Locus 10723

Sequence ID dm3.chr3R
Location 16,026,877 – 16,026,976
Length 99
Max. P 0.834424
window14736 window14737 window14738

overview

Window 6

Location 16,026,877 – 16,026,972
Length 95
Sequences 11
Columns 111
Reading direction forward
Mean pairwise identity 80.38
Shannon entropy 0.41822
G+C content 0.44063
Mean single sequence MFE -29.85
Consensus MFE -15.67
Energy contribution -15.61
Covariance contribution -0.06
Combinations/Pair 1.12
Mean z-score -1.86
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.63
SVM RNA-class probability 0.768510
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 16026877 95 + 27905053
----------------CUGCGGGAGUGUGUUUGUGUGGCAAGUAUUUCUGUUGCAAUUUCCGGCUACUAUAACCGGAAGUGAAGCUGCUCAAAAAUUCAUGCAACCGUAAA
----------------.(((((..(((((((((.(..((..(((.......))).((((((((.........))))))))...))..).))))....)))))..))))).. ( -30.90, z-score =  -2.77, R)
>droSim1.chr3R 22061677 95 - 27517382
----------------CUGCGGGAGUGUGUUUGUGUGGCAAGUAUUUCUGUUGCAAUUUCCGGCUACUAUAACCGGAAGUGAAGCUGCUCAAAAAUUCAUGCAACCGUAAA
----------------.(((((..(((((((((.(..((..(((.......))).((((((((.........))))))))...))..).))))....)))))..))))).. ( -30.90, z-score =  -2.77, R)
>droSec1.super_27 94038 95 - 799419
----------------CUGCGGGAGUGUGUUUGUGUGGCAAGUAUUUCUGUUGCAAUUUCCGGCUACUAUAAGCGGAAGUGAAGCUGCUCAAAAAUUCAUGCAACCGUAAA
----------------.(((((..(((((((((.(..((..(((.......))).(((((((.((......)))))))))...))..).))))....)))))..))))).. ( -29.70, z-score =  -2.14, R)
>droYak2.chr3R_random 294863 95 + 3277457
----------------CUGCGGGAGUGUGUUUGUGUGGCAAGUAUUUCUGUUGCAAUUUCCGGCUACUAUAACCGGAAGUGAAGCUGCUCAAAAAUUCAUGCAACCGUAAA
----------------.(((((..(((((((((.(..((..(((.......))).((((((((.........))))))))...))..).))))....)))))..))))).. ( -30.90, z-score =  -2.77, R)
>droEre2.scaffold_4770 12100125 95 - 17746568
----------------CAGCGGGAGUGUGUUUGUGUGGCAAGUAUUUCUGUUGCAAUUUCCGGCUACUAUAACCGGAAGUGAAGCUGCUCAAAAAUUCAUGCAACCGUAAA
----------------..((((..(((((((((.(..((..(((.......))).((((((((.........))))))))...))..).))))....)))))..))))... ( -30.00, z-score =  -2.33, R)
>droAna3.scaffold_13340 2577622 107 + 23697760
-AUGUUUGCGAGCGU-AUAUGGUAGUGUAUG--UGCGGCAAGUAUUUCUGUUGCAAUUUCCGGCGACUGUAACCGGAAGUGAAGCUGCUCAAAAAUUCAUGCAACCGUAAA
-(((.(((((.((((-((((....)))))))--)(((((..(((.......))).((((((((.........))))))))...)))))...........))))).)))... ( -30.70, z-score =  -0.98, R)
>dp4.chr2 3131831 100 - 30794189
----------UGUGU-GUGUUGCUGUGUGUGGGUGUGGCAAGUAUUUCUGUUGCAAUUUCCGGCUACUAUAACCGGAAGUGAAGCUGCUCAAAAAUUCAUGCAACCGUAAA
----------.....-(.(((((((.((.((((((..(((........)))..).((((((((.........))))))))......)))))...)).)).))))))..... ( -27.20, z-score =  -0.94, R)
>droPer1.super_6 3155124 100 - 6141320
----------UGUGU-GUGUUGCUGUGUGUGGGUGUGGCAAGUAUUUCUGUUGCAAUUUCCGGCUACUAUAACCGGAAGUGAAGCUGCUCAAAAAUUCAUGCAACCGUAAA
----------.....-(.(((((((.((.((((((..(((........)))..).((((((((.........))))))))......)))))...)).)).))))))..... ( -27.20, z-score =  -0.94, R)
>droVir3.scaffold_13047 2866779 104 + 19223366
-------GCAUUCGCACAGUUUAAGUGUGUAUGUGCUCAUAGAGUUUCUGUUGCAAUUUCCUGUUGCUAUACCAGGAAGUGAAGCCACUCAAAAAUGUAUGCAACAUUAAA
-------((((.(((((.......)))))...))))............(((((((..((((((.........))))))(((....)))...........)))))))..... ( -26.40, z-score =  -1.37, R)
>droMoj3.scaffold_6540 14211867 107 - 34148556
UUCGCUAGUGUGAGU-GUGCGCUAGUGUGUGCGUGUGU---GCACUUCAGUUGCAAUUUCCGGAUGCUAUAACCGGAAGUGAAGCUGCUCAAAAAUUCGUGCAGCCGUAAA
..(((((((((....-..))))))))).(((((....)---)))).....((((.((((((((.........))))))))...(((((.(........).))))).)))). ( -36.90, z-score =  -2.13, R)
>droGri2.scaffold_15074 480603 103 - 7742996
--------CGAGCUCAGUCUGAAUGUGAUUGUGUGCUCGGAGUAUUUCUGUUGCAAUUUCCGGCUACUACAACCGGAUGUGAAGCUGCUCAAAAAUUCAUGCAACCGUAAA
--------(((((.(((((.......)))))...)))))..........(((((....(((((.........))))).(((((..(......)..))))))))))...... ( -27.60, z-score =  -1.26, R)
>consensus
________________CUGCGGGAGUGUGUGUGUGUGGCAAGUAUUUCUGUUGCAAUUUCCGGCUACUAUAACCGGAAGUGAAGCUGCUCAAAAAUUCAUGCAACCGUAAA
.................................................((((((((((((((.........))))))))((......)).........))))))...... (-15.67 = -15.61 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,026,877 – 16,026,972
Length 95
Sequences 11
Columns 111
Reading direction reverse
Mean pairwise identity 80.38
Shannon entropy 0.41822
G+C content 0.44063
Mean single sequence MFE -21.65
Consensus MFE -16.44
Energy contribution -16.82
Covariance contribution 0.38
Combinations/Pair 1.06
Mean z-score -1.20
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.85
SVM RNA-class probability 0.834424
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 16026877 95 - 27905053
UUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGGUUAUAGUAGCCGGAAAUUGCAACAGAAAUACUUGCCACACAAACACACUCCCGCAG----------------
......((.(((.(.(((((((.((((......(((((((((...))))))))).))))..))))))).).))).))..................---------------- ( -21.00, z-score =  -1.43, R)
>droSim1.chr3R 22061677 95 + 27517382
UUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGGUUAUAGUAGCCGGAAAUUGCAACAGAAAUACUUGCCACACAAACACACUCCCGCAG----------------
......((.(((.(.(((((((.((((......(((((((((...))))))))).))))..))))))).).))).))..................---------------- ( -21.00, z-score =  -1.43, R)
>droSec1.super_27 94038 95 + 799419
UUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGCUUAUAGUAGCCGGAAAUUGCAACAGAAAUACUUGCCACACAAACACACUCCCGCAG----------------
......((.(((.(.(((((((.((((......(((((((......)).))))).))))..))))))).).))).))..................---------------- ( -16.60, z-score =  -0.22, R)
>droYak2.chr3R_random 294863 95 - 3277457
UUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGGUUAUAGUAGCCGGAAAUUGCAACAGAAAUACUUGCCACACAAACACACUCCCGCAG----------------
......((.(((.(.(((((((.((((......(((((((((...))))))))).))))..))))))).).))).))..................---------------- ( -21.00, z-score =  -1.43, R)
>droEre2.scaffold_4770 12100125 95 + 17746568
UUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGGUUAUAGUAGCCGGAAAUUGCAACAGAAAUACUUGCCACACAAACACACUCCCGCUG----------------
......((.(((.(.(((((((.((((......(((((((((...))))))))).))))..))))))).).))).))..................---------------- ( -21.00, z-score =  -1.25, R)
>droAna3.scaffold_13340 2577622 107 - 23697760
UUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGGUUACAGUCGCCGGAAAUUGCAACAGAAAUACUUGCCGCA--CAUACACUACCAUAU-ACGCUCGCAAACAU-
......((((((........((((....)))).(((((((.......)))))))..))))))........((((.((.--.(((........)))-..))..))))....- ( -20.20, z-score =  -0.17, R)
>dp4.chr2 3131831 100 + 30794189
UUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGGUUAUAGUAGCCGGAAAUUGCAACAGAAAUACUUGCCACACCCACACACAGCAACAC-ACACA----------
.....(((.(((.(.(((((((.((((......(((((((((...))))))))).))))..))))))).).)))...)))...............-.....---------- ( -21.40, z-score =  -1.79, R)
>droPer1.super_6 3155124 100 + 6141320
UUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGGUUAUAGUAGCCGGAAAUUGCAACAGAAAUACUUGCCACACCCACACACAGCAACAC-ACACA----------
.....(((.(((.(.(((((((.((((......(((((((((...))))))))).))))..))))))).).)))...)))...............-.....---------- ( -21.40, z-score =  -1.79, R)
>droVir3.scaffold_13047 2866779 104 - 19223366
UUUAAUGUUGCAUACAUUUUUGAGUGGCUUCACUUCCUGGUAUAGCAACAGGAAAUUGCAACAGAAACUCUAUGAGCACAUACACACUUAAACUGUGCGAAUGC-------
.....(((((((...........(((....)))((((((.........))))))..))))))).......(((..(((((.............)))))..))).------- ( -23.12, z-score =  -0.92, R)
>droMoj3.scaffold_6540 14211867 107 + 34148556
UUUACGGCUGCACGAAUUUUUGAGCAGCUUCACUUCCGGUUAUAGCAUCCGGAAAUUGCAACUGAAGUGC---ACACACGCACACACUAGCGCAC-ACUCACACUAGCGAA
.....((((((.(((....))).))))))....((((((.........)))))).((((.......((((---......))))....(((.(...-.....).))))))). ( -27.20, z-score =  -1.81, R)
>droGri2.scaffold_15074 480603 103 + 7742996
UUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACAUCCGGUUGUAGUAGCCGGAAAUUGCAACAGAAAUACUCCGAGCACACAAUCACAUUCAGACUGAGCUCG--------
......((((((........((((....))))..((((((((...))))))))...))))))..........(((((...((.((.......)).)).)))))-------- ( -24.20, z-score =  -1.01, R)
>consensus
UUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGGUUAUAGUAGCCGGAAAUUGCAACAGAAAUACUUGCCACACAAACACACUCCCGCAG________________
......((((((........((((....)))).((((((((.....))))))))..))))))................................................. (-16.44 = -16.82 +   0.38)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,026,877 – 16,026,976
Length 99
Sequences 11
Columns 113
Reading direction reverse
Mean pairwise identity 81.30
Shannon entropy 0.40915
G+C content 0.44070
Mean single sequence MFE -21.39
Consensus MFE -16.44
Energy contribution -16.82
Covariance contribution 0.38
Combinations/Pair 1.06
Mean z-score -1.06
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.57
SVM RNA-class probability 0.746702
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 16026877 99 - 27905053
UCCUUUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGGUUAUAGUAGCCGGAAAUUGCAACAGAAAUACUUGCCACACAAACACACUCCCGCAG--------------
..........((.(((.(.(((((((.((((......(((((((((...))))))))).))))..))))))).).))).))..................-------------- ( -21.00, z-score =  -1.29, R)
>droSim1.chr3R 22061677 99 + 27517382
UCCUUUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGGUUAUAGUAGCCGGAAAUUGCAACAGAAAUACUUGCCACACAAACACACUCCCGCAG--------------
..........((.(((.(.(((((((.((((......(((((((((...))))))))).))))..))))))).).))).))..................-------------- ( -21.00, z-score =  -1.29, R)
>droSec1.super_27 94038 99 + 799419
UCCUUUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGCUUAUAGUAGCCGGAAAUUGCAACAGAAAUACUUGCCACACAAACACACUCCCGCAG--------------
..........((.(((.(.(((((((.((((......(((((((......)).))))).))))..))))))).).))).))..................-------------- ( -16.60, z-score =  -0.17, R)
>droYak2.chr3R_random 294863 99 - 3277457
UCCUUUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGGUUAUAGUAGCCGGAAAUUGCAACAGAAAUACUUGCCACACAAACACACUCCCGCAG--------------
..........((.(((.(.(((((((.((((......(((((((((...))))))))).))))..))))))).).))).))..................-------------- ( -21.00, z-score =  -1.29, R)
>droEre2.scaffold_4770 12100125 99 + 17746568
UCCUUUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGGUUAUAGUAGCCGGAAAUUGCAACAGAAAUACUUGCCACACAAACACACUCCCGCUG--------------
..........((.(((.(.(((((((.((((......(((((((((...))))))))).))))..))))))).).))).))..................-------------- ( -21.00, z-score =  -1.15, R)
>droAna3.scaffold_13340 2577622 111 - 23697760
UCCUUUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGGUUACAGUCGCCGGAAAUUGCAACAGAAAUACUUGCCGCAC--AUACACUACCAUAUACGCUCGCAAACAU
..........((((((........((((....)))).(((((((.......)))))))..))))))........((((.((..--(((........)))..))..)))).... ( -20.20, z-score =  -0.13, R)
>dp4.chr2 3131832 103 + 30794189
UCCUUUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGGUUAUAGUAGCCGGAAAUUGCAACAGAAAUACUUGCCACACCCACACACAGCAACACACAC----------
.........(((.(((.(.(((((((.((((......(((((((((...))))))))).))))..))))))).).)))...)))...................---------- ( -21.40, z-score =  -1.68, R)
>droPer1.super_6 3155125 103 + 6141320
UCCUUUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGGUUAUAGUAGCCGGAAAUUGCAACAGAAAUACUUGCCACACCCACACACAGCAACACACAC----------
.........(((.(((.(.(((((((.((((......(((((((((...))))))))).))))..))))))).).)))...)))...................---------- ( -21.40, z-score =  -1.68, R)
>droVir3.scaffold_13047 2866783 104 - 19223366
UUCUUUUAAUGUUGCAUACAUUUUUGAGUGGCUUCACUUCCUGGUAUAGCAACAGGAAAUUGCAACAGAAACUCUAUGAGCACAUACACACUUAAACUGUGCGA---------
.........(((((((...........(((....)))((((((.........))))))..)))))))............(((((.............)))))..--------- ( -22.82, z-score =  -1.16, R)
>droMoj3.scaffold_6540 14211868 110 + 34148556
UUCUUUUACGGCUGCACGAAUUUUUGAGCAGCUUCACUUCCGGUUAUAGCAUCCGGAAAUUGCAACUGAAGUGCA---CACACGCACACACUAGCGCACACUCACACUAGCGA
(((......((((((.(((....))).))))))....((((((.........)))))).........)))((((.---.....)))).(.((((.(........).)))).). ( -27.10, z-score =  -1.74, R)
>droGri2.scaffold_15074 480604 106 + 7742996
UUCUUUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACAUCCGGUUGUAGUAGCCGGAAAUUGCAACAGAAAUACUCCGAGCACACAAUCACAUUCAGACUGAGCUC-------
..........((((((........((((....))))..((((((((...))))))))...))))))...........((((...((.((.......)).)).))))------- ( -21.80, z-score =  -0.09, R)
>consensus
UCCUUUUACGGUUGCAUGAAUUUUUGAGCAGCUUCACUUCCGGUUAUAGUAGCCGGAAAUUGCAACAGAAAUACUUGCCACACAAACACACUCCCGCAG______________
..........((((((........((((....)))).((((((((.....))))))))..))))))............................................... (-16.44 = -16.82 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:29:16 2011