignment

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secondary structure

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dotplot

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Window 8

Location 24,276,560 – 24,276,664
Length 104
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 61.99
Shannon entropy 0.59247
G+C content 0.54637
Mean single sequence MFE -38.98
Consensus MFE -22.10
Energy contribution -22.85
Covariance contribution 0.75
Combinations/Pair 1.36
Mean z-score -1.50
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.92
SVM RNA-class probability 0.975216
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 24276560 104 - 24543557
ACAGCGCGGCGGCAGCGUGUGGUCGCUGUCGCCGAGUGUGGUUCG--------AAGGAUAGCACGGAGAAGAAGUGAGUGACACAAAUUAAUUGUGU-GUAGAUCUUCGGUGC----
...((((((((((((((......))))))))))..((((...((.--------...))..))))...(((((..((....((((((.....))))))-.))..))))).))))---- ( -42.30, z-score =  -3.38, R)
>droYak2.chrU 20653638 111 + 28119190
AUAGCGCGGCGCCAGCGUGUUGUUGCUGAUGCCGAGUGUGUUUCGCUGCACAUGUGGUAAGCACGUAGAAGAGGUGUGCGACACACGGCAGUUGUGC-GUAGAACUUCAGUC-----
...((((((((((...((((.(((((...(((((.((((((......)))))).))))).((((.(.....).)))))))))))))))).)))))))-..............----- ( -41.50, z-score =  -0.17, R)
>droAna3.scaffold_13260 592174 109 - 2125536
GUAGCGAGGCGACAGCGUUGUGUCGCUGUCGCCGAUCGAGGUUUG--------GUAGUAUGCACAGUAGGUACACAGUUGGACGCCGGCAGUUGCGUACCAGAACUGGAACAGUGUA
(((((..((((((((((......))))))))))(.(((..(((..--------(..((.(((.......))).))..)..)))..)))).)))))((.(((....))).))...... ( -40.50, z-score =  -1.30, R)
>droMoj3.scaffold_6498 3063543 104 - 3408170
UUAGCGGGGCGACAGCGUCGUGUCGCUGUCGCCGAGUGAGGUUCG--------AUGGUAGGCACAAAGAAUAAUUGAGAGACACAAGUUAGUUGCGU-CCAGAAUUCAAGUGC----
...(((.((((((((((......))))))))))((((...((((.--------.((.......))..))))......(.(((.(((.....))).))-))...))))...)))---- ( -31.60, z-score =  -1.14, R)
>consensus
AUAGCGCGGCGACAGCGUGGUGUCGCUGUCGCCGAGUGAGGUUCG________AUGGUAAGCACAGAGAAGAAGUGAGUGACACAAGGCAGUUGCGU_CCAGAACUUCAGUGC____
(((((..((((((((((......))))))))))..((((.(((((...........(....)............))))).))))......)))))...................... (-22.10 = -22.85 +   0.75)

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 23:47:05 2011