Locus 4889

Sequence ID	3R_DroMel_CAF1
Location	12,855,492 – 12,855,676
Length	184
Max. P	0.977620

overview

Window 0

Location	12,855,492 – 12,855,612
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	93.89
Mean single sequence MFE	-35.67
Consensus MFE	-31.45
Energy contribution	-30.90
Covariance contribution	-0.55
Combinations/Pair	1.11
Mean z-score	-2.14
Structure conservation index	0.88
SVM decision value	0.51
SVM RNA-class probability	0.765651
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12855492 120 + 27905053
AAGGGCGGACACCACCAUCACUAUUAUCCACCAGGACACGAUAAGGGAGGCUACUAUCCGUAUCCACCCCACGGUGGCCAUGGAGGCCAUCACCAUCCAGGCCACAAUUAUCCAGGCCCC
..((((((......))....((....(((....)))...((((((((.((.(((.....))).)).)))....((((((.((((((......)).))))))))))..))))).)))))). ( -41.70)
>DroSim_CAF1 25842 120 + 1
AAGGGCGGACACCACCAUCACUAUUACCCACCAGGACACGAUAAGGGAGGCCACUAUCCGUAUCCACCCCACGGCGGCCAUGGAGGCCAUCACCAUCCAGGUCAUAACUAUCCAGGACCC
..((..((..................(((....(....).....))).((((....(((((..((.((....)).))..)))))))))....))..)).((((............)))). ( -29.60)
>DroYak_CAF1 25161 120 + 1
AAGGGCGGACACCACCAUCACUAUUAUCCUCCAGGACACGAUAAGGGAGGCCACUACCCGUAUCCACCCCACGGCGGCCAUGGAGACCAUCAUCAUCCAGGCCAUAAUUAUCCAGGCCCC
..(((((((.....((..........(((....)))...((((.(((((....)).))).))))........)).((((.((((((......)).)))))))).......)))..)))). ( -35.70)
>consensus
AAGGGCGGACACCACCAUCACUAUUAUCCACCAGGACACGAUAAGGGAGGCCACUAUCCGUAUCCACCCCACGGCGGCCAUGGAGGCCAUCACCAUCCAGGCCAUAAUUAUCCAGGCCCC
..((((((......)).................(((...((((.(((((....)).))).))))...........((((.((((((......)).)))))))).......)))..)))). (-31.45 = -30.90 +  -0.55)

alignment

secondary structure

dotplot

Window 1

Location	12,855,492 – 12,855,612
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	93.89
Mean single sequence MFE	-49.27
Consensus MFE	-45.80
Energy contribution	-45.70
Covariance contribution	-0.10
Combinations/Pair	1.12
Mean z-score	-1.82
Structure conservation index	0.93
SVM decision value	0.43
SVM RNA-class probability	0.734762
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12855492 120 - 27905053
GGGGCCUGGAUAAUUGUGGCCUGGAUGGUGAUGGCCUCCAUGGCCACCGUGGGGUGGAUACGGAUAGUAGCCUCCCUUAUCGUGUCCUGGUGGAUAAUAGUGAUGGUGGUGUCCGCCCUU
((((((.(((((...((((((((((.(((....))))))).))))))((.((((.((.(((.....))).)).))))...))))))).)))(((((.((....))....))))).))).. ( -52.60)
>DroSim_CAF1 25842 120 - 1
GGGUCCUGGAUAGUUAUGACCUGGAUGGUGAUGGCCUCCAUGGCCGCCGUGGGGUGGAUACGGAUAGUGGCCUCCCUUAUCGUGUCCUGGUGGGUAAUAGUGAUGGUGGUGUCCGCCCUU
.((((.((((..(((((.(((.....))).))))).)))).)))).....(((((((((((.....)).(((.((.((((..(..((....))..)...)))).)).)))))))))))). ( -46.20)
>DroYak_CAF1 25161 120 - 1
GGGGCCUGGAUAAUUAUGGCCUGGAUGAUGAUGGUCUCCAUGGCCGCCGUGGGGUGGAUACGGGUAGUGGCCUCCCUUAUCGUGUCCUGGAGGAUAAUAGUGAUGGUGGUGUCCGCCCUU
((((((((((.......((((...........)))))))).)))).))..(((((((((((((((....))))((.((((..(((((....)))))...)))).))..))))))))))). ( -49.01)
>consensus
GGGGCCUGGAUAAUUAUGGCCUGGAUGGUGAUGGCCUCCAUGGCCGCCGUGGGGUGGAUACGGAUAGUGGCCUCCCUUAUCGUGUCCUGGUGGAUAAUAGUGAUGGUGGUGUCCGCCCUU
((((((((((..(((((.(((.....))).))))).)))).)))).))..(((((((((((.....)))(((.((.((((..(((((....)))))...)))).)).))).)))))))). (-45.80 = -45.70 +  -0.10)

alignment

secondary structure

dotplot

Window 2

Location	12,855,532 – 12,855,651
Length	119
Sequences	3
Columns	119
Reading direction	forward
Mean pairwise identity	94.12
Mean single sequence MFE	-35.27
Consensus MFE	-31.85
Energy contribution	-30.97
Covariance contribution	-0.88
Combinations/Pair	1.11
Mean z-score	-3.60
Structure conservation index	0.90
SVM decision value	1.80
SVM RNA-class probability	0.977620
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12855532 119 + 27905053
AUAAGGGAGGCUACUAUCCGUAUCCACCCCACGGUGGCCAUGGAGGCCAUCACCAUCCAGGCCACAAUUAUCCAGGCCCCUAUCCGCCACCAUAUCCACCUCACCAUCCACAUGAUGGC
....(((.((.(((.....))).)).)))...(((((..((((.((((...........))))...........(((........))).))))..)))))...(((((.....))))). ( -38.40)
>DroSim_CAF1 25882 119 + 1
AUAAGGGAGGCCACUAUCCGUAUCCACCCCACGGCGGCCAUGGAGGCCAUCACCAUCCAGGUCAUAACUAUCCAGGACCCUAUCCGCCACCCUAUCCACCUCACCAUCCACAUGAUGGC
...((((.(((......((((.........)))).((((.((((((......)).))))))))...........(((.....)))))).))))..........(((((.....))))). ( -33.70)
>DroYak_CAF1 25201 119 + 1
AUAAGGGAGGCCACUACCCGUAUCCACCCCACGGCGGCCAUGGAGACCAUCAUCAUCCAGGCCAUAAUUAUCCAGGCCCCUAUCCGCCACCUUAUCCACCUCACCAUCCACAUGAUGGC
....(((.((((.....((((.........)))).((((.((((((......)).))))))))...........)))))))......................(((((.....))))). ( -33.70)
>consensus
AUAAGGGAGGCCACUAUCCGUAUCCACCCCACGGCGGCCAUGGAGGCCAUCACCAUCCAGGCCAUAAUUAUCCAGGCCCCUAUCCGCCACCAUAUCCACCUCACCAUCCACAUGAUGGC
....(((.((..((.....))..)).)))...(((((((.((((((......)).))))))))...........((.......)))))...............(((((.....))))). (-31.85 = -30.97 +  -0.88)

alignment

secondary structure

dotplot

Window 3

Location	12,855,532 – 12,855,651
Length	119
Sequences	3
Columns	119
Reading direction	reverse
Mean pairwise identity	94.12
Mean single sequence MFE	-45.73
Consensus MFE	-41.72
Energy contribution	-41.50
Covariance contribution	-0.22
Combinations/Pair	1.09
Mean z-score	-1.83
Structure conservation index	0.91
SVM decision value	0.31
SVM RNA-class probability	0.682411
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12855532 119 - 27905053
GCCAUCAUGUGGAUGGUGAGGUGGAUAUGGUGGCGGAUAGGGGCCUGGAUAAUUGUGGCCUGGAUGGUGAUGGCCUCCAUGGCCACCGUGGGGUGGAUACGGAUAGUAGCCUCCCUUAU
((((((.....))))))..(((((.(((((.(((.(((..(((((...........)))))..)).....).))).))))).)))))..((((.((.(((.....))).)).))))... ( -48.20)
>DroSim_CAF1 25882 119 - 1
GCCAUCAUGUGGAUGGUGAGGUGGAUAGGGUGGCGGAUAGGGUCCUGGAUAGUUAUGACCUGGAUGGUGAUGGCCUCCAUGGCCGCCGUGGGGUGGAUACGGAUAGUGGCCUCCCUUAU
((((((.....))))))........((.((((((((((...))))((((..(((((.(((.....))).))))).))))..)))))).))(((.((.(((.....))).)).))).... ( -45.60)
>DroYak_CAF1 25201 119 - 1
GCCAUCAUGUGGAUGGUGAGGUGGAUAAGGUGGCGGAUAGGGGCCUGGAUAAUUAUGGCCUGGAUGAUGAUGGUCUCCAUGGCCGCCGUGGGGUGGAUACGGGUAGUGGCCUCCCUUAU
((((((.....))))))...........((((((......(((((...........)))))(((.(((....))))))...))))))..((((.((.(((.....))).)).))))... ( -43.40)
>consensus
GCCAUCAUGUGGAUGGUGAGGUGGAUAAGGUGGCGGAUAGGGGCCUGGAUAAUUAUGGCCUGGAUGGUGAUGGCCUCCAUGGCCGCCGUGGGGUGGAUACGGAUAGUGGCCUCCCUUAU
((((((.....))))))...........((((((......(((((...........)))))(((.(((....))))))...))))))..((((.((.(((.....))).)).))))... (-41.72 = -41.50 +  -0.22)

alignment

secondary structure

dotplot

Window 4

Location	12,855,572 – 12,855,676
Length	104
Sequences	3
Columns	104
Reading direction	forward
Mean pairwise identity	92.63
Mean single sequence MFE	-26.51
Consensus MFE	-21.13
Energy contribution	-21.68
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-3.07
Structure conservation index	0.80
SVM decision value	0.79
SVM RNA-class probability	0.851249
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12855572 104 + 27905053
UGGAGGCCAUCACCAUCCAGGCCACAAUUAUCCAGGCCCCUAUCCGCCACCAUAUCCACCUCACCAUCCACAUGAUGGCGGAGACAAGGGUUAUCACCAUUAUC
(((.((((...........))))...........(((((...(((((((.(((..................))).))))))).....)))))....)))..... ( -28.67)
>DroSim_CAF1 25922 104 + 1
UGGAGGCCAUCACCAUCCAGGUCAUAACUAUCCAGGACCCUAUCCGCCACCCUAUCCACCUCACCAUCCACAUGAUGGCGGUGACAAGGGACAUCACCAUCAUC
(((.(((....(((.....)))............(((.....)))))).((((...((((...(((((.....))))).))))...))))......)))..... ( -27.60)
>DroYak_CAF1 25241 104 + 1
UGGAGACCAUCAUCAUCCAGGCCAUAAUUAUCCAGGCCCCUAUCCGCCACCUUAUCCACCUCACCAUCCACAUGAUGGCGGAGACAAGGGACAUCACCAUCAUC
((((((......)).))))((((...........))))(((.(((((((.(......................).)))))))....)))............... ( -23.25)
>consensus
UGGAGGCCAUCACCAUCCAGGCCAUAAUUAUCCAGGCCCCUAUCCGCCACCAUAUCCACCUCACCAUCCACAUGAUGGCGGAGACAAGGGACAUCACCAUCAUC
(((.((((...........))))..............((((.(((((((.(......................).)))))))....))))......)))..... (-21.13 = -21.68 +   0.56)

alignment

secondary structure

dotplot

Window 5

Location	12,855,572 – 12,855,676
Length	104
Sequences	3
Columns	104
Reading direction	reverse
Mean pairwise identity	92.63
Mean single sequence MFE	-38.87
Consensus MFE	-30.61
Energy contribution	-30.07
Covariance contribution	-0.55
Combinations/Pair	1.17
Mean z-score	-2.46
Structure conservation index	0.79
SVM decision value	0.25
SVM RNA-class probability	0.655068
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12855572 104 - 27905053
GAUAAUGGUGAUAACCCUUGUCUCCGCCAUCAUGUGGAUGGUGAGGUGGAUAUGGUGGCGGAUAGGGGCCUGGAUAAUUGUGGCCUGGAUGGUGAUGGCCUCCA
(((((.(((....))).)))))(((((((((((((..((......))..)))))))))))))...(((((...........)))))(((.(((....)))))). ( -41.80)
>DroSim_CAF1 25922 104 - 1
GAUGAUGGUGAUGUCCCUUGUCACCGCCAUCAUGUGGAUGGUGAGGUGGAUAGGGUGGCGGAUAGGGUCCUGGAUAGUUAUGACCUGGAUGGUGAUGGCCUCCA
............(((((((((((((((((((.....))))))..))).))))))).)))((((...)))).(((..(((((.(((.....))).))))).))). ( -37.60)
>DroYak_CAF1 25241 104 - 1
GAUGAUGGUGAUGUCCCUUGUCUCCGCCAUCAUGUGGAUGGUGAGGUGGAUAAGGUGGCGGAUAGGGGCCUGGAUAAUUAUGGCCUGGAUGAUGAUGGUCUCCA
(((.((.((.(((((((((((((((((((((.....))))))..)).)))))))).)))......(((((...........)))))..)).)).)).))).... ( -37.20)
>consensus
GAUGAUGGUGAUGUCCCUUGUCUCCGCCAUCAUGUGGAUGGUGAGGUGGAUAAGGUGGCGGAUAGGGGCCUGGAUAAUUAUGGCCUGGAUGGUGAUGGCCUCCA
......(((.(((..(((((((.((((((((.....))))))).)...))))))).(((........)))........))).))).(((.(((....)))))). (-30.61 = -30.07 +  -0.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:19 2006