Locus 478

Sequence ID 2R_DroMel_CAF1
Location 2,685,223 – 2,685,388
Length 165
Max. P 0.983431
window905 window906 window907 window908

overview

Window 5

Location 2,685,223 – 2,685,328
Length 105
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 77.68
Mean single sequence MFE -37.27
Consensus MFE -15.68
Energy contribution -17.65
Covariance contribution 1.97
Combinations/Pair 1.19
Mean z-score -3.22
Structure conservation index 0.42
SVM decision value 1.94
SVM RNA-class probability 0.983431
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2685223 105 + 20766785
------GACUCGAUUGCACCAGCGAACCGCUCUAGCGGUCCAAGGCGGCGGCA-----GCACUUGUCGCCACGGCACUAUUCAAUAAAAGUGCAGUUAUUUGUAACGCACUU-UUAU
------.....((.(((......(.(((((....))))).)..((((((((..-----....))))))))...)))....)).((((((((((.((((....))))))))))-)))) ( -35.70)
>DroSec_CAF1 117825 105 + 1
------GACUCGAUUGCACCAGCGGACCGCUCUAGCGGUCCAAGACGGCGGCA-----GCACUUGUCGCCACGGCACUAUUCAAUAAAAGUGCAGUUAUUUGUAACGCACUU-UUAU
------.....((.(((......(((((((....))))))).....(((((((-----(...))))))))...)))....)).((((((((((.((((....))))))))))-)))) ( -42.40)
>DroSim_CAF1 116116 105 + 1
------GACUCGCUUGCACCAGCGGACCGCUCUAGCGGUCCAAGGCGGCGGCA-----GCACUUGUCGCCACGGCACUAUUCAAUAAAAGUGCAGUUAUUUGUAACGCACUU-UUAU
------.....((((((....))(((((((....))))))).))))(((((((-----(...)))))))).............((((((((((.((((....))))))))))-)))) ( -44.40)
>DroEre_CAF1 116772 87 + 1
------GACU----UGCACGAGCGGACUUCUCCAGCGGUCC-------------------ACUUGUCGCCACACCACUAUUCAAUAAAAGUGCAGUUAUUUGUAACGCACUU-UUAU
------....----.(((((((.(((((.(....).)))))-------------------.))))).))..............((((((((((.((((....))))))))))-)))) ( -27.60)
>DroYak_CAF1 114049 111 + 1
------GACUCGAUUGCACCAGCGGACCUCUCUAGCGGUCCAAGGCAGCGGCAGUGGGGCACUUGCUGCCACAGCACUAUCCAAUAAAAGUGCAGUUAUUUGUAACGCACUUUUUAU
------.....((((((......(((((.(....).)))))..(((((((..((((...)))))))))))...)))..)))....((((((((.((((....))))))))))))... ( -37.70)
>DroPer_CAF1 138263 98 + 1
UCCUGGGGCG----U-GGGGAACAGGCGUCUCUAACGGUCCAAGGCAGCCGCU-----GGAGUC--------GGUGCCAUUCAAUAAAAGUGCAGUUAUUUGUAACGCACUU-UUAU
...((((.((----(-(((((.......))))).))).)))).((((.((((.-----...).)--------)))))).....((((((((((.((((....))))))))))-)))) ( -35.80)
>consensus
______GACUCGAUUGCACCAGCGGACCGCUCUAGCGGUCCAAGGCGGCGGCA_____GCACUUGUCGCCACGGCACUAUUCAAUAAAAGUGCAGUUAUUUGUAACGCACUU_UUAU
.....................(((((((........)))))......((((((..........))))))....))........((((((((((.((((....)))))))))).)))) (-15.68 = -17.65 +   1.97)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,685,223 – 2,685,328
Length 105
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 77.68
Mean single sequence MFE -37.72
Consensus MFE -16.15
Energy contribution -19.37
Covariance contribution 3.22
Combinations/Pair 1.13
Mean z-score -2.82
Structure conservation index 0.43
SVM decision value 1.40
SVM RNA-class probability 0.950239
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2685223 105 - 20766785
AUAA-AAGUGCGUUACAAAUAACUGCACUUUUAUUGAAUAGUGCCGUGGCGACAAGUGC-----UGCCGCCGCCUUGGACCGCUAGAGCGGUUCGCUGGUGCAAUCGAGUC------
.(((-((((((((((....)))).)))))))))((((...(..((((((((.((.....-----)).))))))...(((((((....)))))))...))..)..))))...------ ( -42.30)
>DroSec_CAF1 117825 105 - 1
AUAA-AAGUGCGUUACAAAUAACUGCACUUUUAUUGAAUAGUGCCGUGGCGACAAGUGC-----UGCCGCCGUCUUGGACCGCUAGAGCGGUCCGCUGGUGCAAUCGAGUC------
.(((-((((((((((....)))).)))))))))((((...(..((((((((.(....).-----))))))......(((((((....)))))))...))..)..))))...------ ( -42.70)
>DroSim_CAF1 116116 105 - 1
AUAA-AAGUGCGUUACAAAUAACUGCACUUUUAUUGAAUAGUGCCGUGGCGACAAGUGC-----UGCCGCCGCCUUGGACCGCUAGAGCGGUCCGCUGGUGCAAGCGAGUC------
((((-((((((((((....)))).))))))))))......(..((((((((.((.....-----)).))))))...(((((((....)))))))...))..).........------ ( -44.70)
>DroEre_CAF1 116772 87 - 1
AUAA-AAGUGCGUUACAAAUAACUGCACUUUUAUUGAAUAGUGGUGUGGCGACAAGU-------------------GGACCGCUGGAGAAGUCCGCUCGUGCA----AGUC------
((((-((((((((((....)))).))))))))))..............((.((.(((-------------------((((..(....)..))))))).)))).----....------ ( -25.80)
>DroYak_CAF1 114049 111 - 1
AUAAAAAGUGCGUUACAAAUAACUGCACUUUUAUUGGAUAGUGCUGUGGCAGCAAGUGCCCCACUGCCGCUGCCUUGGACCGCUAGAGAGGUCCGCUGGUGCAAUCGAGUC------
...((((((((((((....)))).))))))))(((.(((.(..((((((((((.((((...))))...))))))..(((((........))))))).))..).))).))).------ ( -42.10)
>DroPer_CAF1 138263 98 - 1
AUAA-AAGUGCGUUACAAAUAACUGCACUUUUAUUGAAUGGCACC--------GACUCC-----AGCGGCUGCCUUGGACCGUUAGAGACGCCUGUUCCCC-A----CGCCCCAGGA
((((-((((((((((....)))).)))))))))).....((((((--------(.(...-----.)))).))))((((..(((..(..((....))..)..-)----))..)))).. ( -28.70)
>consensus
AUAA_AAGUGCGUUACAAAUAACUGCACUUUUAUUGAAUAGUGCCGUGGCGACAAGUGC_____UGCCGCCGCCUUGGACCGCUAGAGAGGUCCGCUGGUGCAAUCGAGUC______
((((.((((((((((....)))).))))))))))......(((((((((((.............))))))......(((((........)))))...)))))............... (-16.15 = -19.37 +   3.22)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,685,289 – 2,685,388
Length 99
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 84.76
Mean single sequence MFE -29.30
Consensus MFE -20.27
Energy contribution -20.40
Covariance contribution 0.13
Combinations/Pair 1.09
Mean z-score -1.65
Structure conservation index 0.69
SVM decision value 0.20
SVM RNA-class probability 0.630021
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2685289 99 + 20766785
UAUUCAAUAAAAGUGCAGUUAUUUGUAACGCACUU-UUAUGGCCACACAUGCGAUGCGAACCCGCACGAUUGGAGCGUUUUGGAUCGGGCGGGGCGGUUC
......((((((((((.((((....))))))))))-))))((((.(...(((...)))..(((((.(((((.(((...))).))))).)))))).)))). ( -33.80)
>DroSec_CAF1 117891 99 + 1
UAUUCAAUAAAAGUGCAGUUAUUUGUAACGCACUU-UUAUGGCCACACAUGCGAUGCGAACCCGCACGAUUGGAUCGUUUUGGACCGGGCGGGGCGGUUC
......((((((((((.((((....))))))))))-))))((((.(...(((...)))..(((((.((.((.((.....)).)).)).)))))).)))). ( -30.30)
>DroSim_CAF1 116182 99 + 1
UAUUCAAUAAAAGUGCAGUUAUUUGUAACGCACUU-UUAUGGCCACACAUGCGAUGCGAACCCGCACGAUUGGAUCGUUUUGGACCGGGCGGGGCGGUUC
......((((((((((.((((....))))))))))-))))((((.(...(((...)))..(((((.((.((.((.....)).)).)).)))))).)))). ( -30.30)
>DroYak_CAF1 114120 78 + 1
UAUCCAAUAAAAGUGCAGUUAUUUGUAACGCACUUUUUAUGGCCACACAUGCGAUGCGAACCCUCGCGAUUGGAACCG----------------------
..((((((((((((((.((((....))))))))))))((((......))))...(((((....)))))))))))....---------------------- ( -22.80)
>consensus
UAUUCAAUAAAAGUGCAGUUAUUUGUAACGCACUU_UUAUGGCCACACAUGCGAUGCGAACCCGCACGAUUGGAUCGUUUUGGACCGGGCGGGGCGGUUC
..((((((..((((((.((((....))))))))))..((((......))))((.((((....)))))))))))).......((((((.......)))))) (-20.27 = -20.40 +   0.13)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,685,289 – 2,685,388
Length 99
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 84.76
Mean single sequence MFE -27.29
Consensus MFE -17.85
Energy contribution -18.35
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.82
Structure conservation index 0.65
SVM decision value 0.26
SVM RNA-class probability 0.655709
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2685289 99 - 20766785
GAACCGCCCCGCCCGAUCCAAAACGCUCCAAUCGUGCGGGUUCGCAUCGCAUGUGUGGCCAUAA-AAGUGCGUUACAAAUAACUGCACUUUUAUUGAAUA
...(((((((((.((((.............)))).)))))...((((...))))))))(.((((-((((((((((....)))).)))))))))).).... ( -29.02)
>DroSec_CAF1 117891 99 - 1
GAACCGCCCCGCCCGGUCCAAAACGAUCCAAUCGUGCGGGUUCGCAUCGCAUGUGUGGCCAUAA-AAGUGCGUUACAAAUAACUGCACUUUUAUUGAAUA
...(((((((((.((((.............)))).)))))...((((...))))))))(.((((-((((((((((....)))).)))))))))).).... ( -28.42)
>DroSim_CAF1 116182 99 - 1
GAACCGCCCCGCCCGGUCCAAAACGAUCCAAUCGUGCGGGUUCGCAUCGCAUGUGUGGCCAUAA-AAGUGCGUUACAAAUAACUGCACUUUUAUUGAAUA
...(((((((((.((((.............)))).)))))...((((...))))))))(.((((-((((((((((....)))).)))))))))).).... ( -28.42)
>DroYak_CAF1 114120 78 - 1
----------------------CGGUUCCAAUCGCGAGGGUUCGCAUCGCAUGUGUGGCCAUAAAAAGUGCGUUACAAAUAACUGCACUUUUAUUGGAUA
----------------------.(((..((...((((..(....).))))...))..)))...((((((((((((....)))).))))))))........ ( -23.30)
>consensus
GAACCGCCCCGCCCGGUCCAAAACGAUCCAAUCGUGCGGGUUCGCAUCGCAUGUGUGGCCAUAA_AAGUGCGUUACAAAUAACUGCACUUUUAUUGAAUA
...........................(((..(((((((.......)))))))..))).((....((((((((((....)))).))))))....)).... (-17.85 = -18.35 +   0.50)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:36 2006