Locus 15407

Sequence ID	dm3.chrX
Location	18,892,143 – 18,892,256
Length	113
Max. P	0.829306

overview

Window 3

Location	18,892,143 – 18,892,237
Length	94
Sequences	11
Columns	103
Reading direction	forward
Mean pairwise identity	86.03
Shannon entropy	0.30034
G+C content	0.44844
Mean single sequence MFE	-25.90
Consensus MFE	-16.84
Energy contribution	-17.03
Covariance contribution	0.19
Combinations/Pair	1.07
Mean z-score	-2.10
Structure conservation index	0.65
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.83
SVM RNA-class probability	0.829306
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18892143 94 + 22422827
------UACUUAUAUUCAUAUCCAUAUCCUUU-UGCUGGAACGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACU
------..........................-...((((..(((((..((((((((((.....)))))).).).))..)).))))))).--........... ( -25.30, z-score =  -2.17, R)
>dp4.chrXL_group1e 10577002 95 + 12523060
------UACUCAUAUUCAUAUCCAUAUCCUUUCUGGCAUGGAGCCGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACU
------.....................((.....))..((((((.((..((((((((((.....)))))).).).))..))..)))))).--........... ( -28.50, z-score =  -2.53, R)
>droPer1.super_1203 3352 95 + 9866
------UACUCAUAUUCAUAUCCAUAUCCUUUCUGGCAUGGAGCCGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACU
------.....................((.....))..((((((.((..((((((((((.....)))))).).).))..))..)))))).--........... ( -28.50, z-score =  -2.53, R)
>droAna3.scaffold_13047 1773680 94 + 1816235
------UACUUGUAUUCAUAUCCAUAUCCUUU-GGCUGGAACGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACU
------...............(((.......)-)).((((..(((((..((((((((((.....)))))).).).))..)).))))))).--........... ( -26.40, z-score =  -1.61, R)
>droEre2.scaffold_4690 9173669 100 + 18748788
UACUUAUAUUCAUAUCCAUAUCCAUAUCCUUU-UGCUGGAACGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACU
................................-...((((..(((((..((((((((((.....)))))).).).))..)).))))))).--........... ( -25.30, z-score =  -2.05, R)
>droYak2.chrX 17498072 94 + 21770863
------UACUUAUAUUCAUAUCCAUAUCGCUU-UGCUGGAACGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACU
------..........................-...((((..(((((..((((((((((.....)))))).).).))..)).))))))).--........... ( -25.30, z-score =  -1.57, R)
>droSec1.super_8 1186670 94 + 3762037
------UAGUUAUAUUCAUAUCCAUAUCCUUU-UGCUGGAACGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACU
------.(((((........((((((......-)).))))..(((((..((((((((((.....)))))).).).))..)).))).....--......))))) ( -26.80, z-score =  -2.02, R)
>droSim1.chrX 14597911 94 + 17042790
------UACUUAUAUUCAUAUCCAUAUCCUUU-UGCUGGAACGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACU
------..........................-...((((..(((((..((((((((((.....)))))).).).))..)).))))))).--........... ( -25.30, z-score =  -2.17, R)
>droWil1.scaffold_181096 8113176 86 + 12416693
------------UACUUGAAUUCAUAUGCU-----GCAUAUCCUUGGUGCAGCUGCCGCAAAUUACAGUAAGACUUGUGGCAUGCUUCACACUUUUAUUAACU
------------....((((.......(((-----((((.......)))))))((((((((.((.......)).))))))))...)))).............. ( -21.70, z-score =  -1.66, R)
>droVir3.scaffold_12726 829827 95 + 2840439
------UACUUAUAUUCAUAUCCAUAUCCAUAUCCUUGUGCUGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACU
------...............................(((..(((((..((((((((((.....)))))).).).))..)).)))..)))--........... ( -25.90, z-score =  -2.42, R)
>droMoj3.scaffold_6473 7560548 95 - 16943266
------UACUUAUAUUCAUAUCCAUAUCCAUAUCCUUGUGCUGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACU
------...............................(((..(((((..((((((((((.....)))))).).).))..)).)))..)))--........... ( -25.90, z-score =  -2.42, R)
>consensus
______UACUUAUAUUCAUAUCCAUAUCCUUU_UGCUGGAACGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC__UUUUAUUAACU
.............................................((((((((((((((.....)))))).).).))))))...................... (-16.84 = -17.03 +   0.19)

alignment

secondary structure

dotplot

Window 4

Location	18,892,150 – 18,892,256
Length	106
Sequences	11
Columns	116
Reading direction	forward
Mean pairwise identity	86.98
Shannon entropy	0.27961
G+C content	0.45343
Mean single sequence MFE	-31.12
Consensus MFE	-22.92
Energy contribution	-23.70
Covariance contribution	0.78
Combinations/Pair	1.04
Mean z-score	-1.83
Structure conservation index	0.74
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.76
SVM RNA-class probability	0.809976
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18892150 106 + 22422827
------AUUCAUAUCCAUAUCCUUUU--GCUGGAACGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACUUUUUAAUGCAGCAAUGCCA
------.......((((((......)--).))))..((((((((((.((((((.....))))))).....((((......))))--.................))))))..))).. ( -30.10, z-score =  -1.49, R)
>dp4.chrXL_group1e 10577009 107 + 12523060
------AUUCAUAUCCAUAUCCUUUCUGGCAUGGA-GCCGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACUUUUUAAUGCAGCAAUGCCA
------.....................((((((((-((.((..((((((((((.....)))))).).).))..))..)))))..--...((((((....)))))).....))))). ( -35.10, z-score =  -2.58, R)
>droPer1.super_1203 3359 104 + 9866
------AUUCAUAUCCAUAUCCUUUCUGGCAUGGA-GCCGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACUUUUUAAUGC---AAUGCCA
------.....................((((((((-((.((..((((((((((.....)))))).).).))..))..)))))..--...((((((....)))))).---.))))). ( -35.10, z-score =  -3.34, R)
>droAna3.scaffold_13047 1773687 106 + 1816235
------AUUCAUAUCCAUAUCCUUU--GGCUGGAACGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACUUUUUAAUGCAGCUAUGCCA
------..................(--(((((((..(((((..((((((((((.....)))))).).).))..)).))))))).--...((((((....)))))).......)))) ( -30.40, z-score =  -1.26, R)
>droEre2.scaffold_4690 9173676 112 + 18748788
AUUCAUAUCCAUAUCCAUAUCCUUUU--GCUGGAACGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACUUUUUAAUGCAGCAAUGCCA
.............((((((......)--).))))..((((((((((.((((((.....))))))).....((((......))))--.................))))))..))).. ( -30.10, z-score =  -1.42, R)
>droYak2.chrX 17498079 106 + 21770863
------AUUCAUAUCCAUAUCGCUUU--GCUGGAACGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACUUUUUAAUGCAGCAAUGCCA
------...............((.((--((((....(((((..((((((((((.....)))))).).).))..)).))).....--...((((((....)))))))))))).)).. ( -33.10, z-score =  -1.90, R)
>droSec1.super_8 1186677 106 + 3762037
------AUUCAUAUCCAUAUCCUUUU--GCUGGAACGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACUUUUUAAUGCAGCAAUGCCA
------.......((((((......)--).))))..((((((((((.((((((.....))))))).....((((......))))--.................))))))..))).. ( -30.10, z-score =  -1.49, R)
>droSim1.chrX 14597918 106 + 17042790
------AUUCAUAUCCAUAUCCUUUU--GCUGGAACGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACUUUUUAAUGCAGCAAUGCCA
------.......((((((......)--).))))..((((((((((.((((((.....))))))).....((((......))))--.................))))))..))).. ( -30.10, z-score =  -1.49, R)
>droWil1.scaffold_181096 8113183 94 + 12416693
------------AUUCAUAUGCU-----GCAU-AUCCUUGGUGCAGCUGCCGCAAAUUACAGUAAGACUUGUGGCAUGCUUCACACUUUUAUUAACUUUUGAAUGCAGCUCA----
------------........(((-----((((-.......(((.(((((((((((.((.......)).)))))))).))).)))....(((........))))))))))...---- ( -28.20, z-score =  -2.41, R)
>droVir3.scaffold_12726 829834 107 + 2840439
------AUUCAUAUCCAUAUCCAUAU-CCUUGUGCUGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACUUUUUAAUGCAGCGUUGCCA
------...............((..(-(.....(((((....)))))((((((.....)))))).))..))(((((((((.((.--.................)).)))).))))) ( -28.87, z-score =  -1.13, R)
>droMoj3.scaffold_6473 7560555 107 - 16943266
------AUUCAUAUCCAUAUCCAUAU-CCUUGUGCUGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC--UUUUAUUAACUUUUUAAUGCAGCGCUGCCA
------....................-....(((((((.((..((((((((((.....)))))).).).))..)).........--....(((((....))))))))))))..... ( -31.20, z-score =  -1.62, R)
>consensus
______AUUCAUAUCCAUAUCCUUUU__GCUGGAACGCAGCUGCAGCUGCCGCAAAUUGCGGCACGACUUGUGGCAUGCUCCAC__UUUUAUUAACUUUUUAAUGCAGCAAUGCCA
....................................(((((((((((((((((((.(((.....))).)))))))).)))..........(((((....))))))))))..))).. (-22.92 = -23.70 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:58:40 2011