Locus 4885

Sequence ID 2L_DroMel_CAF1
Location 13,947,634 – 13,947,796
Length 162
Max. P 0.987459
window7744 window7745 window7746

overview

Window 4

Location 13,947,634 – 13,947,725
Length 91
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 73.73
Mean single sequence MFE -29.72
Consensus MFE -17.71
Energy contribution -18.88
Covariance contribution 1.17
Combinations/Pair 1.25
Mean z-score -1.88
Structure conservation index 0.60
SVM decision value 1.40
SVM RNA-class probability 0.950647
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13947634 91 + 22407834
UGCGCUUGUAUUGGUUAUAUUU----GUGUGUAUU--AGUGCGGCACGGAAAGUUGCAAGCGGAAGCGCU-----CACCAAUACACUGGCAUGCCACCAAUA
........(((((((.......----..(((((((--.(((.(((((.....)).....((....)))))-----))).))))))).((....))))))))) ( -26.10)
>DroVir_CAF1 45331 95 + 1
UGCCUUGGUAUUGGUGAGCUUUGUGCAUUUGUGUG--CGUUGCGCUCGGAAAGUUUGCAGCGGAAGCACU-----CACUAAUACAGACGCGCCGCACUAAUA
.((.((.(((((((((((((((..((((....)))--)((((((..(.....)..)))))).)))))..)-----))))))))).)).))............ ( -31.50)
>DroSec_CAF1 35431 91 + 1
UGCGCUUGUAUUGGUAAUGCUU----GUGUGUAUU--AGUGCGGCACGGAAAGUUGCAAGCGGAAGCACU-----CACCAACACACUGGCAUGCCACCAAUA
........(((((((.(((((.----((((((...--..((((((.......)))))).((....))...-----.....)))))).)))))...))))))) ( -32.80)
>DroEre_CAF1 36651 91 + 1
UUUGCUUGUAUUGGUAAUAUUU----GUGAGUGUU--AGUGCGGCACGGAAAGUUGCAAGCGGAAGCGCU-----CACCAAUACAUUGGCAGACCACCAAUA
(((((((((((((((.......----..((((...--..((((((.......)))))).((....)))))-----))))))))))..))))))......... ( -29.40)
>DroYak_CAF1 37007 91 + 1
UUCGCUUGUAUUGGUAAAAUGU----UUAAGUGUU--AGUGCCGCACGGAAAGUUGCAAGCGGAAGCGCU-----CACCAAUACAUUGGCAAAGCACCAAUA
...((((((((((((......(----((..((((.--......))))..)))......((((....))))-----.)))))))))..)))............ ( -23.20)
>DroAna_CAF1 35730 94 + 1
UGCGCCUGUAUUGGUGGGUUUU----GCAGGUGUGAGAGUUUGGCUCGGAAAGUUCCAAGCGGAAGCACCACCUCUACCAAUGCAAG----AGGCACCAACA
...(((((((((((((((....----.).(((((....((((((..(.....)..))))))....)))))....))))))))))...----))))....... ( -35.30)
>consensus
UGCGCUUGUAUUGGUAAUAUUU____GUGUGUGUU__AGUGCGGCACGGAAAGUUGCAAGCGGAAGCACU_____CACCAAUACACUGGCAAGCCACCAAUA
...((((((((((((........................((((((.......)))))).((....)).........)))))))))..)))............ (-17.71 = -18.88 +   1.17)

alignment

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secondary structure

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Window 5

Location 13,947,698 – 13,947,796
Length 98
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 72.56
Mean single sequence MFE -32.35
Consensus MFE -14.89
Energy contribution -15.33
Covariance contribution 0.45
Combinations/Pair 1.40
Mean z-score -2.36
Structure conservation index 0.46
SVM decision value 1.88
SVM RNA-class probability 0.981277
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13947698 98 + 22407834
CACCAAUAC------------ACUGGCAUGCCACCAAUACUCACGCAAUUGCGGCUUUUCUCUGUGUGUAUUGGUGACUUUAGCCGCCAACUUGAAAGUGGCUUAUAAAA
(((((((((------------(((((....)))..........(((....)))............))))))))))).....((((((..........))))))....... ( -30.30)
>DroPse_CAF1 41630 110 + 1
CACCACUACCGACACAGACAUACGAGUGUGCCACCAAUACAACGGCAAAGGCGGCUCGGCUGUGCAUGUGUGGGUAGAGCGAGCAGUCGUCUUGGAAGUGCCGCAUAAAA
.....(((((.(((((..(((((((((.((((.((........))....)))))))))..))))..))))).))))).(((.(((.((......))..))))))...... ( -39.80)
>DroSec_CAF1 35495 98 + 1
CACCAACAC------------ACUGGCAUGCCACCAAUACUCGCGCAAUCGCGGCUUUUCUUUCUGUGUAUUGGUGACUUUAGCCGCCGACUUGAAAGUGGCUUAUAAAA
((((((.((------------(((((....))).......(((((....)))))...........)))).)))))).....((((((..........))))))....... ( -27.10)
>DroEre_CAF1 36715 98 + 1
CACCAAUAC------------AUUGGCAGACCACCAAUACUCGCGCAAUCGUGGCUUUCCUCUUUGUGUAUUGGUGACUUUAGCCGCCGACUUGAAAGUGGCUUAUAAAA
(((((((((------------((.((.(((((((................)))).))))).....))))))))))).....((((((..........))))))....... ( -27.19)
>DroYak_CAF1 37071 98 + 1
CACCAAUAC------------AUUGGCAAAGCACCAAUACUCGCGCAAUCGUGGAUUUUCGCUUUGUGUAUUGGUGACUUUAGCCGCCGACUUGAAAGUGGCUUAUAAAA
.........------------...((((((((((((((((....((((..((((....)))).))))))))))))).)))).)))(((.(((....))))))........ ( -29.90)
>DroPer_CAF1 43553 110 + 1
CACCACUACCGACACAGACAUACGAGUGUGCCACCAAUACAACGGCAAAGGCGGCUCGGCUGUGCAUGUGUGGGUAGAGCGAGCAGUCGUCUUGGAAGUGCCGCAUAAAA
.....(((((.(((((..(((((((((.((((.((........))....)))))))))..))))..))))).))))).(((.(((.((......))..))))))...... ( -39.80)
>consensus
CACCAAUAC____________ACUGGCAUGCCACCAAUACUCGCGCAAUCGCGGCUUUUCUCUGUGUGUAUUGGUGACUUUAGCCGCCGACUUGAAAGUGGCUUAUAAAA
........................(((.((.(((((((((...(((....)))((........))..)))))))))...)).)))((((.((....))))))........ (-14.89 = -15.33 +   0.45)

alignment

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secondary structure

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Window 6

Location 13,947,698 – 13,947,796
Length 98
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 72.56
Mean single sequence MFE -34.40
Consensus MFE -18.16
Energy contribution -19.63
Covariance contribution 1.48
Combinations/Pair 1.20
Mean z-score -2.32
Structure conservation index 0.53
SVM decision value 2.08
SVM RNA-class probability 0.987459
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13947698 98 - 22407834
UUUUAUAAGCCACUUUCAAGUUGGCGGCUAAAGUCACCAAUACACACAGAGAAAAGCCGCAAUUGCGUGAGUAUUGGUGGCAUGCCAGU------------GUAUUGGUG
.......((((.((........)).)))).....(((((((((((...(.(....(((((...(((....)))...)))))...)).))------------))))))))) ( -34.60)
>DroPse_CAF1 41630 110 - 1
UUUUAUGCGGCACUUCCAAGACGACUGCUCGCUCUACCCACACAUGCACAGCCGAGCCGCCUUUGCCGUUGUAUUGGUGGCACACUCGUAUGUCUGUGUCGGUAGUGGUG
......((((((..((......)).))).))).(((((.(((((.(.(((..(((((((((..(((....)))..))))))....)))..))))))))).)))))..... ( -37.00)
>DroSec_CAF1 35495 98 - 1
UUUUAUAAGCCACUUUCAAGUCGGCGGCUAAAGUCACCAAUACACAGAAAGAAAAGCCGCGAUUGCGCGAGUAUUGGUGGCAUGCCAGU------------GUGUUGGUG
........((((((....))).)))(((....)))((((((((((..........(((((.(.(((....))).).)))))......))------------)))))))). ( -33.89)
>DroEre_CAF1 36715 98 - 1
UUUUAUAAGCCACUUUCAAGUCGGCGGCUAAAGUCACCAAUACACAAAGAGGAAAGCCACGAUUGCGCGAGUAUUGGUGGUCUGCCAAU------------GUAUUGGUG
........((((((....))).)))(((....)))(((((((((......((...(((((.(.(((....))).).)))))...))..)------------)))))))). ( -32.90)
>DroYak_CAF1 37071 98 - 1
UUUUAUAAGCCACUUUCAAGUCGGCGGCUAAAGUCACCAAUACACAAAGCGAAAAUCCACGAUUGCGCGAGUAUUGGUGCUUUGCCAAU------------GUAUUGGUG
........((((((....))).)))(((.((((.(((((((((.....(((..((((...)))).)))..))))))))))))))))...------------......... ( -31.00)
>DroPer_CAF1 43553 110 - 1
UUUUAUGCGGCACUUCCAAGACGACUGCUCGCUCUACCCACACAUGCACAGCCGAGCCGCCUUUGCCGUUGUAUUGGUGGCACACUCGUAUGUCUGUGUCGGUAGUGGUG
......((((((..((......)).))).))).(((((.(((((.(.(((..(((((((((..(((....)))..))))))....)))..))))))))).)))))..... ( -37.00)
>consensus
UUUUAUAAGCCACUUUCAAGUCGGCGGCUAAAGUCACCAAUACACACAGAGAAAAGCCGCGAUUGCGCGAGUAUUGGUGGCAUGCCAGU____________GUAUUGGUG
........((((((....))).))).........(((((((((.(.....)....(((((.(.(((....))).).)))))....................))))))))) (-18.16 = -19.63 +   1.48)

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 11:30:07 2006