Locus 317

Sequence ID dm3.chr2L
Location 2,266,208 – 2,266,338
Length 130
Max. P 0.984834
window431 window432 window433

overview

Window 1

Location 2,266,208 – 2,266,306
Length 98
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 77.68
Shannon entropy 0.39411
G+C content 0.44105
Mean single sequence MFE -26.73
Consensus MFE -18.81
Energy contribution -19.67
Covariance contribution 0.86
Combinations/Pair 1.07
Mean z-score -2.26
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.18
SVM RNA-class probability 0.984834
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2266208 98 + 23011544
GCAAAUAUCCAUAGACACACAGACAGAUAC------------GUAUACGAUACAU--AUACGUGUUACUGGCAUCACGUCAAAGUUGGUUGGCGUAAUGCCACAGAAAUUUC
.........................(((((------------(((((.......)--)))))))))..((((((.(((((((......))))))).)))))).......... ( -25.80, z-score =  -2.68, R)
>droSim1.chr2L 2224939 87 + 22036055
GCAAAUAUCCAUAGACACACAGACAGAUAC------------GUAUACG-------------UGUUGCUGGCAUCACGUCAAAGUUGGUUGGCGUGAUGCCACAGAAAUUUC
....................((...(((((------------(....))-------------)))).))(((((((((((((......)))))))))))))........... ( -28.60, z-score =  -3.18, R)
>droSec1.super_5 441109 87 + 5866729
GCAAAUAUCCAUAGACACACAGACAGAUAC------------GUAUACG-------------UGUUGCUGGCAUCACGUUAAAGUUGGUUGGCGUGAUGCCACAGAAAUUUC
....................((...(((((------------(....))-------------)))).))(((((((((((((......)))))))))))))........... ( -26.50, z-score =  -2.65, R)
>droEre2.scaffold_4929 2303370 94 + 26641161
GCAAAUAUCCAUAGGCACACAGACAGAUAC------------GUAUACG-UA-----AUACGUGUUACUGGCAUCACGUCAAAGUUGGUUGGCGUGAUGCCACAGAAAUUCC
.........................(((((------------((((...-..-----)))))))))..((((((((((((((......)))))))))))))).......... ( -31.40, z-score =  -3.65, R)
>droYak2.chr2L 2247316 112 + 22324452
GCAAAUAUCCAUAGACACACACACACACACCAAUAUGUACAGGUAUACGUAUACGUAAUACGUGUUACUGGCAUCACGUCAAAGUUGGCUGGCGUGAUGCCACAGAAAUUCC
.............(((((........(((......)))....(((((((....))).)))))))))..(((((((((((((........))))))))))))).......... ( -32.10, z-score =  -2.45, R)
>droAna3.scaffold_12916 9981664 96 - 16180835
ACAAAUACCCGUAGACAUACACACCCACUCAUG-------GCGCACACA---------CAUGUAGGUCUGGCAUUACAUCAAAGUUGGCUGGCAUCAUGCCACAGAAAUUUC
..........(((....)))....((...((((-------.........---------))))..))((((((...((......))..))((((.....))))))))...... ( -16.00, z-score =   1.07, R)
>consensus
GCAAAUAUCCAUAGACACACAGACAGAUAC____________GUAUACG_________UACGUGUUACUGGCAUCACGUCAAAGUUGGUUGGCGUGAUGCCACAGAAAUUUC
....................................................................((((((((((((((......)))))))))))))).......... (-18.81 = -19.67 +   0.86)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,266,208 – 2,266,306
Length 98
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 77.68
Shannon entropy 0.39411
G+C content 0.44105
Mean single sequence MFE -28.11
Consensus MFE -20.02
Energy contribution -19.63
Covariance contribution -0.38
Combinations/Pair 1.38
Mean z-score -1.58
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.07
SVM RNA-class probability 0.886129
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2266208 98 - 23011544
GAAAUUUCUGUGGCAUUACGCCAACCAACUUUGACGUGAUGCCAGUAACACGUAU--AUGUAUCGUAUAC------------GUAUCUGUCUGUGUGUCUAUGGAUAUUUGC
..........((((((((((.(((......))).))))))))))((((.((((((--(((...)))))))------------))...((((((((....)))))))).)))) ( -29.00, z-score =  -2.47, R)
>droSim1.chr2L 2224939 87 - 22036055
GAAAUUUCUGUGGCAUCACGCCAACCAACUUUGACGUGAUGCCAGCAACA-------------CGUAUAC------------GUAUCUGUCUGUGUGUCUAUGGAUAUUUGC
..........((((((((((.(((......))).))))))))))((((.(-------------((....)------------))...((((((((....)))))))).)))) ( -26.50, z-score =  -2.32, R)
>droSec1.super_5 441109 87 - 5866729
GAAAUUUCUGUGGCAUCACGCCAACCAACUUUAACGUGAUGCCAGCAACA-------------CGUAUAC------------GUAUCUGUCUGUGUGUCUAUGGAUAUUUGC
..........((((((((((..............))))))))))((((.(-------------((....)------------))...((((((((....)))))))).)))) ( -23.34, z-score =  -1.65, R)
>droEre2.scaffold_4929 2303370 94 - 26641161
GGAAUUUCUGUGGCAUCACGCCAACCAACUUUGACGUGAUGCCAGUAACACGUAU-----UA-CGUAUAC------------GUAUCUGUCUGUGUGCCUAUGGAUAUUUGC
.((((.((((((((((((((.(((......))).)))))))))((..(((((.((-----((-((....)------------)))...)).)))))..))))))).)))).. ( -29.20, z-score =  -2.36, R)
>droYak2.chr2L 2247316 112 - 22324452
GGAAUUUCUGUGGCAUCACGCCAGCCAACUUUGACGUGAUGCCAGUAACACGUAUUACGUAUACGUAUACCUGUACAUAUUGGUGUGUGUGUGUGUGUCUAUGGAUAUUUGC
.((((.((..((((((((((.(((......))).))))))))))......((((.((((((((((((((((..........))))))))))))))))..)))))).)))).. ( -36.20, z-score =  -1.42, R)
>droAna3.scaffold_12916 9981664 96 + 16180835
GAAAUUUCUGUGGCAUGAUGCCAGCCAACUUUGAUGUAAUGCCAGACCUACAUG---------UGUGUGCGC-------CAUGAGUGGGUGUGUAUGUCUACGGGUAUUUGU
.((((.(((((((((((......((..((......))...))((.((((((.((---------((.(....)-------)))).)))))).)))))).))))))).)))).. ( -24.40, z-score =   0.75, R)
>consensus
GAAAUUUCUGUGGCAUCACGCCAACCAACUUUGACGUGAUGCCAGUAACACGUA_________CGUAUAC____________GUAUCUGUCUGUGUGUCUAUGGAUAUUUGC
..........((((((((((.(((......))).))))))))))......................................(((..((((((((....))))))))..))) (-20.02 = -19.63 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,266,233 – 2,266,338
Length 105
Sequences 8
Columns 116
Reading direction forward
Mean pairwise identity 66.85
Shannon entropy 0.62446
G+C content 0.46344
Mean single sequence MFE -30.23
Consensus MFE -11.37
Energy contribution -11.69
Covariance contribution 0.31
Combinations/Pair 1.33
Mean z-score -2.29
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.01
SVM RNA-class probability 0.978938
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2266233 105 + 23011544
GAUACGUAUACG-AUACAUA-UACGUGUUACUGGCAUCACGUCAAAGUUG-GUUGGCGUAAUGCCACAGAAAUUUCAGCAGCCUGCAACAA--------AAGCGAGUCAACCAAAA
((((((((((..-.....))-))))))))..((((((.(((((((.....-.))))))).))))))..............((.(((.....--------..))).))......... ( -27.20, z-score =  -1.73, R)
>droSim1.chr2L 2224964 94 + 22036055
-----------G-AUACGUA-UACGUGUUGCUGGCAUCACGUCAAAGUUG-GUUGGCGUGAUGCCACAGAAAUUUCAGCUGCCUGCAACAA--------AAGCGAGUCAGCCAAAA
-----------(-((.(((.-....((((((((((((((((((((.....-.))))))))))))))(((.........)))...)))))).--------..))).)))........ ( -36.10, z-score =  -3.51, R)
>droSec1.super_5 441134 94 + 5866729
-----------G-AUACGUA-UACGUGUUGCUGGCAUCACGUUAAAGUUG-GUUGGCGUGAUGCCACAGAAAUUUCAGCUGCCUGCAACAA--------AAGCGAGUCAGCCAGAA
-----------(-((.(((.-....((((((((((((((((((((.....-.))))))))))))))(((.........)))...)))))).--------..))).)))........ ( -34.00, z-score =  -2.76, R)
>droEre2.scaffold_4929 2303395 101 + 26641161
------GAUACGUAUACGUAAUACGUGUUACUGGCAUCACGUCAAAGUUG-GUUGGCGUGAUGCCACAGAAAUUCCAGCAGGCUGCAACAA--------AAGCGAGUCAACUGAAA
------(((((((((.....)))))))))..((((((((((((((.....-.)))))))))))))).........(((..((((((.....--------..)).))))..)))... ( -39.00, z-score =  -4.59, R)
>droYak2.chr2L 2247356 104 + 22324452
---AGGUAUACGUAUACGUAAUACGUGUUACUGGCAUCACGUCAAAGUUG-GCUGGCGUGAUGCCACAGAAAUUCCCGCUGGCUGCAGCAA--------AAGCAAGUCAACUGAAA
---.(((((((((((.....))))))).))))((((((((((((......-..)))))))))))).(((........(((.((....))..--------.))).......)))... ( -36.66, z-score =  -2.76, R)
>droAna3.scaffold_12916 9981689 97 - 16180835
---CACUCAUGGCGCACACA-CAUGUAGGUCUGGCAUUACAUCAAAGUUG-GCUGGCAUCAUGCCACAGAAAUUUC------CUGAAACAA--------AAGCAAGUCGACAAAAA
---..((((((.........-)))).))..................((((-((((((.....))).(((.......------)))......--------.....)))))))..... ( -18.60, z-score =   0.51, R)
>droPer1.super_1 4638714 101 - 10282868
--------------CACACA-CACACUCGCUGUGUGGCACGUCAAAGUUGGCCUGGCAUCGUGCCACUGGAAUUUCCGUUGGCCACAUCACCUUCCUUCACACACAACAGCAAAAA
--------------......-.......((((((((((..((((....))))...))...((((((.(((.....))).))).)))................))).)))))..... ( -27.10, z-score =  -1.00, R)
>droWil1.scaffold_180708 2215471 82 + 12563649
------------CACAGGCG-UAAAU-UUUCUGGCGUCAUGUCAAAGUUGUGUUGGCAGCAUGCCACAAAAAUUUA------CUCCAACAA--------G-GAGAAACAAC-----
------------....((.(-(((((-(((.((((((..((((((.......))))))..))))))..))))))))------).)).....--------.-..........----- ( -23.20, z-score =  -2.46, R)
>consensus
___________G_AUACGUA_UACGUGUUACUGGCAUCACGUCAAAGUUG_GUUGGCGUGAUGCCACAGAAAUUUCAGCUGCCUGCAACAA________AAGCGAGUCAACCAAAA
...............................((((((.((((((.........)))))).)))))).................................................. (-11.37 = -11.69 +   0.31)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:10:40 2011