Locus 4000

Sequence ID dm3.chr2R
Location 9,558,694 – 9,558,797
Length 103
Max. P 0.999834
window5473 window5474

overview

Window 3

Location 9,558,694 – 9,558,797
Length 103
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 77.28
Shannon entropy 0.44002
G+C content 0.47816
Mean single sequence MFE -39.72
Consensus MFE -28.25
Energy contribution -28.03
Covariance contribution -0.21
Combinations/Pair 1.37
Mean z-score -4.65
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.52
SVM RNA-class probability 0.999834
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9558694 103 + 21146708
CCAUCCCUUGAAUUCUUGUAACCCUUUCGGCAAACGGUGCUACAAAAGGGACGAUUUCUGCAGGGGUUCGUCCUUUUUGUAUCCCUUUACUGAAAUGGUUACG
.................((((((.((((((.(((.((.(.(((((((((((((((..(....)..).)))))))))))))).)))))).)))))).)))))). ( -39.80, z-score =  -5.46, R)
>droSim1.chr2R 8004781 103 + 19596830
CCAUCCCUUGAAUUCUUGUAACCCUUUCGGCAAACGGUGCUACAAAAGGGACGAUUUCUGCAUGGGUUCGUCCUUUUUGUAUCCCUUUACUGAAAUGGGUAGG
....................((((((((((.(((.((.(.((((((((((((((.(((.....))).)))))))))))))).)))))).)))))).))))... ( -36.40, z-score =  -3.89, R)
>droSec1.super_1 7085505 103 + 14215200
CCAUCCCUUGAAUUCUUGUAACCCUUUCGGCAAACGGUGCUACAAAAGGGACGAUUUCAGCAUGGGUUCGUCCUUUUUGUAUCCCUUUACUGAAAUGGGUAGG
....................((((((((((.(((.((.(.((((((((((((((.(((.....))).)))))))))))))).)))))).)))))).))))... ( -36.20, z-score =  -3.64, R)
>droYak2.chr2R 13750125 103 - 21139217
CCAACGCAUAACUUCUUCUAGCCCUUUCGGCAAACGCGGUUACAAAAGGGACGAUCUCUGCAGGGUGUCGUCCUCUUUGUAUCCCUUUACCGAAAUUUGUAAA
........................((((((.(((.(.((.((((((..((((((((((....))).)))))))..)))))).)))))).))))))........ ( -30.60, z-score =  -3.09, R)
>droEre2.scaffold_4845 6338883 100 - 22589142
CCAUCGCAUCACUUC---UAGCCCUUUCGGCAAACGGGGCUACAAAAGGGACGAUCUCUGCAGGGGUUCGUCCUUUUUGUAUCCCUUUACUGAAAUUGGUGGA
(((((((........---..))..((((((.(((.((((.((((((((((((((((((....)))).))))))))))))))))))))).))))))..))))). ( -41.10, z-score =  -4.62, R)
>droAna3.scaffold_13266 16868177 103 + 19884421
CGACGCGAUGUUCUCGUCGACCACAUUUAGCAGGAGAGGCUACACCAGGGACGAAUCAGGUAGAUAUUCGUCCUUGGUGUGGCCCUAUGCUACAUUUGGUGGC
(((((.(.....).)))))((((.((.(((((..((.(((((((((((((((((((.........))))))))))))))))))))).))))).)).))))... ( -54.20, z-score =  -7.20, R)
>consensus
CCAUCCCAUGAAUUCUUGUAACCCUUUCGGCAAACGGGGCUACAAAAGGGACGAUUUCUGCAGGGGUUCGUCCUUUUUGUAUCCCUUUACUGAAAUGGGUAGG
.....................((.((((((.(((.((...((((((((((((((.(((.....))).)))))))))))))).)).))).)))))).))..... (-28.25 = -28.03 +  -0.21)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 9,558,694 – 9,558,797
Length 103
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 77.28
Shannon entropy 0.44002
G+C content 0.47816
Mean single sequence MFE -34.39
Consensus MFE -24.28
Energy contribution -23.95
Covariance contribution -0.33
Combinations/Pair 1.31
Mean z-score -3.35
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.85
SVM RNA-class probability 0.999393
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9558694 103 - 21146708
CGUAACCAUUUCAGUAAAGGGAUACAAAAAGGACGAACCCCUGCAGAAAUCGUCCCUUUUGUAGCACCGUUUGCCGAAAGGGUUACAAGAAUUCAAGGGAUGG
.((((((.((((.(((((.((.(((((((.((((((.............)))))).)))))))...)).))))).)))).))))))................. ( -35.32, z-score =  -3.89, R)
>droSim1.chr2R 8004781 103 - 19596830
CCUACCCAUUUCAGUAAAGGGAUACAAAAAGGACGAACCCAUGCAGAAAUCGUCCCUUUUGUAGCACCGUUUGCCGAAAGGGUUACAAGAAUUCAAGGGAUGG
(((((((.((((.(((((.((.(((((((.((((((.............)))))).)))))))...)).))))).)))))))).....(....).)))..... ( -32.42, z-score =  -3.04, R)
>droSec1.super_1 7085505 103 - 14215200
CCUACCCAUUUCAGUAAAGGGAUACAAAAAGGACGAACCCAUGCUGAAAUCGUCCCUUUUGUAGCACCGUUUGCCGAAAGGGUUACAAGAAUUCAAGGGAUGG
(((((((.((((.(((((.((.(((((((.((((((.............)))))).)))))))...)).))))).)))))))).....(....).)))..... ( -32.42, z-score =  -2.79, R)
>droYak2.chr2R 13750125 103 + 21139217
UUUACAAAUUUCGGUAAAGGGAUACAAAGAGGACGACACCCUGCAGAGAUCGUCCCUUUUGUAACCGCGUUUGCCGAAAGGGCUAGAAGAAGUUAUGCGUUGG
....(((.(((((((((((((.(((((((.(((((((.(......).).)))))).))))))).)).).)))))))))).((((......)))).....))). ( -30.50, z-score =  -1.93, R)
>droEre2.scaffold_4845 6338883 100 + 22589142
UCCACCAAUUUCAGUAAAGGGAUACAAAAAGGACGAACCCCUGCAGAGAUCGUCCCUUUUGUAGCCCCGUUUGCCGAAAGGGCUA---GAAGUGAUGCGAUGG
.((((((((((((((...(((.(((((((.((((((.((......).).)))))).)))))))..))).....((....))))).---)))))..)).).))) ( -31.30, z-score =  -2.55, R)
>droAna3.scaffold_13266 16868177 103 - 19884421
GCCACCAAAUGUAGCAUAGGGCCACACCAAGGACGAAUAUCUACCUGAUUCGUCCCUGGUGUAGCCUCUCCUGCUAAAUGUGGUCGACGAGAACAUCGCGUCG
(((((......(((((.(((((.((((((.((((((((.........)))))))).)))))).))).))..)))))...)))))(((((.(.....).))))) ( -44.40, z-score =  -5.88, R)
>consensus
CCUACCAAUUUCAGUAAAGGGAUACAAAAAGGACGAACCCCUGCAGAAAUCGUCCCUUUUGUAGCACCGUUUGCCGAAAGGGUUACAAGAAUUCAAGGGAUGG
.....((.((((.(((((.((.(((((((.((((((.............)))))).)))))))...)).))))).)))).))..................... (-24.28 = -23.95 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:20:44 2011