Locus 4502

Sequence ID	dm3.chr2R
Location	13,540,920 – 13,541,052
Length	132
Max. P	0.997276

overview

Window 6

Location	13,540,920 – 13,541,010
Length	90
Sequences	7
Columns	113
Reading direction	reverse
Mean pairwise identity	64.33
Shannon entropy	0.65241
G+C content	0.47676
Mean single sequence MFE	-29.05
Consensus MFE	-13.09
Energy contribution	-13.29
Covariance contribution	0.19
Combinations/Pair	1.47
Mean z-score	-2.39
Structure conservation index	0.45
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.07
SVM RNA-class probability	0.997276
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13540920 90 - 21146708
------GAAAGAGGCUGCCAGGCGGCGUUGAUAAUGGUAAUGUCGUUGCCGCCUCCGCAUGGAAA-UUGCUUAAAAUUUC-CCAUUCACAUAUGCACC---------------
------....(((((.((..((((((((((.......)))))))))))).))))).(((((((((-((......))))))-).........))))...--------------- ( -29.20, z-score =  -1.96, R)
>droPer1.super_4 1165268 75 + 7162766
----GCUGGAAGGACCGGCA--UUGUGAUGAUAAUGGUAAUGCUGUUACGUCCUCC-UGCCGGAAUUUACUUAAAACUCCCC-------------------------------
----((.(((.(((((((((--(((..((....))..))))))))....)))))))-.)).(((.(((.....))).)))..------------------------------- ( -22.10, z-score =  -2.66, R)
>droAna3.scaffold_13266 9243281 102 + 19884421
-----------AGUCAGGCAGGCAACGAUGAUAAUGGUAAUGUUGUUACCGCCUUCGUCUCGAAAUUUACUCAAAACUCUGCCAAUUAUAUAUUGCACAGGCAUAAGGACAAA
-----------.(((.((((((....(((((...(((((((...)))))))...)))))..((.......)).....))))))..........(((....)))....)))... ( -24.70, z-score =  -1.55, R)
>droEre2.scaffold_4845 7770174 96 - 22589142
------------GGCUGUCG-GCGGCGAUGAUAAUGGCAAUGUCGUUGCCGCCUCCGCAUGGAAA-UCACUUAAAAUUUU-CCUUUCACAUGUGCCCCAAAGCUCCCCACA--
------------((((...(-((((((((((((.......)))))))))))))..((((((((((-..............-..)))).))))))......)))).......-- ( -31.99, z-score =  -2.66, R)
>droYak2.chr2R 5496143 92 + 21139217
-----------AGGCUGUCGUGUGGCGAUGAUAAUGCUAAUGUCGUUGCCGCCUCCGCAUGGAAA-UCACUUAAAAUUUU-CCUUUCACAUGUGUCCCAAAUCUA--------
-----------.((.....(.((((((((((((.......)))))))))))))..((((((((((-..............-..)))).))))))..)).......-------- ( -24.69, z-score =  -2.45, R)
>droSec1.super_1 11040377 96 - 14215200
GGAAGAGGAAGAGGCUGCCAGGCGGCGAUGAUAAUGGUAAUGUCGUUGCCGCCUCCGCAUGGAAA-UUGCUUAAAAUUUC-CCAUUCACAUAUGCACC---------------
(((...((.((...)).)).(((((((((((((.......))))))))))))))))(((((((((-((......))))))-).........))))...--------------- ( -34.40, z-score =  -2.51, R)
>droSim1.chr2R 12277705 96 - 19596830
GGAAGUGGAAGAGGCUGCCAGGCGGCGAUGAUAAUGGUAAUGUCGUUGCCGCCUCCGCAUGGAAA-UUGCUUAAAAUUUC-CCAUUCACAUAUGCACC---------------
....(((((......(((.((((((((((((((.......))))))))))))))..))).(((((-((......))))))-)..))))).........--------------- ( -36.30, z-score =  -2.96, R)
>consensus
_________A_AGGCUGCCAGGCGGCGAUGAUAAUGGUAAUGUCGUUGCCGCCUCCGCAUGGAAA_UUACUUAAAAUUUC_CCAUUCACAUAUGCACC_______________
...............(((...((((((((((((.......))))))))))))....)))...................................................... (-13.09 = -13.29 +   0.19)

alignment

secondary structure

dotplot

Window 7

Location	13,540,944 – 13,541,046
Length	102
Sequences	8
Columns	109
Reading direction	reverse
Mean pairwise identity	62.11
Shannon entropy	0.74939
G+C content	0.49455
Mean single sequence MFE	-30.47
Consensus MFE	-15.79
Energy contribution	-15.58
Covariance contribution	-0.21
Combinations/Pair	1.84
Mean z-score	-1.45
Structure conservation index	0.52
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.68
SVM RNA-class probability	0.994231
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13540944 102 - 21146708
UUAAUUAAGUGGCAAGCAGGAAGAGGAACA------GGAAGUGAAAGAGGCUGCCAGGCGGCGUUGAUAAUGGUAAUGUCGUUGCCGCCUCCGCAUGGAAA-UUGCUUA
.....((((..(((.((.(((.........------((.(((.......))).)).(((((((.(((((.......))))).)))))))))))).))....-)..)))) ( -28.90, z-score =  -0.45, R)
>dp4.chr3 9111298 92 + 19779522
UUAAUUAAGUGCUCGGCUGGGCCUGGGCUG--------------GAAGGACCGGCAG--UGUGAUGAUAAUGGUAAUGCUGUUACGUCCUCCUCCCAGAAU-UUACUUA
.....(((((((((....))))(((((..(--------------((.((((.(((((--(((.............))))))))..))))))).)))))...-..))))) ( -30.32, z-score =  -1.48, R)
>droAna3.scaffold_13266 9243321 94 + 19884421
UUAAUUAAGUGGCAUGCCG--AGCCGAACG-------------AGGCAGUCAGGCAGGCAACGAUGAUAAUGGUAAUGUUGUUACCGCCUUCGUCUCGAAAUUUACUCA
.....(((((..(.((((.--.(((..((.-------------.....))..))).))))..(((((...(((((((...)))))))...)))))..)..))))).... ( -26.30, z-score =  -1.03, R)
>droEre2.scaffold_4845 7770211 87 - 22589142
--------GUAAUGAGUCGGGUGGCAGGCG------------GGAAGGGGCUGUC-GGCGGCGAUGAUAAUGGCAAUGUCGUUGCCGCCUCCGCAUGGAAA-UCACUUA
--------....(((.(((.((((..((((------------(.......)))))-(((((((((((((.......))))))))))))).)))).)))...-))).... ( -34.70, z-score =  -1.83, R)
>droYak2.chr2R 5496174 94 + 21139217
UUAAUUAAGUGGCAGGCGGGCAGGCGAACA--------------GGGAGGCUGUCGUGUGGCGAUGAUAAUGCUAAUGUCGUUGCCGCCUCCGCAUGGAAA-UCACUUA
.....(((((((((.(((((...((((.((--------------(.....)))))))((((((((((((.......)))))))))))).))))).))....-))))))) ( -35.20, z-score =  -1.86, R)
>droSec1.super_1 11040401 108 - 14215200
UUAAUUAAGUGGCAGGCAGGAAGAGGAACAGGAAGUGGAAGAGGAAGAGGCUGCCAGGCGGCGAUGAUAAUGGUAAUGUCGUUGCCGCCUCCGCAUGGAAA-UUGCUUA
.....((((((((((.(...........((.....))...........).))))).(((((((((((((.......)))))))))))))(((....)))..-..))))) ( -34.55, z-score =  -2.07, R)
>droSim1.chr2R 12277729 108 - 19596830
UUAAUUAAGUGGCAGGCAGGAAGAGGAACAGGAAGUGGAAGUGGAAGAGGCUGCCAGGCGGCGAUGAUAAUGGUAAUGUCGUUGCCGCCUCCGCAUGGAAA-UUGCUUA
........((((..(((((........((...........))........)))))((((((((((((((.......)))))))))))))))))).......-....... ( -34.79, z-score =  -1.92, R)
>droWil1.scaffold_180569 515508 94 - 1405142
CUAAUUAAGUGGUUGCCCAAGCUGAUGAUG--------------AUACAGUUGAU-GAUGAUUGUGAUGCGGAAAAUGUCGAAGUUGGUUUUUGGCUAGAAAUUACUUA
.....((((((((((((.((((..((....--------------.(((((((...-...)))))))...(((......)))..))..))))..)))....))))))))) ( -19.00, z-score =  -0.95, R)
>consensus
UUAAUUAAGUGGCAGGCAGGAAGAGGAACA______________AAGAGGCUGCCAGGCGGCGAUGAUAAUGGUAAUGUCGUUGCCGCCUCCGCAUGGAAA_UUACUUA
.....((((((((.(((................................))))))((((((((((((((.......))))))))))))))..............))))) (-15.79 = -15.58 +  -0.21)

alignment

secondary structure

dotplot

Window 8

Location	13,540,954 – 13,541,052
Length	98
Sequences	7
Columns	110
Reading direction	reverse
Mean pairwise identity	63.68
Shannon entropy	0.67433
G+C content	0.52408
Mean single sequence MFE	-29.78
Consensus MFE	-11.21
Energy contribution	-10.46
Covariance contribution	-0.74
Combinations/Pair	1.90
Mean z-score	-1.23
Structure conservation index	0.38
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.32
SVM RNA-class probability	0.643876
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13540954 98 - 21146708
-----CAUCGGUUAAUUAAGUGGCAAGCAGGAAGAGGAACAGGAAGUGAAA------GAGGCUGCCAGGCGGCGUUGAUAAUGGUAAUGUCGUUGCC-GCCUCCGCAUGG
-----((((((.........(((((.((..........((.....))....------...)))))))(((((((.(((((.......))))).))))-))).))).))). ( -30.53, z-score =  -1.20, R)
>dp4.chr3 9111308 88 + 19779522
-----CAUCAGUUAAUUAAGUGCUCGGCUGG-GCCUGGGCUGGA-------------AGGACCGGCAG--UGUGAUGAUAAUGGUAAUGCUGUUACG-UCCUCCUCCCAG
-----..(((((..(........)..)))))-..(((((..(((-------------.((((.(((((--(((.............))))))))..)-)))))).))))) ( -27.92, z-score =  -0.47, R)
>droAna3.scaffold_13266 9243332 89 + 19884421
-----CAUCAGUUAAUUAAGUGGCAUGCCG--AGCCGAACGAGG-------------CAGUCAGGCAGGCAACGAUGAUAAUGGUAAUGUUGUUACC-GCCUUCGUCUCG
-----..............((.((.(((((--((((......))-------------)..)).)))).)).))(((((...(((((((...))))))-)...)))))... ( -26.00, z-score =  -1.08, R)
>droYak2.chr2R 5496184 95 + 21139217
AGACGCGUCGGUUAAUUAAGUGGCAGGCGGGCAGGCGAACAGG--------------GAGGCUGUCGUGUGGCGAUGAUAAUGCUAAUGUCGUUGCC-GCCUCCGCAUGG
....((((((.((....)).)))).((.(((((.((((.(((.--------------....))))))).)((((((((((.......))))))))))-)))))))).... ( -35.20, z-score =  -0.74, R)
>droSec1.super_1 11040411 104 - 14215200
-----CAUCGUUUAAUUAAGUGGCAGGCAGGAAGAGGAACAGGAAGUGGAAGAGGAAGAGGCUGCCAGGCGGCGAUGAUAAUGGUAAUGUCGUUGCC-GCCUCCGCAUGG
-----..............((((..(((((...............................)))))((((((((((((((.......))))))))))-)))))))).... ( -33.98, z-score =  -2.14, R)
>droSim1.chr2R 12277739 104 - 19596830
-----CAUCGGUUAAUUAAGUGGCAGGCAGGAAGAGGAACAGGAAGUGGAAGUGGAAGAGGCUGCCAGGCGGCGAUGAUAAUGGUAAUGUCGUUGCC-GCCUCCGCAUGG
-----((((((.........((((((.(...........((.....))...........).))))))(((((((((((((.......))))))))))-))).))).))). ( -36.85, z-score =  -2.82, R)
>droWil1.scaffold_180569 515518 90 - 1405142
-----CUGCUGCUAAUUAAGUGGUUGCCCA--AGCUGAUGAUGA------------UACAGUUGAUGA-UGAUUGUGAUGCGGAAAAUGUCGAAGUUGGUUUUUGGCUAG
-----..((..((.....))..)).(((.(--(((..((.....------------(((((((.....-.)))))))...(((......)))..))..))))..)))... ( -18.00, z-score =  -0.16, R)
>consensus
_____CAUCGGUUAAUUAAGUGGCAGGCAGG_AGAGGAACAGGA_____________GAGGCUGCCAGGCGGCGAUGAUAAUGGUAAUGUCGUUGCC_GCCUCCGCAUGG
.....................(((.(((................................))))))((((((((((((((.......)))))))))).))))........ (-11.21 = -10.46 +  -0.74)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:30:15 2011