Locus 199

Sequence ID	dm3.chr2L
Location	1,405,819 – 1,405,941
Length	122
Max. P	0.995545

overview

Window 7

Location	1,405,819 – 1,405,931
Length	112
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	53.08
Shannon entropy	0.84907
G+C content	0.32602
Mean single sequence MFE	-20.40
Consensus MFE	-7.54
Energy contribution	-7.32
Covariance contribution	-0.22
Combinations/Pair	1.50
Mean z-score	-0.96
Structure conservation index	0.37
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.76
SVM RNA-class probability	0.810633
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1405819 112 - 23011544
-GAUACUCUAAGCGAAGGGUAUUUUAAAACCUUAUGAGCUCAGCUCCU-AAGAGAGGAACAACAUUAAAAGAUAUAGAAAUUGUUAAUUAAAUUAUGUUCUUAUGGAUCAUUAC
-((((((((......)))))))).......((((.((((...)))).)-)))..(((((((...((((..((((.......))))..))))....)))))))............ ( -19.10, z-score =  -0.48, R)
>droSim1.chr2L 1379072 94 - 22036055
-AAUACCCUAACCAAAGGGUAUUCAUUAACAAUAUG-----AUCGCCU-AGGAG-------------AAAGAUAUAGAAAUUGUUAAUUAAAUUAAAUUGUUAUGGAUCAUUGC
-..((((((......))))))(((((.((((((.((-----(((.(..-..).)-------------)..((((.......)))).......))).)))))))))))....... ( -15.00, z-score =  -0.52, R)
>droSec1.super_14 1353520 107 - 2068291
-AAUACCCUAACCAAAGGGUAUUCAUUAACAAUAUG-----AUCUCCU-AGGAGUGGAACAACAUUAAAAGAUAUAGAAGUUGUUAAUUCAAUUAAAUUGUUAUGGAUCAUUGU
-..((((((......))))))(((((.((((((.((-----(((((..-..)))...((((((................))))))......)))).)))))))))))....... ( -21.69, z-score =  -1.26, R)
>droYak2.chr2L 1380250 96 - 22324452
-GAUACCCUAAACGCAGGGUAUCUCAAAACAUUCAG-----AGCUCUUGGGGAGUGAAGCAAUAUUACAAGAUAUAGCAAUAAUGGGAUAG--UGGAUCGUUAA----------
-((((((((......))))))))....((((((((.-----.((((.....))))...((.(((((....))))).)).............--))))).)))..---------- ( -23.20, z-score =  -1.84, R)
>dp4.chr4_group3 9924161 102 - 11692001
GAAUACCCUAUCGAAAGGGGGUUGCAUUGAAAUUCGAUAUACAUUUUAUAGGGUUAUAGAAUCAUAAUUUGAUGCUGCGAUUGCUUGUAAUUGCAGAUUUGU------------
....(((((((.((((....((...((((.....))))..)).)))))))))))......((((.....)))).(((((((((....)))))))))......------------ ( -23.20, z-score =  -1.20, R)
>droPer1.super_8 1131488 101 - 3966273
GAAUACCCUAUCGAAA-GGGGUUGCAUUGAAAUUCGAUAUACAUUUUAUAGGCAUAUAGAAUCAUAAUUUGAUGCUGCGAUUGCUUGUAAUUGGAGAUUUGU------------
(...(((((.......-)))))..)((((.....))))...((..(((((((((..(((.((((.....)))).)))....))))))))).)).........------------ ( -20.20, z-score =  -0.44, R)
>consensus
_AAUACCCUAACCAAAGGGUAUUCCAUAACAAUAUG_____AACUCCU_AGGAGUGGAGCAACAUUAAAAGAUAUAGAAAUUGUUAAUUAAAUUAGAUUGUUAU__________
.((((((((......))))))))........................................................................................... ( -7.54 =  -7.32 +  -0.22)

alignment

secondary structure

dotplot

Window 8

Location	1,405,829 – 1,405,941
Length	112
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	55.61
Shannon entropy	0.79049
G+C content	0.33409
Mean single sequence MFE	-18.57
Consensus MFE	-5.17
Energy contribution	-6.12
Covariance contribution	0.95
Combinations/Pair	1.12
Mean z-score	-1.67
Structure conservation index	0.28
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.78
SVM RNA-class probability	0.815591
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1405829 112 + 23011544
AUAAGAACAUAAUUUAAUUAACAAUUUCUAUAUCUUUUAAUGUUGUUCCUCUCUUAGGAGCUG-AGCUCAUAAGGUUUUAAAAUACCCUUCGCUUAGAGUAUCCACUUAGCGA-
...(((((...........((((((................)))))).....((((.((((..-.)))).)))))))))..........(((((..((((....)))))))))- ( -16.99, z-score =  -0.04, R)
>droSim1.chr2L 1379082 94 + 22036055
AUAACAAUUUAAUUUAAUUAACAAUUUCUAUAUCUUU-------------CUCCUAGG------CGAUCAUAUUGUUAAUGAAUACCCUUUGGUUAGGGUAUUCACUUAGCGA-
................(((((((((.......(((..-------------.....)))------.......)))))))))(((((((((......))))))))).........- ( -19.64, z-score =  -2.91, R)
>droSec1.super_14 1353530 107 + 2068291
AUAACAAUUUAAUUGAAUUAACAACUUCUAUAUCUUUUAAUGUUGUUCCACUCCUAGG------AGAUCAUAUUGUUAAUGAAUACCCUUUGGUUAGGGUAUUCACUUAGCGA-
.(((((((.....(((...((((((................))))))...(((....)------)).))).))))))).((((((((((......))))))))))........- ( -26.49, z-score =  -3.40, R)
>droYak2.chr2L 1380260 96 + 22324452
------------ACUAUCCCAUUAUUGCUAUAUCUUGUAAUAUUGCUUCACUCCCCAA----G-AGCUCUGAAUGUUUUGAGAUACCCUGCGUUUAGGGUAUCCACUUAGCGA-
------------.......((.((((((........)))))).)).(((((((.....----)-))...))))((((.((.(((((((((....)))))))))))...)))).- ( -21.20, z-score =  -1.95, R)
>dp4.chr4_group3 9924171 102 + 11692001
------------AAUUACAAGCAAUCGCAGCAUCAAAUUAUGAUUCUAUAACCCUAUAAAAUGUAUAUCGAAUUUCAAUGCAACCCCCUUUCGAUAGGGUAUUCCAUUCACCAG
------------...((((.((....))((.((((.....)))).))..............))))...........((((.((..((((......))))..)).))))...... ( -12.20, z-score =  -0.68, R)
>droPer1.super_8 1131498 101 + 3966273
------------AAUUACAAGCAAUCGCAGCAUCAAAUUAUGAUUCUAUAUGCCUAUAAAAUGUAUAUCGAAUUUCAAUGCAACCCC-UUUCGAUAGGGUAUUCCAUUCACCAG
------------........((....)).((((........(((((.((((((.........)))))).)))))...))))...(((-(......))))............... ( -14.90, z-score =  -1.03, R)
>consensus
____________AUUAACUAACAAUUGCUAUAUCUUUUAAUGUUGCUACACUCCUAGA____G_AGAUCAUAUUGUUAUGAAAUACCCUUUGGUUAGGGUAUUCACUUAGCGA_
.................................................................................((((((((......))))))))........... ( -5.17 =  -6.12 +   0.95)

alignment

secondary structure

dotplot

Window 9

Location	1,405,829 – 1,405,941
Length	112
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	55.61
Shannon entropy	0.79049
G+C content	0.33409
Mean single sequence MFE	-22.25
Consensus MFE	-10.19
Energy contribution	-10.75
Covariance contribution	0.56
Combinations/Pair	1.58
Mean z-score	-1.66
Structure conservation index	0.46
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.82
SVM RNA-class probability	0.995545
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1405829 112 - 23011544
-UCGCUAAGUGGAUACUCUAAGCGAAGGGUAUUUUAAAACCUUAUGAGCU-CAGCUCCUAAGAGAGGAACAACAUUAAAAGAUAUAGAAAUUGUUAAUUAAAUUAUGUUCUUAU
-(((((.((.(....).)).)))))...............((((.((((.-..)))).))))..(((((((...((((..((((.......))))..))))....))))))).. ( -20.90, z-score =  -0.59, R)
>droSim1.chr2L 1379082 94 - 22036055
-UCGCUAAGUGAAUACCCUAACCAAAGGGUAUUCAUUAACAAUAUGAUCG------CCUAGGAG-------------AAAGAUAUAGAAAUUGUUAAUUAAAUUAAAUUGUUAU
-......((((((((((((......))))))))))))((((((.(((((.------(....).)-------------)..((((.......)))).......))).)))))).. ( -20.10, z-score =  -2.94, R)
>droSec1.super_14 1353530 107 - 2068291
-UCGCUAAGUGAAUACCCUAACCAAAGGGUAUUCAUUAACAAUAUGAUCU------CCUAGGAGUGGAACAACAUUAAAAGAUAUAGAAGUUGUUAAUUCAAUUAAAUUGUUAU
-......((((((((((((......))))))))))))((((((.((((((------(....)))...((((((................))))))......)))).)))))).. ( -26.79, z-score =  -3.62, R)
>droYak2.chr2L 1380260 96 - 22324452
-UCGCUAAGUGGAUACCCUAAACGCAGGGUAUCUCAAAACAUUCAGAGCU-C----UUGGGGAGUGAAGCAAUAUUACAAGAUAUAGCAAUAAUGGGAUAGU------------
-..((((..((((((((((......)))))))).))...((((....(((-(----.....))))...((.(((((....))))).))...))))...))))------------ ( -23.10, z-score =  -1.56, R)
>dp4.chr4_group3 9924171 102 - 11692001
CUGGUGAAUGGAAUACCCUAUCGAAAGGGGGUUGCAUUGAAAUUCGAUAUACAUUUUAUAGGGUUAUAGAAUCAUAAUUUGAUGCUGCGAUUGCUUGUAAUU------------
....(.((((.((..((((......))))..)).)))).)...............(((((((((..(((.((((.....)))).)))..))..)))))))..------------ ( -20.30, z-score =  -0.24, R)
>droPer1.super_8 1131498 101 - 3966273
CUGGUGAAUGGAAUACCCUAUCGAAA-GGGGUUGCAUUGAAAUUCGAUAUACAUUUUAUAGGCAUAUAGAAUCAUAAUUUGAUGCUGCGAUUGCUUGUAAUU------------
....(.((((.(((.((((......)-)))))).)))).)...............(((((((((..(((.((((.....)))).)))....)))))))))..------------ ( -22.30, z-score =  -1.04, R)
>consensus
_UCGCUAAGUGAAUACCCUAACCAAAGGGUAUUCCAUAACAAUAUGAUCU_C____CCUAGGAGUGGAGCAACAUUAAAAGAUAUAGAAAUUGUUAAUUAAA____________
.......((((((((((((......))))))))))))............................................................................. (-10.19 = -10.75 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:08:31 2011