Locus 3510

Sequence ID	dm3.chr2R
Location	5,896,232 – 5,896,293
Length	61
Max. P	0.990274

overview

Window 5

Location	5,896,232 – 5,896,293
Length	61
Sequences	6
Columns	61
Reading direction	forward
Mean pairwise identity	79.23
Shannon entropy	0.39799
G+C content	0.41440
Mean single sequence MFE	-15.05
Consensus MFE	-9.46
Energy contribution	-11.13
Covariance contribution	1.67
Combinations/Pair	1.25
Mean z-score	-2.59
Structure conservation index	0.63
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.41
SVM RNA-class probability	0.990274
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5896232 61 + 21146708
AAGUCAGCUGACUCAGACUUUAAUACGCGCAACCUACGAAUUUAACUGAGUUAAGCUGAUU
.(((((((((((((((...((((....((.......))...))))))))))).)))))))) ( -18.70, z-score =  -4.22, R)
>droSim1.chr2R 4525562 61 + 19596830
AAGUCAGCUGACUCAGACUUUAAUACGCGCACCCUACGAAUUUAACUGAGUUAAGCUGAUU
.(((((((((((((((...((((....((.......))...))))))))))).)))))))) ( -18.70, z-score =  -4.40, R)
>droSec1.super_1 3508887 56 + 14215200
-----AGCUGACUCAGACUUUAAUACGCGCACCCUACGAAAAUAACUGAGUUAAGCUGAUU
-----(((((((((((...(((.....((.......))....)))))))))).)))).... ( -10.80, z-score =  -2.25, R)
>droYak2.chr2L 18523714 61 + 22324452
AAGUCAGCUGAGUCAGACUUUAAUACGCGCACUCCACGAAUUUAACUGAGUUAAGCUGAUU
.((((((((((.((((.....(((.((.(.....).)).)))...)))).)).)))))))) ( -14.90, z-score =  -1.81, R)
>droEre2.scaffold_4929 18166897 61 - 26641161
AAGUCAGCUGACUCAGACUUUAAUACGCGCACUGCACGAAUUUAACUGAGCUAAGCUGAUU
.((((((((..(((((.....(((.((.((...)).)).)))...)))))...)))))))) ( -18.80, z-score =  -3.20, R)
>droAna3.scaffold_13266 2625838 55 - 19884421
-----AGC-AACAAGGACUUUAAGACCUGACUGUUAAGGACCUGACUGUGGUAAGCGAAUU
-----.((-(...(((.((((((.(......).)))))).)))...)))............ (  -8.40, z-score =   0.35, R)
>consensus
AAGUCAGCUGACUCAGACUUUAAUACGCGCACCCUACGAAUUUAACUGAGUUAAGCUGAUU
..((((((((((((((...((((....((.......))...))))))))))).))))))). ( -9.46 = -11.13 +   1.67)

alignment

secondary structure

dotplot

Window 6

Location	5,896,232 – 5,896,293
Length	61
Sequences	6
Columns	61
Reading direction	reverse
Mean pairwise identity	79.23
Shannon entropy	0.39799
G+C content	0.41440
Mean single sequence MFE	-14.47
Consensus MFE	-10.09
Energy contribution	-10.96
Covariance contribution	0.87
Combinations/Pair	1.27
Mean z-score	-1.62
Structure conservation index	0.70
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.12
SVM RNA-class probability	0.895728
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5896232 61 - 21146708
AAUCAGCUUAACUCAGUUAAAUUCGUAGGUUGCGCGUAUUAAAGUCUGAGUCAGCUGACUU
..((((((..((((((...(((.(((.......))).))).....)))))).))))))... ( -16.20, z-score =  -2.22, R)
>droSim1.chr2R 4525562 61 - 19596830
AAUCAGCUUAACUCAGUUAAAUUCGUAGGGUGCGCGUAUUAAAGUCUGAGUCAGCUGACUU
..((((((..((((((...(((.(((.......))).))).....)))))).))))))... ( -16.20, z-score =  -2.05, R)
>droSec1.super_1 3508887 56 - 14215200
AAUCAGCUUAACUCAGUUAUUUUCGUAGGGUGCGCGUAUUAAAGUCUGAGUCAGCU-----
....((((..((((((..(((((.(((.(.....).))).))))))))))).))))----- ( -12.60, z-score =  -1.49, R)
>droYak2.chr2L 18523714 61 - 22324452
AAUCAGCUUAACUCAGUUAAAUUCGUGGAGUGCGCGUAUUAAAGUCUGACUCAGCUGACUU
..((((((....((((...(((.((((.....)))).))).....))))...))))))... ( -14.60, z-score =  -1.19, R)
>droEre2.scaffold_4929 18166897 61 + 26641161
AAUCAGCUUAGCUCAGUUAAAUUCGUGCAGUGCGCGUAUUAAAGUCUGAGUCAGCUGACUU
..((((((..((((((...(((.(((((...))))).))).....)))))).))))))... ( -21.20, z-score =  -3.28, R)
>droAna3.scaffold_13266 2625838 55 + 19884421
AAUUCGCUUACCACAGUCAGGUCCUUAACAGUCAGGUCUUAAAGUCCUUGUU-GCU-----
.....((..(((.......)))....((((...(((.(.....).)))))))-)).----- (  -6.00, z-score =   0.50, R)
>consensus
AAUCAGCUUAACUCAGUUAAAUUCGUAGGGUGCGCGUAUUAAAGUCUGAGUCAGCUGACUU
..((((((..((((((.......(((.......))).........)))))).))))))... (-10.09 = -10.96 +   0.87)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:11:32 2011