Locus 4573

Sequence ID dm3.chr2R
Location 14,173,368 – 14,173,489
Length 121
Max. P 0.957631
window6267 window6268 window6269

overview

Window 7

Location 14,173,368 – 14,173,468
Length 100
Sequences 9
Columns 100
Reading direction forward
Mean pairwise identity 75.79
Shannon entropy 0.50167
G+C content 0.68085
Mean single sequence MFE -43.82
Consensus MFE -25.73
Energy contribution -24.72
Covariance contribution -1.01
Combinations/Pair 1.31
Mean z-score -1.73
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.64
SVM RNA-class probability 0.957631
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14173368 100 + 21146708
CCGGUCGCUGCCAGAAGUGAGGCAGCGGCAGGCACCACGGUCGAUGGUGAACCGGUGGAAGGAGAGCCCGCUGAAGGUGUGAACACACCCGGUGGCACUG
((.(((((((((........))))))))).....(((((((((....)).))).))))..))((.(((.((((..(((((....)))))))))))).)). ( -43.20, z-score =  -1.42, R)
>droGri2.scaffold_15245 11428529 85 + 18325388
GUUGUAGCAGCCAGCAGCGAUGCUGCAGCAGAGACAACAGCAGCUGG---------------UGAGCCAGCAGAGGGCGUAAAUACGCCUGGUGGCACAG
(((((..(.((..(((((...))))).)).)..))))).((.(((((---------------....)))))...((((((....))))))....)).... ( -35.50, z-score =  -2.16, R)
>droVir3.scaffold_12875 502954 85 - 20611582
GUCGUUGCAGCCAGCAGCGAGGCAGCCGCCGAGACAACAGCUGCCGG---------------GGAGCCAGCCGAGGGCGUGAAUACGCCCGGCGGCACAG
.(((((((.....)))))))((((((.(.........).))))))((---------------....)).((((.((((((....))))))..)))).... ( -42.70, z-score =  -2.85, R)
>droPer1.super_4 6853555 100 + 7162766
GUUGUGGCUGCCAGCAGAGAGGCGGCUGCUGGGACGACGGCCGAUGGAGAUCCCGCCGAGGGUGAGCCGGCCGACGGUGUAAACACCCCCGGCGGCACAG
..((((((((((........))))))(((((((....(((((...((....(((.....)))....)))))))..((((....))))))))))).)))). ( -48.40, z-score =  -1.84, R)
>dp4.chr3 11449302 100 + 19779522
GUUGUGGCUGCCAGCAGAGAGGCGGCUGCUGGGACGACGGCCGAUGGAGAUCCCGCCGAGGGUGAGCCGGCCGACGGUGUAAACACCCCCGGCGGCACAG
..((((((((((........))))))(((((((....(((((...((....(((.....)))....)))))))..((((....))))))))))).)))). ( -48.40, z-score =  -1.84, R)
>droSim1.chr2R 12909916 100 + 19596830
CCGGUCGCCGCCAGAAGUGAGGCAGCGGCAGGCACCACGGUCGAUGGUGAACCGGCGGAAGGAGAGCCCGCUGAAGGUGUGAACACACCCGGUGGCACUG
.((((.((((((...((((.(((..(((....((((((....).)))))..))).(....)....)))))))...(((((....))))).)))))))))) ( -42.90, z-score =  -1.05, R)
>droSec1.super_1 11663273 100 + 14215200
CCGGUCGCCGCCAGAAGUGAGGCAGCGGCAGGCACCACGGUCGAUGGUGAACCGGCGGAAGGAGAGCCCGCUGAAGGUGUGAACACACCCGGUGGCACUG
.((((.((((((...((((.(((..(((....((((((....).)))))..))).(....)....)))))))...(((((....))))).)))))))))) ( -42.90, z-score =  -1.05, R)
>droYak2.chr2R 6131306 100 - 21139217
CCGGUCGCCGCCAGAAGUGAGGCAGCCGCAGGCACCACGUUCGAAGGUGAACCGGCGGAAGGAGAGCCCGCUGAAGGUGUGAACACACCCGGUGGCACUG
.((((.((((((...((((.(((.(((...))).((...((((..((....))..)))).))...)))))))...(((((....))))).)))))))))) ( -44.30, z-score =  -1.92, R)
>droEre2.scaffold_4845 8394419 100 + 22589142
CCGGUCGCCGCCAGAAGUGAGGCAGCCGCAGGCACCACGGUCGACGGUGAGCCGGCGGAUGGAGAGCCCGCUGAAGGUGUGAACACACCCGGUGGCACUG
.((((.((((((...((((.(((..((((.(((..(((.(....).))).))).)))).......)))))))...(((((....))))).)))))))))) ( -46.10, z-score =  -1.45, R)
>consensus
CCGGUCGCCGCCAGAAGUGAGGCAGCCGCAGGCACCACGGUCGAUGGUGAACCGGCGGAAGGAGAGCCCGCUGAAGGUGUGAACACACCCGGUGGCACUG
.((((.((((((..........((((.((.(......).))....((....((.......))....)).))))..(((((....))))).)))))))))) (-25.73 = -24.72 +  -1.01)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,173,368 – 14,173,468
Length 100
Sequences 9
Columns 100
Reading direction reverse
Mean pairwise identity 75.79
Shannon entropy 0.50167
G+C content 0.68085
Mean single sequence MFE -40.53
Consensus MFE -20.00
Energy contribution -21.08
Covariance contribution 1.08
Combinations/Pair 1.32
Mean z-score -1.30
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.01
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>dm3.chr2R 14173368 100 - 21146708
CAGUGCCACCGGGUGUGUUCACACCUUCAGCGGGCUCUCCUUCCACCGGUUCACCAUCGACCGUGGUGCCUGCCGCUGCCUCACUUCUGGCAGCGACCGG
........((((((((....)))))....((((((.......((((.((((.......)))))))).))))))(((((((........)))))))..))) ( -41.80, z-score =  -2.37, R)
>droGri2.scaffold_15245 11428529 85 - 18325388
CUGUGCCACCAGGCGUAUUUACGCCCUCUGCUGGCUCA---------------CCAGCUGCUGUUGUCUCUGCUGCAGCAUCGCUGCUGGCUGCUACAAC
.((.((((.(((((((....)))))...)).)))).))---------------(((((.((((((((.......))))))..)).))))).......... ( -30.20, z-score =  -0.94, R)
>droVir3.scaffold_12875 502954 85 + 20611582
CUGUGCCGCCGGGCGUAUUCACGCCCUCGGCUGGCUCC---------------CCGGCAGCUGUUGUCUCGGCGGCUGCCUCGCUGCUGGCUGCAACGAC
....((((((((((((....))))))..))).)))...---------------..(((((((((((...)))))))))))(((.(((.....))).))). ( -43.40, z-score =  -2.48, R)
>droPer1.super_4 6853555 100 - 7162766
CUGUGCCGCCGGGGGUGUUUACACCGUCGGCCGGCUCACCCUCGGCGGGAUCUCCAUCGGCCGUCGUCCCAGCAGCCGCCUCUCUGCUGGCAGCCACAAC
..((.((((((((((((......(((.....)))..)))))))))))).)).......(((.(.....(((((((........)))))))).)))..... ( -43.30, z-score =  -1.04, R)
>dp4.chr3 11449302 100 - 19779522
CUGUGCCGCCGGGGGUGUUUACACCGUCGGCCGGCUCACCCUCGGCGGGAUCUCCAUCGGCCGUCGUCCCAGCAGCCGCCUCUCUGCUGGCAGCCACAAC
..((.((((((((((((......(((.....)))..)))))))))))).)).......(((.(.....(((((((........)))))))).)))..... ( -43.30, z-score =  -1.04, R)
>droSim1.chr2R 12909916 100 - 19596830
CAGUGCCACCGGGUGUGUUCACACCUUCAGCGGGCUCUCCUUCCGCCGGUUCACCAUCGACCGUGGUGCCUGCCGCUGCCUCACUUCUGGCGGCGACCGG
........((((((((....)))))....((((((.......((((.((((.......)))))))).))))))(((((((........)))))))..))) ( -40.70, z-score =  -1.26, R)
>droSec1.super_1 11663273 100 - 14215200
CAGUGCCACCGGGUGUGUUCACACCUUCAGCGGGCUCUCCUUCCGCCGGUUCACCAUCGACCGUGGUGCCUGCCGCUGCCUCACUUCUGGCGGCGACCGG
........((((((((....)))))....((((((.......((((.((((.......)))))))).))))))(((((((........)))))))..))) ( -40.70, z-score =  -1.26, R)
>droYak2.chr2R 6131306 100 + 21139217
CAGUGCCACCGGGUGUGUUCACACCUUCAGCGGGCUCUCCUUCCGCCGGUUCACCUUCGAACGUGGUGCCUGCGGCUGCCUCACUUCUGGCGGCGACCGG
........((((((((....))))).((.((((((.......((((..((((......)))))))).)))))).((((((........)))))))).))) ( -39.10, z-score =  -0.65, R)
>droEre2.scaffold_4845 8394419 100 - 22589142
CAGUGCCACCGGGUGUGUUCACACCUUCAGCGGGCUCUCCAUCCGCCGGCUCACCGUCGACCGUGGUGCCUGCGGCUGCCUCACUUCUGGCGGCGACCGG
........((((((((....))))).((.((((((...((((.((.(((....))).))...)))).)))))).((((((........)))))))).))) ( -42.30, z-score =  -0.66, R)
>consensus
CAGUGCCACCGGGUGUGUUCACACCUUCAGCGGGCUCUCCUUCCGCCGGUUCACCAUCGACCGUGGUGCCUGCCGCUGCCUCACUUCUGGCGGCGACCGG
.((.(((..(.(((((....)))))....)..))).)).....((((((.((......)).).)))))......((((((........))))))...... (-20.00 = -21.08 +   1.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,173,398 – 14,173,489
Length 91
Sequences 12
Columns 110
Reading direction forward
Mean pairwise identity 62.36
Shannon entropy 0.71424
G+C content 0.65475
Mean single sequence MFE -35.01
Consensus MFE -13.63
Energy contribution -13.98
Covariance contribution 0.36
Combinations/Pair 1.50
Mean z-score -1.45
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.20
SVM RNA-class probability 0.908678
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14173398 91 + 21146708
GGCACCACGGUCGAUGGUGAACCGGUGGAAGGAGAGCCCGCUGAAGGUGUGAACACACCCGGUGGCACUGCUGACAUGGAGGAUG-AACCAC------------------
((((((((....).)))))..((.(((..((.((.(((.((((..(((((....)))))))))))).)).))..)))...))...-..))..------------------ ( -31.80, z-score =  -0.73, R)
>droGri2.scaffold_15245 11428559 72 + 18325388
---------------GAGACAACAGCAGCUGGUGAGCCAGCAGAGGGCGUAAAUACGCCUGGUGGCACAGCGGAUGCAGAGGAAUUG-----------------------
---------------.........(((.(((.((.((((.((...(((((....))))))).)))).)).))).)))..........----------------------- ( -26.90, z-score =  -3.02, R)
>droMoj3.scaffold_6496 6073348 72 + 26866924
---------------GAGACCACAGCAGCCGGCGAGCCGGCAGAGGGCGUAAAUACGCCGGGCGGCACAGCCGUGGCUGUGGCAUUG-----------------------
---------------..(.(((((((.(((((....)))))....(((((....)))))..(((((...))))).))))))))....----------------------- ( -38.90, z-score =  -3.82, R)
>droVir3.scaffold_12875 502984 72 - 20611582
---------------GAGACAACAGCUGCCGGGGAGCCAGCCGAGGGCGUGAAUACGCCCGGCGGCACAGCCGUUGCGCUCGAGCUG-----------------------
---------------(((.((((.((((..((....)).((((.((((((....))))))..)))).)))).))))..)))......----------------------- ( -35.70, z-score =  -2.28, R)
>droAna3.scaffold_13266 15534900 91 - 19884421
GGCACAACAGCCGAUGGCGACCCACCGGAUGGGGAUCCAGCCGACGGCGUGAACACCCCCGGGGGCACAGCGGACAUGGAGGAGC-UACUGU------------------
(((.(..((.(((.((..(.(((.((((..((((.((..(((...)))..)).).))))))))))).)).)))...))...).))-).....------------------ ( -31.20, z-score =   0.62, R)
>droPer1.super_4 6853585 104 + 7162766
GGGACGACGGCCGAUGGAGAUCCCGCCGAGGGUGAGCCGGCCGACGGUGUAAACACCCCCGGCGGCACAGCUGACAUGGAGGAGGCAGCUGCAGCUGCAGCAGC------
(((((..((.....))..).))))((((.(((((.((((.....)))).....))))).)))).((...(((..(.....)..))).(((((....))))).))------ ( -44.60, z-score =  -1.01, R)
>dp4.chr3 11449332 110 + 19779522
GGGACGACGGCCGAUGGAGAUCCCGCCGAGGGUGAGCCGGCCGACGGUGUAAACACCCCCGGCGGCACAGCUGACAUGGAGGAGGCAGCUGCAGCUGCAGCUGCAGCAGC
(((((..((.....))..).))))((((.(((((.((((.....)))).....))))).)))).((...(((..(.....)..))).((((((((....)))))))).)) ( -52.10, z-score =  -2.07, R)
>droWil1.scaffold_181141 1675111 76 - 5303230
---------------GACACCACAGCUGCCGGUGAACCAGCCGAUGGUGUAAACACUCCCGGAGGCACCGCCGACAUGGAGGCAGAGGCAG-------------------
---------------..........(((((((((..((..(((..((((....))))..))).))))))(((........)))...)))))------------------- ( -28.60, z-score =  -1.78, R)
>droSim1.chr2R 12909946 91 + 19596830
GGCACCACGGUCGAUGGUGAACCGGCGGAAGGAGAGCCCGCUGAAGGUGUGAACACACCCGGUGGCACUGCUGACAUGGAGGAUG-AACCAC------------------
....(((..((((..((((.((((((((.........))))....(((((....)))))))))..))))..)))).))).((...-..))..------------------ ( -32.10, z-score =  -0.81, R)
>droSec1.super_1 11663303 91 + 14215200
GGCACCACGGUCGAUGGUGAACCGGCGGAAGGAGAGCCCGCUGAAGGUGUGAACACACCCGGUGGCACUGCUGACAUGGAGGAUG-AACCAC------------------
....(((..((((..((((.((((((((.........))))....(((((....)))))))))..))))..)))).))).((...-..))..------------------ ( -32.10, z-score =  -0.81, R)
>droYak2.chr2R 6131336 91 - 21139217
GGCACCACGUUCGAAGGUGAACCGGCGGAAGGAGAGCCCGCUGAAGGUGUGAACACACCCGGUGGCACUGCUGACAUGGAGGAUG-AGCCAC------------------
(((....((((((..((....))..)(..((.((.(((.((((..(((((....)))))))))))).)).))..).....)))))-.)))..------------------ ( -32.20, z-score =  -0.87, R)
>droEre2.scaffold_4845 8394449 91 + 22589142
GGCACCACGGUCGACGGUGAGCCGGCGGAUGGAGAGCCCGCUGAAGGUGUGAACACACCCGGUGGCACUGCAGACAUGGAGGAUG-AACCAC------------------
....(((..(((..(((((.((((((((.........))))....(((((....)))))))))..)))))..))).))).((...-..))..------------------ ( -33.90, z-score =  -0.84, R)
>consensus
GGCACCACGGUCGAUGGUGAACCAGCGGAAGGAGAGCCCGCCGAAGGUGUGAACACACCCGGUGGCACAGCUGACAUGGAGGAUG_AACCAC__________________
.............................((.((.(((.((((..(((((....)))))))))))).)).))...................................... (-13.63 = -13.98 +   0.36)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:31:47 2011