Locus 10213

Sequence ID	3R_DroMel_CAF1
Location	27,395,942 – 27,396,059
Length	117
Max. P	0.992473

overview

Window 2

Location	27,395,942 – 27,396,043
Length	101
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	99.01
Mean single sequence MFE	-26.36
Consensus MFE	-26.36
Energy contribution	-25.96
Covariance contribution	-0.40
Combinations/Pair	1.07
Mean z-score	-1.76
Structure conservation index	1.00
SVM decision value	2.02
SVM RNA-class probability	0.985849
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27395942 101 - 27905053
UCGUGCCCAGAAAACGGGCAACGGCAGGAACAACAGACUAAUUAACAUAUUCAAAUAUUUGUCGCAUUGUUUCGCCAGUUUCCCAGCUCCAUCUGGCAGUU
...((((.(((....(((.((((((.(((((((..(((.(((..............))).)))...)))))))))).))).))).......)))))))... ( -26.24)
>DroSec_CAF1 12019 101 - 1
UCGUGCCCAGAAAACGGGCAACGGCAGGAACAACAGACUAAUUAACAUAUUCAAAUAUUUGUCGCAUUGUUUCGCCAGUUUCCCAGCUCCAUCUGGCAGCU
.(((((((.......)))).)))((.(((((((..(((.(((..............))).)))...)))))))(((((..............))))).)). ( -27.68)
>DroSim_CAF1 12069 101 - 1
UCGUGCCCAGAAAACGGGCAACGGCAGGAACAACAGACUAAUUAACAUAUUCAAAUAUUUGUCGCAUUGUUUCGCUAGUUUCCCAGCUCCAUCUGGCAGCU
.(((((((.......)))).)))((.(((((((..(((.(((..............))).)))...)))))))(((((..............))))).)). ( -25.38)
>DroEre_CAF1 12687 101 - 1
UCGUGCCCAGAAAACGGGCAACGGCAGGAACAACAGACUAAUUAACAUAUUCAAAUAUUUGUCGCAUUGUUUCGCCAGUUUCCCAGCUCCAUCUGGCAGUU
...((((.(((....(((.((((((.(((((((..(((.(((..............))).)))...)))))))))).))).))).......)))))))... ( -26.24)
>DroYak_CAF1 12089 101 - 1
UCGUGCCCAGAAAACGGGCAACGGCAGGAACAACAGACUAAUUAACAUAUUCAAAUAUUUGUCGCAUUGUUUCGCCAGUUUCCCAGCUCCAUCUGGCAGUU
...((((.(((....(((.((((((.(((((((..(((.(((..............))).)))...)))))))))).))).))).......)))))))... ( -26.24)
>consensus
UCGUGCCCAGAAAACGGGCAACGGCAGGAACAACAGACUAAUUAACAUAUUCAAAUAUUUGUCGCAUUGUUUCGCCAGUUUCCCAGCUCCAUCUGGCAGUU
.(((((((.......)))).)))((.(((((((..(((.(((..............))).)))...)))))))(((((..............))))).)). (-26.36 = -25.96 +  -0.40)

alignment

secondary structure

dotplot

Window 3

Location	27,395,963 – 27,396,059
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	99.17
Mean single sequence MFE	-22.88
Consensus MFE	-22.96
Energy contribution	-22.80
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.88
Structure conservation index	1.00
SVM decision value	2.33
SVM RNA-class probability	0.992473
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27395963 96 - 27905053
AAGAAGAACGAACUGAUCGUGCCCAGAAAACGGGCAACGGCAGGAACAACAGACUAAUUAACAUAUUCAAAUAUUUGUCGCAUUGUUUCGCCAGUU
.......((((.....))))((((.......))))...(((.(((((((..(((.(((..............))).)))...)))))))))).... ( -23.24)
>DroSec_CAF1 12040 96 - 1
AAGAAGAACGAACUGAUCGUGCCCAGAAAACGGGCAACGGCAGGAACAACAGACUAAUUAACAUAUUCAAAUAUUUGUCGCAUUGUUUCGCCAGUU
.......((((.....))))((((.......))))...(((.(((((((..(((.(((..............))).)))...)))))))))).... ( -23.24)
>DroSim_CAF1 12090 96 - 1
AAGAAGAACGAACUGAUCGUGCCCAGAAAACGGGCAACGGCAGGAACAACAGACUAAUUAACAUAUUCAAAUAUUUGUCGCAUUGUUUCGCUAGUU
.((..((((((.(((.((((((((.......)))).)))))))........(((.(((..............))).)))...))))))..)).... ( -21.44)
>DroEre_CAF1 12708 96 - 1
AAGAAGAACGAACUGAUCGUGCCCAGAAAACGGGCAACGGCAGGAACAACAGACUAAUUAACAUAUUCAAAUAUUUGUCGCAUUGUUUCGCCAGUU
.......((((.....))))((((.......))))...(((.(((((((..(((.(((..............))).)))...)))))))))).... ( -23.24)
>DroYak_CAF1 12110 96 - 1
AAAAAGAACGAACUGAUCGUGCCCAGAAAACGGGCAACGGCAGGAACAACAGACUAAUUAACAUAUUCAAAUAUUUGUCGCAUUGUUUCGCCAGUU
.......((((.....))))((((.......))))...(((.(((((((..(((.(((..............))).)))...)))))))))).... ( -23.24)
>consensus
AAGAAGAACGAACUGAUCGUGCCCAGAAAACGGGCAACGGCAGGAACAACAGACUAAUUAACAUAUUCAAAUAUUUGUCGCAUUGUUUCGCCAGUU
..........(((((..(((((((.......)))).)))((.(((((((..(((.(((..............))).)))...)))))))))))))) (-22.96 = -22.80 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:51:33 2006