Locus 10373

Sequence ID	dm3.chr3R
Location	13,445,865 – 13,445,950
Length	85
Max. P	0.979574

overview

Window 7

Location	13,445,865 – 13,445,950
Length	85
Sequences	13
Columns	85
Reading direction	forward
Mean pairwise identity	88.24
Shannon entropy	0.28917
G+C content	0.56876
Mean single sequence MFE	-24.04
Consensus MFE	-22.58
Energy contribution	-22.62
Covariance contribution	0.04
Combinations/Pair	1.17
Mean z-score	-0.80
Structure conservation index	0.94
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.41
SVM RNA-class probability	0.682119
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13445865 85 + 27905053
UGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUCAGAAACUGU
.((((.(((((((.......))))))).)))).....(((.....)))((((........))))..................... ( -23.70, z-score =  -0.47, R)
>droSim1.chr3R 19485020 85 - 27517382
UGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUUGCUAACGCU
.((((.(((((((.......))))))).)))).........(((((((((((........)))).((......)).)))..)))) ( -26.60, z-score =  -1.27, R)
>droSec1.super_12 1407740 85 - 2123299
UGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGACGCAAAUACC
.((((.(((((((.......))))))).))))..........(((...((((........))))..(......).)))....... ( -23.90, z-score =  -1.14, R)
>droYak2.chr3R 2006652 85 + 28832112
UGGAGAUGCUGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUUGCAGAAAGU
.((.((((..(((........)))......((((.(((.(((((....))).)).))).))))...)))).))............ ( -17.80, z-score =   1.29, R)
>droEre2.scaffold_4770 9560487 85 - 17746568
UGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGAUGCGACUGAG
..(((.(((((((.......))))))).)))((.((((((.....)))((((........))))..........))).))..... ( -25.10, z-score =  -0.56, R)
>droAna3.scaffold_13340 5736719 85 + 23697760
UGGAGAUGCGGGGUAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGAUGUACAUGGU
.((((.(((((((.......))))))).))))..((((..........((((........))))((((((...)))))))))).. ( -29.40, z-score =  -1.78, R)
>dp4.chr2 7041878 85 - 30794189
UGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUUGUCAACUAU
.((((.(((((((.......))))))).)))).....(((.....)))((((........))))..................... ( -23.70, z-score =  -0.81, R)
>droPer1.super_3 845234 85 - 7375914
UGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUUGCCAACUGU
.((((.(((((((.......))))))).)))).....(((.....)))((((........))))..................... ( -23.70, z-score =  -0.36, R)
>droWil1.scaffold_181089 3825657 74 - 12369635
UGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCG-----------
.((((.(((((((.......))))))).)))).....(((.....)))((((........))))..........----------- ( -23.70, z-score =  -1.57, R)
>droVir3.scaffold_13047 2062971 84 - 19223366
UGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUUGGAAUCGU-
.((((.(((((((.......))))))).))))..........((((..((((........))))....(((.....))).))))- ( -26.10, z-score =  -0.73, R)
>droMoj3.scaffold_6540 19611495 75 - 34148556
UGGAGAUGCGGGGUAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGU----------
.((((.(((((((.......))))))).)))).....(((.....)))((((........))))...........---------- ( -24.70, z-score =  -1.60, R)
>droGri2.scaffold_14906 1941405 84 - 14172833
UGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCAUU-GAAACUGU
.((((.(((((((.......))))))).)))).....(((.....)))((((........))))............-........ ( -23.70, z-score =  -1.04, R)
>anoGam1.chr2R 51279388 76 - 62725911
UGGAGAUACCGGGGAUCGAACCCGGGGCCUUUCACAUGCAAAGCGAACGCUCUACCA-CUGAGCUAUAUCCCCCUCA--------
.((.(((((((((.......))))).......................((((.....-..))))..)))).))....-------- ( -20.40, z-score =  -0.36, R)
>consensus
UGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUUGCAAACGGU
.((((.(((((((.......))))))).)))).....(((.....)))((((........))))..................... (-22.58 = -22.62 +   0.04)

alignment

secondary structure

dotplot

Window 8

Location	13,445,865 – 13,445,950
Length	85
Sequences	13
Columns	85
Reading direction	reverse
Mean pairwise identity	88.24
Shannon entropy	0.28917
G+C content	0.56876
Mean single sequence MFE	-32.70
Consensus MFE	-31.49
Energy contribution	-31.53
Covariance contribution	0.04
Combinations/Pair	1.08
Mean z-score	-1.79
Structure conservation index	0.96
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.03
SVM RNA-class probability	0.979574
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13445865 85 - 27905053
ACAGUUUCUGACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCA
.(((...)))..((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))). ( -33.20, z-score =  -1.62, R)
>droSim1.chr3R 19485020 85 + 27517382
AGCGUUAGCAACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCA
.((....))...((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))). ( -35.00, z-score =  -2.09, R)
>droSec1.super_12 1407740 85 + 2123299
GGUAUUUGCGUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCA
............((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))). ( -33.10, z-score =  -1.30, R)
>droYak2.chr3R 2006652 85 - 28832112
ACUUUCUGCAACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCAGCAUCUCCA
............((((((((..((((.(((.(.((((....))))).))).))))......(((........))).)))))))). ( -30.20, z-score =  -0.92, R)
>droEre2.scaffold_4770 9560487 85 + 17746568
CUCAGUCGCAUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCA
............((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))). ( -33.10, z-score =  -1.08, R)
>droAna3.scaffold_13340 5736719 85 - 23697760
ACCAUGUACAUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUACCCCGCAUCUCCA
............((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))). ( -32.90, z-score =  -1.86, R)
>dp4.chr2 7041878 85 + 30794189
AUAGUUGACAACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCA
............((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))). ( -33.10, z-score =  -2.04, R)
>droPer1.super_3 845234 85 + 7375914
ACAGUUGGCAACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCA
......(....)((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))). ( -34.10, z-score =  -1.85, R)
>droWil1.scaffold_181089 3825657 74 + 12369635
-----------CGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCA
-----------.((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))). ( -33.10, z-score =  -2.57, R)
>droVir3.scaffold_13047 2062971 84 + 19223366
-ACGAUUCCAACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCA
-...........((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))). ( -33.10, z-score =  -1.77, R)
>droMoj3.scaffold_6540 19611495 75 + 34148556
----------ACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUACCCCGCAUCUCCA
----------..((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))). ( -32.90, z-score =  -2.86, R)
>droGri2.scaffold_14906 1941405 84 + 14172833
ACAGUUUC-AAUGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCA
........-..(((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))) ( -33.00, z-score =  -2.10, R)
>anoGam1.chr2R 51279388 76 + 62725911
--------UGAGGGGGAUAUAGCUCAG-UGGUAGAGCGUUCGCUUUGCAUGUGAAAGGCCCCGGGUUCGAUCCCCGGUAUCUCCA
--------....(((((((..(((((.-..(((((((....)))))))...)))...)).(((((.......)))))))))))). ( -28.30, z-score =  -1.23, R)
>consensus
ACAGUUUGCAACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCA
............((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))). (-31.49 = -31.53 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:22:46 2011