Locus 8353

Sequence ID	dm3.chr3L
Location	22,192,898 – 22,192,996
Length	98
Max. P	0.920758

overview

Window 5

Location	22,192,898 – 22,192,996
Length	98
Sequences	10
Columns	115
Reading direction	forward
Mean pairwise identity	84.59
Shannon entropy	0.30731
G+C content	0.29694
Mean single sequence MFE	-17.69
Consensus MFE	-11.67
Energy contribution	-11.83
Covariance contribution	0.16
Combinations/Pair	1.16
Mean z-score	-1.83
Structure conservation index	0.66
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.44
SVM RNA-class probability	0.696949
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 22192898 98 + 24543557
ACAGACG-UCAGCUUAACAAUAUGACAAAUACAAUUUUUCGUCU----------------UUAUAAUUUAAUUUUGCUAUAAAAACGCAUUAUUGUAUAAUGCGUUGGGCUAUCU
.......-..((((((((......................((.(----------------(((((............)))))).))(((((((...))))))))))))))).... ( -17.60, z-score =  -1.53, R)
>droVir3.scaffold_13049 14755929 101 + 25233164
ACAGCCA-UCAGCUUAACAAUGUGACAAAUACAAUUUUUCGUCUU-------------UUUUAUUAUUUCAUUUAACUAUAAAAACGCAUUAUUAUAUAAUGCGCUGGGCGUUGC
...(((.-.((((..........((((((.......))).))).(-------------((((((..((......))..))))))).(((((((...))))))))))))))..... ( -17.50, z-score =  -1.27, R)
>droGri2.scaffold_15110 6599488 99 - 24565398
ACAGCCAGUCAGCUUAACAAUAUGACAAAUACAAUUUUUCGUCUU-------------UUU-AUAAUUUCAUUUUACUAUGAAAACGCAUUAUUAUGUAAUGCGCUGGGC--UGC
.(((((...((((..........((((((.......))).)))..-------------...-....((((((......))))))..(((((((...))))))))))))))--)). ( -23.20, z-score =  -3.03, R)
>droWil1.scaffold_180698 109116 96 + 11422946
ACGUCUG-UCAGCUUAACAAUAUGACAAAUACAAUUUUUCGUCUC-------------UUU-AUAAUUUCAUUUUACUAUAAAAACGCAUUAUUAUAUAAUGCGUUAUGCU----
.....((-(((...........)))))..................-------------...-.....................((((((((((...)))))))))).....---- ( -13.40, z-score =  -1.63, R)
>droPer1.super_45 410381 114 - 618639
ACAGACG-UCAGCUUAACAAUAUGACAAAUACAAUUUUUCGUCUCUCUCCCUUUUUUUUAUUAUAAUUUCAUUUUACUAUAAAAACGCAUUAUUAUAUAAUGCGUUGGGCAUCCC
..(((((-(((...........))))(((......)))..))))....(((.....(((((..(((.......)))..)))))((((((((((...)))))))))))))...... ( -18.40, z-score =  -3.06, R)
>droAna3.scaffold_13337 21355172 94 + 23293914
ACAGUCG-UCAGCUUAACAAUAUGACAAAUACAAUUUUUCGUCU----------------UUAUAAUUCCAUUUCACUAUAAAAACGCAUUAUUAUAUAAUGCG---AGCAUCC-
.......-...((((.........................((.(----------------(((((............)))))).))(((((((...))))))))---)))....- ( -12.10, z-score =  -1.72, R)
>droEre2.scaffold_4784 21864366 97 + 25762168
ACAGACG-CGAGCUUAACAAUAUGACAAAUACAAUUUUUCGUCU----------------UUAUAAUUUCAUUUUGCUAUAACAACGCAUUAUUGUAUAAUGCGUUGGGCUAUU-
.......-..((((.........((((((.......))).))).----------------......................(((((((((((...)))))))))))))))...- ( -17.80, z-score =  -1.47, R)
>droYak2.chr3L 22577227 98 + 24197627
ACAGGCA-UCAGCUGAACAAUAUGACAAAAACAAUUUUUCGUCU----------------UUAUAAUUUAAUUUUGCUAUAAAAACGCAUUAUUGUAUAAUGCGUUGGGCUUGCU
...((((-..((((.(((.....(((.((((....)))).))).----------------..........................(((((((...)))))))))).)))))))) ( -19.80, z-score =  -1.50, R)
>droSec1.super_11 2123264 98 + 2888827
ACAGACG-UCAGCUUAACAAUAUGACAAAUACAAUUUUUCGUCU----------------UUAUAAUUUAAUUUUGCUAUAAAAACGCAUUAUUGUAUAAUGCGUUGGGCUAUCU
.......-..((((((((......................((.(----------------(((((............)))))).))(((((((...))))))))))))))).... ( -17.60, z-score =  -1.53, R)
>droSim1.chr3L 21543003 98 + 22553184
ACAGACG-UCAGCUUAACAAUAUGACAAAUACAAUUUUUCGUCU----------------UUAUAAUUUAAUUUUGCUAUAAAAACGCAUUAUGGUAUAAUGCGUUGGGCUAUGU
....(((-(.((((((((......................((.(----------------(((((............)))))).))(((((((...))))))))))))))))))) ( -19.50, z-score =  -1.53, R)
>consensus
ACAGACG_UCAGCUUAACAAUAUGACAAAUACAAUUUUUCGUCU________________UUAUAAUUUCAUUUUACUAUAAAAACGCAUUAUUAUAUAAUGCGUUGGGCUAUCU
...........(((((.......((((((.......))).)))..........................................((((((((...)))))))).)))))..... (-11.67 = -11.83 +   0.16)

alignment

secondary structure

dotplot

Window 6

Location	22,192,898 – 22,192,996
Length	98
Sequences	10
Columns	115
Reading direction	reverse
Mean pairwise identity	84.59
Shannon entropy	0.30731
G+C content	0.29694
Mean single sequence MFE	-21.77
Consensus MFE	-14.61
Energy contribution	-14.77
Covariance contribution	0.16
Combinations/Pair	1.06
Mean z-score	-2.24
Structure conservation index	0.67
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.28
SVM RNA-class probability	0.920758
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 22192898 98 - 24543557
AGAUAGCCCAACGCAUUAUACAAUAAUGCGUUUUUAUAGCAAAAUUAAAUUAUAA----------------AGACGAAAAAUUGUAUUUGUCAUAUUGUUAAGCUGA-CGUCUGU
(((((((..((((((((((...))))))))))....((((((..(((.....)))----------------.((((((........))))))...)))))).)))..-.)))).. ( -19.20, z-score =  -1.65, R)
>droVir3.scaffold_13049 14755929 101 - 25233164
GCAACGCCCAGCGCAUUAUAUAAUAAUGCGUUUUUAUAGUUAAAUGAAAUAAUAAAA-------------AAGACGAAAAAUUGUAUUUGUCACAUUGUUAAGCUGA-UGGCUGU
.....((((((((((((((...))))))).(((((((.(((......))).))))))-------------).((((((........))))))..........)))).-.)))... ( -22.60, z-score =  -1.86, R)
>droGri2.scaffold_15110 6599488 99 + 24565398
GCA--GCCCAGCGCAUUACAUAAUAAUGCGUUUUCAUAGUAAAAUGAAAUUAU-AAA-------------AAGACGAAAAAUUGUAUUUGUCAUAUUGUUAAGCUGACUGGCUGU
(((--(((((((((((((.....))))))..((((((......))))))....-...-------------..((((((........))))))..........))))...)))))) ( -27.10, z-score =  -3.50, R)
>droWil1.scaffold_180698 109116 96 - 11422946
----AGCAUAACGCAUUAUAUAAUAAUGCGUUUUUAUAGUAAAAUGAAAUUAU-AAA-------------GAGACGAAAAAUUGUAUUUGUCAUAUUGUUAAGCUGA-CAGACGU
----(((.(((((((((((...))))))).((((((((((........)))))-)))-------------))((((((........)))))).....)))).)))..-....... ( -21.00, z-score =  -2.46, R)
>droPer1.super_45 410381 114 + 618639
GGGAUGCCCAACGCAUUAUAUAAUAAUGCGUUUUUAUAGUAAAAUGAAAUUAUAAUAAAAAAAAGGGAGAGAGACGAAAAAUUGUAUUUGUCAUAUUGUUAAGCUGA-CGUCUGU
.((((((((((((((((((...)))))))))).(((((((........))))))).........))).....((((((........))))))...............-))))).. ( -25.10, z-score =  -2.87, R)
>droAna3.scaffold_13337 21355172 94 - 23293914
-GGAUGCU---CGCAUUAUAUAAUAAUGCGUUUUUAUAGUGAAAUGGAAUUAUAA----------------AGACGAAAAAUUGUAUUUGUCAUAUUGUUAAGCUGA-CGACUGU
-((((((.---.(((((((...)))))))(((((((((((........)))))))----------------))))........))))))((((...........)))-)...... ( -20.40, z-score =  -1.79, R)
>droEre2.scaffold_4784 21864366 97 - 25762168
-AAUAGCCCAACGCAUUAUACAAUAAUGCGUUGUUAUAGCAAAAUGAAAUUAUAA----------------AGACGAAAAAUUGUAUUUGUCAUAUUGUUAAGCUCG-CGUCUGU
-....((.(((((((((((...)))))))))))...((((((.((((...(((((----------------..........)))))....)))).)))))).....)-)...... ( -22.00, z-score =  -2.39, R)
>droYak2.chr3L 22577227 98 - 24197627
AGCAAGCCCAACGCAUUAUACAAUAAUGCGUUUUUAUAGCAAAAUUAAAUUAUAA----------------AGACGAAAAAUUGUUUUUGUCAUAUUGUUCAGCUGA-UGCCUGU
.(((.((..((((((((((...))))))))))....((((..(((...((.((((----------------((((((....)))))))))).))...)))..)))).-.)).))) ( -22.20, z-score =  -2.46, R)
>droSec1.super_11 2123264 98 - 2888827
AGAUAGCCCAACGCAUUAUACAAUAAUGCGUUUUUAUAGCAAAAUUAAAUUAUAA----------------AGACGAAAAAUUGUAUUUGUCAUAUUGUUAAGCUGA-CGUCUGU
(((((((..((((((((((...))))))))))....((((((..(((.....)))----------------.((((((........))))))...)))))).)))..-.)))).. ( -19.20, z-score =  -1.65, R)
>droSim1.chr3L 21543003 98 - 22553184
ACAUAGCCCAACGCAUUAUACCAUAAUGCGUUUUUAUAGCAAAAUUAAAUUAUAA----------------AGACGAAAAAUUGUAUUUGUCAUAUUGUUAAGCUGA-CGUCUGU
...((((..((((((((((...))))))))))....((((((..(((.....)))----------------.((((((........))))))...)))))).)))).-....... ( -18.90, z-score =  -1.73, R)
>consensus
AGAAAGCCCAACGCAUUAUACAAUAAUGCGUUUUUAUAGCAAAAUGAAAUUAUAA________________AGACGAAAAAUUGUAUUUGUCAUAUUGUUAAGCUGA_CGUCUGU
.....((..((((((((((...))))))))))........................................((((((........))))))..........))........... (-14.61 = -14.77 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:44:03 2011