Locus 12068

Sequence ID dm3.chr3R
Location 25,406,082 – 25,406,220
Length 138
Max. P 0.955004
window16591 window16592 window16593 window16594

overview

Window 1

Location 25,406,082 – 25,406,180
Length 98
Sequences 8
Columns 113
Reading direction forward
Mean pairwise identity 70.52
Shannon entropy 0.57149
G+C content 0.56205
Mean single sequence MFE -32.84
Consensus MFE -15.57
Energy contribution -16.39
Covariance contribution 0.81
Combinations/Pair 1.21
Mean z-score -1.85
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.61
SVM RNA-class probability 0.955004
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25406082 98 + 27905053
UAGACGACGGAUCGGGCAUCGGGAACGAAG---------------GGGUAUGCGGAGUUGGCCACGGAGCCAAAGCCACUCAUUCAAUGGCCAAAAACGGGCCAUGGAAACCG
.......(((...(((..(((....)))..---------------........((..(((((......)))))..)).))).(((.((((((.......)))))).))).))) ( -31.40, z-score =  -0.95, R)
>droSim1.chr3R 25078399 98 + 27517382
UAGACGACGGAUCGGGAAUCGGGAACGGAG---------------GGGUAUGCGGAGUUGGCCACGGAGCCAAAGCCACUCAUUCAAUGGCCAAAAACGGGCCAUGGAAACCG
.......(((...(((..(((....)))..---------------........((..(((((......)))))..)).))).(((.((((((.......)))))).))).))) ( -31.20, z-score =  -0.92, R)
>droSec1.super_4 4263723 98 + 6179234
UAGACGACGGAUCGGGAAUCGGGAACGGAG---------------GGGUAUGCGGAGUUGGCCACGGAGCCAAAGCCACUCAUUCAAUGGCCAAAAACGGGCCAUGGAAACCG
.......(((...(((..(((....)))..---------------........((..(((((......)))))..)).))).(((.((((((.......)))))).))).))) ( -31.20, z-score =  -0.92, R)
>droYak2.chr3R 7761038 113 - 28832112
UAGACGACCGAUCGGGAAUCGGGAAUGGGGAAUGGGGAACACAGGGGGGAUUUGGAGUUGGCCACGAAGCCAAAGCCUCUCAUUCAAUGGCCAAAAACGGGCCAUGGAAACUG
.......(((((.....)))))((((......(((....).))((((((.(((((..(((....)))..))))).)))))))))).((((((.......))))))(....).. ( -36.80, z-score =  -1.50, R)
>droEre2.scaffold_4820 7873684 97 - 10470090
UAGACGGCGGAUCGGGAAACGGGAGCGGAG---------------GGGGCUUUGCAGUUGGCCACGAAGCCAAAGCCACUCAUUCAAUGGCCAAAA-CGGGCCAUGGAAACUG
....(.((...((.(....).)).)).).(---------------(((((((((...(((....)))...))))))).))).(((.((((((....-..)))))).))).... ( -34.40, z-score =  -1.69, R)
>droAna3.scaffold_12911 5101465 76 + 5364042
-------------------------------------UGGUAGUUGGGGAAACCGAGUUGGCCACGGAGCCAAAGCGAUUCAUUGAAUGGCCAAAAACAGGCCAUGGAAACUG
-------------------------------------...(((((.((....))(..(((((......)))))..)..........((((((.......))))))...))))) ( -23.30, z-score =  -1.47, R)
>dp4.chr2 2276653 98 + 30794189
GAAGAGUCGGACACAGAGCCAGAGCCAGAG---------------CUGGAGCUGGAGCUGAAGCCGGAGCCAAAGCGAUUCAUUGAAUGGCCAAAAACAGGCCAUCGAAACUG
...(((((((...(((..((((..(((...---------------.)))..))))..)))...))...((....))))))).((((.(((((.......)))))))))..... ( -37.20, z-score =  -3.67, R)
>droPer1.super_7 2441529 98 + 4445127
GAAGAGUCGGACACAGAGCCAGAGCCAGAG---------------CUGGAGCUGGAGCUGAAGCCGGAGCCAAAGCGAUUCAUUGAAUGGCCAAAAACAGGCCAUCGAAACUG
...(((((((...(((..((((..(((...---------------.)))..))))..)))...))...((....))))))).((((.(((((.......)))))))))..... ( -37.20, z-score =  -3.67, R)
>consensus
UAGACGACGGAUCGGGAAUCGGGAACGGAG_______________GGGGAUGCGGAGUUGGCCACGGAGCCAAAGCCACUCAUUCAAUGGCCAAAAACGGGCCAUGGAAACUG
...................(((...............................((..(((((......)))))..)).....((((.(((((.......)))))))))..))) (-15.57 = -16.39 +   0.81)

alignment

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secondary structure

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dotplot

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Window 2

Location 25,406,082 – 25,406,180
Length 98
Sequences 8
Columns 113
Reading direction reverse
Mean pairwise identity 70.52
Shannon entropy 0.57149
G+C content 0.56205
Mean single sequence MFE -27.88
Consensus MFE -14.09
Energy contribution -14.12
Covariance contribution 0.03
Combinations/Pair 1.29
Mean z-score -1.06
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.41
SVM RNA-class probability 0.682735
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25406082 98 - 27905053
CGGUUUCCAUGGCCCGUUUUUGGCCAUUGAAUGAGUGGCUUUGGCUCCGUGGCCAACUCCGCAUACCC---------------CUUCGUUCCCGAUGCCCGAUCCGUCGUCUA
.((((((.((((((.......)))))).)))...((((..((((((....))))))..))))..))).---------------.........(((((.......))))).... ( -29.40, z-score =  -1.01, R)
>droSim1.chr3R 25078399 98 - 27517382
CGGUUUCCAUGGCCCGUUUUUGGCCAUUGAAUGAGUGGCUUUGGCUCCGUGGCCAACUCCGCAUACCC---------------CUCCGUUCCCGAUUCCCGAUCCGUCGUCUA
(((.(((.((((((.......)))))).)))...((((..((((((....))))))..))))......---------------........))).....(((....))).... ( -28.10, z-score =  -0.94, R)
>droSec1.super_4 4263723 98 - 6179234
CGGUUUCCAUGGCCCGUUUUUGGCCAUUGAAUGAGUGGCUUUGGCUCCGUGGCCAACUCCGCAUACCC---------------CUCCGUUCCCGAUUCCCGAUCCGUCGUCUA
(((.(((.((((((.......)))))).)))...((((..((((((....))))))..))))......---------------........))).....(((....))).... ( -28.10, z-score =  -0.94, R)
>droYak2.chr3R 7761038 113 + 28832112
CAGUUUCCAUGGCCCGUUUUUGGCCAUUGAAUGAGAGGCUUUGGCUUCGUGGCCAACUCCAAAUCCCCCCUGUGUUCCCCAUUCCCCAUUCCCGAUUCCCGAUCGGUCGUCUA
(((.(((.((((((.......)))))).))).....((..((((((....))))))..)).........)))...................((((((...))))))....... ( -27.50, z-score =  -0.55, R)
>droEre2.scaffold_4820 7873684 97 + 10470090
CAGUUUCCAUGGCCCG-UUUUGGCCAUUGAAUGAGUGGCUUUGGCUUCGUGGCCAACUGCAAAGCCCC---------------CUCCGCUCCCGUUUCCCGAUCCGCCGUCUA
....(((.((((((..-....)))))).))).((((((....(((((.(..(....)..).)))))..---------------..))))))...................... ( -29.80, z-score =  -1.59, R)
>droAna3.scaffold_12911 5101465 76 - 5364042
CAGUUUCCAUGGCCUGUUUUUGGCCAUUCAAUGAAUCGCUUUGGCUCCGUGGCCAACUCGGUUUCCCCAACUACCA-------------------------------------
.((((...((((((.......)))))).....((((((..((((((....))))))..))))))....))))....------------------------------------- ( -22.10, z-score =  -2.03, R)
>dp4.chr2 2276653 98 - 30794189
CAGUUUCGAUGGCCUGUUUUUGGCCAUUCAAUGAAUCGCUUUGGCUCCGGCUUCAGCUCCAGCUCCAG---------------CUCUGGCUCUGGCUCUGUGUCCGACUCUUC
.((..(((((((((.......))))))..........(((..((((..((((..(((....)))..))---------------))..))))..)))........)))..)).. ( -29.00, z-score =  -0.72, R)
>droPer1.super_7 2441529 98 - 4445127
CAGUUUCGAUGGCCUGUUUUUGGCCAUUCAAUGAAUCGCUUUGGCUCCGGCUUCAGCUCCAGCUCCAG---------------CUCUGGCUCUGGCUCUGUGUCCGACUCUUC
.((..(((((((((.......))))))..........(((..((((..((((..(((....)))..))---------------))..))))..)))........)))..)).. ( -29.00, z-score =  -0.72, R)
>consensus
CAGUUUCCAUGGCCCGUUUUUGGCCAUUGAAUGAGUGGCUUUGGCUCCGUGGCCAACUCCACAUCCCC_______________CUCCGUUCCCGAUUCCCGAUCCGUCGUCUA
........((((((.......))))))........(((..(((((......)))))..))).................................................... (-14.09 = -14.12 +   0.03)

alignment

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secondary structure

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dotplot

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Window 3

Location 25,406,110 – 25,406,220
Length 110
Sequences 8
Columns 113
Reading direction forward
Mean pairwise identity 81.76
Shannon entropy 0.34647
G+C content 0.50402
Mean single sequence MFE -33.91
Consensus MFE -19.85
Energy contribution -20.66
Covariance contribution 0.81
Combinations/Pair 1.06
Mean z-score -1.79
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.22
SVM RNA-class probability 0.601235
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25406110 110 + 27905053
---AGGGGUAUGCGGAGUUGGCCACGGAGCCAAAGCCACUCAUUCAAUGGCCAAAAACGGGCCAUGGAAACCGGCCAACGAAAUUGCAAAUAUACGAGUAACCACAUACAGUG
---....(((((.((.(((((((..((........)).....(((.((((((.......)))))).)))...)))))))....((((..........)))))).))))).... ( -35.80, z-score =  -2.29, R)
>droSim1.chr3R 25078427 110 + 27517382
---AGGGGUAUGCGGAGUUGGCCACGGAGCCAAAGCCACUCAUUCAAUGGCCAAAAACGGGCCAUGGAAACCGGCCAACGAAAUUGCAAAUAUACGAGUAACCACAUACAGUG
---....(((((.((.(((((((..((........)).....(((.((((((.......)))))).)))...)))))))....((((..........)))))).))))).... ( -35.80, z-score =  -2.29, R)
>droSec1.super_4 4263751 110 + 6179234
---AGGGGUAUGCGGAGUUGGCCACGGAGCCAAAGCCACUCAUUCAAUGGCCAAAAACGGGCCAUGGAAACCGGCCAACGAAAUUGCAAAUAUACGAGUAACCACAUACAGUG
---....(((((.((.(((((((..((........)).....(((.((((((.......)))))).)))...)))))))....((((..........)))))).))))).... ( -35.80, z-score =  -2.29, R)
>droYak2.chr3R 7761078 113 - 28832112
ACAGGGGGGAUUUGGAGUUGGCCACGAAGCCAAAGCCUCUCAUUCAAUGGCCAAAAACGGGCCAUGGAAACUGGCCAACGAAAUUGCAAAUAUACGAGUGACCACAUACAGUG
...((((((.(((((..(((....)))..))))).))))((((((..((........))(((((.(....))))))...................)))))))).......... ( -33.70, z-score =  -1.43, R)
>droEre2.scaffold_4820 7873712 109 - 10470090
---AGGGGGCUUUGCAGUUGGCCACGAAGCCAAAGCCACUCAUUCAAUGGCCAAAA-CGGGCCAUGGAAACUGGCCAACGAAAUUGCAAAUAUACGAGUGACCACAUACAGUG
---.((..((((((((((((((((....((....))......(((.((((((....-..)))))).)))..)))))))).....)))).......))))..)).......... ( -33.71, z-score =  -1.51, R)
>droAna3.scaffold_12911 5101471 105 + 5364042
---UUGGGGAAACCGAGUUGGCCACGGAGCCAAAGCGAUUCAUUGAAUGGCCAAAAACAGGCCAUGGAAACUGGCCAACAAAAUUGCCAAUAUAUGG-----CACAUACAGUG
---...((....))..((((((((.(...((....(((....))).((((((.......))))))))...))))))))).....(((((.....)))-----))......... ( -36.70, z-score =  -3.38, R)
>dp4.chr2 2276681 105 + 30794189
---AGCUGGAGCUGGAGCUGAAGCCGGAGCCAAAGCGAUUCAUUGAAUGGCCAAAAACAGGCCAUCGAAACUGGCCAACAGAAUUGGGAAUAUUGCA-----CACGCACAGGU
---.(((((..((((........))))..)))..(((((((.((((.(((((.......)))))))))..(((.....)))......))..))))).-----...))...... ( -29.90, z-score =  -0.58, R)
>droPer1.super_7 2441557 105 + 4445127
---AGCUGGAGCUGGAGCUGAAGCCGGAGCCAAAGCGAUUCAUUGAAUGGCCAAAAACAGGCCAUCGAAACUGGCCAACAGAAUUGGGAAUAUUGCA-----CACGCACAGGU
---.(((((..((((........))))..)))..(((((((.((((.(((((.......)))))))))..(((.....)))......))..))))).-----...))...... ( -29.90, z-score =  -0.58, R)
>consensus
___AGGGGGAUGCGGAGUUGGCCACGGAGCCAAAGCCACUCAUUCAAUGGCCAAAAACGGGCCAUGGAAACUGGCCAACGAAAUUGCAAAUAUACGAGU_ACCACAUACAGUG
................(((((((.....((....))......((((.(((((.......)))))))))....))))))).................................. (-19.85 = -20.66 +   0.81)

alignment

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secondary structure

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dotplot

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Window 4

Location 25,406,110 – 25,406,220
Length 110
Sequences 8
Columns 113
Reading direction reverse
Mean pairwise identity 81.76
Shannon entropy 0.34647
G+C content 0.50402
Mean single sequence MFE -34.57
Consensus MFE -21.09
Energy contribution -22.00
Covariance contribution 0.91
Combinations/Pair 1.18
Mean z-score -1.71
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.596666
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25406110 110 - 27905053
CACUGUAUGUGGUUACUCGUAUAUUUGCAAUUUCGUUGGCCGGUUUCCAUGGCCCGUUUUUGGCCAUUGAAUGAGUGGCUUUGGCUCCGUGGCCAACUCCGCAUACCCCU---
....((((((((......(((....)))......((((((((..(((.((((((.......)))))).)))...(..((....))..).)))))))).))))))))....--- ( -39.50, z-score =  -2.88, R)
>droSim1.chr3R 25078427 110 - 27517382
CACUGUAUGUGGUUACUCGUAUAUUUGCAAUUUCGUUGGCCGGUUUCCAUGGCCCGUUUUUGGCCAUUGAAUGAGUGGCUUUGGCUCCGUGGCCAACUCCGCAUACCCCU---
....((((((((......(((....)))......((((((((..(((.((((((.......)))))).)))...(..((....))..).)))))))).))))))))....--- ( -39.50, z-score =  -2.88, R)
>droSec1.super_4 4263751 110 - 6179234
CACUGUAUGUGGUUACUCGUAUAUUUGCAAUUUCGUUGGCCGGUUUCCAUGGCCCGUUUUUGGCCAUUGAAUGAGUGGCUUUGGCUCCGUGGCCAACUCCGCAUACCCCU---
....((((((((......(((....)))......((((((((..(((.((((((.......)))))).)))...(..((....))..).)))))))).))))))))....--- ( -39.50, z-score =  -2.88, R)
>droYak2.chr3R 7761078 113 + 28832112
CACUGUAUGUGGUCACUCGUAUAUUUGCAAUUUCGUUGGCCAGUUUCCAUGGCCCGUUUUUGGCCAUUGAAUGAGAGGCUUUGGCUUCGUGGCCAACUCCAAAUCCCCCCUGU
...((((((.(....).))))))...........((((((((..(((.((((((.......)))))).)))...(((((....))))).))))))))................ ( -35.70, z-score =  -2.09, R)
>droEre2.scaffold_4820 7873712 109 + 10470090
CACUGUAUGUGGUCACUCGUAUAUUUGCAAUUUCGUUGGCCAGUUUCCAUGGCCCG-UUUUGGCCAUUGAAUGAGUGGCUUUGGCUUCGUGGCCAACUGCAAAGCCCCCU---
...((((((.(....).))))))((((((.....((((((((..(((.((((((..-....)))))).)))...(.(((....))).).)))))))))))))).......--- ( -36.10, z-score =  -1.67, R)
>droAna3.scaffold_12911 5101471 105 - 5364042
CACUGUAUGUG-----CCAUAUAUUGGCAAUUUUGUUGGCCAGUUUCCAUGGCCUGUUUUUGGCCAUUCAAUGAAUCGCUUUGGCUCCGUGGCCAACUCGGUUUCCCCAA---
.((((....((-----(((.....))))).....((((((((......((((((.......))))))..........((....))....)))))))).))))........--- ( -33.30, z-score =  -2.01, R)
>dp4.chr2 2276681 105 - 30794189
ACCUGUGCGUG-----UGCAAUAUUCCCAAUUCUGUUGGCCAGUUUCGAUGGCCUGUUUUUGGCCAUUCAAUGAAUCGCUUUGGCUCCGGCUUCAGCUCCAGCUCCAGCU---
..((((((...-----.)))......(((((...))))).)))....(((((((.......))))))).........(((..((((..(((....)))..))))..))).--- ( -26.50, z-score =   0.36, R)
>droPer1.super_7 2441557 105 - 4445127
ACCUGUGCGUG-----UGCAAUAUUCCCAAUUCUGUUGGCCAGUUUCGAUGGCCUGUUUUUGGCCAUUCAAUGAAUCGCUUUGGCUCCGGCUUCAGCUCCAGCUCCAGCU---
..((((((...-----.)))......(((((...))))).)))....(((((((.......))))))).........(((..((((..(((....)))..))))..))).--- ( -26.50, z-score =   0.36, R)
>consensus
CACUGUAUGUGGU_ACUCGUAUAUUUGCAAUUUCGUUGGCCAGUUUCCAUGGCCCGUUUUUGGCCAUUGAAUGAGUGGCUUUGGCUCCGUGGCCAACUCCACAUCCCCCU___
...((((((........))))))...........((((((((......((((((.......))))))..........((....))....))))))))................ (-21.09 = -22.00 +   0.91)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:55:07 2011