Locus 6465

Sequence ID dm3.chr3L
Location 6,892,529 – 6,892,684
Length 155
Max. P 0.997115
window8904 window8905 window8906 window8907

overview

Window 4

Location 6,892,529 – 6,892,646
Length 117
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 88.12
Shannon entropy 0.19206
G+C content 0.45253
Mean single sequence MFE -26.49
Consensus MFE -19.32
Energy contribution -22.14
Covariance contribution 2.81
Combinations/Pair 1.03
Mean z-score -2.63
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.43
SVM RNA-class probability 0.939536
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6892529 117 + 24543557
UACGCAUGCGUCCGAUUUCCUGUUGCUGUGGCAACCCCCACAUGGACACACACUUUUAUCUAUAUACAUAUAUCUACACACACACAAACACACAGAUAUAUGUGUCGAGAGCACCCA
...((.((.(((((.......(((((....))))).......))))).))........(((..((((((((((((..................))))))))))))..)))))..... ( -29.01, z-score =  -3.21, R)
>droSim1.chr3L 6365579 113 + 22553184
UACGCAUGCGUCCGAUUUCCUGUUGCUGUGGCAACCCCCACAUGGACACACACUUUUAUCUAUAUACAUAUAUCUACACACAC----ACACACAGAUAUAUGUGUCGAGAGCACCCA
...((.((.(((((.......(((((....))))).......))))).))........(((..((((((((((((........----......))))))))))))..)))))..... ( -29.28, z-score =  -3.23, R)
>droSec1.super_2 6814647 97 + 7591821
UACGCAUGCGUCCGAUUUCCUGUUGCUGUGGCAACCCCCACAUGGACACACACUUUUAUCUAUAUACAUAUAUCUACACACAC----ACACACAGA-GCACC---------------
...((.((.(((((.......(((((....))))).......))))).))..........((((....))))...........----.........-))...--------------- ( -14.64, z-score =  -0.55, R)
>droEre2.scaffold_4784 21286637 111 - 25762168
UACGCAUGCGUCCGAUUUCCUGUUGCUGUGGCAACCCCCACAUGGACACACACUUUUAUCUAUAUACAUAUAUCUACACAC------ACACACAGAUAUAUGUGUCGAGAGCAGGCA
...((.((((((((.......(((((....))))).......)))))...........(((..((((((((((((......------......))))))))))))..)))))).)). ( -33.04, z-score =  -3.54, R)
>consensus
UACGCAUGCGUCCGAUUUCCUGUUGCUGUGGCAACCCCCACAUGGACACACACUUUUAUCUAUAUACAUAUAUCUACACACAC____ACACACAGAUAUAUGUGUCGAGAGCACCCA
...((.((.(((((.......(((((....))))).......))))).))........(((..((((((((((((..................))))))))))))..)))))..... (-19.32 = -22.14 +   2.81)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,892,529 – 6,892,646
Length 117
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 88.12
Shannon entropy 0.19206
G+C content 0.45253
Mean single sequence MFE -36.79
Consensus MFE -31.47
Energy contribution -32.09
Covariance contribution 0.62
Combinations/Pair 1.07
Mean z-score -1.81
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.02
SVM RNA-class probability 0.874584
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6892529 117 - 24543557
UGGGUGCUCUCGACACAUAUAUCUGUGUGUUUGUGUGUGUGUAGAUAUAUGUAUAUAGAUAAAAGUGUGUGUCCAUGUGGGGGUUGCCACAGCAACAGGAAAUCGGACGCAUGCGUA
.(.((((.....((((((.((((((((((..(((((........)))))..))))))))))...))))))((((........(((((....)))))........)))))))).)... ( -36.19, z-score =  -0.91, R)
>droSim1.chr3L 6365579 113 - 22553184
UGGGUGCUCUCGACACAUAUAUCUGUGUGU----GUGUGUGUAGAUAUAUGUAUAUAGAUAAAAGUGUGUGUCCAUGUGGGGGUUGCCACAGCAACAGGAAAUCGGACGCAUGCGUA
.(.((((.....((((((.((((((((((.----.(((((....)))))..))))))))))...))))))((((........(((((....)))))........)))))))).)... ( -39.39, z-score =  -2.12, R)
>droSec1.super_2 6814647 97 - 7591821
---------------GGUGC-UCUGUGUGU----GUGUGUGUAGAUAUAUGUAUAUAGAUAAAAGUGUGUGUCCAUGUGGGGGUUGCCACAGCAACAGGAAAUCGGACGCAUGCGUA
---------------..(((-((((((((.----.(((((....)))))..)))))))).....((((((((((........(((((....)))))........))))))))))))) ( -34.09, z-score =  -2.59, R)
>droEre2.scaffold_4784 21286637 111 + 25762168
UGCCUGCUCUCGACACAUAUAUCUGUGUGU------GUGUGUAGAUAUAUGUAUAUAGAUAAAAGUGUGUGUCCAUGUGGGGGUUGCCACAGCAACAGGAAAUCGGACGCAUGCGUA
.((.(((.....((((((.((((((((((.------.((((....))))..))))))))))...))))))((((........(((((....)))))........))))))).))... ( -37.49, z-score =  -1.62, R)
>consensus
UGGGUGCUCUCGACACAUAUAUCUGUGUGU____GUGUGUGUAGAUAUAUGUAUAUAGAUAAAAGUGUGUGUCCAUGUGGGGGUUGCCACAGCAACAGGAAAUCGGACGCAUGCGUA
..............(((((((((((..((........))..)))))))))))............((((((((((........(((((....)))))........))))))))))... (-31.47 = -32.09 +   0.62)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,892,569 – 6,892,684
Length 115
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 95.31
Shannon entropy 0.06388
G+C content 0.34927
Mean single sequence MFE -19.00
Consensus MFE -17.87
Energy contribution -17.87
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.50
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.04
SVM RNA-class probability 0.997115
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6892569 115 + 24543557
CAUGGACACACACUUUUAUCUAUAUACAUAUAUCUACACACACACAAACACACAGAUAUAUGUGUCGAGAGCACCCAACGCAAUAUUUGAAUAUUCACGCAUACCAUAAACUAAA
.((((.............(((..((((((((((((..................))))))))))))..)))((.......))......................))))........ ( -17.87, z-score =  -3.34, R)
>droSim1.chr3L 6365619 111 + 22553184
CAUGGACACACACUUUUAUCUAUAUACAUAUAUCUACACACACAC----ACACAGAUAUAUGUGUCGAGAGCACCCAACGCAAUAUUUGAAUAUUCACGCAUACCAUAAACUAAA
.((((.............(((..((((((((((((..........----....))))))))))))..)))((.......))......................))))........ ( -18.14, z-score =  -3.45, R)
>droEre2.scaffold_4784 21286677 109 - 25762168
CAUGGACACACACUUUUAUCUAUAUACAUAUAUCUACACACACAC------ACAGAUAUAUGUGUCGAGAGCAGGCAACGCAAUAUUUGAAUAUUCACGCAUACCAUAAACUAAA
.((((.............(((..((((((((((((..........------..))))))))))))..)))((.(....)(.(((((....))))))..))...))))........ ( -21.00, z-score =  -3.72, R)
>consensus
CAUGGACACACACUUUUAUCUAUAUACAUAUAUCUACACACACAC____ACACAGAUAUAUGUGUCGAGAGCACCCAACGCAAUAUUUGAAUAUUCACGCAUACCAUAAACUAAA
.((((.............(((..((((((((((((..................))))))))))))..)))((.......))......................))))........ (-17.87 = -17.87 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,892,569 – 6,892,684
Length 115
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 95.31
Shannon entropy 0.06388
G+C content 0.34927
Mean single sequence MFE -30.47
Consensus MFE -23.67
Energy contribution -24.67
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.23
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.595339
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6892569 115 - 24543557
UUUAGUUUAUGGUAUGCGUGAAUAUUCAAAUAUUGCGUUGGGUGCUCUCGACACAUAUAUCUGUGUGUUUGUGUGUGUGUAGAUAUAUGUAUAUAGAUAAAAGUGUGUGUCCAUG
.......(((((....((.((.(((((((........))))))).)).))((((((.((((((((((..(((((........)))))..))))))))))...))))))..))))) ( -28.10, z-score =  -1.15, R)
>droSim1.chr3L 6365619 111 - 22553184
UUUAGUUUAUGGUAUGCGUGAAUAUUCAAAUAUUGCGUUGGGUGCUCUCGACACAUAUAUCUGUGU----GUGUGUGUGUAGAUAUAUGUAUAUAGAUAAAAGUGUGUGUCCAUG
.......(((((....((.((.(((((((........))))))).)).))((((((.(((((((((----(..(((((....)))))..))))))))))...))))))..))))) ( -31.30, z-score =  -2.43, R)
>droEre2.scaffold_4784 21286677 109 + 25762168
UUUAGUUUAUGGUAUGCGUGAAUAUUCAAAUAUUGCGUUGCCUGCUCUCGACACAUAUAUCUGU------GUGUGUGUGUAGAUAUAUGUAUAUAGAUAAAAGUGUGUGUCCAUG
...(((....((((.((((.(((((....))))))))))))).)))...(((((((((((((((------(((..((((....))))..)))))))))....))))))))).... ( -32.00, z-score =  -3.12, R)
>consensus
UUUAGUUUAUGGUAUGCGUGAAUAUUCAAAUAUUGCGUUGGGUGCUCUCGACACAUAUAUCUGUGU____GUGUGUGUGUAGAUAUAUGUAUAUAGAUAAAAGUGUGUGUCCAUG
.......((((((((((((.(((((....)))))))))...))))....(((((((((((((((((....((((((......))))))..))))))))....))))))))))))) (-23.67 = -24.67 +   1.00)

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 23:08:22 2011