Locus 5133

Sequence ID	3R_DroMel_CAF1
Location	13,515,162 – 13,515,360
Length	198
Max. P	0.999821

overview

Window 5

Location	13,515,162 – 13,515,280
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.28
Mean single sequence MFE	-27.14
Consensus MFE	-25.64
Energy contribution	-25.64
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.32
Structure conservation index	0.94
SVM decision value	0.91
SVM RNA-class probability	0.880540
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13515162 118 + 27905053
GGUUUAGUUAUCAUAUUUACUAUUUUU--AGAUUUGAGUGAAAAAAUAUACAGUUGUUAUUGUAUUGACUGUUACAGUGAUGGAUUGGCGAGCCAUUCCAUCGCAGAUACAUUGCAGGCG
.((((.((((((.......(((....)--))......((((......(((((((....)))))))......)))).((((((((.(((....))).)))))))).))))....)))))). ( -29.80)
>DroSec_CAF1 4136 118 + 1
GGUUUAGUUAUCAUAUUUACUAUUUUU--AGAUUUGAGUGAAAAAAUAUACAGUUGUUAUUGUAUUGACUGUUACAGUGAUGGAUAGGCGAGCCAUUCCAUCGCAGAUACAUUGCAGGCG
.((((.((((((.......(((....)--))......((((......(((((((....)))))))......)))).((((((((..((....))..)))))))).))))....)))))). ( -27.00)
>DroSim_CAF1 4513 118 + 1
GGUUUAGUUAUCAUAUUUACUAUUUUU--AGAUUUGAGUGAAAAAAUAUACAGUUGUUAUUGUAUUGACUGUUACAGUGAUGGAUAGGCGAGCCAUUCCAUCGCAGAUACAUUGCAGGCG
.((((.((((((.......(((....)--))......((((......(((((((....)))))))......)))).((((((((..((....))..)))))))).))))....)))))). ( -27.00)
>DroEre_CAF1 4589 116 + 1
----UAGUUAUCAUAUUUACUAUUUUUUAAGAUUUGAGUGAAAAAAUAUACAGUUGUUAUUGUAUUGACUGUUACAGUGAUGGAUAGGUGAGCCAUUCCAUCGCAGAUACAUUGCAGGCG
----..((.(((.........................((((......(((((((....)))))))......)))).((((((((..((....))..)))))))).))))).......... ( -25.50)
>DroYak_CAF1 4866 114 + 1
----UAGUUAUCAUAUUUACUAUUUUU--AGAUUUGAGUGAAAAAAUAUACAGUUGUUAUUGUAUUGACUGUUACAGUGAUGGAUAGGCGAGCCAUUCCAUCGCAGAUACAUUGCAGACG
----..(((.(((.(((((.......)--)))).)))((((......(((((((....)))))))......)))).((((((((..((....))..))))))))............))). ( -26.40)
>consensus
GGUUUAGUUAUCAUAUUUACUAUUUUU__AGAUUUGAGUGAAAAAAUAUACAGUUGUUAUUGUAUUGACUGUUACAGUGAUGGAUAGGCGAGCCAUUCCAUCGCAGAUACAUUGCAGGCG
......((.(((.........................((((......(((((((....)))))))......)))).((((((((..((....))..)))))))).))))).......... (-25.64 = -25.64 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	13,515,200 – 13,515,320
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.00
Mean single sequence MFE	-33.24
Consensus MFE	-32.40
Energy contribution	-32.08
Covariance contribution	-0.32
Combinations/Pair	1.03
Mean z-score	-1.29
Structure conservation index	0.97
SVM decision value	0.90
SVM RNA-class probability	0.877711
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13515200 120 + 27905053
AAAAAAUAUACAGUUGUUAUUGUAUUGACUGUUACAGUGAUGGAUUGGCGAGCCAUUCCAUCGCAGAUACAUUGCAGGCGCUGCACCUGCUGAGUUCCCGUUUACGUAUCCUUAGAGUUC
.......(((((((....))))))).((((......((((((((.(((....))).)))))))).(((((...(((((.......)))))...((........))))))).....)))). ( -35.20)
>DroSec_CAF1 4174 120 + 1
AAAAAAUAUACAGUUGUUAUUGUAUUGACUGUUACAGUGAUGGAUAGGCGAGCCAUUCCAUCGCAGAUACAUUGCAGGCGCUGCACCUGCUGAGUUCCCGUUUACGUAUCCUUGGAGUUC
.......(((((((....))))))).((((......((((((((..((....))..)))))))).(((((...(((((.......)))))...((........))))))).....)))). ( -32.40)
>DroSim_CAF1 4551 120 + 1
AAAAAAUAUACAGUUGUUAUUGUAUUGACUGUUACAGUGAUGGAUAGGCGAGCCAUUCCAUCGCAGAUACAUUGCAGGCGCUGCACCUGCUGAGUUCCCGUUUACGUAUCCUUGGAGUUC
.......(((((((....))))))).((((......((((((((..((....))..)))))))).(((((...(((((.......)))))...((........))))))).....)))). ( -32.40)
>DroEre_CAF1 4625 120 + 1
AAAAAAUAUACAGUUGUUAUUGUAUUGACUGUUACAGUGAUGGAUAGGUGAGCCAUUCCAUCGCAGAUACAUUGCAGGCGUUGCACCUGCUGAGUUCCCGUUUACGUAUCCGUGGAGUUC
.......(((((((....))))))).((((.((((.((((((((..((....))..)))))))).(((((...(((((.......)))))...((........))))))).)))))))). ( -34.80)
>DroYak_CAF1 4900 120 + 1
AAAAAAUAUACAGUUGUUAUUGUAUUGACUGUUACAGUGAUGGAUAGGCGAGCCAUUCCAUCGCAGAUACAUUGCAGACGCUGCAUCUGCUGAGUUCCCUUUUACGUAUCCUUGGAGUUA
.......(((((((....)))))))(((((......((((((((..((....))..)))))))).(((((...(((((.......)))))...((........))))))).....))))) ( -31.40)
>consensus
AAAAAAUAUACAGUUGUUAUUGUAUUGACUGUUACAGUGAUGGAUAGGCGAGCCAUUCCAUCGCAGAUACAUUGCAGGCGCUGCACCUGCUGAGUUCCCGUUUACGUAUCCUUGGAGUUC
.......(((((((....))))))).((((......((((((((..((....))..)))))))).(((((...(((((.......)))))...((........))))))).....)))). (-32.40 = -32.08 +  -0.32)

alignment

secondary structure

dotplot

Window 7

Location	13,515,200 – 13,515,320
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.00
Mean single sequence MFE	-33.32
Consensus MFE	-32.68
Energy contribution	-32.36
Covariance contribution	-0.32
Combinations/Pair	1.03
Mean z-score	-2.37
Structure conservation index	0.98
SVM decision value	4.16
SVM RNA-class probability	0.999821
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13515200 120 - 27905053
GAACUCUAAGGAUACGUAAACGGGAACUCAGCAGGUGCAGCGCCUGCAAUGUAUCUGCGAUGGAAUGGCUCGCCAAUCCAUCACUGUAACAGUCAAUACAAUAACAACUGUAUAUUUUUU
.........((((((((....(....)...(((((((...))))))).))))))))..((((((.(((....))).))))))((((...))))..(((((........)))))....... ( -35.60)
>DroSec_CAF1 4174 120 - 1
GAACUCCAAGGAUACGUAAACGGGAACUCAGCAGGUGCAGCGCCUGCAAUGUAUCUGCGAUGGAAUGGCUCGCCUAUCCAUCACUGUAACAGUCAAUACAAUAACAACUGUAUAUUUUUU
.........((((((((....(....)...(((((((...))))))).))))))))..((((((..((....))..))))))((((...))))..(((((........)))))....... ( -33.00)
>DroSim_CAF1 4551 120 - 1
GAACUCCAAGGAUACGUAAACGGGAACUCAGCAGGUGCAGCGCCUGCAAUGUAUCUGCGAUGGAAUGGCUCGCCUAUCCAUCACUGUAACAGUCAAUACAAUAACAACUGUAUAUUUUUU
.........((((((((....(....)...(((((((...))))))).))))))))..((((((..((....))..))))))((((...))))..(((((........)))))....... ( -33.00)
>DroEre_CAF1 4625 120 - 1
GAACUCCACGGAUACGUAAACGGGAACUCAGCAGGUGCAACGCCUGCAAUGUAUCUGCGAUGGAAUGGCUCACCUAUCCAUCACUGUAACAGUCAAUACAAUAACAACUGUAUAUUUUUU
........(((((((((....(....)...(((((((...))))))).))))))))).((((((..((....))..))))))((((...))))..(((((........)))))....... ( -33.50)
>DroYak_CAF1 4900 120 - 1
UAACUCCAAGGAUACGUAAAAGGGAACUCAGCAGAUGCAGCGUCUGCAAUGUAUCUGCGAUGGAAUGGCUCGCCUAUCCAUCACUGUAACAGUCAAUACAAUAACAACUGUAUAUUUUUU
.........((((((((...((....))..(((((((...))))))).))))))))..((((((..((....))..))))))((((...))))..(((((........)))))....... ( -31.50)
>consensus
GAACUCCAAGGAUACGUAAACGGGAACUCAGCAGGUGCAGCGCCUGCAAUGUAUCUGCGAUGGAAUGGCUCGCCUAUCCAUCACUGUAACAGUCAAUACAAUAACAACUGUAUAUUUUUU
.........((((((((....(....)...(((((((...))))))).))))))))..((((((..((....))..))))))((((...))))..(((((........)))))....... (-32.68 = -32.36 +  -0.32)

alignment

secondary structure

dotplot

Window 8

Location	13,515,240 – 13,515,360
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.45
Mean single sequence MFE	-38.56
Consensus MFE	-31.54
Energy contribution	-31.78
Covariance contribution	0.24
Combinations/Pair	1.06
Mean z-score	-1.59
Structure conservation index	0.82
SVM decision value	0.62
SVM RNA-class probability	0.803528
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13515240 120 - 27905053
GAGAGAGAGAGAGAGUCACGAUGUGCGAGAACUCGUGUCCGAACUCUAAGGAUACGUAAACGGGAACUCAGCAGGUGCAGCGCCUGCAAUGUAUCUGCGAUGGAAUGGCUCGCCAAUCCA
.....((((...(.(.(((((.((......))))))).))...))))..((((((((....(....)...(((((((...))))))).))))))))....((((.(((....))).)))) ( -39.30)
>DroSec_CAF1 4214 113 - 1
G-------GAGAGAGUCAAGGUGUGCGAGAACUCGUGUCCGAACUCCAAGGAUACGUAAACGGGAACUCAGCAGGUGCAGCGCCUGCAAUGUAUCUGCGAUGGAAUGGCUCGCCUAUCCA
(-------((..((((((.((.(..(((....)))..)))....((((.((((((((....(....)...(((((((...))))))).))))))))....)))).)))))).....))). ( -41.80)
>DroSim_CAF1 4591 113 - 1
G-------UAGAGAGUCAUGGUGUGCGAGAACUCGUGUCCGAACUCCAAGGAUACGUAAACGGGAACUCAGCAGGUGCAGCGCCUGCAAUGUAUCUGCGAUGGAAUGGCUCGCCUAUCCA
(-------(((.(((((((((.(..(((....)))..)))....((((.((((((((....(....)...(((((((...))))))).))))))))....)))))))))))..))))... ( -41.20)
>DroEre_CAF1 4665 113 - 1
G-------GAGAAAGUCACGAUGUGCGAGAACACGUGUCCGAACUCCACGGAUACGUAAACGGGAACUCAGCAGGUGCAACGCCUGCAAUGUAUCUGCGAUGGAAUGGCUCACCUAUCCA
(-------(((...(.((((.(((......))))))).)....)))).(((((((((....(....)...(((((((...))))))).)))))))))...((((..((....))..)))) ( -38.00)
>DroYak_CAF1 4940 113 - 1
G-------GAGAGAUUCACGAUGUGCGAGAACACUUGUCCUAACUCCAAGGAUACGUAAAAGGGAACUCAGCAGAUGCAGCGUCUGCAAUGUAUCUGCGAUGGAAUGGCUCGCCUAUCCA
.-------...........((((.(((((....(...(((....((...((((((((...((....))..(((((((...))))))).))))))))..)).)))..).))))).)))).. ( -32.50)
>consensus
G_______GAGAGAGUCACGAUGUGCGAGAACUCGUGUCCGAACUCCAAGGAUACGUAAACGGGAACUCAGCAGGUGCAGCGCCUGCAAUGUAUCUGCGAUGGAAUGGCUCGCCUAUCCA
...................((((.(((((....(((.((((...((...((((((((....(....)...(((((((...))))))).))))))))..))))))))).))))).)))).. (-31.54 = -31.78 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:11 2006