Locus 1834

Sequence ID dm3.chr2L
Location 14,243,274 – 14,243,405
Length 131
Max. P 0.994521
window2522 window2523 window2524

overview

Window 2

Location 14,243,274 – 14,243,375
Length 101
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 87.35
Shannon entropy 0.23977
G+C content 0.53254
Mean single sequence MFE -37.10
Consensus MFE -26.30
Energy contribution -27.75
Covariance contribution 1.45
Combinations/Pair 1.14
Mean z-score -3.08
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.34
SVM RNA-class probability 0.988852
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14243274 101 + 23011544
GGCAAGUGGGAGCAAAGUCCUGGCAAAAAGCCUACGUCAACA----GCAUCCAGACUAUGUAUCCCAAAAAUCCUGGCAGACAGCUGCCAGGAUGAGUCAUCGUC
(((...((((((((.((((..(((.....)))...((.....----)).....)))).))).)))))...((((((((((....))))))))))..)))...... ( -38.40, z-score =  -4.22, R)
>droSim1.chr2L 13986486 99 + 22036055
GGCCAGUGGGAGCAAAGUCCUGGCAAACAGCCUACGUCAACG----GCAUCCAGACUAUGUAUCCCAAAAUUCCUGGCAGACAGCUGCCAGGAUGAGUCAUCG--
(((((.((((((((.((((.(((......(((.........)----))..))))))).))).)))))....(((((((((....))))))))))).)))....-- ( -39.20, z-score =  -3.72, R)
>droSec1.super_3 500765 99 + 7220098
GGCCAGUGGGAGCAAAGUCCUGGCAAACAGCCUACGUCAACG----GCAUCCAGACUAUGUAUCCCAAAAUUCCUGGCAGACAGCUGCCAGGAUGAGUCAUCG--
(((((.((((((((.((((.(((......(((.........)----))..))))))).))).)))))....(((((((((....))))))))))).)))....-- ( -39.20, z-score =  -3.72, R)
>droYak2.chr2L 14341687 101 + 22324452
GGCAAGUGGGAGCAAAGUCCUGGGAAACAGCCUACGUCAACA----GCAUCCAGACUGUGUAUCCCAAAAAUCCUGGCAGACAGCUGCUAGGAUGAGUCAUCGUC
(((...((((((((.((((.(((....).((...........----))...)))))).))).)))))...((((((((((....))))))))))..)))...... ( -35.40, z-score =  -2.38, R)
>droEre2.scaffold_4929 15418020 101 - 26641161
GGCCAGUGGGAGCAAAGUCCUGGCAAACAGCCUACGUCAACA----GCAUCCAGACUAUGUAUCCCAAAAAUCCUGGCAGACAGCUACCAGGAUGAGUCAUCGUC
((((..((((((((.((((..(((.....)))...((.....----)).....)))).))).)))))...(((((((.((....)).)))))))).)))...... ( -31.10, z-score =  -2.03, R)
>droAna3.scaffold_12916 4640859 100 - 16180835
----AGGGGCAGAAAGGUCCUGGCAAAAAGCCUACGUCAACAUCCAGCAUCCAGACUCUGCAACAUAGAG-UCCUGGCAGACGUCUGGCUGGAUGAGUCAUGGCU
----.(((((......)))))(((.....)))...((((.((((((((..((((((((((.....)))))-).))))(((....))))))))))).....)))). ( -39.30, z-score =  -2.43, R)
>consensus
GGCCAGUGGGAGCAAAGUCCUGGCAAACAGCCUACGUCAACA____GCAUCCAGACUAUGUAUCCCAAAAAUCCUGGCAGACAGCUGCCAGGAUGAGUCAUCGUC
(((...((((((((.((((..(((.....)))...(....)............)))).))).)))))....(((((((((....)))))))))...)))...... (-26.30 = -27.75 +   1.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 14,243,314 – 14,243,405
Length 91
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 79.76
Shannon entropy 0.35772
G+C content 0.51627
Mean single sequence MFE -28.65
Consensus MFE -20.13
Energy contribution -21.22
Covariance contribution 1.09
Combinations/Pair 1.16
Mean z-score -2.80
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.71
SVM RNA-class probability 0.994521
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14243314 91 + 23011544
----CAGCAUCCAGACUAUGUAUCCCAAAAAUCCUGGCAGACAGCUGCCAGGAUGAGUCAUCGUCGACAUUCGCUUCGAAACAGGAUACAGCCGC-----
----..............(((((((.....((((((((((....))))))))))..(((......))).((((...))))...))))))).....----- ( -30.30, z-score =  -3.51, R)
>droSim1.chr2L 13986526 79 + 22036055
----CGGCAUCCAGACUAUGUAUCCCAAAAUUCCUGGCAGACAGCUGCCAGGAUGAGUCAUCGUCGA------------AACAGGAUACAGCCGC-----
----((((..........(((((((........(((((((....)))))))(((((....)))))..------------....))))))))))).----- ( -30.10, z-score =  -4.11, R)
>droSec1.super_3 500805 79 + 7220098
----CGGCAUCCAGACUAUGUAUCCCAAAAUUCCUGGCAGACAGCUGCCAGGAUGAGUCAUCGUCGA------------AACAGGAUACAGCCGC-----
----((((..........(((((((........(((((((....)))))))(((((....)))))..------------....))))))))))).----- ( -30.10, z-score =  -4.11, R)
>droYak2.chr2L 14341727 91 + 22324452
----CAGCAUCCAGACUGUGUAUCCCAAAAAUCCUGGCAGACAGCUGCUAGGAUGAGUCAUCGUCGACAUUCGCUUCGAAACAGGAUACAGCCGC-----
----(((........)))(((((((.....((((((((((....))))))))))..(((......))).((((...))))...))))))).....----- ( -28.20, z-score =  -2.19, R)
>droEre2.scaffold_4929 15418060 91 - 26641161
----CAGCAUCCAGACUAUGUAUCCCAAAAAUCCUGGCAGACAGCUACCAGGAUGAGUCAUCGUCGACAUUCGCUUCGAAACAGGAUACGGCCGC-----
----..............(((((((.....(((((((.((....)).)))))))..(((......))).((((...))))...))))))).....----- ( -23.00, z-score =  -1.16, R)
>droAna3.scaffold_12916 4640895 99 - 16180835
CAUCCAGCAUCCAGACUCUGCAACAUAGAG-UCCUGGCAGACGUCUGGCUGGAUGAGUCAUGGCUGCCAUUCAUUUUGAAACAGGAUAUACACACAAAGC
((((((((..((((((((((.....)))))-).))))(((....))))))))))).((.(((.(((...(((.....))).)))..)))))......... ( -30.20, z-score =  -1.73, R)
>consensus
____CAGCAUCCAGACUAUGUAUCCCAAAAAUCCUGGCAGACAGCUGCCAGGAUGAGUCAUCGUCGACAUUCGCUUCGAAACAGGAUACAGCCGC_____
..................(((((((......(((((((((....)))))))))...(((......)))...............))))))).......... (-20.13 = -21.22 +   1.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 14,243,314 – 14,243,405
Length 91
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 79.76
Shannon entropy 0.35772
G+C content 0.51627
Mean single sequence MFE -30.15
Consensus MFE -21.23
Energy contribution -22.95
Covariance contribution 1.72
Combinations/Pair 1.07
Mean z-score -1.75
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.01
SVM RNA-class probability 0.873403
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14243314 91 - 23011544
-----GCGGCUGUAUCCUGUUUCGAAGCGAAUGUCGACGAUGACUCAUCCUGGCAGCUGUCUGCCAGGAUUUUUGGGAUACAUAGUCUGGAUGCUG----
-----..(((((((((((((((((...((.....)).))).)))..((((((((((....))))))))))....)))))))..)))).........---- ( -32.80, z-score =  -2.19, R)
>droSim1.chr2L 13986526 79 - 22036055
-----GCGGCUGUAUCCUGUU------------UCGACGAUGACUCAUCCUGGCAGCUGUCUGCCAGGAAUUUUGGGAUACAUAGUCUGGAUGCCG----
-----.(((((((((((((((------------........)))...(((((((((....))))))))).....))))))))..........))))---- ( -30.40, z-score =  -2.76, R)
>droSec1.super_3 500805 79 - 7220098
-----GCGGCUGUAUCCUGUU------------UCGACGAUGACUCAUCCUGGCAGCUGUCUGCCAGGAAUUUUGGGAUACAUAGUCUGGAUGCCG----
-----.(((((((((((((((------------........)))...(((((((((....))))))))).....))))))))..........))))---- ( -30.40, z-score =  -2.76, R)
>droYak2.chr2L 14341727 91 - 22324452
-----GCGGCUGUAUCCUGUUUCGAAGCGAAUGUCGACGAUGACUCAUCCUAGCAGCUGUCUGCCAGGAUUUUUGGGAUACACAGUCUGGAUGCUG----
-----..(((((((((((((((((...((.....)).))).)))..(((((.((((....)))).)))))....)))))..)))))).........---- ( -26.60, z-score =  -0.27, R)
>droEre2.scaffold_4929 15418060 91 + 26641161
-----GCGGCCGUAUCCUGUUUCGAAGCGAAUGUCGACGAUGACUCAUCCUGGUAGCUGUCUGCCAGGAUUUUUGGGAUACAUAGUCUGGAUGCUG----
-----(((.(((((((((((((((...((.....)).))).)))..((((((((((....))))))))))....))))))).......)).)))..---- ( -30.11, z-score =  -1.44, R)
>droAna3.scaffold_12916 4640895 99 + 16180835
GCUUUGUGUGUAUAUCCUGUUUCAAAAUGAAUGGCAGCCAUGACUCAUCCAGCCAGACGUCUGCCAGGA-CUCUAUGUUGCAGAGUCUGGAUGCUGGAUG
...(..((.((....((...(((.....))).))..))))..)..(((((((((((((.(((((...((-(.....)))))))))))))...)))))))) ( -30.60, z-score =  -1.08, R)
>consensus
_____GCGGCUGUAUCCUGUUUCGAAGCGAAUGUCGACGAUGACUCAUCCUGGCAGCUGUCUGCCAGGAUUUUUGGGAUACAUAGUCUGGAUGCUG____
...........((((((...(((.....)))....(((.(((.(((((((((((((....)))))))))....))))...))).))).))))))...... (-21.23 = -22.95 +   1.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:39:44 2011