Locus 10379

Sequence ID	dm3.chr3R
Location	13,471,312 – 13,471,416
Length	104
Max. P	0.996935

overview

Window 5

Location	13,471,312 – 13,471,416
Length	104
Sequences	12
Columns	106
Reading direction	forward
Mean pairwise identity	73.25
Shannon entropy	0.60963
G+C content	0.52610
Mean single sequence MFE	-33.91
Consensus MFE	-31.53
Energy contribution	-29.43
Covariance contribution	-2.10
Combinations/Pair	1.48
Mean z-score	-0.81
Structure conservation index	0.93
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.66
SVM RNA-class probability	0.959142
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13471312 104 + 27905053
GGCCGUCCCCAAACUAAGAGGCUCAAUGGUCUAGGGGU-AUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCAG-UAUAUAAUUUU
((((..((((........(((((....))))).)))).-.....((((((.......))))))))))..((((((((.......))))))))..-........... ( -34.40, z-score =  -0.66, R)
>droEre2.scaffold_4770 9585429 104 - 17746568
GGCCAUUCUGAAAUUAAUAGGCUCAAUGGUCUAGGGGU-AUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCGAUUUAUUUCUUU-
.........(((((.(((.((((((((.......(((.-....(((((((.......)))))))..)))(((.......))).))))))))..))).)))))...- ( -35.20, z-score =  -1.37, R)
>droYak2.chr3R 2039048 104 + 28832112
GGCGGUCCUAAAAUUAAGAGGCUCAAUGGUCUAGGGGU-AUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCGACUUUUUUAUUU-
...((((((.......)).((((((((.......(((.-....(((((((.......)))))))..)))(((.......))).)))))))).)))).........- ( -33.10, z-score =  -0.38, R)
>droSec1.super_12 1431964 105 - 2123299
UGCCGCCCGAAAACUAAGAGGCUCAAUGGUCUAGGGGU-AUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCAGCUAUACAAUUUU
....((((.........).)))...(((((....(((.-....(((((((.......)))))))..)))((((((((.......)))))))).)))))........ ( -32.60, z-score =   0.06, R)
>droSim1.chr3R 19509738 105 - 27517382
GGCCGCCCGAAAACUAAGAGGCUCAAUGGUCUAGGGGU-AUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCAGCUAUACAAUUUU
((((((((.........).))).....))))((((((.-....(((((((.......)))))))..)))((((((((.......))))))))..)))......... ( -33.60, z-score =   0.02, R)
>droAna3.scaffold_13340 5764535 103 + 23697760
CGCCACGACAAAAUCAAGCGGCUCAAUGGUCUAGGGGU-AUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCGGAUUAAUUUUU--
.(((.(...........).)))....((((((..(((.-....(((((((.......)))))))..)))((((((((.......))))))))))))))......-- ( -34.70, z-score =  -0.85, R)
>dp4.chr2 7071374 103 - 30794189
GGACGCCUCAAAUGGAAGAGGCUCAAUGGUCUAGGGGU-AUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCGGAUUUAUUUUU--
.((.(((((........)))))))...(((((..(((.-....(((((((.......)))))))..)))((((((((.......))))))))))))).......-- ( -38.20, z-score =  -1.30, R)
>droPer1.super_3 874803 93 - 7375914
GGACGCCCAAAAUGGAAGAGGCUCAAUGGUCUAGGGGU-AUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCGG------------
((((((((..........(((((....)))))..))))-....(((((((.......)))))))))))(((((((((.......))))))))).------------ ( -37.30, z-score =  -1.47, R)
>droWil1.scaffold_181089 3831596 104 - 12369635
GAAUGGGGUAUGUUAACAGGUUUCCGUAGUGUAGUGGUUAUCACGUGUGCUUCACACGCACAAGGUCCCCGGUUCGAACCCGGGCGGAAACAGAUAUCAAUUUU--
......((((((....)..(((((((..((((.(((.....)))(((((...)))))))))......(((((.......))))))))))))..)))))......-- ( -30.40, z-score =  -0.72, R)
>droVir3.scaffold_13047 2095435 102 - 19223366
GGCGAUCAUAAAUGCAUGAGGCUCAAUGGUCUAGGGGU-AUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCGA-CGAACUUUU--
((.((((....((((...(((((....)))))....))-))...((((((.......))))))))))))((((((((.......))))))))..-.........-- ( -34.40, z-score =  -0.65, R)
>droMoj3.scaffold_6540 14509523 101 + 34148556
GGCGAUCGUCAACGCAAGAGGCUCAAUGGUCUAGGGGU-AUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCG--CAAAUUUUU--
.(((........(....).((((((((.......(((.-....(((((((.......)))))))..)))(((.......))).))))))))))--)........-- ( -37.40, z-score =  -1.51, R)
>droGri2.scaffold_15074 2188636 80 - 7742996
-------------------GUUUCCGUAGUGUAGCGGUUAUCACGUGUGCUUCACACGCACAAGGUCCCCGGUUCGAACCCGGGCGGGAACAAGUCUUU-------
-------------------(((((((..((((...(.......)(((((...)))))))))......(((((.......))))))))))))........------- ( -25.60, z-score =  -0.95, R)
>consensus
GGCCGCCCUAAAAGUAAGAGGCUCAAUGGUCUAGGGGU_AUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCGG_UUUAUUUUU__
...................((((((((.......(((......(((((((.......)))))))..)))(((.......))).))))))))............... (-31.53 = -29.43 +  -2.10)

alignment

secondary structure

dotplot

Window 6

Location	13,471,312 – 13,471,416
Length	104
Sequences	12
Columns	106
Reading direction	reverse
Mean pairwise identity	73.25
Shannon entropy	0.60963
G+C content	0.52610
Mean single sequence MFE	-31.98
Consensus MFE	-30.10
Energy contribution	-28.13
Covariance contribution	-1.97
Combinations/Pair	1.44
Mean z-score	-2.15
Structure conservation index	0.94
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.01
SVM RNA-class probability	0.996935
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13471312 104 - 27905053
AAAAUUAUAUA-CUGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAU-ACCCCUAGACCAUUGAGCCUCUUAGUUUGGGGACGGCC
.((((((....-..(((((((((((((.......)))))((..((((((.......)))))).))..-............))))))))..))))))(....).... ( -32.60, z-score =  -1.60, R)
>droEre2.scaffold_4770 9585429 104 + 17746568
-AAAGAAAUAAAUCGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAU-ACCCCUAGACCAUUGAGCCUAUUAAUUUCAGAAUGGCC
-...(((((.(((.(((((((((((((.......)))))((..((((((.......)))))).))..-............))))))))))).)))))......... ( -35.20, z-score =  -4.13, R)
>droYak2.chr3R 2039048 104 - 28832112
-AAAUAAAAAAGUCGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAU-ACCCCUAGACCAUUGAGCCUCUUAAUUUUAGGACCGCC
-..........((((((((((((((((.......)))))((..((((((.......)))))).))..-............))))))))((.......))))).... ( -31.50, z-score =  -2.65, R)
>droSec1.super_12 1431964 105 + 2123299
AAAAUUGUAUAGCUGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAU-ACCCCUAGACCAUUGAGCCUCUUAGUUUUCGGGCGGCA
...........((((((((((((((((.......)))))((..((((((.......)))))).))..-............)))))))(((........))))))). ( -33.50, z-score =  -1.35, R)
>droSim1.chr3R 19509738 105 + 27517382
AAAAUUGUAUAGCUGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAU-ACCCCUAGACCAUUGAGCCUCUUAGUUUUCGGGCGGCC
....((((..(((((((((((((((((.......)))))((..((((((.......)))))).))..-............))))))))...)))).....)))).. ( -32.90, z-score =  -1.15, R)
>droAna3.scaffold_13340 5764535 103 - 23697760
--AAAAAUUAAUCCGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAU-ACCCCUAGACCAUUGAGCCGCUUGAUUUUGUCGUGGCG
--.............((((((((((((.......)))))((..((((((.......)))))).))..-............)))))))(((((((...)))).))). ( -33.30, z-score =  -2.41, R)
>dp4.chr2 7071374 103 + 30794189
--AAAAAUAAAUCCGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAU-ACCCCUAGACCAUUGAGCCUCUUCCAUUUGAGGCGUCC
--............(((((((((((((.......)))))((..((((((.......)))))).))..-............))))(((((........))))))))) ( -34.00, z-score =  -3.07, R)
>droPer1.super_3 874803 93 + 7375914
------------CCGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAU-ACCCCUAGACCAUUGAGCCUCUUCCAUUUUGGGCGUCC
------------..(((((((((((((.......)))))((..((((((.......)))))).))..-............))))))))..(((.....)))..... ( -31.60, z-score =  -1.94, R)
>droWil1.scaffold_181089 3831596 104 + 12369635
--AAAAUUGAUAUCUGUUUCCGCCCGGGUUCGAACCGGGGACCUUGUGCGUGUGAAGCACACGUGAUAACCACUACACUACGGAAACCUGUUAACAUACCCCAUUC
--....((((((...((((((((((((.......)))))....(((((((((((...))))))).))))...........))))))).))))))............ ( -29.60, z-score =  -1.68, R)
>droVir3.scaffold_13047 2095435 102 + 19223366
--AAAAGUUCG-UCGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAU-ACCCCUAGACCAUUGAGCCUCAUGCAUUUAUGAUCGCC
--..((((.((-(.(((((((((((((.......)))))((..((((((.......)))))).))..-............)))))))).))).))))......... ( -33.90, z-score =  -3.06, R)
>droMoj3.scaffold_6540 14509523 101 - 34148556
--AAAAAUUUG--CGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAU-ACCCCUAGACCAUUGAGCCUCUUGCGUUGACGAUCGCC
--........(--((((((((((((((.......)))))((..((((((.......)))))).))..-............))))))).....((....))..))). ( -33.00, z-score =  -2.74, R)
>droGri2.scaffold_15074 2188636 80 + 7742996
-------AAAGACUUGUUCCCGCCCGGGUUCGAACCGGGGACCUUGUGCGUGUGAAGCACACGUGAUAACCGCUACACUACGGAAAC-------------------
-------........(((.((((((((.......)))))....(((((((((((...))))))).))))...........))).)))------------------- ( -22.70, z-score =  -0.03, R)
>consensus
__AAAAAUAAA_CCGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAU_ACCCCUAGACCAUUGAGCCUCUUAAUUUUAGGACGGCC
...............((((((((((((.......)))))....((((((.......))))))..................)))))))................... (-30.10 = -28.13 +  -1.97)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:22:53 2011