Locus 2797

Sequence ID dm3.chr2L
Location 22,438,761 – 22,438,874
Length 113
Max. P 0.995464
window3851 window3852

overview

Window 1

Location 22,438,761 – 22,438,874
Length 113
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 84.89
Shannon entropy 0.26739
G+C content 0.48190
Mean single sequence MFE -34.26
Consensus MFE -23.82
Energy contribution -24.70
Covariance contribution 0.88
Combinations/Pair 1.05
Mean z-score -1.80
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.31
SVM RNA-class probability 0.640591
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22438761 113 + 23011544
UAAU-UUUAUUUUCGUUAUGUUGGAGAAGUGAGAGGCUUACCAAGAUCCCAGGAACCGAAUACG-CGAGCUUAGGCUGGCAAACUGGUGCCUGAACAU-GGCUGCCUCUCCCUC-GC
....-....((((((......))))))((.(((((((...(((.(....((((.((((.....(-(.(((....))).))....)))).))))..).)-))..))))))).)).-.. ( -35.10, z-score =  -1.46, R)
>droSim1.chr2h_random 1258893 116 + 3178526
UAAUUUUUAUUCUCUUUAUGUUGAUGAGGUGAGAGGCUUACCAAGAUCCCAUGAACCAAAUACG-CGAGCUUAGGCUUGCAAACUGGUGUCUGAACAUCGGAUGCCUCUCCCUCUGC
.........................((((.(((((((..........................(-(((((....))))))...(((((((....)))))))..)))))))))))... ( -37.50, z-score =  -3.45, R)
>droSec1.super_42 47745 116 + 298440
UAAUAUUUAUUCUCUUUAUGUUGAUGAGGUGAGAGGCUUACCAAGAUCCCAUGAACCAAAUACG-CGAGCUUAGGCUUGCAAACUGGUGUCUGAACAUCGGAUGCCUCUCCCUCUGC
.........................((((.(((((((..........................(-(((((....))))))...(((((((....)))))))..)))))))))))... ( -37.50, z-score =  -3.48, R)
>droEre2.scaffold_4784 24210917 112 + 25762168
---UAAAUAUUUUCGUUAUGUUGGAGAGGUAAGAGGCUUACCAAGAUCCCACGA-CUAAAUACGACGAGCUUACGCUGGCAACCUGGUGCCUGAACAUCGGAUGCCUCUCCCUCGG-
---...............((..(((((((((..((((..((((.(...((.((.-.......))...(((....)))))...).))))))))(.....)...)))))))))..)).- ( -27.50, z-score =  -0.15, R)
>droYak2.chr2R 20773049 114 - 21139217
UAAAAUUUAUUGUCGUUAUGUUGGGGAGGUAAGGGGCUUACCAAGAUCCCACGACCCAAAAUCGACGAGCUUACGCCGGCAUCCUGGUCCCUGAACAUCGGAUGCCCCUCCCUC---
.........((((((.....(((((..(....((((((.....)).)))).)..)))))...))))))((....)).(((((((.(((........))))))))))........--- ( -33.70, z-score =  -0.45, R)
>consensus
UAAUAUUUAUUCUCGUUAUGUUGGAGAGGUGAGAGGCUUACCAAGAUCCCACGAACCAAAUACG_CGAGCUUAGGCUGGCAAACUGGUGCCUGAACAUCGGAUGCCUCUCCCUC_GC
.........................((((.(((((((..........................(.(.(((....))).))...((((((......))))))..)))))))))))... (-23.82 = -24.70 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 22,438,761 – 22,438,874
Length 113
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 84.89
Shannon entropy 0.26739
G+C content 0.48190
Mean single sequence MFE -40.10
Consensus MFE -32.10
Energy contribution -31.98
Covariance contribution -0.12
Combinations/Pair 1.16
Mean z-score -3.03
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.81
SVM RNA-class probability 0.995464
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22438761 113 - 23011544
GC-GAGGGAGAGGCAGCC-AUGUUCAGGCACCAGUUUGCCAGCCUAAGCUCG-CGUAUUCGGUUCCUGGGAUCUUGGUAAGCCUCUCACUUCUCCAACAUAACGAAAAUAAA-AUUA
..-(((((((((((.(((-(..((((((.((((((.(((.(((....))).)-)).))).))).))))))....))))..))))))).))))....................-.... ( -41.00, z-score =  -3.40, R)
>droSim1.chr2h_random 1258893 116 - 3178526
GCAGAGGGAGAGGCAUCCGAUGUUCAGACACCAGUUUGCAAGCCUAAGCUCG-CGUAUUUGGUUCAUGGGAUCUUGGUAAGCCUCUCACCUCAUCAACAUAAAGAGAAUAAAAAUUA
...(((((((((((..((((.((((.((.(((((..(((.(((....))).)-))...)))))))...)))).))))...))))))).))))......................... ( -40.20, z-score =  -3.90, R)
>droSec1.super_42 47745 116 - 298440
GCAGAGGGAGAGGCAUCCGAUGUUCAGACACCAGUUUGCAAGCCUAAGCUCG-CGUAUUUGGUUCAUGGGAUCUUGGUAAGCCUCUCACCUCAUCAACAUAAAGAGAAUAAAUAUUA
...(((((((((((..((((.((((.((.(((((..(((.(((....))).)-))...)))))))...)))).))))...))))))).))))......................... ( -40.20, z-score =  -3.86, R)
>droEre2.scaffold_4784 24210917 112 - 25762168
-CCGAGGGAGAGGCAUCCGAUGUUCAGGCACCAGGUUGCCAGCGUAAGCUCGUCGUAUUUAG-UCGUGGGAUCUUGGUAAGCCUCUUACCUCUCCAACAUAACGAAAAUAUUUA---
-..(((((((((((..((((.((((.((((......))))(((....)))............-.....)))).))))...))))))).))))......................--- ( -35.10, z-score =  -1.82, R)
>droYak2.chr2R 20773049 114 + 21139217
---GAGGGAGGGGCAUCCGAUGUUCAGGGACCAGGAUGCCGGCGUAAGCUCGUCGAUUUUGGGUCGUGGGAUCUUGGUAAGCCCCUUACCUCCCCAACAUAACGACAAUAAAUUUUA
---(((((((((((.(((........)))((((((((.(((((....)))...((((.....)))).)).))))))))..))))))).))))......................... ( -44.00, z-score =  -2.16, R)
>consensus
GC_GAGGGAGAGGCAUCCGAUGUUCAGGCACCAGUUUGCCAGCCUAAGCUCG_CGUAUUUGGUUCAUGGGAUCUUGGUAAGCCUCUCACCUCACCAACAUAACGAAAAUAAAUAUUA
...(((((((((((..((((.((((.((.(((((..(((.(((....))).).))...)))))))...)))).))))...))))))).))))......................... (-32.10 = -31.98 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:58:10 2011