Locus 8308

Sequence ID dm3.chr3L
Location 21,886,936 – 21,887,026
Length 90
Max. P 0.902725
window11414 window11415

overview

Window 4

Location 21,886,936 – 21,887,026
Length 90
Sequences 8
Columns 90
Reading direction forward
Mean pairwise identity 86.50
Shannon entropy 0.27727
G+C content 0.44617
Mean single sequence MFE -18.82
Consensus MFE -13.17
Energy contribution -13.76
Covariance contribution 0.59
Combinations/Pair 1.06
Mean z-score -2.00
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.78
SVM RNA-class probability 0.816077
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 21886936 90 + 24543557
CACUCGCAAUGGCGCAAAAGUUCCUAGACCACUCCAAAAAAGAGAGAAAUAAAAAAGCACAAAAUUUAUAUGCGCCGUCGCGCAUGCAGU
((..(((.((((((((...(((....)))..((((......).)))........................)))))))).)))..)).... ( -19.70, z-score =  -1.76, R)
>droEre2.scaffold_4784 21562320 90 + 25762168
CACUCGCAACGGCGCAAAAGUUCCUAGACCACUCCAAAAAAGAGAAAAAUAAAAAAGCACAAAAUUUAUAUGCGCCGUCGCGCAUGCAGU
((..(((.((((((((...(((....)))..(((.......)))..........................)))))))).)))..)).... ( -21.00, z-score =  -2.62, R)
>droYak2.chr3L 22186919 88 + 24197627
CACUCGCAACGGCGCAAAAGUUCCUAGACCACUCCAAAAAAGAGAAA--UAAAAAAGCACAAAAUUUAUAUGCGCCGUCGCGCAUGCAGU
((..(((.((((((((...(((....)))..(((.......)))...--.....................)))))))).)))..)).... ( -21.00, z-score =  -2.57, R)
>droSec1.super_11 1814315 89 + 2888827
CACUCGCAACGGCGCAAAAGUUCCUAGACCACUCCAAAAAAGAGAGAAAUAAAAA-GCACAAAAUUUAUAUGCGCCGUCGCGCAUGCAGU
((..(((.((((((((...(((....)))..((((......).))).........-..............)))))))).)))..)).... ( -21.50, z-score =  -2.45, R)
>droSim1.chr3L 21225508 89 + 22553184
CACUCGCAACGGCGCAAAAGUUCCUAGACCACUCCAAAAAAGAGAGAAAUAAAAA-GCACAAAAUUUAUAUGCGCCGUCGCGCAUGCAGU
((..(((.((((((((...(((....)))..((((......).))).........-..............)))))))).)))..)).... ( -21.50, z-score =  -2.45, R)
>droAna3.scaffold_13337 21018803 77 + 23293914
CACUCGCAACGGCGCAAAAGUUCCUAGACCACUCCAAAAAAGAA-------------CACAGAAUUUAUAUGCGCCGUCGCGCACUCAGU
....(((.((((((((.((((((.....................-------------....))))))...)))))))).)))........ ( -20.01, z-score =  -3.12, R)
>droWil1.scaffold_180949 4417909 75 - 6375548
CACUCG-------GCAAAAGUUCCUAGACCACUCCAAAAAGAAUACC--------ACGAAAAAAUUUAUAUGCGCCGUCGCGCAUGCAGU
..((.(-------(........)).))....................--------.............(((((((....))))))).... (  -9.80, z-score =   0.29, R)
>droGri2.scaffold_15110 1692672 87 - 24565398
CACUCGCAAUGGCGCAAAAGUUCCUAGACCACUCAAAAAACAUAAAA---AAAAGAACACAAAAUUUAUAUGCGCCGUCGCGCAUGCAGU
((..(((.((((((((...(((....)))............(((((.---..............))))).)))))))).)))..)).... ( -16.06, z-score =  -1.31, R)
>consensus
CACUCGCAACGGCGCAAAAGUUCCUAGACCACUCCAAAAAAGAGAAA__UAAAAAAGCACAAAAUUUAUAUGCGCCGUCGCGCAUGCAGU
....(((.((((((((.(((((........................................)))))...)))))))).)))........ (-13.17 = -13.76 +   0.59)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,886,936 – 21,887,026
Length 90
Sequences 8
Columns 90
Reading direction reverse
Mean pairwise identity 86.50
Shannon entropy 0.27727
G+C content 0.44617
Mean single sequence MFE -26.96
Consensus MFE -17.55
Energy contribution -18.69
Covariance contribution 1.14
Combinations/Pair 1.04
Mean z-score -2.39
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.16
SVM RNA-class probability 0.902725
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 21886936 90 - 24543557
ACUGCAUGCGCGACGGCGCAUAUAAAUUUUGUGCUUUUUUAUUUCUCUCUUUUUUGGAGUGGUCUAGGAACUUUUGCGCCAUUGCGAGUG
((((((.((((((.((((((.........))))))((((((..((.((((.....)))).))..))))))...))))))...))).))). ( -26.20, z-score =  -2.05, R)
>droEre2.scaffold_4784 21562320 90 - 25762168
ACUGCAUGCGCGACGGCGCAUAUAAAUUUUGUGCUUUUUUAUUUUUCUCUUUUUUGGAGUGGUCUAGGAACUUUUGCGCCGUUGCGAGUG
....(((.((((((((((((......(((((.(((...........((((.....)))).))).))))).....)))))))))))).))) ( -29.60, z-score =  -3.13, R)
>droYak2.chr3L 22186919 88 - 24197627
ACUGCAUGCGCGACGGCGCAUAUAAAUUUUGUGCUUUUUUA--UUUCUCUUUUUUGGAGUGGUCUAGGAACUUUUGCGCCGUUGCGAGUG
....(((.((((((((((((......(((((.(((......--...((((.....)))).))).))))).....)))))))))))).))) ( -29.80, z-score =  -3.14, R)
>droSec1.super_11 1814315 89 - 2888827
ACUGCAUGCGCGACGGCGCAUAUAAAUUUUGUGC-UUUUUAUUUCUCUCUUUUUUGGAGUGGUCUAGGAACUUUUGCGCCGUUGCGAGUG
....(((.((((((((((((((((.....)))).-((((((..((.((((.....)))).))..))))))....)))))))))))).))) ( -31.30, z-score =  -3.57, R)
>droSim1.chr3L 21225508 89 - 22553184
ACUGCAUGCGCGACGGCGCAUAUAAAUUUUGUGC-UUUUUAUUUCUCUCUUUUUUGGAGUGGUCUAGGAACUUUUGCGCCGUUGCGAGUG
....(((.((((((((((((((((.....)))).-((((((..((.((((.....)))).))..))))))....)))))))))))).))) ( -31.30, z-score =  -3.57, R)
>droAna3.scaffold_13337 21018803 77 - 23293914
ACUGAGUGCGCGACGGCGCAUAUAAAUUCUGUG-------------UUCUUUUUUGGAGUGGUCUAGGAACUUUUGCGCCGUUGCGAGUG
........((((((((((((((((.....))))-------------)...((((((((....)))))))).....))))))))))).... ( -27.20, z-score =  -2.39, R)
>droWil1.scaffold_180949 4417909 75 + 6375548
ACUGCAUGCGCGACGGCGCAUAUAAAUUUUUUCGU--------GGUAUUCUUUUUGGAGUGGUCUAGGAACUUUUGC-------CGAGUG
(((..((((((....)))))).............(--------((((...((((((((....))))))))....)))-------))))). ( -18.10, z-score =  -0.34, R)
>droGri2.scaffold_15110 1692672 87 + 24565398
ACUGCAUGCGCGACGGCGCAUAUAAAUUUUGUGUUCUUUU---UUUUAUGUUUUUUGAGUGGUCUAGGAACUUUUGCGCCAUUGCGAGUG
....(((.(((((.((((((............((((((..---..((((.........))))...))))))...)))))).))))).))) ( -22.16, z-score =  -0.95, R)
>consensus
ACUGCAUGCGCGACGGCGCAUAUAAAUUUUGUGCUUUUUUA__UCUCUCUUUUUUGGAGUGGUCUAGGAACUUUUGCGCCGUUGCGAGUG
....(((.(((((.((((((((((.....)))).................((((((((....))))))))....)))))).))))).))) (-17.55 = -18.69 +   1.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:43:13 2011