Locus 929

Sequence ID 2R_DroMel_CAF1
Location 4,066,664 – 4,066,927
Length 263
Max. P 0.952118
window1640 window1641 window1642

overview

Window 0

Location 4,066,664 – 4,066,784
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.58
Mean single sequence MFE -36.44
Consensus MFE -29.60
Energy contribution -30.04
Covariance contribution 0.44
Combinations/Pair 1.07
Mean z-score -1.48
Structure conservation index 0.81
SVM decision value 0.14
SVM RNA-class probability 0.604117
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4066664 120 + 20766785
GACAUCGUCAAAUUAAAUGGCCUGGCCAGAAUGCAACAGUUAAAACGGCACACAACAAUGGCCAGAAGCGGGCACUUGAAGUCCGGCCAAAUGGCCUACUGGGCGCAGUCCGGAAAACUG
(((...))).........(((((((((.....((....((....))(((.((......)))))....))((((.......)))))))))...))))..((((((...))))))....... ( -35.40)
>DroSec_CAF1 49208 120 + 1
GACAUCGUCAAAUUAAAUGGCCUGGCCACAAUGCAACAGUUAAAACGGCAGACAACAAUGGCCAGAAGCGGGCACUUGAAGUCCGGCCAAAUGGCCUACUGGGCGCAGCCCGGAAAACUG
(((...))).........(((((((((....(((....((....)).)))(((..(((((.((......)).)).)))..))).)))))...))))..((((((...))))))....... ( -37.90)
>DroSim_CAF1 57448 120 + 1
GACAUCGUCAAAUUAAAUGGCCUGGCCACAAUGCAACAGUUAAAACGGCAGACAACAAUGGCCAGAAGCGGGCACUUGAAGUCCGGCCAAAUGGCCUACUGGGCGCAGCCCGGAAAACUG
(((...))).........(((((((((....(((....((....)).)))(((..(((((.((......)).)).)))..))).)))))...))))..((((((...))))))....... ( -37.90)
>DroEre_CAF1 50526 120 + 1
GCCAUCGUCAAACCCAAUGGCCUGGCCACAAUGCAACAGCUAAAACGGCGGAGAACAAUGGCCAGAAGCAGGCACUUGAAGUCCGGCCAAAUGGCCUACUGGCCGCAGUGCGGAAAACUG
(((((.(.......).)))))....((.((.(((....(((.....)))..........((((((.....((.((.....))))((((....))))..))))))))).)).))....... ( -37.80)
>DroYak_CAF1 53290 120 + 1
GACAUCGUCAAAUUAAAUGGCCUGGCCACAAUGCAACAGUUAAAACAGCGGACAACAAUGGCCAGAAGCAGGCACUUGAAGUCCGGCCAAAUGGCCUACUGGGCGCAGCACGGAAAACUG
....(((((........((((...))))...(((..((((.........((((..(((..(((.......)))..)))..))))((((....)))).))))...)))).))))....... ( -33.20)
>consensus
GACAUCGUCAAAUUAAAUGGCCUGGCCACAAUGCAACAGUUAAAACGGCAGACAACAAUGGCCAGAAGCGGGCACUUGAAGUCCGGCCAAAUGGCCUACUGGGCGCAGCCCGGAAAACUG
(((.((((((.......))))(((((((...(((....(......).)))........)))))))............)).))).((((....))))..((((((...))))))....... (-29.60 = -30.04 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 4,066,744 – 4,066,847
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 70.75
Mean single sequence MFE -29.81
Consensus MFE -21.30
Energy contribution -21.46
Covariance contribution 0.16
Combinations/Pair 1.06
Mean z-score -0.81
Structure conservation index 0.71
SVM decision value -0.01
SVM RNA-class probability 0.529742
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4066744 103 - 20766785
AGCUGUUCUUAAGGUUGCCCCCAC------UAACCGC----CCAUUCG-------CAUCCCCGUUGGGAUGCUGAUGUUGCAGUUUUCCGGACUGCGCCCAGUAGGCCAUUUGGCCGGAC
.((((.......(((((.......------)))))((----.((((.(-------((((((....))))))).))))..((((((.....)))))))).)))).((((....)))).... ( -39.10)
>DroSec_CAF1 49288 86 - 1
AGCUGUUCUUAAGUUUGCCCCC----------------------------------AUCCCCGUUGCGAUGCUGAUGUUGCAGUUUUCCGGGCUGCGCCCAGUAGGCCAUUUGGCCGGAC
((((((.....(((((((....----------------------------------.........)))).)))......)))))).(((((((...))))....((((....))))))). ( -25.92)
>DroSim_CAF1 57528 86 - 1
AGCUGUUCUUAAGUUUGCCCCC----------------------------------CUCCCCGUUGCGAUGCUGAUGUUGCAGUUUUCCGGGCUGCGCCCAGUAGGCCAUUUGGCCGGAC
((((((.....(((((((....----------------------------------.........)))).)))......)))))).(((((((...))))....((((....))))))). ( -25.92)
>DroEre_CAF1 50606 97 - 1
GUCUGUUCUCAAGGC----------------AUCCCCACCACCAUCCC-------CAUUCCCAUUCCGAUGCUGAUGUUGCAGUUUUCCGCACUGCGGCCAGUAGGCCAUUUGGCCGGAC
((((.......))))----------------.................-------.........(((..(((((..((((((((.......)))))))))))))((((....))))))). ( -28.60)
>DroYak_CAF1 53370 120 - 1
GGCAUUUUAUAAGGCUUAACCCACCUGCCCUAUCCGCAUCCGCAUCCCCCCCCAGCAUCCCCAAUCCGCUGCUGAUGUUGCAGUUUUCCGUGCUGCGCCCAGUAGGCCAUUUGGCCGGAC
.((.....(((.(((...........))).)))..)).(((((.........(((((.(........).))))).....(((((.......)))))))......((((....))))))). ( -29.50)
>consensus
AGCUGUUCUUAAGGUUGCCCCC_________A_CC_C_____CAU_C________CAUCCCCGUUGCGAUGCUGAUGUUGCAGUUUUCCGGGCUGCGCCCAGUAGGCCAUUUGGCCGGAC
............................................................((.......(((((..(..((((((.....))))))..))))))((((....)))))).. (-21.30 = -21.46 +   0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 4,066,816 – 4,066,927
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.18
Mean single sequence MFE -34.48
Consensus MFE -22.86
Energy contribution -24.34
Covariance contribution 1.48
Combinations/Pair 1.04
Mean z-score -2.28
Structure conservation index 0.66
SVM decision value 1.42
SVM RNA-class probability 0.952118
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4066816 111 + 20766785
---GCGGUUA------GUGGGGGCAACCUUAAGAACAGCUGGCACUCGACACUGGACUUUAAGUCAAUCGAGGCAUAAAAAGUGUGCGCAGGAGAAGCUCAAGAGUUUUUCCUUCCACAU
---((.(((.------.(((((....)))))..))).))..((.(((((.....(((.....)))..))))))).......(((((.(.((((((((((....)))))))))).)))))) ( -41.70)
>DroSec_CAF1 49352 96 + 1
------------------GGGGGCAAACUUAAGAACAGCUGGCACUCGACACCGGACUUUAAGUCAAUCGAGGCAUAAAAAGUGUGCACAGGAGAAGCUCAAGAGUU------UCCACAU
------------------((..((..............(((((.(((((.....(((.....)))..)))))((((.....)))))).)))(((...)))....)).------.)).... ( -24.50)
>DroSim_CAF1 57592 102 + 1
------------------GGGGGCAAACUUAAGAACAGCUGGCACUCGACACUGGACUUUAAGUCAAUCGAGGCAUAAAAAGUGUGCACAGGAGAAGCUCAAGAGUUUUUCCUUCCACAU
------------------.((((((.((((.((.....)).((.(((((.....(((.....)))..))))))).....)))).)))..((((((((((....))))))))))))).... ( -29.90)
>DroEre_CAF1 50679 104 + 1
GGUGGGGAU----------------GCCUUGAGAACAGACGGCACUCGACACUGGACUUUAAGUCAAUCGAGGCAUAAAAAGUGUGCGCAGGAGGAGCUCAAGAGUGUUUCCUUCCACAG
((.((..((----------------((((((((..(...(.((.(((((.....(((.....)))..)))))(((((.....))))))).)...)..)))))).))))..))..)).... ( -36.60)
>DroYak_CAF1 53450 120 + 1
GAUGCGGAUAGGGCAGGUGGGUUAAGCCUUAUAAAAUGCCGGCACUCGACACUGGACUUUAAGUCAAUCGAGGCAUAAAAAGUGUGCGCAGGAGAAGCUCAAGAGUUUUUCCUUCCACAU
.(((.(((...((((.(((((......)))))....)))).((.(((((.....(((.....)))..)))))(((((.....)))))))((((((((((....))))))))))))).))) ( -39.70)
>consensus
___G_GG_U_________GGGGGCAACCUUAAGAACAGCUGGCACUCGACACUGGACUUUAAGUCAAUCGAGGCAUAAAAAGUGUGCGCAGGAGAAGCUCAAGAGUUUUUCCUUCCACAU
.........................................((.(((((.....(((.....)))..))))))).......(((((...((((((((((....))))))))))..))))) (-22.86 = -24.34 +   1.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:41 2006