Locus 5905

Sequence ID dm3.chr3L
Location 2,362,816 – 2,362,986
Length 170
Max. P 0.996760
window8121 window8122 window8123 window8124

overview

Window 1

Location 2,362,816 – 2,362,926
Length 110
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 92.45
Shannon entropy 0.12902
G+C content 0.50452
Mean single sequence MFE -34.32
Consensus MFE -31.44
Energy contribution -31.92
Covariance contribution 0.48
Combinations/Pair 1.08
Mean z-score -3.08
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.81
SVM RNA-class probability 0.995529
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2362816 110 - 24543557
CUGUGUGUAUGUCCUGCAUGCACGCGUUUUCCAGGCGCCAAAAACUGAUGGCCCCUCCGACUGGAAAACAAUGAAACUCAUUUGCAUUUUCCCCCGCUGGUCGGAAAAUG
..(((((((((.....)))))))))((((((((((.((((........)))).)))..((((((((((.((((.....))))....))))))......))))))))))). ( -37.30, z-score =  -3.73, R)
>droSec1.super_2 2387599 110 - 7591821
AUGUGUGUAUGUCCGCCAUGCACGCGUUUUCCAGGCGCCAAAAACUGAUGGCCCCUCCGACUGGAAAACAAUGAAACUCAUUUGCAUUUUCCCCCGCUCGUCGGAAAAUG
..(((((((((.....)))))))))((((((((((.((((........)))).))......))))))))((((.....))))..((((((((..(....)..)))))))) ( -36.50, z-score =  -3.78, R)
>droYak2.chr3L 14623176 108 + 24197627
AUGUGUGUAUGUCCUGUAUGCACGCGUUUUCCAGGCGCCAAAA-CUGAUGGCUCCUCUGACUGCGAAACAAUGAAACUCAUUUGCA-UUUGCCCCGCUCGUCGCAAAAUG
..(((((((((.....)))))))))(((((.((((.((((...-....)))).)))..(((.(((....((((.....)))).((.-...))..)))..)))).))))). ( -27.80, z-score =  -1.31, R)
>droEre2.scaffold_4784 2377755 109 - 25762168
AUGUGUGUAUGUCCUGUACUCACGCGUUUUCCAGGCGCCAAAACCUGAUGGCUCCUCUGACUGGGAAACAAUGAAACUCAUUUGCA-UUUGCCCCGCUCGCCGGAAAAUG
..(((.((((.....)))).))).((((((((.(((((((........))))......((.((((....((((.....)))).((.-...)))))).))))))))))))) ( -33.50, z-score =  -2.81, R)
>droSim1.chr3L 1925054 110 - 22553184
AUGUGUGUAUGUCCGCCAUGCACGCGUUUUCCAGGCGCCAAAAACUGAUGGCCCCUCCGACUGGAAAACAAUGAAACUCAUUUGCAUUUUCCCCCGCUCGUCGGAAAAUG
..(((((((((.....)))))))))((((((((((.((((........)))).))......))))))))((((.....))))..((((((((..(....)..)))))))) ( -36.50, z-score =  -3.78, R)
>consensus
AUGUGUGUAUGUCCUGCAUGCACGCGUUUUCCAGGCGCCAAAAACUGAUGGCCCCUCCGACUGGAAAACAAUGAAACUCAUUUGCAUUUUCCCCCGCUCGUCGGAAAAUG
..(((((((((.....)))))))))((((((((((.((((........)))).))......))))))))((((.....))))..((((((((..(....)..)))))))) (-31.44 = -31.92 +   0.48)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,362,849 – 2,362,955
Length 106
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 83.68
Shannon entropy 0.28594
G+C content 0.50132
Mean single sequence MFE -32.64
Consensus MFE -26.26
Energy contribution -27.14
Covariance contribution 0.88
Combinations/Pair 1.07
Mean z-score -1.30
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.25
SVM RNA-class probability 0.612735
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2362849 106 + 24543557
GUUUCAUUGUUUUCCAGUCGGAGGGGCCAUCAGUUUUUGGCGCCUGGAAAACGCGUGCAUGCAGGACAUACACACAGGCACUGAGAGAAAACAGUGCUAUGCAGCC-------
........((((((((......((.((((........)))).))))))))))(((((.(((.....))).)))...(((((((........)))))))..))....------- ( -35.20, z-score =  -1.55, R)
>droSec1.super_2 2387632 98 + 7591821
GUUUCAUUGUUUUCCAGUCGGAGGGGCCAUCAGUUUUUGGCGCCUGGAAAACGCGUGCAUGGCGGACAUACACACAUGCACUGAGAGAAACCAGUGCU---------------
(((((...((((((((......((.((((........)))).))))))))))..((((((((.(......).).))))))).....))))).......--------------- ( -34.70, z-score =  -2.01, R)
>droYak2.chr3L 14623208 105 - 24197627
GUUUCAUUGUUUCGCAGUCAGAGGAGCCAUCAG-UUUUGGCGCCUGGAAAACGCGUGCAUACAGGACAUACACACAUGCACUGAGAAGAACCAGUGCUACUAAAAC-------
((((...(((..(((..((..(((.((((....-...)))).))).))....))).)))....))))..........((((((........)))))).........------- ( -27.40, z-score =  -0.83, R)
>droEre2.scaffold_4784 2377787 113 + 25762168
GUUUCAUUGUUUCCCAGUCAGAGGAGCCAUCAGGUUUUGGCGCCUGGAAAACGCGUGAGUACAGGACAUACACACAUGCACUGAGAAGAACCAGUACUACGAAGCCAUUUGCC
(((((...((((.((((.(...((((((....))))))...).)))).))))(((((.((...........)).)))))((((........)))).....)))))........ ( -27.00, z-score =  -0.02, R)
>droSim1.chr3L 1925087 113 + 22553184
GUUUCAUUGUUUUCCAGUCGGAGGGGCCAUCAGUUUUUGGCGCCUGGAAAACGCGUGCAUGGCGGACAUACACACAUGCACUGAGAGAAAUUAGUGCUAUCCAGCCAUAUGCU
........((((((((......((.((((........)))).))))))))))((((..((((((((...........(((((((......)))))))..))).))))))))). ( -38.92, z-score =  -2.09, R)
>consensus
GUUUCAUUGUUUUCCAGUCGGAGGGGCCAUCAGUUUUUGGCGCCUGGAAAACGCGUGCAUGCAGGACAUACACACAUGCACUGAGAGAAACCAGUGCUACGAAGCC_______
........((((((((......((.((((........)))).))))))))))(.(((.(((.....))).))).)..((((((........))))))................ (-26.26 = -27.14 +   0.88)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,362,849 – 2,362,955
Length 106
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 83.68
Shannon entropy 0.28594
G+C content 0.50132
Mean single sequence MFE -35.72
Consensus MFE -34.08
Energy contribution -34.32
Covariance contribution 0.24
Combinations/Pair 1.13
Mean z-score -2.72
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.98
SVM RNA-class probability 0.996760
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2362849 106 - 24543557
-------GGCUGCAUAGCACUGUUUUCUCUCAGUGCCUGUGUGUAUGUCCUGCAUGCACGCGUUUUCCAGGCGCCAAAAACUGAUGGCCCCUCCGACUGGAAAACAAUGAAAC
-------.........((((((........))))))..(((((((((.....)))))))))((((((((((.((((........)))).))......))))))))........ ( -38.10, z-score =  -3.53, R)
>droSec1.super_2 2387632 98 - 7591821
---------------AGCACUGGUUUCUCUCAGUGCAUGUGUGUAUGUCCGCCAUGCACGCGUUUUCCAGGCGCCAAAAACUGAUGGCCCCUCCGACUGGAAAACAAUGAAAC
---------------.(((((((......)))))))..(((((((((.....)))))))))((((((((((.((((........)))).))......))))))))........ ( -38.30, z-score =  -4.32, R)
>droYak2.chr3L 14623208 105 + 24197627
-------GUUUUAGUAGCACUGGUUCUUCUCAGUGCAUGUGUGUAUGUCCUGUAUGCACGCGUUUUCCAGGCGCCAAAA-CUGAUGGCUCCUCUGACUGCGAAACAAUGAAAC
-------(((((.((((((((((......)))))))..(((((((((.....)))))))))(((....(((.((((...-....)))).)))..)))))))))))........ ( -33.90, z-score =  -2.58, R)
>droEre2.scaffold_4784 2377787 113 - 25762168
GGCAAAUGGCUUCGUAGUACUGGUUCUUCUCAGUGCAUGUGUGUAUGUCCUGUACUCACGCGUUUUCCAGGCGCCAAAACCUGAUGGCUCCUCUGACUGGGAAACAAUGAAAC
.((.............(((((((......)))))))..(((.((((.....)))).)))))(((((((((..((((........))))((....)))))))))))........ ( -33.20, z-score =  -1.34, R)
>droSim1.chr3L 1925087 113 - 22553184
AGCAUAUGGCUGGAUAGCACUAAUUUCUCUCAGUGCAUGUGUGUAUGUCCGCCAUGCACGCGUUUUCCAGGCGCCAAAAACUGAUGGCCCCUCCGACUGGAAAACAAUGAAAC
(((.....))).....(((((..........)))))..(((((((((.....)))))))))((((((((((.((((........)))).))......))))))))........ ( -35.10, z-score =  -1.86, R)
>consensus
_______GGCUGCAUAGCACUGGUUUCUCUCAGUGCAUGUGUGUAUGUCCUGCAUGCACGCGUUUUCCAGGCGCCAAAAACUGAUGGCCCCUCCGACUGGAAAACAAUGAAAC
................(((((((......)))))))..(((((((((.....)))))))))((((((((((.((((........)))).))......))))))))........ (-34.08 = -34.32 +   0.24)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,362,886 – 2,362,986
Length 100
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 71.59
Shannon entropy 0.49336
G+C content 0.44842
Mean single sequence MFE -29.98
Consensus MFE -20.12
Energy contribution -21.28
Covariance contribution 1.16
Combinations/Pair 1.19
Mean z-score -1.04
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.75
SVM RNA-class probability 0.805341
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2362886 100 - 24543557
-------UUCAGAGAUAAUACAGCUAAGAAAGG-AAUAU--------GGCUGCAUAGCACUGUUUUCUCUCAGUGCCUGUGUGUAUGUCCUGCAUGCACGCGUUUUCCAGGCGCCA
-------...(((((.((((..((((.(...((-.....--------..)).).))))..)))).)))))..(((((((((((((((.....)))))))))(.....))))))).. ( -30.60, z-score =  -1.11, R)
>droSec1.super_2 2387669 100 - 7591821
GCAAUCAUUCAGAGAUAAUACAGAUAUGAAAUU-AAUGU---------------UAGCACUGGUUUCUCUCAGUGCAUGUGUGUAUGUCCGCCAUGCACGCGUUUUCCAGGCGCCA
...........((((............((((((-(.((.---------------...)).))))))))))).(((((((.(((......))))))))))(((((.....))))).. ( -26.10, z-score =  -0.92, R)
>droYak2.chr3L 14623244 101 + 24197627
GGAAUCAUAUAUGGAUAAUAUAAGUAAAUAUG---------------GUUUUAGUAGCACUGGUUCUUCUCAGUGCAUGUGUGUAUGUCCUGUAUGCACGCGUUUUCCAGGCGCCA
((..((.(((((.....)))))........((---------------(........(((((((......)))))))(((((((((((.....)))))))))))...)))))..)). ( -28.10, z-score =  -1.48, R)
>droEre2.scaffold_4784 2377824 116 - 25762168
GGAGUCAUAUGGGGAUCAUACAGGUAAAAAAGCGAGUGUUGGCAAAUGGCUUCGUAGUACUGGUUCUUCUCAGUGCAUGUGUGUAUGUCCUGUACUCACGCGUUUUCCAGGCGCCA
.((((.(((.(((.((((((((.........(((((.((((.....))))))))).(((((((......))))))).)))))).)).))))))))))..(((((.....))))).. ( -34.10, z-score =  -0.72, R)
>droSim1.chr3L 1925124 106 - 22553184
---------CAGUGAUAAUACAGCUAUGAAAUU-AAUGUUAGCAUAUGGCUGGAUAGCACUAAUUUCUCUCAGUGCAUGUGUGUAUGUCCGCCAUGCACGCGUUUUCCAGGCGCCA
---------.............((((.......-.....))))....(.(((((..(((((..........)))))(((((((((((.....)))))))))))..))))).).... ( -31.00, z-score =  -0.96, R)
>consensus
G_A_UCAUACAGAGAUAAUACAGCUAAGAAAGU_AAUGU________GGCUGCAUAGCACUGGUUUCUCUCAGUGCAUGUGUGUAUGUCCUGCAUGCACGCGUUUUCCAGGCGCCA
...............................................(((......(((((((......)))))))(((((((((((.....))))))))))).........))). (-20.12 = -21.28 +   1.16)

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 22:57:31 2011