Locus 3444

Sequence ID	2R_DroMel_CAF1
Location	11,592,236 – 11,592,429
Length	193
Max. P	0.933291

overview

Window 2

Location	11,592,236 – 11,592,356
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.32
Mean single sequence MFE	-36.67
Consensus MFE	-35.10
Energy contribution	-35.10
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.45
Structure conservation index	0.96
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11592236 120 - 20766785
AGCCUCGGAACACUCCCACUAAUCCGUGGCUCUUCGCCGCGACUCGAAAGUCAAUCUUCUGCGGCUAAUGGAAGUUGCUUGUUGUGGGAGUACUCAGCUCCUGCCUGCCUGCCACUCAUC
((((.(((((...............(((((.....)))))((((....))))....))))).))))....((.((.((..((.(..(((((.....)))))..)..))..)).))))... ( -39.40)
>DroSec_CAF1 25789 118 - 1
AGCCUCGGAACACUCCCACUAAUCCGUGGCUCUUCACC--GACUCGAAAGUCAAUCUUCUGCGGCUAAUGGAAGUUGCUUGUUGUGGGAGUACUCAGCUCCUGCCUGCCUGCCACUCAUC
((((.(((((.....((((......)))).........--((((....))))....))))).))))....((.((.((..((.(..(((((.....)))))..)..))..)).))))... ( -35.30)
>DroSim_CAF1 29072 118 - 1
AGCCUCGGAACACUCCCACUAAUCCGUGGCUCUUCGCC--GACUCGAAAGUCAAUCUUCUGCGGCUAAUGGAAGUUGCUUGUUGUGGGAGUACUCAGCUCCUGCCUGCCUGCCACUCAUC
((((.(((((.....((((......)))).........--((((....))))....))))).))))....((.((.((..((.(..(((((.....)))))..)..))..)).))))... ( -35.30)
>consensus
AGCCUCGGAACACUCCCACUAAUCCGUGGCUCUUCGCC__GACUCGAAAGUCAAUCUUCUGCGGCUAAUGGAAGUUGCUUGUUGUGGGAGUACUCAGCUCCUGCCUGCCUGCCACUCAUC
((((.(((((.....((((......))))...........((((....))))....))))).))))....((.((.((..((.(..(((((.....)))))..)..))..)).))))... (-35.10 = -35.10 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	11,592,276 – 11,592,396
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.21
Mean single sequence MFE	-38.40
Consensus MFE	-36.69
Energy contribution	-36.47
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-2.31
Structure conservation index	0.96
SVM decision value	1.23
SVM RNA-class probability	0.933291
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11592276 120 + 20766785
AAGCAACUUCCAUUAGCCGCAGAAGAUUGACUUUCGAGUCGCGGCGAAGAGCCACGGAUUAGUGGGAGUGUUCCGAGGCUAAUGAUAUACACUAGCGUCGAGUGAAAUUAUAAAGUGCGC
..(((((((((((((((((.........((((....))))..(((.....))).))).)))))))))))....(((.((((.((.....)).)))).)))...............))).. ( -39.40)
>DroSec_CAF1 25829 118 + 1
AAGCAACUUCCAUUAGCCGCAGAAGAUUGACUUUCGAGUC--GGUGAAGAGCCACGGAUUAGUGGGAGUGUUCCGAGGCUAAUGAUAUACACUAGCGUCGAGUGAAAUUAUAAAGAGCGC
..((.((((((((((((((.........((((....))))--(((.....))).))).)))))))))))....(((.((((.((.....)).)))).)))................)).. ( -36.40)
>DroSim_CAF1 29112 118 + 1
AAGCAACUUCCAUUAGCCGCAGAAGAUUGACUUUCGAGUC--GGCGAAGAGCCACGGAUUAGUGGGAGUGUUCCGAGGCUAAUGAUAUACACUAGCGUCGAAUGAAAUUAUAAAGUGCGC
..(((((((((((((((((.........((((....))))--(((.....))).))).)))))))))))....(((.((((.((.....)).)))).)))...............))).. ( -39.40)
>consensus
AAGCAACUUCCAUUAGCCGCAGAAGAUUGACUUUCGAGUC__GGCGAAGAGCCACGGAUUAGUGGGAGUGUUCCGAGGCUAAUGAUAUACACUAGCGUCGAGUGAAAUUAUAAAGUGCGC
..((.((((((((((((((.........((((....))))..(((.....))).))).)))))))))))....(((.((((.((.....)).)))).)))................)).. (-36.69 = -36.47 +  -0.22)

alignment

secondary structure

dotplot

Window 4

Location	11,592,276 – 11,592,396
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.21
Mean single sequence MFE	-33.60
Consensus MFE	-30.45
Energy contribution	-30.57
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-2.41
Structure conservation index	0.91
SVM decision value	0.91
SVM RNA-class probability	0.879553
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11592276 120 - 20766785
GCGCACUUUAUAAUUUCACUCGACGCUAGUGUAUAUCAUUAGCCUCGGAACACUCCCACUAAUCCGUGGCUCUUCGCCGCGACUCGAAAGUCAAUCUUCUGCGGCUAAUGGAAGUUGCUU
(((.(((((.......((((.......)))).....((((((((.(((((...............(((((.....)))))((((....))))....))))).)))))))))))))))).. ( -36.80)
>DroSec_CAF1 25829 118 - 1
GCGCUCUUUAUAAUUUCACUCGACGCUAGUGUAUAUCAUUAGCCUCGGAACACUCCCACUAAUCCGUGGCUCUUCACC--GACUCGAAAGUCAAUCUUCUGCGGCUAAUGGAAGUUGCUU
(((..((((.......((((.......)))).....((((((((.(((((.....((((......)))).........--((((....))))....))))).)))))))))))).))).. ( -30.90)
>DroSim_CAF1 29112 118 - 1
GCGCACUUUAUAAUUUCAUUCGACGCUAGUGUAUAUCAUUAGCCUCGGAACACUCCCACUAAUCCGUGGCUCUUCGCC--GACUCGAAAGUCAAUCUUCUGCGGCUAAUGGAAGUUGCUU
..(((.............(((((.(((((((.....))))))).)))))..(((.(((.((..(((((((.....)))--((((....))))........)))).)).))).)))))).. ( -33.10)
>consensus
GCGCACUUUAUAAUUUCACUCGACGCUAGUGUAUAUCAUUAGCCUCGGAACACUCCCACUAAUCCGUGGCUCUUCGCC__GACUCGAAAGUCAAUCUUCUGCGGCUAAUGGAAGUUGCUU
(((.(((((.......((((.......)))).....((((((((.(((((.....((((......))))...........((((....))))....))))).)))))))))))))))).. (-30.45 = -30.57 +   0.11)

alignment

secondary structure

dotplot

Window 5

Location	11,592,316 – 11,592,429
Length	113
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	90.88
Mean single sequence MFE	-36.03
Consensus MFE	-30.05
Energy contribution	-30.50
Covariance contribution	0.45
Combinations/Pair	1.09
Mean z-score	-2.37
Structure conservation index	0.83
SVM decision value	0.59
SVM RNA-class probability	0.792818
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11592316 113 + 20766785
GCGGCGAAGAGCCACGGAUUAGUGGGAGUGUUCCGAGGCUAAUGAUAUACACUAGCGUCGAGUGAAAUUAUAAAGUGCGCAGCAGCCACUACAAUUAAUUUCGGAGCA--U-----UGCA
...((......((((......)))).((((((((((.((((.((.....)).)))).))....(((((((...((((.((....)))))).....)))))))))))))--)-----))). ( -37.50)
>DroSec_CAF1 25869 111 + 1
--GGUGAAGAGCCACGGAUUAGUGGGAGUGUUCCGAGGCUAAUGAUAUACACUAGCGUCGAGUGAAAUUAUAAAGAGCGCAGCAGCCACUACAAUUAAUUUCGGAGCA--U-----UGCA
--.........((((......)))).((((((((((.((((.((.....)).)))).))....(((((((.....((.((....))..)).....)))))))))))))--)-----)... ( -31.20)
>DroSim_CAF1 29152 117 + 1
--GGCGAAGAGCCACGGAUUAGUGGGAGUGUUCCGAGGCUAAUGAUAUACACUAGCGUCGAAUGAAAUUAUAAAGUGCGCAGCAGCCACUACAAUUAAU-UCGGAGCGAAUCCCACCACA
--(((.....)))........((((((.((((((((.((((.((.....)).)))).))((((..((((....((((.((....))))))..)))).))-))))))))..)))))).... ( -39.40)
>consensus
__GGCGAAGAGCCACGGAUUAGUGGGAGUGUUCCGAGGCUAAUGAUAUACACUAGCGUCGAGUGAAAUUAUAAAGUGCGCAGCAGCCACUACAAUUAAUUUCGGAGCA__U_____UGCA
...(((.....((((......))))...((((((((.((((.((.....)).)))).))....(((((((...((((.((....)))))).....)))))))))))))........))). (-30.05 = -30.50 +   0.45)

alignment

secondary structure

dotplot

Window 6

Location	11,592,316 – 11,592,429
Length	113
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	90.88
Mean single sequence MFE	-32.63
Consensus MFE	-28.53
Energy contribution	-28.70
Covariance contribution	0.17
Combinations/Pair	1.06
Mean z-score	-2.39
Structure conservation index	0.87
SVM decision value	0.93
SVM RNA-class probability	0.883595
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11592316 113 - 20766785
UGCA-----A--UGCUCCGAAAUUAAUUGUAGUGGCUGCUGCGCACUUUAUAAUUUCACUCGACGCUAGUGUAUAUCAUUAGCCUCGGAACACUCCCACUAAUCCGUGGCUCUUCGCCGC
....-----.--((.((((((((((.....((((((....)).))))...)))))))....((.(((((((.....))))))).))))).)).............(((((.....))))) ( -32.40)
>DroSec_CAF1 25869 111 - 1
UGCA-----A--UGCUCCGAAAUUAAUUGUAGUGGCUGCUGCGCUCUUUAUAAUUUCACUCGACGCUAGUGUAUAUCAUUAGCCUCGGAACACUCCCACUAAUCCGUGGCUCUUCACC--
....-----.--((.((((((((((..((((((....)))))).......)))))))....((.(((((((.....))))))).))))).))...((((......)))).........-- ( -26.60)
>DroSim_CAF1 29152 117 - 1
UGUGGUGGGAUUCGCUCCGA-AUUAAUUGUAGUGGCUGCUGCGCACUUUAUAAUUUCAUUCGACGCUAGUGUAUAUCAUUAGCCUCGGAACACUCCCACUAAUCCGUGGCUCUUCGCC--
..((((((((...(.(((((-((.((((((((((((....)).))))..))))))..))))((.(((((((.....))))))).))))).)..))))))))......(((.....)))-- ( -38.90)
>consensus
UGCA_____A__UGCUCCGAAAUUAAUUGUAGUGGCUGCUGCGCACUUUAUAAUUUCACUCGACGCUAGUGUAUAUCAUUAGCCUCGGAACACUCCCACUAAUCCGUGGCUCUUCGCC__
.((((......))))((((((((((.....((((((....)).))))...)))))))....((.(((((((.....))))))).)))))......((((......))))........... (-28.53 = -28.70 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:45 2006