Locus 2557

Sequence ID	dm3.chr2L
Location	19,996,147 – 19,996,286
Length	139
Max. P	0.977442

overview

Window 5

Location	19,996,147 – 19,996,264
Length	117
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	75.25
Shannon entropy	0.46678
G+C content	0.52986
Mean single sequence MFE	-42.65
Consensus MFE	-24.80
Energy contribution	-25.67
Covariance contribution	0.87
Combinations/Pair	1.40
Mean z-score	-2.13
Structure conservation index	0.58
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.97
SVM RNA-class probability	0.977442
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19996147 117 + 23011544
GCUCCUUUGCUCCACUUCGCAUCCAGAGGCGGGUCGGAUUGAAGGGGGGACUGGUUGUUUGCAGGAAAUAGUGGGGAUGUUGGGGACCGGCAUCGCCUCCAAACAAUUACGUCAGUU
.(((((((..((((((.(((........)))))).)))..))))))).(((((((((((((.........(.((.((((((((...)))))))).)).))))))))))).))).... ( -43.10, z-score =  -1.02, R)
>droSim1.chr2L 19656690 115 + 22036055
GCUCCUUUGCUCCACUCCGCAUCCAGAGGCGGGUCGGAUUGAAGGGGG--CUGGUUGUUUGGAGGAAAUAGUGGGGAUGUUGGGGACCGGCAUCGCCUCCAAACAAUUACGUCAGUU
.(((((((..(((((.((((........)))))).)))..)))))))(--(((((((((((((((..........((((((((...)))))))).)))))))))))))).))..... ( -48.40, z-score =  -2.34, R)
>droSec1.super_7 3607511 116 + 3727775
GCUCCUUUGCUCCACUCCGCAUCCAGAGGCGGGUCGGAUUGAAGGGGGG-CUGGUUGUUUGGAGGAAAUAGUGGGGAUGUUGGGGACCGGCAUCGCCUCCAAACAAUUACGUCAGUU
.(((((((..(((((.((((........)))))).)))..)))))))((-(((((((((((((((..........((((((((...)))))))).)))))))))))))).))).... ( -51.60, z-score =  -2.96, R)
>droYak2.chr2R 6465355 106 + 21139217
GCUGAUUUGCUGCACUCCGCAUCCAGAGGCGGGUUG------AUGGG-----GGUUGUUUGGAGGAAAUAGUGGGGAUGUUGGGGACCGGCAUCGCCUCCAAACAAUUAAGUCAGUU
(((((((((.....((((((((((......))).))------.))))-----)((((((((((((..........((((((((...)))))))).))))))))))))))))))))). ( -42.30, z-score =  -2.53, R)
>droEre2.scaffold_4845 18257463 108 - 22589142
ACUCCUUUGCUCCACUCCGCAUCCGGAGGCGGGUUG------AGGGG---CUGGUUGUUUGGAGGAAAUAGUGGGGAUGUUGGGGACCGGUAUUGCCUCCAAACAAUUACGUCAGUU
...((((.((((..(((((....)))))..)))).)------)))((---(((((((((((((((.((((.(((............))).)))).)))))))))))))).))).... ( -47.20, z-score =  -2.99, R)
>droWil1.scaffold_180708 8900069 111 - 12563649
ACUAACCAAACUAACUAUGUAUUUAUUUAUGUUUUA-----AACCGCGAAACACUUGGA-GACGGAGACGAAGAGGGGACGGAAAUGCGGCAACUCCCCUAAAUAAUUACGUCAGUU
............(((((((((.((((((.((((((.-----......))))))((((..-..)(....).)))((((((.(......)(....))))))))))))).))))).)))) ( -23.30, z-score =  -0.94, R)
>consensus
GCUCCUUUGCUCCACUCCGCAUCCAGAGGCGGGUCG_____AAGGGGG__CUGGUUGUUUGGAGGAAAUAGUGGGGAUGUUGGGGACCGGCAUCGCCUCCAAACAAUUACGUCAGUU
.(((((.........(((((........))))).........))))).....(((((((((((((..........(((((((.....))))))).)))))))))))))......... (-24.80 = -25.67 +   0.87)

alignment

secondary structure

dotplot

Window 6

Location	19,996,147 – 19,996,264
Length	117
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	75.25
Shannon entropy	0.46678
G+C content	0.52986
Mean single sequence MFE	-29.88
Consensus MFE	-17.92
Energy contribution	-18.12
Covariance contribution	0.20
Combinations/Pair	1.52
Mean z-score	-1.08
Structure conservation index	0.60
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.10
SVM RNA-class probability	0.544019
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19996147 117 - 23011544
AACUGACGUAAUUGUUUGGAGGCGAUGCCGGUCCCCAACAUCCCCACUAUUUCCUGCAAACAACCAGUCCCCCCUUCAAUCCGACCCGCCUCUGGAUGCGAAGUGGAGCAAAGGAGC
....(((....(((((((.(((.((((..((............))..)))).))).)))))))...)))...((((...((((...(((........)))...))))...))))... ( -28.30, z-score =   0.22, R)
>droSim1.chr2L 19656690 115 - 22036055
AACUGACGUAAUUGUUUGGAGGCGAUGCCGGUCCCCAACAUCCCCACUAUUUCCUCCAAACAACCAG--CCCCCUUCAAUCCGACCCGCCUCUGGAUGCGGAGUGGAGCAAAGGAGC
...........(((((((((((.((((..((............))..)))).)))))))))))...(--(..((((...((((..((((........))))..))))...)))).)) ( -35.00, z-score =  -1.57, R)
>droSec1.super_7 3607511 116 - 3727775
AACUGACGUAAUUGUUUGGAGGCGAUGCCGGUCCCCAACAUCCCCACUAUUUCCUCCAAACAACCAG-CCCCCCUUCAAUCCGACCCGCCUCUGGAUGCGGAGUGGAGCAAAGGAGC
...........(((((((((((.((((..((............))..)))).)))))))))))....-....((((...((((..((((........))))..))))...))))... ( -34.50, z-score =  -1.30, R)
>droYak2.chr2R 6465355 106 - 21139217
AACUGACUUAAUUGUUUGGAGGCGAUGCCGGUCCCCAACAUCCCCACUAUUUCCUCCAAACAACC-----CCCAU------CAACCCGCCUCUGGAUGCGGAGUGCAGCAAAUCAGC
..((((.....(((((((((((.((((..((............))..)))).)))))))))))..-----.....------......(((((((....))))).))......)))). ( -30.20, z-score =  -2.42, R)
>droEre2.scaffold_4845 18257463 108 + 22589142
AACUGACGUAAUUGUUUGGAGGCAAUACCGGUCCCCAACAUCCCCACUAUUUCCUCCAAACAACCAG---CCCCU------CAACCCGCCUCCGGAUGCGGAGUGGAGCAAAGGAGU
...........(((((((((((.((((..((............))..)))).)))))))))))...(---(.(((------...(((((.((((....)))))))).)...))).)) ( -31.80, z-score =  -1.65, R)
>droWil1.scaffold_180708 8900069 111 + 12563649
AACUGACGUAAUUAUUUAGGGGAGUUGCCGCAUUUCCGUCCCCUCUUCGUCUCCGUC-UCCAAGUGUUUCGCGGUU-----UAAAACAUAAAUAAAUACAUAGUUAGUUUGGUUAGU
((((((((((.((((((((((((...............))))).........((((.-............))))..-----.......))))))).)))...)))))))........ ( -19.48, z-score =   0.24, R)
>consensus
AACUGACGUAAUUGUUUGGAGGCGAUGCCGGUCCCCAACAUCCCCACUAUUUCCUCCAAACAACCAG__CCCCCUU_____CAACCCGCCUCUGGAUGCGGAGUGGAGCAAAGGAGC
...........(((((((((((.((((..((............))..)))).))))))))))).........((((.....((..((((........))))..)).....))))... (-17.92 = -18.12 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	19,996,187 – 19,996,286
Length	99
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	79.46
Shannon entropy	0.38934
G+C content	0.47275
Mean single sequence MFE	-29.30
Consensus MFE	-18.57
Energy contribution	-19.35
Covariance contribution	0.78
Combinations/Pair	1.31
Mean z-score	-1.90
Structure conservation index	0.63
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.15
SVM RNA-class probability	0.899449
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19996187 99 + 23011544
GAAGGGGGGACUGGUUGUUUGCAG---GAAAUAGUGGGGAUGUUGGGGACCGGCAUCGCCUCCAAACAAUUACGUCAGUUUAGGCAUGACUUCUAAUUAACU
...((((((((((((((((((...---......(.((.((((((((...)))))))).)).))))))))))).))).((....))....)))))........ ( -28.00, z-score =  -0.78, R)
>droSim1.chr2L 19656730 97 + 22036055
--GAAGGGGGCUGGUUGUUUGGAG---GAAAUAGUGGGGAUGUUGGGGACCGGCAUCGCCUCCAAACAAUUACGUCAGUUUAGGCAUGACUUCUAAUUAACU
--((((..((((((((((((((((---(..........((((((((...)))))))).)))))))))))))).))).((....))....))))......... ( -33.40, z-score =  -2.72, R)
>droSec1.super_7 3607551 98 + 3727775
-GAAGGGGGGCUGGUUGUUUGGAG---GAAAUAGUGGGGAUGUUGGGGACCGGCAUCGCCUCCAAACAAUUACGUCAGUUUAGGCAUGACUUCUAAUUAACU
-..(((((((((((((((((((((---(..........((((((((...)))))))).)))))))))))))).))).((....))....)))))........ ( -33.50, z-score =  -2.61, R)
>droYak2.chr2R 6465391 92 + 21139217
-------AUGGGGGUUGUUUGGAG---GAAAUAGUGGGGAUGUUGGGGACCGGCAUCGCCUCCAAACAAUUAAGUCAGUUUAGGCAUGACUUAUAAUUAACU
-------......(((((((((((---(..........((((((((...)))))))).))))))))))))(((((((((....)).)))))))......... ( -31.80, z-score =  -3.54, R)
>droEre2.scaffold_4845 18257499 94 - 22589142
-----AGGGGCUGGUUGUUUGGAG---GAAAUAGUGGGGAUGUUGGGGACCGGUAUUGCCUCCAAACAAUUACGUCAGUUUAGGCAUGACUUCUAAUUAACU
-----(((((.(((((((((((((---(.((((.(((............))).)))).)))))))))))))).(((......)))....)))))........ ( -31.00, z-score =  -2.51, R)
>droWil1.scaffold_180708 8900105 97 - 12563649
-----AACCGCGAAACACUUGGAGACGGAGACGAAGAGGGGACGGAAAUGCGGCAACUCCCCUAAAUAAUUACGUCAGUUUAGUCACGAUGCCUAAUUAACU
-----...((.(((((..(((....))).((((((.((((((.(......)(....)))))))......)).)))).)))...)).)).............. ( -18.10, z-score =   0.79, R)
>consensus
_____GGGGGCUGGUUGUUUGGAG___GAAAUAGUGGGGAUGUUGGGGACCGGCAUCGCCUCCAAACAAUUACGUCAGUUUAGGCAUGACUUCUAAUUAACU
............(((((((((((............((.(((((((.....))))))).)))))))))))))..((((((....)).))))............ (-18.57 = -19.35 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:53:33 2011