Locus 6002

Sequence ID dm3.chr3L
Location 2,991,619 – 2,991,743
Length 124
Max. P 0.994817
window8258 window8259 window8260 window8261

overview

Window 8

Location 2,991,619 – 2,991,712
Length 93
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 93.05
Shannon entropy 0.11939
G+C content 0.36533
Mean single sequence MFE -19.96
Consensus MFE -18.38
Energy contribution -17.82
Covariance contribution -0.56
Combinations/Pair 1.14
Mean z-score -1.33
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.39
SVM RNA-class probability 0.670513
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2991619 93 + 24543557
AAUGGCCCAUAAAAAUAUGAAAACGCAUAUACAAAUUGUGCUGUAUGGACGGGUUUACAGCUGAAGUGUUUCAAAAGCUGCAAACUACCCGUA
......(((((......(....).(((((.......)))))..)))))((((((...(((((.............)))))......)))))). ( -21.72, z-score =  -1.08, R)
>droSim1.chr3L 2523886 91 + 22553184
AAUGGCCCAUAAAAAUAUGAAAACGCAUAUACAAAUU-UG-UGUAUGGACGAGUUUACAGCUGAAGUGUUUCAAAAGCUGCAAACUACCCGUA
.((((..((((....))))......((((((((....-))-))))))....(((((.(((((.............))))).)))))..)))). ( -20.22, z-score =  -1.75, R)
>droSec1.super_2 2995710 91 + 7591821
AAUGGCCCAUAAAAAUAUGAAAACGCAUAUACAAAUU--UCUGUAUGGACGGGUUUACAGCUGAAGUGUUUCAAAAGCUGCAAACUACCCGUA
......((((....(((((......)))))(((....--..)))))))((((((...(((((.............)))))......)))))). ( -19.92, z-score =  -1.26, R)
>droYak2.chr3L 15249506 91 - 24197627
GAUGGCCCAUAAAAAUAUGAAAACGCAUAUACAAAUU--UCUGUAUGAAUGGGUUUACAGCUGAAAUGUUUCAAAGGCUGCAAACUAUCCGUA
((((((((((.....((((......))))((((....--..))))...)))))....((((((((....)))...)))))....))))).... ( -17.00, z-score =  -0.59, R)
>droEre2.scaffold_4784 3009019 91 + 25762168
GAUGGGCCAUAAAAAUAUAAAAACGCAUAUACAAAUU--UCUGUAUGGAUGGGUUUACAGCUGAAGUGUUUCAAAAGCUGAAAACUACCCGUA
.(((((.................((..((((((....--..))))))..))(((((.(((((.............))))).))))).))))). ( -20.92, z-score =  -2.01, R)
>consensus
AAUGGCCCAUAAAAAUAUGAAAACGCAUAUACAAAUU__UCUGUAUGGACGGGUUUACAGCUGAAGUGUUUCAAAAGCUGCAAACUACCCGUA
.((((..................((..((((((........))))))..))(((((.(((((.............))))).)))))..)))). (-18.38 = -17.82 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,991,619 – 2,991,712
Length 93
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 93.05
Shannon entropy 0.11939
G+C content 0.36533
Mean single sequence MFE -21.78
Consensus MFE -18.82
Energy contribution -18.90
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -2.23
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.29
SVM RNA-class probability 0.922367
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2991619 93 - 24543557
UACGGGUAGUUUGCAGCUUUUGAAACACUUCAGCUGUAAACCCGUCCAUACAGCACAAUUUGUAUAUGCGUUUUCAUAUUUUUAUGGGCCAUU
...((((...((((((((...(((....)))))))))))))))(((((((..(((.....)))(((((......)))))...))))))).... ( -23.90, z-score =  -2.29, R)
>droSim1.chr3L 2523886 91 - 22553184
UACGGGUAGUUUGCAGCUUUUGAAACACUUCAGCUGUAAACUCGUCCAUACA-CA-AAUUUGUAUAUGCGUUUUCAUAUUUUUAUGGGCCAUU
....((((((((((((((...(((....))))))))))))))(((..(((((-..-....)))))..)))...(((((....))))))))... ( -23.30, z-score =  -2.83, R)
>droSec1.super_2 2995710 91 - 7591821
UACGGGUAGUUUGCAGCUUUUGAAACACUUCAGCUGUAAACCCGUCCAUACAGA--AAUUUGUAUAUGCGUUUUCAUAUUUUUAUGGGCCAUU
...((((...((((((((...(((....)))))))))))))))(((((((..((--(((.((............)).)))))))))))).... ( -23.90, z-score =  -2.51, R)
>droYak2.chr3L 15249506 91 + 24197627
UACGGAUAGUUUGCAGCCUUUGAAACAUUUCAGCUGUAAACCCAUUCAUACAGA--AAUUUGUAUAUGCGUUUUCAUAUUUUUAUGGGCCAUC
...((((.(((((((((...((((....)))))))))))))..))))((((((.--...))))))(((.((..(((((....)))))))))). ( -20.10, z-score =  -1.96, R)
>droEre2.scaffold_4784 3009019 91 - 25762168
UACGGGUAGUUUUCAGCUUUUGAAACACUUCAGCUGUAAACCCAUCCAUACAGA--AAUUUGUAUAUGCGUUUUUAUAUUUUUAUGGCCCAUC
...((((.((((.(((((...(((....)))))))).))))......((((((.--...)))))).....................))))... ( -17.70, z-score =  -1.57, R)
>consensus
UACGGGUAGUUUGCAGCUUUUGAAACACUUCAGCUGUAAACCCGUCCAUACAGA__AAUUUGUAUAUGCGUUUUCAUAUUUUUAUGGGCCAUU
.(((.((((((((((((...((((....))))))))))))).......(((((......)))))))).)))..(((((....)))))...... (-18.82 = -18.90 +   0.08)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,991,650 – 2,991,743
Length 93
Sequences 7
Columns 101
Reading direction forward
Mean pairwise identity 64.83
Shannon entropy 0.66354
G+C content 0.38986
Mean single sequence MFE -21.45
Consensus MFE -10.04
Energy contribution -12.07
Covariance contribution 2.03
Combinations/Pair 1.42
Mean z-score -1.62
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.97
SVM RNA-class probability 0.977301
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2991650 93 + 24543557
--CAAAUUGUGCUGUAUGGACGGGUUUACAGCU--GAAGUGUUUCAAAAGCUGCAAACUACCCGUAUAUAAGCUCAAUGGAUUCUGCCG----AUUGGCUU
--...((((.(((.((((.((((((...(((((--.............)))))......)))))).))))))).)))).......(((.----...))).. ( -26.42, z-score =  -1.73, R)
>droSim1.chr3L 2523917 91 + 22553184
--CAAAUUU--GUGUAUGGACGAGUUUACAGCU--GAAGUGUUUCAAAAGCUGCAAACUACCCGUAUAUAAGCUCAUUGGAUUCUGCCG----AUUGGCUU
--.....((--((((((((...(((((.(((((--.............))))).)))))..))))))))))(((.(((((......)))----)).))).. ( -29.22, z-score =  -3.53, R)
>droSec1.super_2 2995741 91 + 7591821
--CAAAUUU--CUGUAUGGACGGGUUUACAGCU--GAAGUGUUUCAAAAGCUGCAAACUACCCGUAUAUAAGCUCAUUGGAUUCUGCCG----AUUGGCUU
--.......--.(((((((...(((((.(((((--.............))))).)))))..))))))).(((((.(((((......)))----)).))))) ( -26.92, z-score =  -2.51, R)
>droYak2.chr3L 15249537 91 - 24197627
--CAAAUUU--CUGUAUGAAUGGGUUUACAGCU--GAAAUGUUUCAAAGGCUGCAAACUAUCCGUAUAUAAGCUCGUUGGAUGCUGCCG----AUUGGCUU
--.......--.((((((....(((((.(((((--(((....)))...))))).)))))...)))))).(((((.(((((......)))----)).))))) ( -23.20, z-score =  -1.26, R)
>droEre2.scaffold_4784 3009050 91 + 25762168
--CAAAUUU--CUGUAUGGAUGGGUUUACAGCU--GAAGUGUUUCAAAAGCUGAAAACUACCCGUAUAUAAGCUCAUUCGAUUCUGCCG----AUUGGCUU
--.......--.(((((((...(((((.(((((--.............))))).)))))..))))))).((((.((.(((.......))----).)))))) ( -24.32, z-score =  -2.27, R)
>droVir3.scaffold_13049 15140220 99 + 25233164
UCAAUUUGUGUGUGCAAUAAAUAAAACAUGGCCCAAAAAUAUUCGAAUAAACACAACCGAAU--UGUACAAUCUUUACGGUCUACACCAGAACAUUGGCUU
.(((((((..((((.....................................))))..)))))--))..((((.(((..(((....))).))).)))).... ( -10.69, z-score =   1.39, R)
>droMoj3.scaffold_6680 3024406 79 - 24764193
----------------UCAAUUUGUGCAUUAUC---GAAUAUUCGAAAAAACACUAA-AUAU--UUUACAAUCUUUAUGGCCACCCACACAACUCUGGCUU
----------------...(((((((..((.((---((....)))).))..))).))-))..--..............(((((............))))). (  -9.40, z-score =  -1.40, R)
>consensus
__CAAAUUU__CUGUAUGGACGGGUUUACAGCU__GAAGUGUUUCAAAAGCUGCAAACUACCCGUAUAUAAGCUCAUUGGAUUCUGCCG____AUUGGCUU
............(((((((...(((((.(((((..(((....)))...))))).)))))..))))))).................((((......)))).. (-10.04 = -12.07 +   2.03)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,991,650 – 2,991,743
Length 93
Sequences 7
Columns 101
Reading direction reverse
Mean pairwise identity 64.83
Shannon entropy 0.66354
G+C content 0.38986
Mean single sequence MFE -20.14
Consensus MFE -12.07
Energy contribution -12.00
Covariance contribution -0.07
Combinations/Pair 1.74
Mean z-score -1.54
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.74
SVM RNA-class probability 0.994817
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2991650 93 - 24543557
AAGCCAAU----CGGCAGAAUCCAUUGAGCUUAUAUACGGGUAGUUUGCAGCUUUUGAAACACUUC--AGCUGUAAACCCGUCCAUACAGCACAAUUUG--
..(((...----.))).......((((.((((((..((((((...((((((((...(((....)))--))))))))))))))..))).))).))))...-- ( -28.40, z-score =  -3.88, R)
>droSim1.chr3L 2523917 91 - 22553184
AAGCCAAU----CGGCAGAAUCCAAUGAGCUUAUAUACGGGUAGUUUGCAGCUUUUGAAACACUUC--AGCUGUAAACUCGUCCAUACAC--AAAUUUG--
..(((...----.)))......................(((((((((((((((...(((....)))--))))))))))).))))......--.......-- ( -21.00, z-score =  -1.79, R)
>droSec1.super_2 2995741 91 - 7591821
AAGCCAAU----CGGCAGAAUCCAAUGAGCUUAUAUACGGGUAGUUUGCAGCUUUUGAAACACUUC--AGCUGUAAACCCGUCCAUACAG--AAAUUUG--
..(((...----.)))......(((....(((((..((((((...((((((((...(((....)))--))))))))))))))..))).))--....)))-- ( -23.50, z-score =  -2.46, R)
>droYak2.chr3L 15249537 91 + 24197627
AAGCCAAU----CGGCAGCAUCCAACGAGCUUAUAUACGGAUAGUUUGCAGCCUUUGAAACAUUUC--AGCUGUAAACCCAUUCAUACAG--AAAUUUG--
..(((...----.)))(((.((....))))).......((((.(((((((((...((((....)))--))))))))))..))))......--.......-- ( -20.80, z-score =  -2.49, R)
>droEre2.scaffold_4784 3009050 91 - 25762168
AAGCCAAU----CGGCAGAAUCGAAUGAGCUUAUAUACGGGUAGUUUUCAGCUUUUGAAACACUUC--AGCUGUAAACCCAUCCAUACAG--AAAUUUG--
((((((.(----(((.....)))).)).))))......((((.((((.(((((...(((....)))--))))).))))..))))......--.......-- ( -20.10, z-score =  -1.86, R)
>droVir3.scaffold_13049 15140220 99 - 25233164
AAGCCAAUGUUCUGGUGUAGACCGUAAAGAUUGUACA--AUUCGGUUGUGUUUAUUCGAAUAUUUUUGGGCCAUGUUUUAUUUAUUGCACACACAAAUUGA
....((((......((((((...((((((...(..((--(((((..((....))..))))).....))..)....))))))...))))))......)))). ( -14.30, z-score =   1.73, R)
>droMoj3.scaffold_6680 3024406 79 + 24764193
AAGCCAGAGUUGUGUGGGUGGCCAUAAAGAUUGUAAA--AUAU-UUAGUGUUUUUUCGAAUAUUC---GAUAAUGCACAAAUUGA----------------
.....(.((((.(((((....)))))..)))).)...--....-...((((.((.((((....))---)).)).)))).......---------------- ( -12.90, z-score =  -0.01, R)
>consensus
AAGCCAAU____CGGCAGAAUCCAAUGAGCUUAUAUACGGGUAGUUUGCAGCUUUUGAAACACUUC__AGCUGUAAACCCAUCCAUACAG__AAAUUUG__
..(((........)))......................(((..((((((((((...(((....)))..))))))))))...)))................. (-12.07 = -12.00 +  -0.07)

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 22:59:24 2011