Locus 8118

Sequence ID dm3.chr3L
Location 20,382,537 – 20,382,628
Length 91
Max. P 0.834168
window11168 window11169

overview

Window 8

Location 20,382,537 – 20,382,628
Length 91
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 58.77
Shannon entropy 0.70363
G+C content 0.35380
Mean single sequence MFE -17.42
Consensus MFE -6.44
Energy contribution -5.84
Covariance contribution -0.60
Combinations/Pair 1.60
Mean z-score -1.39
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.76
SVM RNA-class probability 0.810392
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20382537 91 + 24543557
----UAUUUUUGGUGUAAAUGUCCUACAAUU--AAUUGCUUAUUUAAAAC-AUCGGGGUAAAUGCCCC---GCGC--CGAAAUAGUUUGUUAUUCAAAGAGUG
----...(((((((((.............((--((........))))...-...(((((....)))))---))))--)))))...((((.....))))..... ( -19.20, z-score =  -1.25, R)
>droYak2.chr3L 4019759 94 - 24197627
---CAUUCUUAAAAUUAAUUGCUGUUAAAUU--AAUUGUUUAUUUAAAAC-CUCGGGGUAAAUACCCC---ACACAGCAGAAUAGUUUAUUAUUCAAUGACUG
---((((............(((((((((((.--....)))))........-...(((((....)))))---..))))))((((((....)))))))))).... ( -20.10, z-score =  -3.09, R)
>droSec1.super_11 276385 70 + 2888827
------------------------UGUU-UU--AAUUGUUUAUUUAAAAC-CUCGGGGUAAAUGCCCC---GCGC--CAAAAUAGUUUGUUAUUCAAUGAGUG
------------------------.(((-((--((........)))))))-((((((((....)))))---....--((((....)))).........))).. ( -14.70, z-score =  -1.62, R)
>droSim1.chr3L 19738940 70 + 22553184
------------------------UGUU-UU--AAUUGUUUAUUUAAAAC-CUCGGGGUAAAUGCCCC---GCGC--CAAAAUAGUUUGUUAUUCAAUGAGUG
------------------------.(((-((--((........)))))))-((((((((....)))))---....--((((....)))).........))).. ( -14.70, z-score =  -1.62, R)
>triCas2.ChLG6 4396166 101 - 13544221
AUUCGUUGACAAAUAUCUGUGAUAUCAGGCUCGAAAGUCUUAGUUGAGACACCCUGUAUAAACGUACCUUGAAGCACCAGAACAGU--GAAAAUGGGAGAGUG
.((((((..((....((((((...(((((.......(((((....))))).....((((....)))))))))..)).))))....)--)..))))))...... ( -18.40, z-score =   0.66, R)
>consensus
______U________U___UG___UGAA_UU__AAUUGUUUAUUUAAAAC_CUCGGGGUAAAUGCCCC___GCGC__CAAAAUAGUUUGUUAUUCAAUGAGUG
......................................................(((((....)))))................................... ( -6.44 =  -5.84 +  -0.60)

alignment

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secondary structure

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dotplot

Postscript

Window 9

Location 20,382,537 – 20,382,628
Length 91
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 58.77
Shannon entropy 0.70363
G+C content 0.35380
Mean single sequence MFE -16.62
Consensus MFE -5.98
Energy contribution -5.54
Covariance contribution -0.44
Combinations/Pair 1.50
Mean z-score -1.49
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.85
SVM RNA-class probability 0.834168
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20382537 91 - 24543557
CACUCUUUGAAUAACAAACUAUUUCG--GCGC---GGGGCAUUUACCCCGAU-GUUUUAAAUAAGCAAUU--AAUUGUAGGACAUUUACACCAAAAAUA----
.........................(--(.((---((((......)))))((-((((((..(((....))--)....))))))))...).)).......---- ( -16.30, z-score =  -1.16, R)
>droYak2.chr3L 4019759 94 + 24197627
CAGUCAUUGAAUAAUAAACUAUUCUGCUGUGU---GGGGUAUUUACCCCGAG-GUUUUAAAUAAACAAUU--AAUUUAACAGCAAUUAAUUUUAAGAAUG---
...((...(((((......)))))((((((.(---(((((....))))))..-((((.....))))....--......))))))...........))...--- ( -20.20, z-score =  -2.29, R)
>droSec1.super_11 276385 70 - 2888827
CACUCAUUGAAUAACAAACUAUUUUG--GCGC---GGGGCAUUUACCCCGAG-GUUUUAAAUAAACAAUU--AA-AACA------------------------
..(((.........((((....))))--....---((((......)))))))-(((((((........))--))-))).------------------------ ( -15.10, z-score =  -2.53, R)
>droSim1.chr3L 19738940 70 - 22553184
CACUCAUUGAAUAACAAACUAUUUUG--GCGC---GGGGCAUUUACCCCGAG-GUUUUAAAUAAACAAUU--AA-AACA------------------------
..(((.........((((....))))--....---((((......)))))))-(((((((........))--))-))).------------------------ ( -15.10, z-score =  -2.53, R)
>triCas2.ChLG6 4396166 101 + 13544221
CACUCUCCCAUUUUC--ACUGUUCUGGUGCUUCAAGGUACGUUUAUACAGGGUGUCUCAACUAAGACUUUCGAGCCUGAUAUCACAGAUAUUUGUCAACGAAU
...............--.....(((((((((....))))).......((((.(((((......)))).....).))))......)))).(((((....))))) ( -16.40, z-score =   1.06, R)
>consensus
CACUCAUUGAAUAACAAACUAUUUUG__GCGC___GGGGCAUUUACCCCGAG_GUUUUAAAUAAACAAUU__AA_AACA___CA___A________A______
...................................((((......))))...................................................... ( -5.98 =  -5.54 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:39:46 2011