Locus 15299

Sequence ID	dm3.chrX
Location	18,329,461 – 18,329,560
Length	99
Max. P	0.964213

overview

Window 7

Location	18,329,461 – 18,329,560
Length	99
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	69.60
Shannon entropy	0.48479
G+C content	0.45650
Mean single sequence MFE	-31.42
Consensus MFE	-16.82
Energy contribution	-16.66
Covariance contribution	-0.16
Combinations/Pair	1.26
Mean z-score	-2.05
Structure conservation index	0.54
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.73
SVM RNA-class probability	0.964213
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18329461 99 + 22422827
------------------CCGAUUAGGAAUGACCCAUCAUUA---GCCAUGAUGAAUCUGGUAAGUGGGGCCAGUUAACUGACCAGCUAGAUUCCACGGAGCACGUGCCGAUGGUUUAUU
------------------((.....))(((((.(((((....---........(((((((((...(((...(((....))).))))))))))))((((.....))))..))))).))))) ( -30.00, z-score =  -1.60, R)
>droSec1.super_8 633174 102 + 3762037
------------------CCGAUUAGGAAUGACCCAUCAUUAUGAAUCGUGAUGAAUCUCAAAAGUGGGGCCAGUUAACUGGCCAGCUAGAUUCCACGGAACACGUGCCGAUGGGUUGUU
------------------((.....))((..(((((((..((((..(((((..((((((....(((..((((((....)))))).))))))))))))))....))))..)))))))..)) ( -40.30, z-score =  -4.16, R)
>droSim1.chrX 14142824 102 + 17042790
------------------CCGAUUAGGAAUGACCCAUCAUUAUGAAUCGUGAUGAAUCUGAAAAGUGGGGCCAGUUAACUGGGCAGCUAGAUUCCACGGAGCACGUGCCGAUGGGUUGUU
------------------((.....))((..(((((((........(((((..((((((....(((..(.((((....)))).).)))))))))))))).((....)).)))))))..)) ( -36.30, z-score =  -2.74, R)
>droYak2.chrX 16947743 113 + 21770863
GCCAUAAGUAUUUAUACGCCGAUUAGGCAUGACCUAUCAUUA---GCAAUGAUGAAUCUGAAUAAUGGGGCCAGUAAGCUGGUUAACUGGAUUCCAUCAAACACGUGCUGCUGAUU----
..(((..(((....)))(((.....))))))....((((.((---(((.((((((((((.........((((((....))))))....))))).)))))......))))).)))).---- ( -27.52, z-score =  -0.46, R)
>droEre2.scaffold_4690 8648841 90 + 18748788
------------------CCGAGCAGGAAUGACCCAUCAUUA---GCUAUGAUGAAUCUGGCAAAUGUGGCCAGUAAGCUGGUUAACUAGAUGCUGAUGGAAAUAU-UUAUU--------
------------------((((((..........((((((..---...)))))).((((((......(((((((....))))))).)))))))))..)))......-.....-------- ( -23.00, z-score =  -1.30, R)
>consensus
__________________CCGAUUAGGAAUGACCCAUCAUUA___GCCAUGAUGAAUCUGAAAAGUGGGGCCAGUUAACUGGCCAGCUAGAUUCCACGGAACACGUGCCGAUGGGUU_UU
.........................(((((((..((((((........))))))..))..........((((((....))))))......)))))......................... (-16.82 = -16.66 +  -0.16)

alignment

secondary structure

dotplot

Window 8

Location	18,329,461 – 18,329,560
Length	99
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	69.60
Shannon entropy	0.48479
G+C content	0.45650
Mean single sequence MFE	-27.06
Consensus MFE	-14.80
Energy contribution	-15.84
Covariance contribution	1.04
Combinations/Pair	1.05
Mean z-score	-1.65
Structure conservation index	0.55
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.05
SVM RNA-class probability	0.881758
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18329461 99 - 22422827
AAUAAACCAUCGGCACGUGCUCCGUGGAAUCUAGCUGGUCAGUUAACUGGCCCCACUUACCAGAUUCAUCAUGGC---UAAUGAUGGGUCAUUCCUAAUCGG------------------
...........(((....)))(((.(((((......((((((....))))))..........((((((((((...---..)))))))))))))))....)))------------------ ( -29.40, z-score =  -1.80, R)
>droSec1.super_8 633174 102 - 3762037
AACAACCCAUCGGCACGUGUUCCGUGGAAUCUAGCUGGCCAGUUAACUGGCCCCACUUUUGAGAUUCAUCACGAUUCAUAAUGAUGGGUCAUUCCUAAUCGG------------------
....((((((((....(((...((((((((((((..((((((....))))))...))....))))))..))))...)))..)))))))).............------------------ ( -33.10, z-score =  -2.87, R)
>droSim1.chrX 14142824 102 - 17042790
AACAACCCAUCGGCACGUGCUCCGUGGAAUCUAGCUGCCCAGUUAACUGGCCCCACUUUUCAGAUUCAUCACGAUUCAUAAUGAUGGGUCAUUCCUAAUCGG------------------
....((((((((((....))).((((((((((((.((.((((....))))...))))....))))))..)))).........))))))).............------------------ ( -26.30, z-score =  -1.50, R)
>droYak2.chrX 16947743 113 - 21770863
----AAUCAGCAGCACGUGUUUGAUGGAAUCCAGUUAACCAGCUUACUGGCCCCAUUAUUCAGAUUCAUCAUUGC---UAAUGAUAGGUCAUGCCUAAUCGGCGUAUAAAUACUUAUGGC
----.((((..((((..((..((((((...(((((..........)))))..))))))..))((....))..)))---)..))))..((((((((.....)))(((....)))..))))) ( -26.80, z-score =  -0.60, R)
>droEre2.scaffold_4690 8648841 90 - 18748788
--------AAUAA-AUAUUUCCAUCAGCAUCUAGUUAACCAGCUUACUGGCCACAUUUGCCAGAUUCAUCAUAGC---UAAUGAUGGGUCAUUCCUGCUCGG------------------
--------.....-........................(((((....((((.......))))((((((((((...---..))))))))))......))).))------------------ ( -19.70, z-score =  -1.47, R)
>consensus
AA_AAACCAUCGGCACGUGUUCCGUGGAAUCUAGCUGACCAGUUAACUGGCCCCACUUUUCAGAUUCAUCAUGGC___UAAUGAUGGGUCAUUCCUAAUCGG__________________
.........................(((((........((((....))))............((((((((((........)))))))))))))))......................... (-14.80 = -15.84 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:56:42 2011