Locus 5944

Sequence ID 2R_DroMel_CAF1
Location 18,745,904 – 18,746,040
Length 136
Max. P 0.998881
window9534 window9535 window9536 window9537

overview

Window 4

Location 18,745,904 – 18,746,002
Length 98
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 88.31
Mean single sequence MFE -30.34
Consensus MFE -23.46
Energy contribution -23.86
Covariance contribution 0.40
Combinations/Pair 1.08
Mean z-score -1.96
Structure conservation index 0.77
SVM decision value 0.84
SVM RNA-class probability 0.864415
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18745904 98 + 20766785
GCCUCGAGUAUCGCCAAGUGGCGGACAGCAUUGUGGUUACUUCGCUCAAGUGUGAAUACAAAUUAUUCACACAGCCGCACAGCUUU-GCGAGUUUGAAU
...((((...((((.((((.((((.(......((((.....))))....(((((((((.....))))))))).)))))...)))).-))))..)))).. ( -33.20)
>DroSec_CAF1 108634 98 + 1
GCCUGGAGUAUCGCCAAGUGGCGGACAGCAUUGUGGUUACUUGGCUCAAGUGUGAAUACAAAUUAUUCACACAGCCGCACAGCUUU-GCGAGUUUGAAU
............((((((((((.(.(......)).))))))))))(((((((((((((.....))))))))).((((((......)-))).)))))).. ( -32.70)
>DroSim_CAF1 109418 98 + 1
GCCUGGAGUAUCGCCAAGUGGCGGACAGCAUUGUGGUUACUUGGCUCAAGUGUGAAUACAAAUUAUUCACACAGCCGCACAGCUUU-GCGAGUUUGAAU
............((((((((((.(.(......)).))))))))))(((((((((((((.....))))))))).((((((......)-))).)))))).. ( -32.70)
>DroEre_CAF1 111099 89 + 1
GCCUCAAGUAUCGCCGAGUGGCGGACAGCAUUGUGGUUACUUCGUUUGAGUGUGAAUACAAAUUAUUCACACAGCCCAACCGUU----------UGAAU
...((((((.(((((....)))))))....(((.((((...((....))(((((((((.....))))))))))))))))....)----------))).. ( -23.70)
>DroYak_CAF1 111342 99 + 1
GCCUCAAGUAUCGCCAAGUGGCGGACAGCAUUGUGGUUACUUCGUUUGAGUGUGAAUACAAAUUAUUCACACAGCCCAGCCGUUUUGGCUAGUUUCAAU
(((.(((((.(((((....)))))...)).))).)))........(((((((((((((.....))))))))).....((((.....))))....)))). ( -29.40)
>consensus
GCCUCGAGUAUCGCCAAGUGGCGGACAGCAUUGUGGUUACUUCGCUCAAGUGUGAAUACAAAUUAUUCACACAGCCGCACAGCUUU_GCGAGUUUGAAU
.......((.(((((....)))))))(((..(((((((...........(((((((((.....))))))))))))))))..)))............... (-23.46 = -23.86 +   0.40)

alignment

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secondary structure

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Window 5

Location 18,745,904 – 18,746,002
Length 98
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 88.31
Mean single sequence MFE -27.78
Consensus MFE -20.04
Energy contribution -20.28
Covariance contribution 0.24
Combinations/Pair 1.08
Mean z-score -1.82
Structure conservation index 0.72
SVM decision value 0.22
SVM RNA-class probability 0.638300
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18745904 98 - 20766785
AUUCAAACUCGC-AAAGCUGUGCGGCUGUGUGAAUAAUUUGUAUUCACACUUGAGCGAAGUAACCACAAUGCUGUCCGCCACUUGGCGAUACUCGAGGC
.......(((((-..((((....))))(((((((((.....)))))))))....))((.(((...(((....))).((((....)))).)))))))).. ( -28.30)
>DroSec_CAF1 108634 98 - 1
AUUCAAACUCGC-AAAGCUGUGCGGCUGUGUGAAUAAUUUGUAUUCACACUUGAGCCAAGUAACCACAAUGCUGUCCGCCACUUGGCGAUACUCCAGGC
........((((-.(((.((.(((((((((((((((.....)))))))))...)))).((((.......))))....))))))).)))).......... ( -27.70)
>DroSim_CAF1 109418 98 - 1
AUUCAAACUCGC-AAAGCUGUGCGGCUGUGUGAAUAAUUUGUAUUCACACUUGAGCCAAGUAACCACAAUGCUGUCCGCCACUUGGCGAUACUCCAGGC
........((((-.(((.((.(((((((((((((((.....)))))))))...)))).((((.......))))....))))))).)))).......... ( -27.70)
>DroEre_CAF1 111099 89 - 1
AUUCA----------AACGGUUGGGCUGUGUGAAUAAUUUGUAUUCACACUCAAACGAAGUAACCACAAUGCUGUCCGCCACUCGGCGAUACUUGAGGC
.((((----------(((((((((((((((((((((.....)))))))))((....)))))..)))....))))).((((....))))....))))).. ( -23.80)
>DroYak_CAF1 111342 99 - 1
AUUGAAACUAGCCAAAACGGCUGGGCUGUGUGAAUAAUUUGUAUUCACACUCAAACGAAGUAACCACAAUGCUGUCCGCCACUUGGCGAUACUUGAGGC
.((((..((((((.....))))))...(((((((((.....))))))))))))).........((.(((.(.((((.(((....))))))))))).)). ( -31.40)
>consensus
AUUCAAACUCGC_AAAGCUGUGCGGCUGUGUGAAUAAUUUGUAUUCACACUUGAGCGAAGUAACCACAAUGCUGUCCGCCACUUGGCGAUACUCGAGGC
........................((((((((((((.....)))))))))(((((...((((.......))))...((((....))))...)))))))) (-20.04 = -20.28 +   0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,745,943 – 18,746,040
Length 97
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 77.29
Mean single sequence MFE -25.70
Consensus MFE -15.68
Energy contribution -16.06
Covariance contribution 0.38
Combinations/Pair 1.14
Mean z-score -3.01
Structure conservation index 0.61
SVM decision value 3.27
SVM RNA-class probability 0.998881
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18745943 97 + 20766785
CUUCGCUCAAGUGUGAAUACAAAUUAUUCACACAGCCGCACAGCUUU-GCGAGUUUGAAUAGCACGGCAAACAGAAGAAACCCCCAAAGGGAAAUAAU
((((......(((((((((.....))))))))).((((((......)-))..(((.....)))..))).....))))...(((.....)))....... ( -26.70)
>DroSec_CAF1 108673 95 + 1
CUUGGCUCAAGUGUGAAUACAAAUUAUUCACACAGCCGCACAGCUUU-GCGAGUUUGAAUAGCACGGCAAACAGAAGAAAGCCC--AAGGGAAAUAUU
(((((((...(((((((((.....))))))))).((((((......)-))..(((.....)))..)))...........)).))--)))......... ( -26.00)
>DroSim_CAF1 109457 95 + 1
CUUGGCUCAAGUGUGAAUACAAAUUAUUCACACAGCCGCACAGCUUU-GCGAGUUUGAAUAGCACGGCAAACAGAAGAAAGCCC--AAGGGAAAUAUU
(((((((...(((((((((.....))))))))).((((((......)-))..(((.....)))..)))...........)).))--)))......... ( -26.00)
>DroEre_CAF1 111138 84 + 1
CUUCGUUUGAGUGUGAAUACAAAUUAUUCACACAGCCCAACCGUU----------UGAAUGGCACGGCAAACAGAAGAAACCCU--A--GGGAAUAUU
((((((((..(((((((((.....))))))))).(((...((((.----------...))))...))))))).))))...((..--.--.))...... ( -25.40)
>DroYak_CAF1 111381 77 + 1
CUUCGUUUGAGUGUGAAUACAAAUUAUUCACACAGCCCAGCCGUUUUGGCUAGUUUCAAUGGCAGGACAAACAGUAG---------------------
....(((((.(((((((((.....)))))))))...((.((((((..((....))..)))))).)).))))).....--------------------- ( -24.40)
>consensus
CUUCGCUCAAGUGUGAAUACAAAUUAUUCACACAGCCGCACAGCUUU_GCGAGUUUGAAUAGCACGGCAAACAGAAGAAACCCC__AAGGGAAAUAUU
((((......(((((((((.....))))))))).((((....(((...............))).)))).....))))....((......))....... (-15.68 = -16.06 +   0.38)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,745,943 – 18,746,040
Length 97
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 77.29
Mean single sequence MFE -26.11
Consensus MFE -20.72
Energy contribution -20.63
Covariance contribution -0.09
Combinations/Pair 1.22
Mean z-score -2.50
Structure conservation index 0.79
SVM decision value 2.61
SVM RNA-class probability 0.995707
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18745943 97 - 20766785
AUUAUUUCCCUUUGGGGGUUUCUUCUGUUUGCCGUGCUAUUCAAACUCGC-AAAGCUGUGCGGCUGUGUGAAUAAUUUGUAUUCACACUUGAGCGAAG
......((((....))))...((((.((((((((..(.............-......)..)))).(((((((((.....)))))))))..)))))))) ( -29.11)
>DroSec_CAF1 108673 95 - 1
AAUAUUUCCCUU--GGGCUUUCUUCUGUUUGCCGUGCUAUUCAAACUCGC-AAAGCUGUGCGGCUGUGUGAAUAAUUUGUAUUCACACUUGAGCCAAG
............--.(((((..........((((..(.............-......)..)))).(((((((((.....)))))))))..)))))... ( -27.21)
>DroSim_CAF1 109457 95 - 1
AAUAUUUCCCUU--GGGCUUUCUUCUGUUUGCCGUGCUAUUCAAACUCGC-AAAGCUGUGCGGCUGUGUGAAUAAUUUGUAUUCACACUUGAGCCAAG
............--.(((((..........((((..(.............-......)..)))).(((((((((.....)))))))))..)))))... ( -27.21)
>DroEre_CAF1 111138 84 - 1
AAUAUUCCC--U--AGGGUUUCUUCUGUUUGCCGUGCCAUUCA----------AACGGUUGGGCUGUGUGAAUAAUUUGUAUUCACACUCAAACGAAG
......((.--.--..))...((((.(((((((..(((.....----------...)))..))).(((((((((.....)))))))))..)))))))) ( -23.20)
>DroYak_CAF1 111381 77 - 1
---------------------CUACUGUUUGUCCUGCCAUUGAAACUAGCCAAAACGGCUGGGCUGUGUGAAUAAUUUGUAUUCACACUCAAACGAAG
---------------------....((((((..............((((((.....))))))...(((((((((.....))))))))).))))))... ( -23.80)
>consensus
AAUAUUUCCCUU__GGGCUUUCUUCUGUUUGCCGUGCUAUUCAAACUCGC_AAAGCUGUGCGGCUGUGUGAAUAAUUUGUAUUCACACUUGAGCGAAG
.......(((....))).........(((((((((((....................))))))).(((((((((.....)))))))))..)))).... (-20.72 = -20.63 +  -0.09)

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 11:58:41 2006