Locus 2380

Sequence ID 3R_DroMel_CAF1
Location 6,738,590 – 6,738,910
Length 320
Max. P 0.973886
window3839 window3840 window3841 window3842 window3843 window3844 window3845

overview

Window 9

Location 6,738,590 – 6,738,710
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 99.44
Mean single sequence MFE -29.23
Consensus MFE -29.03
Energy contribution -29.37
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.57
Structure conservation index 0.99
SVM decision value 1.72
SVM RNA-class probability 0.973886
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6738590 120 - 27905053
CGUGGCUGGAAUAGAGAUUGGCUAAAAGCAUGCCAACAGCAUCUGGGCCAAACGCCAGCGCACAAAAAUUAAUAUGCAAUUAAAUGAAAAUUAGCAAAAAUGUGUGGCGAAUUGAUAAUA
.((((((((......(.((((((...((.((((.....)))))).)))))).).))))).)))....((((((.(((.....(((....))).(((......))).))).)))))).... ( -31.60)
>DroSec_CAF1 3434 120 - 1
CGUGGCUGGAAUAGAGAUUGACUAAAAGCAUGCCAACAGCAUCUGGGCCAAACGCCAGCGCACAAAAAUUAAUAUGCAAUUAAAUGAAAAUUAGCAAAAAUGUGUGGCGAAUUGAUAAUA
.((((((((......(.(((.((...((.((((.....)))))).)).))).).))))).)))....((((((.(((.....(((....))).(((......))).))).)))))).... ( -24.50)
>DroSim_CAF1 7790 120 - 1
CGUGGCUGGAAUAGAGAUUGGCUAAAAGCAUGCCAACAGCAUCUGGGCCAAACGCCAGCGCACAAAAAUUAAUAUGCAAUUAAAUGAAAAUUAGCAAAAAUGUGUGGCGAAUUGAUAAUA
.((((((((......(.((((((...((.((((.....)))))).)))))).).))))).)))....((((((.(((.....(((....))).(((......))).))).)))))).... ( -31.60)
>consensus
CGUGGCUGGAAUAGAGAUUGGCUAAAAGCAUGCCAACAGCAUCUGGGCCAAACGCCAGCGCACAAAAAUUAAUAUGCAAUUAAAUGAAAAUUAGCAAAAAUGUGUGGCGAAUUGAUAAUA
.((((((((......(.((((((...((.((((.....)))))).)))))).).))))).)))....((((((.(((.....(((....))).(((......))).))).)))))).... (-29.03 = -29.37 +   0.33)

alignment

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secondary structure

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Window 0

Location 6,738,630 – 6,738,750
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 99.44
Mean single sequence MFE -28.83
Consensus MFE -28.26
Energy contribution -28.04
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.74
Structure conservation index 0.98
SVM decision value 0.51
SVM RNA-class probability 0.765003
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6738630 120 + 27905053
AUUGCAUAUUAAUUUUUGUGCGCUGGCGUUUGGCCCAGAUGCUGUUGGCAUGCUUUUAGCCAAUCUCUAUUCCAGCCACGCCACCACUCUCACGGCCACACUUUUCACUUGCCACUUGCC
...(((((........)))))((((((((..(((...((((..((((((.........))))))...))))...)))))))))..........(((..............)))....)). ( -28.94)
>DroSec_CAF1 3474 120 + 1
AUUGCAUAUUAAUUUUUGUGCGCUGGCGUUUGGCCCAGAUGCUGUUGGCAUGCUUUUAGUCAAUCUCUAUUCCAGCCACGCCACCACUCUCACGGCCACACUUUUCACUUGCCACUUGCC
...(((((........)))))((((((((.(((((.(((.(.((.((((..(((..(((.......)))....)))...)))).))))))...))))).)).........))))...)). ( -28.60)
>DroSim_CAF1 7830 120 + 1
AUUGCAUAUUAAUUUUUGUGCGCUGGCGUUUGGCCCAGAUGCUGUUGGCAUGCUUUUAGCCAAUCUCUAUUCCAGCCACGCCACCACUCUCACGGCCACACUUUUCACUUGCCACUUGCC
...(((((........)))))((((((((..(((...((((..((((((.........))))))...))))...)))))))))..........(((..............)))....)). ( -28.94)
>consensus
AUUGCAUAUUAAUUUUUGUGCGCUGGCGUUUGGCCCAGAUGCUGUUGGCAUGCUUUUAGCCAAUCUCUAUUCCAGCCACGCCACCACUCUCACGGCCACACUUUUCACUUGCCACUUGCC
...(((((........)))))((((((((..(((...((((..((((((.........))))))...))))...)))))))))..........(((..............)))....)). (-28.26 = -28.04 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,738,630 – 6,738,750
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 99.44
Mean single sequence MFE -36.07
Consensus MFE -35.43
Energy contribution -35.77
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.05
Structure conservation index 0.98
SVM decision value 1.00
SVM RNA-class probability 0.897143
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6738630 120 - 27905053
GGCAAGUGGCAAGUGAAAAGUGUGGCCGUGAGAGUGGUGGCGUGGCUGGAAUAGAGAUUGGCUAAAAGCAUGCCAACAGCAUCUGGGCCAAACGCCAGCGCACAAAAAUUAAUAUGCAAU
.(((...(((.(.(....).)...)))......(((.((((((...(((..(((((.(((((.........)))))...).))))..))).)))))).))).............)))... ( -38.00)
>DroSec_CAF1 3474 120 - 1
GGCAAGUGGCAAGUGAAAAGUGUGGCCGUGAGAGUGGUGGCGUGGCUGGAAUAGAGAUUGACUAAAAGCAUGCCAACAGCAUCUGGGCCAAACGCCAGCGCACAAAAAUUAAUAUGCAAU
.(((...(((.(.(....).)...)))......(((.((((((((((....(((.......)))..((.((((.....)))))).))))..)))))).))).............)))... ( -32.20)
>DroSim_CAF1 7830 120 - 1
GGCAAGUGGCAAGUGAAAAGUGUGGCCGUGAGAGUGGUGGCGUGGCUGGAAUAGAGAUUGGCUAAAAGCAUGCCAACAGCAUCUGGGCCAAACGCCAGCGCACAAAAAUUAAUAUGCAAU
.(((...(((.(.(....).)...)))......(((.((((((...(((..(((((.(((((.........)))))...).))))..))).)))))).))).............)))... ( -38.00)
>consensus
GGCAAGUGGCAAGUGAAAAGUGUGGCCGUGAGAGUGGUGGCGUGGCUGGAAUAGAGAUUGGCUAAAAGCAUGCCAACAGCAUCUGGGCCAAACGCCAGCGCACAAAAAUUAAUAUGCAAU
.(((...(((.(.(....).)...)))......(((.((((((...(((..(((((.(((((.........)))))...).))))..))).)))))).))).............)))... (-35.43 = -35.77 +   0.33)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,738,670 – 6,738,790
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 99.44
Mean single sequence MFE -35.67
Consensus MFE -35.33
Energy contribution -35.33
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.36
Structure conservation index 0.99
SVM decision value -0.00
SVM RNA-class probability 0.531893
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6738670 120 - 27905053
GGCACUGAAAGCAAAAGUGUUUUACUGGACUCUCUCGAGUGGCAAGUGGCAAGUGAAAAGUGUGGCCGUGAGAGUGGUGGCGUGGCUGGAAUAGAGAUUGGCUAAAAGCAUGCCAACAGC
((((((.........))))))...(((.((((((.((.((.(((..(..(....)..)..))).)))).))))))((((((.((((..(........)..))))...)).))))..))). ( -35.90)
>DroSec_CAF1 3514 120 - 1
GGCACUGAAAGCAAAAGUGUUUUACUGGACUCUCUCGAGUGGCAAGUGGCAAGUGAAAAGUGUGGCCGUGAGAGUGGUGGCGUGGCUGGAAUAGAGAUUGACUAAAAGCAUGCCAACAGC
((((((.........))))))...(((.((((((.((.((.(((..(..(....)..)..))).)))).))))))..(((((((.((....(((.......)))..))))))))).))). ( -35.20)
>DroSim_CAF1 7870 120 - 1
GGCACUGAAAGCAAAAGUGUUUUACUGGACUCUCUCGAGUGGCAAGUGGCAAGUGAAAAGUGUGGCCGUGAGAGUGGUGGCGUGGCUGGAAUAGAGAUUGGCUAAAAGCAUGCCAACAGC
((((((.........))))))...(((.((((((.((.((.(((..(..(....)..)..))).)))).))))))((((((.((((..(........)..))))...)).))))..))). ( -35.90)
>consensus
GGCACUGAAAGCAAAAGUGUUUUACUGGACUCUCUCGAGUGGCAAGUGGCAAGUGAAAAGUGUGGCCGUGAGAGUGGUGGCGUGGCUGGAAUAGAGAUUGGCUAAAAGCAUGCCAACAGC
((((((.........))))))...(((.((((((.((.((.(((..(..(....)..)..))).)))).))))))..(((((((.((....(((.......)))..))))))))).))). (-35.33 = -35.33 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,738,710 – 6,738,830
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -36.90
Consensus MFE -36.90
Energy contribution -36.90
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.96
Structure conservation index 1.00
SVM decision value 0.97
SVM RNA-class probability 0.892531
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6738710 120 + 27905053
CCACCACUCUCACGGCCACACUUUUCACUUGCCACUUGCCACUCGAGAGAGUCCAGUAAAACACUUUUGCUUUCAGUGCCUGGCAGGCAGAAGUUUCCGCUGCCGGUGAUUAAUGUGCCG
............((((.(((.(..((((((((((...(((((((....))))..((((((.....))))))....).)).)))))(((((.........))))))))))..).))))))) ( -36.90)
>DroSec_CAF1 3554 120 + 1
CCACCACUCUCACGGCCACACUUUUCACUUGCCACUUGCCACUCGAGAGAGUCCAGUAAAACACUUUUGCUUUCAGUGCCUGGCAGGCAGAAGUUUCCGCUGCCGGUGAUUAAUGUGCCG
............((((.(((.(..((((((((((...(((((((....))))..((((((.....))))))....).)).)))))(((((.........))))))))))..).))))))) ( -36.90)
>DroSim_CAF1 7910 120 + 1
CCACCACUCUCACGGCCACACUUUUCACUUGCCACUUGCCACUCGAGAGAGUCCAGUAAAACACUUUUGCUUUCAGUGCCUGGCAGGCAGAAGUUUCCGCUGCCGGUGAUUAAUGUGCCG
............((((.(((.(..((((((((((...(((((((....))))..((((((.....))))))....).)).)))))(((((.........))))))))))..).))))))) ( -36.90)
>consensus
CCACCACUCUCACGGCCACACUUUUCACUUGCCACUUGCCACUCGAGAGAGUCCAGUAAAACACUUUUGCUUUCAGUGCCUGGCAGGCAGAAGUUUCCGCUGCCGGUGAUUAAUGUGCCG
............((((.(((.(..((((((((((...(((((((....))))..((((((.....))))))....).)).)))))(((((.........))))))))))..).))))))) (-36.90 = -36.90 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,738,710 – 6,738,830
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -42.00
Consensus MFE -42.00
Energy contribution -42.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 1.00
SVM decision value 0.32
SVM RNA-class probability 0.685577
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6738710 120 - 27905053
CGGCACAUUAAUCACCGGCAGCGGAAACUUCUGCCUGCCAGGCACUGAAAGCAAAAGUGUUUUACUGGACUCUCUCGAGUGGCAAGUGGCAAGUGAAAAGUGUGGCCGUGAGAGUGGUGG
............(((((((((.(....)..)))))..(((((((((.........)))))....))))((((((.((.((.(((..(..(....)..)..))).)))).)))))))))). ( -42.00)
>DroSec_CAF1 3554 120 - 1
CGGCACAUUAAUCACCGGCAGCGGAAACUUCUGCCUGCCAGGCACUGAAAGCAAAAGUGUUUUACUGGACUCUCUCGAGUGGCAAGUGGCAAGUGAAAAGUGUGGCCGUGAGAGUGGUGG
............(((((((((.(....)..)))))..(((((((((.........)))))....))))((((((.((.((.(((..(..(....)..)..))).)))).)))))))))). ( -42.00)
>DroSim_CAF1 7910 120 - 1
CGGCACAUUAAUCACCGGCAGCGGAAACUUCUGCCUGCCAGGCACUGAAAGCAAAAGUGUUUUACUGGACUCUCUCGAGUGGCAAGUGGCAAGUGAAAAGUGUGGCCGUGAGAGUGGUGG
............(((((((((.(....)..)))))..(((((((((.........)))))....))))((((((.((.((.(((..(..(....)..)..))).)))).)))))))))). ( -42.00)
>consensus
CGGCACAUUAAUCACCGGCAGCGGAAACUUCUGCCUGCCAGGCACUGAAAGCAAAAGUGUUUUACUGGACUCUCUCGAGUGGCAAGUGGCAAGUGAAAAGUGUGGCCGUGAGAGUGGUGG
............(((((((((.(....)..)))))..(((((((((.........)))))....))))((((((.((.((.(((..(..(....)..)..))).)))).)))))))))). (-42.00 = -42.00 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,738,790 – 6,738,910
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -44.19
Consensus MFE -42.92
Energy contribution -43.26
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.97
SVM decision value 0.79
SVM RNA-class probability 0.850958
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6738790 120 - 27905053
GAGCUGACUAGAUGGCUACCUGGGUAGAUGGCCAAGCCGUAUCUCUUGGCCAUGGUUUAAAGCUGGCCCGAACAUUAUUGCGGCACAUUAAUCACCGGCAGCGGAAACUUCUGCCUGCCA
.((((...(((((..((((....))))(((((((((........))))))))).))))).)))).((((((......))).)))............(((((((((....)))).))))). ( -42.40)
>DroSec_CAF1 3634 120 - 1
GAGCUGACUAGAUGGCUAGCUGGGUAGCUGGCCAAGCCGUAUCUCUUGGCCAUGGUUUAAAGCUGGCCCGAACAUUAUUGCGGCACAUUAAUCACCGGCAGCGGAAACUUCUGCCUGCCA
..(.(((.(((.(((((((((....))))))))).((((((......(((((..((.....)))))))..........))))))...))).))).)(((((((((....)))).))))). ( -45.09)
>DroSim_CAF1 7990 120 - 1
GAGCUGACUAGAUGGCUAGCUGGGUAGCUGGCCAAGCCGUAUCUCUUGGCCAUGGUUUAAAGCUGGCCCGAACAUUAUUGCGGCACAUUAAUCACCGGCAGCGGAAACUUCUGCCUGCCA
..(.(((.(((.(((((((((....))))))))).((((((......(((((..((.....)))))))..........))))))...))).))).)(((((((((....)))).))))). ( -45.09)
>consensus
GAGCUGACUAGAUGGCUAGCUGGGUAGCUGGCCAAGCCGUAUCUCUUGGCCAUGGUUUAAAGCUGGCCCGAACAUUAUUGCGGCACAUUAAUCACCGGCAGCGGAAACUUCUGCCUGCCA
..(.(((.(((.(((((((((....))))))))).((((((......(((((..((.....)))))))..........))))))...))).))).)(((((((((....)))).))))). (-42.92 = -43.26 +   0.33)

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 10:33:59 2006