Locus 8339

Sequence ID dm3.chr3L
Location 22,118,599 – 22,118,720
Length 121
Max. P 0.960084
window11455 window11456 window11457 window11458

overview

Window 5

Location 22,118,599 – 22,118,695
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 99.38
Shannon entropy 0.01011
G+C content 0.50625
Mean single sequence MFE -35.10
Consensus MFE -35.10
Energy contribution -35.10
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.68
SVM RNA-class probability 0.960084
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22118599 96 + 24543557
AAGCCGCUUUGAGCUUUAACGCUUUGUACAGAUUUCCAUUAGUGGAGUGGGUUUUCCACUGCCCACGUGUGCGUGUGCUGCAUGUGUGGGCGCAAA
..((.((...((((......)))).)).............(((((((......)))))))(((((((..((((.....))))..)))))))))... ( -35.10, z-score =  -1.70, R)
>droSim1.chr3L 21465632 96 + 22553184
AAGCCGCUUUGAGCUUUAACGCUUUGUACAGAUUUCCAUUAGUGGAGUGGGUUUUCCACUGCCCACGUGUGCGUGUGCUGCAUGUGUGGGCGCAAA
..((.((...((((......)))).)).............(((((((......)))))))(((((((..((((.....))))..)))))))))... ( -35.10, z-score =  -1.70, R)
>droSec1.super_11 2048007 96 + 2888827
AAGCCGCUUUGAGCUUUAACGCUUUGUACAGAUUUCCAUUAGUGGAGUGGGUUUUCCACUGCCCACGUGUGCGUGUGCUGCAUGUGUGGGCGCAAA
..((.((...((((......)))).)).............(((((((......)))))))(((((((..((((.....))))..)))))))))... ( -35.10, z-score =  -1.70, R)
>droYak2.chr3L 22461975 96 + 24197627
AAGCCGCUUUGAGCUUUAACGCUUUGUACAGAUUUCCAUUAGUGGAGUGUGUUUUCCACUGCCCACGUGUGCGUGUGCUGCAUGUGUGGGCGCAAA
..((.((...((((......)))).)).............(((((((......)))))))(((((((..((((.....))))..)))))))))... ( -35.10, z-score =  -2.20, R)
>droEre2.scaffold_4784 21789504 96 + 25762168
AAGCCGCUUUGAGCUUUAACGCUUUGUACAGAUUUCCAUUAGUGGAGUGUGUUUUCCACUGCCCACGUGUGCGUGUGCUGCAUGUGUGGGCGCAAA
..((.((...((((......)))).)).............(((((((......)))))))(((((((..((((.....))))..)))))))))... ( -35.10, z-score =  -2.20, R)
>consensus
AAGCCGCUUUGAGCUUUAACGCUUUGUACAGAUUUCCAUUAGUGGAGUGGGUUUUCCACUGCCCACGUGUGCGUGUGCUGCAUGUGUGGGCGCAAA
..((.((...((((......)))).)).............(((((((......)))))))(((((((..((((.....))))..)))))))))... (-35.10 = -35.10 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 22,118,599 – 22,118,695
Length 96
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 99.38
Shannon entropy 0.01011
G+C content 0.50625
Mean single sequence MFE -27.60
Consensus MFE -27.60
Energy contribution -27.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.31
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.829145
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22118599 96 - 24543557
UUUGCGCCCACACAUGCAGCACACGCACACGUGGGCAGUGGAAAACCCACUCCACUAAUGGAAAUCUGUACAAAGCGUUAAAGCUCAAAGCGGCUU
...((((((((...(((.......)))...))))))((((((........))))))..................))....(((((......))))) ( -27.60, z-score =  -1.22, R)
>droSim1.chr3L 21465632 96 - 22553184
UUUGCGCCCACACAUGCAGCACACGCACACGUGGGCAGUGGAAAACCCACUCCACUAAUGGAAAUCUGUACAAAGCGUUAAAGCUCAAAGCGGCUU
...((((((((...(((.......)))...))))))((((((........))))))..................))....(((((......))))) ( -27.60, z-score =  -1.22, R)
>droSec1.super_11 2048007 96 - 2888827
UUUGCGCCCACACAUGCAGCACACGCACACGUGGGCAGUGGAAAACCCACUCCACUAAUGGAAAUCUGUACAAAGCGUUAAAGCUCAAAGCGGCUU
...((((((((...(((.......)))...))))))((((((........))))))..................))....(((((......))))) ( -27.60, z-score =  -1.22, R)
>droYak2.chr3L 22461975 96 - 24197627
UUUGCGCCCACACAUGCAGCACACGCACACGUGGGCAGUGGAAAACACACUCCACUAAUGGAAAUCUGUACAAAGCGUUAAAGCUCAAAGCGGCUU
...((((((((...(((.......)))...))))))((((((........))))))..................))....(((((......))))) ( -27.60, z-score =  -1.45, R)
>droEre2.scaffold_4784 21789504 96 - 25762168
UUUGCGCCCACACAUGCAGCACACGCACACGUGGGCAGUGGAAAACACACUCCACUAAUGGAAAUCUGUACAAAGCGUUAAAGCUCAAAGCGGCUU
...((((((((...(((.......)))...))))))((((((........))))))..................))....(((((......))))) ( -27.60, z-score =  -1.45, R)
>consensus
UUUGCGCCCACACAUGCAGCACACGCACACGUGGGCAGUGGAAAACCCACUCCACUAAUGGAAAUCUGUACAAAGCGUUAAAGCUCAAAGCGGCUU
...((((((((...(((.......)))...))))))((((((........))))))..................))....(((((......))))) (-27.60 = -27.60 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 22,118,624 – 22,118,720
Length 96
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 84.10
Shannon entropy 0.30915
G+C content 0.54019
Mean single sequence MFE -34.88
Consensus MFE -26.91
Energy contribution -28.50
Covariance contribution 1.59
Combinations/Pair 1.13
Mean z-score -1.80
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.13
SVM RNA-class probability 0.896212
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22118624 96 + 24543557
GUACAGAUUUCCAUUAGUGGAGUGGGUUUUCCACUGCCCACGUGUGCGUGUGCUGCAUGUGUGGGCGCAAAUCGCUUCGCUCCGAAAGUUGACACG
((.(((.((((....(((((((((((....))...(((((((..((((.....))))..)))))))......)))))))))..)))).)))))... ( -37.60, z-score =  -2.41, R)
>droSim1.chr3L 21465657 96 + 22553184
GUACAGAUUUCCAUUAGUGGAGUGGGUUUUCCACUGCCCACGUGUGCGUGUGCUGCAUGUGUGGGCGCAAAUCGCUUGGCUCCGAAAGUUGACACG
.....(((((.(...(((((((......)))))))(((((((..((((.....))))..)))))))).)))))(.(..(((.....)))..))... ( -35.90, z-score =  -1.64, R)
>droSec1.super_11 2048032 96 + 2888827
GUACAGAUUUCCAUUAGUGGAGUGGGUUUUCCACUGCCCACGUGUGCGUGUGCUGCAUGUGUGGGCGCAAAUCGCUUGGCUCCGAAAGUUGACACG
.....(((((.(...(((((((......)))))))(((((((..((((.....))))..)))))))).)))))(.(..(((.....)))..))... ( -35.90, z-score =  -1.64, R)
>droYak2.chr3L 22462000 96 + 24197627
GUACAGAUUUCCAUUAGUGGAGUGUGUUUUCCACUGCCCACGUGUGCGUGUGCUGCAUGUGUGGGCGCAAAUCGCUUGGCUCCGAAAGUUGACACG
.....(((((.(...(((((((......)))))))(((((((..((((.....))))..)))))))).)))))(.(..(((.....)))..))... ( -35.90, z-score =  -2.02, R)
>droEre2.scaffold_4784 21789529 96 + 25762168
GUACAGAUUUCCAUUAGUGGAGUGUGUUUUCCACUGCCCACGUGUGCGUGUGCUGCAUGUGUGGGCGCAAAUCGCUCGGCUCCGAAAGUUGACACG
.....(((((.(...(((((((......)))))))(((((((..((((.....))))..)))))))).)))))(.((((((.....)))))))... ( -37.30, z-score =  -2.36, R)
>droAna3.scaffold_13337 21283716 81 + 23293914
----GGACUUGCCCGUGUGGGGCAAGUUUGCCAGUCUCCA--------UGUGCAACACGUGCAGAGGAAUCUCGCUCGACUCAGAAA-UUGACA--
----((((((((((.....))))))))))((.((..(((.--------((..(.....)..))..)))..)).))............-......-- ( -26.70, z-score =  -0.75, R)
>consensus
GUACAGAUUUCCAUUAGUGGAGUGGGUUUUCCACUGCCCACGUGUGCGUGUGCUGCAUGUGUGGGCGCAAAUCGCUUGGCUCCGAAAGUUGACACG
.....(((((.(...(((((((......)))))))(((((((..((((.....))))..)))))))).)))))(.((((((.....)))))))... (-26.91 = -28.50 +   1.59)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 22,118,624 – 22,118,720
Length 96
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 84.10
Shannon entropy 0.30915
G+C content 0.54019
Mean single sequence MFE -29.33
Consensus MFE -21.23
Energy contribution -21.90
Covariance contribution 0.67
Combinations/Pair 1.19
Mean z-score -1.48
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.20
SVM RNA-class probability 0.591648
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22118624 96 - 24543557
CGUGUCAACUUUCGGAGCGAAGCGAUUUGCGCCCACACAUGCAGCACACGCACACGUGGGCAGUGGAAAACCCACUCCACUAAUGGAAAUCUGUAC
.(((.((..((((...(((((....)))))((((((...(((.......)))...))))))((((((........))))))....))))..))))) ( -29.50, z-score =  -1.30, R)
>droSim1.chr3L 21465657 96 - 22553184
CGUGUCAACUUUCGGAGCCAAGCGAUUUGCGCCCACACAUGCAGCACACGCACACGUGGGCAGUGGAAAACCCACUCCACUAAUGGAAAUCUGUAC
............((((.(((.((.....))((((((...(((.......)))...))))))((((((........))))))..)))...))))... ( -29.40, z-score =  -1.39, R)
>droSec1.super_11 2048032 96 - 2888827
CGUGUCAACUUUCGGAGCCAAGCGAUUUGCGCCCACACAUGCAGCACACGCACACGUGGGCAGUGGAAAACCCACUCCACUAAUGGAAAUCUGUAC
............((((.(((.((.....))((((((...(((.......)))...))))))((((((........))))))..)))...))))... ( -29.40, z-score =  -1.39, R)
>droYak2.chr3L 22462000 96 - 24197627
CGUGUCAACUUUCGGAGCCAAGCGAUUUGCGCCCACACAUGCAGCACACGCACACGUGGGCAGUGGAAAACACACUCCACUAAUGGAAAUCUGUAC
............((((.(((.((.....))((((((...(((.......)))...))))))((((((........))))))..)))...))))... ( -29.40, z-score =  -1.53, R)
>droEre2.scaffold_4784 21789529 96 - 25762168
CGUGUCAACUUUCGGAGCCGAGCGAUUUGCGCCCACACAUGCAGCACACGCACACGUGGGCAGUGGAAAACACACUCCACUAAUGGAAAUCUGUAC
.(((.((...((((....)))).(((((.(((((((...(((.......)))...))))))((((((........))))))...).)))))))))) ( -30.10, z-score =  -1.51, R)
>droAna3.scaffold_13337 21283716 81 - 23293914
--UGUCAA-UUUCUGAGUCGAGCGAGAUUCCUCUGCACGUGUUGCACA--------UGGAGACUGGCAAACUUGCCCCACACGGGCAAGUCC----
--(((((.-((((((((((......)))))...((((.....))))..--------.))))).))))).((((((((.....))))))))..---- ( -28.20, z-score =  -1.78, R)
>consensus
CGUGUCAACUUUCGGAGCCAAGCGAUUUGCGCCCACACAUGCAGCACACGCACACGUGGGCAGUGGAAAACCCACUCCACUAAUGGAAAUCUGUAC
.......................(((((.(((((((...(((.......)))...))))))((((((........))))))...).)))))..... (-21.23 = -21.90 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:43:49 2011