Locus 7688

Sequence ID dm3.chr3L
Location 16,625,351 – 16,625,476
Length 125
Max. P 0.993658
window10575 window10576 window10577

overview

Window 5

Location 16,625,351 – 16,625,441
Length 90
Sequences 6
Columns 90
Reading direction forward
Mean pairwise identity 81.04
Shannon entropy 0.37200
G+C content 0.52165
Mean single sequence MFE -28.80
Consensus MFE -19.78
Energy contribution -22.25
Covariance contribution 2.47
Combinations/Pair 1.09
Mean z-score -2.70
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.63
SVM RNA-class probability 0.993658
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16625351 90 + 24543557
UGUUGGGUGAGAAAGAGUCGGAGGUAUGGCCAGAGAAAGAGACGGCGAUAGAAACAUGUCUCAAGCCAUGCACAUCCGCCAUCUAGCGAC
.((((((((.((.....))(((.(((((((..((((.........(....).......))))..)))))))...)))..))))))))... ( -28.39, z-score =  -2.32, R)
>droSim1.chr3L 15956521 90 + 22553184
UGUUGGGUGGGAAAGAGGCGGAGGUAUGGCCAGAGACAGAGACGGCGAUAGAAACAUGUCUCAAGACAUGCACAUCCGCCAUCUAGCGAC
.(((((((........((((((.(((((....((((((.......(....).....))))))....)))))...)))))))))))))... ( -30.30, z-score =  -2.79, R)
>droSec1.super_0 8703259 90 + 21120651
UGUUGGGUGGGAAAGAGGCGGAGGUAUGGCCAGAGACAGAGACGGCGAUAGAAACAUGUCUCAAGCCAUGCACAUCCGCCAUCUAGAGAC
.............(((((((((.(((((((..((((((.......(....).....))))))..)))))))...)))))).)))...... ( -34.70, z-score =  -4.12, R)
>droYak2.chr3L 6752027 90 - 24197627
UGUUGGGAGGGAAAGAGGCGGAGGUAUGGCUGGAGACAGAGAUGGCGAUAGAAACAUGUCUCAAGCCAUGCACAUCCGCCAUCUAGCGAC
..........(..(((((((((.((((((((.((((((.......(....).....)))))).))))))))...)))))).)))..)... ( -37.40, z-score =  -4.75, R)
>droEre2.scaffold_4784 8559116 90 - 25762168
UGUUGGGAGAGAAAGAGGCGGAUAUAUGGAUGGAGACAGAGAUGGCGAUAGAAACAUGUCUCAAGCCAUGCACAUCCGCCAUCUAGCGAC
.((((..(((......(((((((.(((((...((((((.......(....).....))))))...)))))...))))))).)))..)))) ( -29.50, z-score =  -3.30, R)
>droAna3.scaffold_13337 9323286 78 - 23293914
------------UGCUUAGAGAAGAAAAAAGAAAGAGAGAGAAGGGGAGAAGACACUGUCUCAAGUCAUGCACAUCCGCCAUCUAGCGGC
------------.(((.(((..........((..((((.((...(........).)).))))...))..((......))..))))))... ( -12.50, z-score =   1.06, R)
>consensus
UGUUGGGUGGGAAAGAGGCGGAGGUAUGGCCAGAGACAGAGACGGCGAUAGAAACAUGUCUCAAGCCAUGCACAUCCGCCAUCUAGCGAC
.............(((((((((.(((((((..((((((..................))))))..)))))))...)))))).)))...... (-19.78 = -22.25 +   2.47)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,625,351 – 16,625,441
Length 90
Sequences 6
Columns 90
Reading direction reverse
Mean pairwise identity 81.04
Shannon entropy 0.37200
G+C content 0.52165
Mean single sequence MFE -24.36
Consensus MFE -18.72
Energy contribution -20.00
Covariance contribution 1.28
Combinations/Pair 1.30
Mean z-score -2.04
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.96
SVM RNA-class probability 0.977034
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16625351 90 - 24543557
GUCGCUAGAUGGCGGAUGUGCAUGGCUUGAGACAUGUUUCUAUCGCCGUCUCUUUCUCUGGCCAUACCUCCGACUCUUUCUCACCCAACA
((((..(((((((((....(((((........))))).....)))))))))........((.....))..))))................ ( -23.00, z-score =  -1.14, R)
>droSim1.chr3L 15956521 90 - 22553184
GUCGCUAGAUGGCGGAUGUGCAUGUCUUGAGACAUGUUUCUAUCGCCGUCUCUGUCUCUGGCCAUACCUCCGCCUCUUUCCCACCCAACA
...(..(((.((((((.(((((((((....))))))).......((((..........))))...)).)))))))))..).......... ( -25.80, z-score =  -2.32, R)
>droSec1.super_0 8703259 90 - 21120651
GUCUCUAGAUGGCGGAUGUGCAUGGCUUGAGACAUGUUUCUAUCGCCGUCUCUGUCUCUGGCCAUACCUCCGCCUCUUUCCCACCCAACA
......(((.((((((.((..((((((.((((((.(...(.......)...))))))).)))))))).)))))))))............. ( -30.00, z-score =  -3.54, R)
>droYak2.chr3L 6752027 90 + 24197627
GUCGCUAGAUGGCGGAUGUGCAUGGCUUGAGACAUGUUUCUAUCGCCAUCUCUGUCUCCAGCCAUACCUCCGCCUCUUUCCCUCCCAACA
...(..(((.((((((.((..((((((.((((((..................)))))).)))))))).)))))))))..).......... ( -30.17, z-score =  -3.90, R)
>droEre2.scaffold_4784 8559116 90 + 25762168
GUCGCUAGAUGGCGGAUGUGCAUGGCUUGAGACAUGUUUCUAUCGCCAUCUCUGUCUCCAUCCAUAUAUCCGCCUCUUUCUCUCCCAACA
...(..(((.(((((((((..((((...((((((..................))))))...))))))))))))))))..).......... ( -26.57, z-score =  -3.08, R)
>droAna3.scaffold_13337 9323286 78 + 23293914
GCCGCUAGAUGGCGGAUGUGCAUGACUUGAGACAGUGUCUUCUCCCCUUCUCUCUCUUUCUUUUUUCUUCUCUAAGCA------------
.(((((....)))))........((...((((.((..............)).))))..))..................------------ ( -10.64, z-score =   1.75, R)
>consensus
GUCGCUAGAUGGCGGAUGUGCAUGGCUUGAGACAUGUUUCUAUCGCCGUCUCUGUCUCUGGCCAUACCUCCGCCUCUUUCCCACCCAACA
......(((.((((((.((..((((((.((((((..................)))))).)))))))).)))))))))............. (-18.72 = -20.00 +   1.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,625,371 – 16,625,476
Length 105
Sequences 7
Columns 110
Reading direction reverse
Mean pairwise identity 76.36
Shannon entropy 0.47987
G+C content 0.49794
Mean single sequence MFE -26.79
Consensus MFE -17.10
Energy contribution -17.23
Covariance contribution 0.13
Combinations/Pair 1.56
Mean z-score -0.89
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.13
SVM RNA-class probability 0.559427
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16625371 105 - 24543557
UGCUCCAAAUUCGCCGCUAAUAACCUGCAUAAGCAGUCGCUAGAUGGCGGAUGUGCAUGGCUUGAGACAUGUUUCUAUCGCCGUCUCUUUCUCUGGCCAUACCUC-----
.((.....(((((((((((.....((((....))))....))).))))))))..))((((((.(((((..............))))).......)))))).....----- ( -30.54, z-score =  -1.50, R)
>droSim1.chr3L 15956541 105 - 22553184
UGCUCCAAAUUCGCCGCUAAUAACCUGCAUAAGCAGUCGCUAGAUGGCGGAUGUGCAUGUCUUGAGACAUGUUUCUAUCGCCGUCUCUGUCUCUGGCCAUACCUC-----
............(((.........((((....))))..((.(((((((((....(((((((....))))))).....)))))))))..))....)))........----- ( -32.40, z-score =  -2.40, R)
>droSec1.super_0 8703279 105 - 21120651
UGCUCCAAAUUCGCCGCUAAUAACCUGCAUAAGCAGUCUCUAGAUGGCGGAUGUGCAUGGCUUGAGACAUGUUUCUAUCGCCGUCUCUGUCUCUGGCCAUACCUC-----
.((.....(((((((((((.....((((....))))....))).))))))))..))((((((.((((((.(...(.......)...))))))).)))))).....----- ( -34.70, z-score =  -3.01, R)
>droYak2.chr3L 6752047 104 + 24197627
UGCUCCAAAUUCA-CGCUAAUAACCUGCAUAAGCAGUCGCUAGAUGGCGGAUGUGCAUGGCUUGAGACAUGUUUCUAUCGCCAUCUCUGUCUCCAGCCAUACCUC-----
.((.(.....((.-(((((.....((((....))))((....))))))))).).))((((((.((((((..................)))))).)))))).....----- ( -27.67, z-score =  -1.07, R)
>droEre2.scaffold_4784 8559136 104 + 25762168
UGCUCCAAAUUCA-CGCUAAUAACCUGCAUAAGCAGUCGCUAGAUGGCGGAUGUGCAUGGCUUGAGACAUGUUUCUAUCGCCAUCUCUGUCUCCAUCCAUAUAUC-----
.............-..........((((....))))..((.(((((((((....(((((........))))).....)))))))))..))...............----- ( -24.00, z-score =  -0.33, R)
>droAna3.scaffold_13337 9323305 93 + 23293914
UGCUCCAAAUUCC-CGCUAAUAGCCUCCAUAAGCAGCCGCUAGAUGGCGGAUGUGCAUGACUUGAGACAGUGUCUUCUCCCCUUCUCUCUCUUU----------------
.............-.((.....))...(((..(((.(((((....))))).)))..)))....((((.((..............)).))))...---------------- ( -16.24, z-score =   1.22, R)
>droWil1.scaffold_180727 2506530 107 + 2741493
UGCUCCAAUUCC--UACUAAUAACUUGCAUAAGUAGCUAUAAUGGCGCGGAGAUGUGACGCUGAAGAUGC-CUCCUCCCAUGCCUCAUGCCGCAUGCCGCAUGCCCGAAU
.((.(((((..(--((((.((.......)).)))))..))..))).))((((....((.((.......))-.))))))(((((..((((...))))..)))))....... ( -22.00, z-score =   0.84, R)
>consensus
UGCUCCAAAUUCG_CGCUAAUAACCUGCAUAAGCAGUCGCUAGAUGGCGGAUGUGCAUGGCUUGAGACAUGUUUCUAUCGCCGUCUCUGUCUCUGGCCAUACCUC_____
........................((((....)))).....(((((((((....(((((........))))).....)))))))))........................ (-17.10 = -17.23 +   0.13)

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 23:31:33 2011