Locus 1394

Sequence ID dm3.chr2L
Location 10,811,510 – 10,811,607
Length 97
Max. P 0.980861
window1898 window1899

overview

Window 8

Location 10,811,510 – 10,811,607
Length 97
Sequences 10
Columns 112
Reading direction forward
Mean pairwise identity 72.76
Shannon entropy 0.55884
G+C content 0.53229
Mean single sequence MFE -34.08
Consensus MFE -15.42
Energy contribution -15.33
Covariance contribution -0.09
Combinations/Pair 1.55
Mean z-score -2.25
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.06
SVM RNA-class probability 0.980861
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10811510 97 + 23011544
GAAAUUGCGCGGAUUUGUCUGCUCUCUCAAGCGGCACGCACUUAAGUGCG----UGUCCUUAUCCCUGC--GCGCAUCGGUAUGCGUGCGAGGGCCCAUGUGU---------
......(((((((....)))((((((..(((.(((((((((....)))))----)))))))......((--((((((....))))))))))))))....))))--------- ( -42.30, z-score =  -2.93, R)
>droSec1.super_3 6229928 97 + 7220098
GAAAUUGCGCGGAUUUGUCUGCUCUCUCAAGCGGCACGCACUUAAGUGCG----UGUCCUUAUCCCUGC--GCGCAUCGGUAUGUGUGCGAGGGCCCAUGUGU---------
......(((((((....)))((((((..(((.(((((((((....)))))----)))))))......((--((((((....))))))))))))))....))))--------- ( -40.40, z-score =  -2.67, R)
>droSim1.chr2L 10617906 101 + 22036055
GAAAUUGCGCGGAUUUGUCUGCUCUCUCAAGCGGCACGCACUUAAGUGCG----UGUCCUUAUCCCUGU--GCGCAUCGGUAUGUGUGCGAGGGCCCAUGUGUGUGU-----
......(((((.((.((...((((((..(((.(((((((((....)))))----)))))))......(.--.(((((....)))))..))))))).)).)).)))))----- ( -41.00, z-score =  -2.74, R)
>droYak2.chr2L 7218532 97 + 22324452
GAAAUUGCGCGGAUUUGUCUGUUCUCUCGAGCGGCACGCACUUAAGUGCG----UGUCCUUAUCCCUGC--GUGCAUCGGUAUGUGUGCCAGUGCCCAUGUGU---------
......((((((........((((....))))(((((((((....)))))----)))).......))))--))((((.((((....)))).))))........--------- ( -36.00, z-score =  -2.47, R)
>droEre2.scaffold_4929 12022371 95 - 26641161
GAAAUUGCGCGGAUUUGUCUGCUCUCUCAAGCGGCACGCACUUAAGUGCG----UGUCCUUAUCCCAGU--G--CAUCGGUGUGUGUGCGAGUGCCCAUGUCU---------
.....(((((((((..(...(((......)))(((((((((....)))))----)))))..))))..))--)--))..((..((.(.((....)))))..)).--------- ( -32.40, z-score =  -1.47, R)
>droAna3.scaffold_12916 14662869 100 + 16180835
GAAAUUGCGCGGAUUUGUCUGCUCUCUCAAGCGGCACGCACUUAAGUGCG----GGUCCUUAUCCUUUUCUAUGUGUCAGUGUGUCUGUGUGUCUCUGCAUGGC--------
......((((((((....(((((......)))(((((((((....))))(----(((....))))........)))))))...))))))))(((.......)))-------- ( -27.50, z-score =  -0.68, R)
>droPer1.super_10 2030643 94 + 3432795
GGAAUUGCGCGGAUUUGUCUGCUUCCUCAAGCGGCACGCACUUAAGUGCG----UGUCUUUGUCCU-----GCAUACUCGUAUGUGUGUGUGUUGCUGAGUGA---------
........(((((....))))).((((((.(((((((((((....(((((----.((...((....-----.)).)).)))))..))))))))))))))).))--------- ( -35.80, z-score =  -2.96, R)
>dp4.chr4_group4 3015992 94 + 6586962
GGGAUUGCGCGGAUUUGUCUGCUCCCUCAAGCGGCACGCACUUAAGUGCG----UGUCUUUGUCCU-----GCAUACUCGUAUGUGUGUGUGUUGCUGAGUGA---------
((((....(((((....)))))))))(((.(((((((((((....(((((----.((...((....-----.)).)).)))))..))))))))))))))....--------- ( -37.10, z-score =  -2.88, R)
>droWil1.scaffold_180703 369708 108 - 3946847
GAAAUUGCGCGGAUUUGUCUGUUCUCUCAAGCGGCACGCACUUAAGUGCA----UGUCCUUUGUCUUUCUCUCUCACUCACUCAUCCAAUCUCCAUCCAAUCCUCUUCUCCU
((.((((.(((((....))))).....((((.((((.((((....)))).----)))).)))).......................)))).))................... ( -17.00, z-score =  -1.61, R)
>droGri2.scaffold_15126 2041137 89 + 8399593
GAAAUUGCGCGGAUUUGGCUGUGCUCCCAAGCGGCACACACUUAACUGUCGAAUUGGGUUUAUCCCUGU--GUGUGUGUGUGUGUCAGCUU---------------------
......((((((......))))))....(((((((((((((...((...((....(((.....)))..)--).))..))))))))).))))--------------------- ( -31.30, z-score =  -2.10, R)
>consensus
GAAAUUGCGCGGAUUUGUCUGCUCUCUCAAGCGGCACGCACUUAAGUGCG____UGUCCUUAUCCCUGC__GCGCAUCGGUAUGUGUGCGAGUGCCCAUGUGU_________
..........((((.((.(((((......)))))))(((((....)))))...........))))......((((((......))))))....................... (-15.42 = -15.33 +  -0.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 10,811,510 – 10,811,607
Length 97
Sequences 10
Columns 112
Reading direction reverse
Mean pairwise identity 72.76
Shannon entropy 0.55884
G+C content 0.53229
Mean single sequence MFE -29.41
Consensus MFE -8.45
Energy contribution -8.47
Covariance contribution 0.02
Combinations/Pair 1.08
Mean z-score -2.42
Structure conservation index 0.29
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.779860
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10811510 97 - 23011544
---------ACACAUGGGCCCUCGCACGCAUACCGAUGCGC--GCAGGGAUAAGGACA----CGCACUUAAGUGCGUGCCGCUUGAGAGAGCAGACAAAUCCGCGCAAUUUC
---------.....((.((....((.(((((....))))).--))..((((..((.((----(((((....)))))))))((((....))))......)))))).))..... ( -40.30, z-score =  -3.82, R)
>droSec1.super_3 6229928 97 - 7220098
---------ACACAUGGGCCCUCGCACACAUACCGAUGCGC--GCAGGGAUAAGGACA----CGCACUUAAGUGCGUGCCGCUUGAGAGAGCAGACAAAUCCGCGCAAUUUC
---------.....((.((.(((((.((........)).))--).))((((..((.((----(((((....)))))))))((((....))))......)))))).))..... ( -35.60, z-score =  -2.94, R)
>droSim1.chr2L 10617906 101 - 22036055
-----ACACACACAUGGGCCCUCGCACACAUACCGAUGCGC--ACAGGGAUAAGGACA----CGCACUUAAGUGCGUGCCGCUUGAGAGAGCAGACAAAUCCGCGCAAUUUC
-----........(((.((....))...))).....(((((--....((((..((.((----(((((....)))))))))((((....))))......)))))))))..... ( -34.70, z-score =  -3.33, R)
>droYak2.chr2L 7218532 97 - 22324452
---------ACACAUGGGCACUGGCACACAUACCGAUGCAC--GCAGGGAUAAGGACA----CGCACUUAAGUGCGUGCCGCUCGAGAGAACAGACAAAUCCGCGCAAUUUC
---------........(((.(((........))).)))..--((..((((..((.((----(((((....)))))))))(.((....)).)......))))..))...... ( -29.60, z-score =  -2.11, R)
>droEre2.scaffold_4929 12022371 95 + 26641161
---------AGACAUGGGCACUCGCACACACACCGAUG--C--ACUGGGAUAAGGACA----CGCACUUAAGUGCGUGCCGCUUGAGAGAGCAGACAAAUCCGCGCAAUUUC
---------.....((.((....((((.......).))--)--....((((..((.((----(((((....)))))))))((((....))))......)))))).))..... ( -32.90, z-score =  -3.01, R)
>droAna3.scaffold_12916 14662869 100 - 16180835
--------GCCAUGCAGAGACACACAGACACACUGACACAUAGAAAAGGAUAAGGACC----CGCACUUAAGUGCGUGCCGCUUGAGAGAGCAGACAAAUCCGCGCAAUUUC
--------....(((.........(((.....)))............((((..((.(.----(((((....))))).)))((((....))))......))))..)))..... ( -26.40, z-score =  -2.95, R)
>droPer1.super_10 2030643 94 - 3432795
---------UCACUCAGCAACACACACACAUACGAGUAUGC-----AGGACAAAGACA----CGCACUUAAGUGCGUGCCGCUUGAGGAAGCAGACAAAUCCGCGCAAUUCC
---------........................((((.(((-----.(((....(.((----(((((....))))))).)((((....)))).......)))..))))))). ( -24.40, z-score =  -2.01, R)
>dp4.chr4_group4 3015992 94 - 6586962
---------UCACUCAGCAACACACACACAUACGAGUAUGC-----AGGACAAAGACA----CGCACUUAAGUGCGUGCCGCUUGAGGGAGCAGACAAAUCCGCGCAAUCCC
---------..((((..................)))).(((-----.(((....(.((----(((((....))))))).)((((....)))).......)))..)))..... ( -23.97, z-score =  -1.44, R)
>droWil1.scaffold_180703 369708 108 + 3946847
AGGAGAAGAGGAUUGGAUGGAGAUUGGAUGAGUGAGUGAGAGAGAAAGACAAAGGACA----UGCACUUAAGUGCGUGCCGCUUGAGAGAACAGACAAAUCCGCGCAAUUUC
.........((((((..((((..(((..((......(....).......(((.((.((----(((((....)))))))))..)))......))..))).))))..)))))). ( -25.10, z-score =  -1.89, R)
>droGri2.scaffold_15126 2041137 89 - 8399593
---------------------AAGCUGACACACACACACAC--ACAGGGAUAAACCCAAUUCGACAGUUAAGUGUGUGCCGCUUGGGAGCACAGCCAAAUCCGCGCAAUUUC
---------------------..((((.........(((((--((.(((.....)))(((......)))..)))))))..(((....))).))))................. ( -21.10, z-score =  -0.66, R)
>consensus
_________ACACAUGGGCACUCGCACACAUACCGAUGCGC__ACAGGGAUAAGGACA____CGCACUUAAGUGCGUGCCGCUUGAGAGAGCAGACAAAUCCGCGCAAUUUC
...............................................................((((....))))((((.(.(((..........)))..).))))...... ( -8.45 =  -8.47 +   0.02)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:31:04 2011