Locus 6415

Sequence ID dm3.chr3L
Location 6,531,541 – 6,531,594
Length 53
Max. P 0.991214
window8826 window8827

overview

Window 6

Location 6,531,541 – 6,531,594
Length 53
Sequences 9
Columns 66
Reading direction forward
Mean pairwise identity 91.95
Shannon entropy 0.14860
G+C content 0.51972
Mean single sequence MFE -19.22
Consensus MFE -13.31
Energy contribution -13.31
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.69
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.46
SVM RNA-class probability 0.991214
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 6531541 53 + 24543557
CAGACACAUGGCAAGCGCCAUAAACAGCCACCACAA-------------UUGGAAGCUUGCCAUGG
......((((((((((((........))..(((...-------------.)))..)))))))))). ( -21.10, z-score =  -4.69, R)
>droSim1.chr3L 6002622 53 + 22553184
CAGACACAUGGCAAGCGCCAUAAACAGCCACCACAA-------------UUGGAAGCUUGCCAUGG
......((((((((((((........))..(((...-------------.)))..)))))))))). ( -21.10, z-score =  -4.69, R)
>droYak2.chr3L 7101500 53 + 24197627
CAGACACAUGGCAAGCGCCAUAAACAGGCACCACAA-------------UUGGAAGCUUGCCAUGG
......(((((((((((((.......))).(((...-------------.)))..)))))))))). ( -25.50, z-score =  -6.34, R)
>droEre2.scaffold_4784 9203058 53 + 25762168
CAGACACAUGGCAAGCGCCAUAAACAGCCACCACAA-------------UUGGAAGCUUGCCAUGG
......((((((((((((........))..(((...-------------.)))..)))))))))). ( -21.10, z-score =  -4.69, R)
>droAna3.scaffold_13337 2858909 53 - 23293914
CAGACACAUGGCAAACGCCAUAAACAGCCACCACAA-------------UUGGAUGCUUGCCAUGG
......((((((((.(((((................-------------.))).)).)))))))). ( -15.23, z-score =  -2.46, R)
>droWil1.scaffold_180916 888225 65 + 2700594
-AGACACAUGGCAAACGCCAUAAACAGCCACCACAAUUGGGGUGCACAAUUGGAAGCUUGCCAUGG
-.....((((((((...(((......(((.(((....)))))).......)))....)))))))). ( -22.32, z-score =  -2.59, R)
>droVir3.scaffold_13049 10886749 53 + 25233164
CAGACACAUGGCAAACGCCAUAAGCAGCCACCACAA-------------UUGGAAGCUUGCCAUGG
......((((((((..((.....)).((..(((...-------------.)))..)))))))))). ( -16.90, z-score =  -2.85, R)
>droMoj3.scaffold_6680 14825492 53 - 24764193
CAGACACAUGGCAAACGCCAUAAACAGCCACCACAA-------------UUGGAAGCUUGCCAUGG
......((((((((.(((........))..(((...-------------.)))..).)))))))). ( -14.50, z-score =  -2.50, R)
>droGri2.scaffold_15110 16138296 53 - 24565398
CAGACACAUGGCAAACGCCAUAAACAGCCACCACAA-------------UUGGAUGCUUGCCAUGG
......((((((((.(((((................-------------.))).)).)))))))). ( -15.23, z-score =  -2.46, R)
>consensus
CAGACACAUGGCAAACGCCAUAAACAGCCACCACAA_____________UUGGAAGCUUGCCAUGG
......((((((((...(((..............................)))....)))))))). (-13.31 = -13.31 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 6,531,541 – 6,531,594
Length 53
Sequences 9
Columns 66
Reading direction reverse
Mean pairwise identity 91.95
Shannon entropy 0.14860
G+C content 0.51972
Mean single sequence MFE -21.16
Consensus MFE -18.42
Energy contribution -18.29
Covariance contribution -0.14
Combinations/Pair 1.06
Mean z-score -2.68
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.16
SVM RNA-class probability 0.984096
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 6531541 53 - 24543557
CCAUGGCAAGCUUCCAA-------------UUGUGGUGGCUGUUUAUGGCGCUUGCCAUGUGUCUG
.((((((((((..(((.-------------...)))..(((......)))))))))))))...... ( -21.60, z-score =  -2.94, R)
>droSim1.chr3L 6002622 53 - 22553184
CCAUGGCAAGCUUCCAA-------------UUGUGGUGGCUGUUUAUGGCGCUUGCCAUGUGUCUG
.((((((((((..(((.-------------...)))..(((......)))))))))))))...... ( -21.60, z-score =  -2.94, R)
>droYak2.chr3L 7101500 53 - 24197627
CCAUGGCAAGCUUCCAA-------------UUGUGGUGCCUGUUUAUGGCGCUUGCCAUGUGUCUG
.((((((((((..(((.-------------...))).(((.......)))))))))))))...... ( -23.60, z-score =  -4.21, R)
>droEre2.scaffold_4784 9203058 53 - 25762168
CCAUGGCAAGCUUCCAA-------------UUGUGGUGGCUGUUUAUGGCGCUUGCCAUGUGUCUG
.((((((((((..(((.-------------...)))..(((......)))))))))))))...... ( -21.60, z-score =  -2.94, R)
>droAna3.scaffold_13337 2858909 53 + 23293914
CCAUGGCAAGCAUCCAA-------------UUGUGGUGGCUGUUUAUGGCGUUUGCCAUGUGUCUG
.((((((((((..(((.-------------...)))..(((......)))))))))))))...... ( -19.70, z-score =  -2.18, R)
>droWil1.scaffold_180916 888225 65 - 2700594
CCAUGGCAAGCUUCCAAUUGUGCACCCCAAUUGUGGUGGCUGUUUAUGGCGUUUGCCAUGUGUCU-
.((((((((((..(((.....((((((((....))).)).)))...))).)))))))))).....- ( -24.10, z-score =  -2.30, R)
>droVir3.scaffold_13049 10886749 53 - 25233164
CCAUGGCAAGCUUCCAA-------------UUGUGGUGGCUGCUUAUGGCGUUUGCCAUGUGUCUG
.(((((((((((.(((.-------------...))).))))((.....))...)))))))...... ( -19.30, z-score =  -2.00, R)
>droMoj3.scaffold_6680 14825492 53 + 24764193
CCAUGGCAAGCUUCCAA-------------UUGUGGUGGCUGUUUAUGGCGUUUGCCAUGUGUCUG
.((((((((((..(((.-------------...)))..(((......)))))))))))))...... ( -19.20, z-score =  -2.42, R)
>droGri2.scaffold_15110 16138296 53 + 24565398
CCAUGGCAAGCAUCCAA-------------UUGUGGUGGCUGUUUAUGGCGUUUGCCAUGUGUCUG
.((((((((((..(((.-------------...)))..(((......)))))))))))))...... ( -19.70, z-score =  -2.18, R)
>consensus
CCAUGGCAAGCUUCCAA_____________UUGUGGUGGCUGUUUAUGGCGUUUGCCAUGUGUCUG
.((((((((((..(((.................)))..(((......)))))))))))))...... (-18.42 = -18.29 +  -0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:07:17 2011