Locus 3715

Sequence ID	dm3.chr2R
Location	7,356,792 – 7,356,892
Length	100
Max. P	0.997582

overview

Window 2

Location	7,356,792 – 7,356,892
Length	100
Sequences	10
Columns	118
Reading direction	forward
Mean pairwise identity	82.89
Shannon entropy	0.32990
G+C content	0.39990
Mean single sequence MFE	-28.23
Consensus MFE	-15.93
Energy contribution	-16.73
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.46
Structure conservation index	0.56
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.16
SVM RNA-class probability	0.901323
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 7356792 100 + 21146708
----------GAGCGAGAGGG--GGAAUGGGUAAAUUGCAUGCGAUUGAAAUU------GAAUGGUUUAAACGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCGUAAUUAGUUGAUUG
----------.(((.....(.--((..((..(((((((((.((.((((((((.------((.((.......)).)))))))))).))))))))))).))..)).).....)))..... ( -28.90, z-score =  -3.31, R)
>droSec1.super_1 4909345 100 + 14215200
----------GAGCGAGAGGG--GGAAUGGGUAAAUUGCAUGCGAUUGAAAUU------GAAUGGUUUAAACGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCGUAAUUAGUUGAUUG
----------.(((.....(.--((..((..(((((((((.((.((((((((.------((.((.......)).)))))))))).))))))))))).))..)).).....)))..... ( -28.90, z-score =  -3.31, R)
>droSim1.chr2R 5883009 100 + 19596830
----------GAGAGAGAGGG--GGAAUGGGUAAAUUGCAUGCGAUUGAAAUU------GAAUGGUUUAAACGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCGUAAUUAGUUGAUUG
----------...........--((..((..(((((((((.((.((((((((.------((.((.......)).)))))))))).))))))))))).))..))............... ( -26.90, z-score =  -3.15, R)
>dp4.chr3 4539147 99 + 19779522
------------GUGCCGCAG-AGAGGUGGGUAAAUUGCAUGCGAUUGAAAUU------GAAUGGUUUAAACGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCGUAAUUAGUGGAUUG
------------...((((.(-(..(((..((((((((((.((.((((((((.------((.((.......)).)))))))))).)))))))))).))..)))....)).)))).... ( -33.10, z-score =  -3.66, R)
>droPer1.super_2 4728064 99 + 9036312
------------GUGCCGCAG-AGAGGUGGGUAAAUUGCAUGCGAUUGAAAUU------GAAUGGUUUAAACGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCGUAAUUAGUGGAUUG
------------...((((.(-(..(((..((((((((((.((.((((((((.------((.((.......)).)))))))))).)))))))))).))..)))....)).)))).... ( -33.10, z-score =  -3.66, R)
>droWil1.scaffold_180745 766819 100 - 2843958
----------UCCUGGAAGGG--GGGUUGGUUAAAUUGCAUGCUAUUGAAAUU------GAAUGGUUUAAAUGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCAUAAUUAGUUGAUUG
----------((((....)))--)((((.(((((((((((.(((((((((((.------((.(.((....)).))))))))))))))))))))))))).))))............... ( -34.20, z-score =  -4.54, R)
>droAna3.scaffold_13266 1072292 103 + 19884421
---------GGACUGGAGGGGCAGGAGGAGCUAAAUUGCAUGCGAUUGAAAUU------GAAUGGUUUAAAUGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCGUAAUUAGUUGAUUG
---------.((((((.(.(((.(......)(((((((((.((.((((((((.------((.(.((....)).))))))))))).)))))))))))....))).)..))))))..... ( -26.20, z-score =  -1.62, R)
>droVir3.scaffold_12875 7487703 117 - 20611582
GGGGGGGGGGGGUUGCAGCAAA-AGGGGCAGCAAAUUGCAUGCGAUUGAAAUUGAAAUUGAAUGGUUUAAAUGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCAUAAUUAGUUUAUUG
.((...(..((((((((((...-....(((((.....)).))).((((((((.((.(((..........)))..)))))))))).))))))))))..)...))............... ( -29.30, z-score =  -1.61, R)
>droMoj3.scaffold_6496 6463488 97 - 26866924
----------AGGCGCAGGGCACAAGGGCAG-----UGCAUGCGAUGGAAAUU------GAAUGGUUUAAAUGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCAUAAUUAGUUGAUUG
----------...((((..((((.......)-----))).)))).....((((------(((((((((((((((((((....))))))...))))))...)))))..))))))..... ( -22.90, z-score =  -0.07, R)
>droGri2.scaffold_15245 7236968 100 + 18325388
----------GAGUGUGAGGA--GCGAGGAGUAAAUGGCAUGCGAUUGAAAUU------GAAUGGUUUAAAUGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCAUAAUUAGUUGAUUG
----------...((((....--((..(...(((((.(((.((.((((((((.------((.(.((....)).))))))))))).))))).))))).)..))))))............ ( -18.80, z-score =   0.38, R)
>consensus
__________GAGUGCAAGGG__GGGGUGGGUAAAUUGCAUGCGAUUGAAAUU______GAAUGGUUUAAACGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCGUAAUUAGUUGAUUG
...............................(((((((((.((.((((((((........((....))........)))))))).)))))))))))...................... (-15.93 = -16.73 +   0.80)

alignment

secondary structure

dotplot

Window 3

Location	7,356,792 – 7,356,892
Length	100
Sequences	10
Columns	118
Reading direction	reverse
Mean pairwise identity	82.89
Shannon entropy	0.32990
G+C content	0.39990
Mean single sequence MFE	-19.93
Consensus MFE	-15.09
Energy contribution	-15.71
Covariance contribution	0.62
Combinations/Pair	1.05
Mean z-score	-3.14
Structure conservation index	0.76
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.13
SVM RNA-class probability	0.997582
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 7356792 100 - 21146708
CAAUCAACUAAUUACGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCGUUUAAACCAUUC------AAUUUCAAUCGCAUGCAAUUUACCCAUUCC--CCCUCUCGCUC----------
...............((..((.(((((((((((.((((((((((..((....))...))------.)))))))).)).)))))))))..))..))--...........---------- ( -20.00, z-score =  -4.02, R)
>droSec1.super_1 4909345 100 - 14215200
CAAUCAACUAAUUACGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCGUUUAAACCAUUC------AAUUUCAAUCGCAUGCAAUUUACCCAUUCC--CCCUCUCGCUC----------
...............((..((.(((((((((((.((((((((((..((....))...))------.)))))))).)).)))))))))..))..))--...........---------- ( -20.00, z-score =  -4.02, R)
>droSim1.chr2R 5883009 100 - 19596830
CAAUCAACUAAUUACGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCGUUUAAACCAUUC------AAUUUCAAUCGCAUGCAAUUUACCCAUUCC--CCCUCUCUCUC----------
...............((..((.(((((((((((.((((((((((..((....))...))------.)))))))).)).)))))))))..))..))--...........---------- ( -20.00, z-score =  -4.81, R)
>dp4.chr3 4539147 99 - 19779522
CAAUCCACUAAUUACGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCGUUUAAACCAUUC------AAUUUCAAUCGCAUGCAAUUUACCCACCUCU-CUGCGGCAC------------
(((.((.........)).))).(((((((((((.((((((((((..((....))...))------.)))))))).)).)))))))))((((.....-.)).))...------------ ( -19.00, z-score =  -2.10, R)
>droPer1.super_2 4728064 99 - 9036312
CAAUCCACUAAUUACGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCGUUUAAACCAUUC------AAUUUCAAUCGCAUGCAAUUUACCCACCUCU-CUGCGGCAC------------
(((.((.........)).))).(((((((((((.((((((((((..((....))...))------.)))))))).)).)))))))))((((.....-.)).))...------------ ( -19.00, z-score =  -2.10, R)
>droWil1.scaffold_180745 766819 100 + 2843958
CAAUCAACUAAUUAUGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCAUUUAAACCAUUC------AAUUUCAAUAGCAUGCAAUUUAACCAACCC--CCCUUCCAGGA----------
...............((.(((((((((((((((.((((((((.................------.)))))))).)).)))))))))).))).))--.((.....)).---------- ( -23.07, z-score =  -4.07, R)
>droAna3.scaffold_13266 1072292 103 - 19884421
CAAUCAACUAAUUACGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCAUUUAAACCAUUC------AAUUUCAAUCGCAUGCAAUUUAGCUCCUCCUGCCCCUCCAGUCC---------
...............(((..(((((((((((((.((((((((.................------.)))))))).)).))))))))))).......)))..........--------- ( -24.37, z-score =  -4.79, R)
>droVir3.scaffold_12875 7487703 117 + 20611582
CAAUAAACUAAUUAUGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCAUUUAAACCAUUCAAUUUCAAUUUCAAUCGCAUGCAAUUUGCUGCCCCU-UUUGCUGCAACCCCCCCCCCCC
...............(((..((.((((((((((.((((((((........................)))))))).)).)))))))))).)))...-...................... ( -21.36, z-score =  -2.51, R)
>droMoj3.scaffold_6496 6463488 97 + 26866924
CAAUCAACUAAUUAUGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCAUUUAAACCAUUC------AAUUUCCAUCGCAUGCA-----CUGCCCUUGUGCCCUGCGCCU----------
...(((.......((((((.((......)))))))).....)))...............------.........((((.(((-----(.......))))..))))...---------- ( -17.80, z-score =  -0.86, R)
>droGri2.scaffold_15245 7236968 100 - 18325388
CAAUCAACUAAUUAUGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCAUUUAAACCAUUC------AAUUUCAAUCGCAUGCCAUUUACUCCUCGC--UCCUCACACUC----------
.............(((((.(((......)))((.((((((((.................------.)))))))).))..)))))...........--...........---------- ( -14.67, z-score =  -2.06, R)
>consensus
CAAUCAACUAAUUACGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCAUUUAAACCAUUC______AAUUUCAAUCGCAUGCAAUUUACCCACCCC__CCCCCGCACUC__________
......................(((((((((((.((((((((........................)))))))).)).)))))))))............................... (-15.09 = -15.71 +   0.62)

alignment

secondary structure

dotplot

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