Locus 2878

Sequence ID 3R_DroMel_CAF1
Location 7,704,752 – 7,704,884
Length 132
Max. P 0.980945
window4646 window4647 window4648

overview

Window 6

Location 7,704,752 – 7,704,844
Length 92
Sequences 6
Columns 93
Reading direction forward
Mean pairwise identity 77.83
Mean single sequence MFE -27.42
Consensus MFE -16.34
Energy contribution -16.57
Covariance contribution 0.22
Combinations/Pair 1.14
Mean z-score -2.49
Structure conservation index 0.60
SVM decision value 1.67
SVM RNA-class probability 0.971396
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7704752 92 + 27905053
CAAAGCCCA-UUACUAAUUGUAGUUACACCUCAUUUAGACCGCAUUCAGCAGUCAGUGGGCUUUGUUUGCCCUUUCAAAGGAGCCGAGGCUCC
(((((((((-((((((....)))).............(((.((.....)).))))))))))))))..............(((((....))))) ( -30.80)
>DroPse_CAF1 48609 93 + 1
CCGAAUUGAUUGACUAAUUCGAAUCCCCUCCCGCACAGACCGCCUUCAGCAGCCAGUGGGCGUUAUUCGUUCUUUCGCGGGAGCCACAGCUGC
.(((((((......)))))))......(((((((..(((.((.....(((.(((....))))))...)).)))...))))))).......... ( -25.80)
>DroSec_CAF1 1694 92 + 1
UAAAGCCCA-UUACUAAUUGUAGUUACACUUCAUACAGACCGCAUUUAGCAGUCAGUGGGCUUUGUUUGCCCUUUCAAAGGAGCCGACGCUCC
(((((((((-((......((((...........))))(((.((.....)).))))))))))))))..............(((((....))))) ( -27.70)
>DroSim_CAF1 1690 92 + 1
UAAAGCCCA-UUACUUAUUGUAGCUACACCUCAUACAGACCGCAUUUAGCAGUCAGUGGGCUUUGUUUGCCCUUUCAAAGGAGCCGACGCUCC
(((((((((-((......((((...........))))(((.((.....)).))))))))))))))..............(((((....))))) ( -27.70)
>DroEre_CAF1 1777 92 + 1
UGGAACCAA-UUACUAAUUGUAGUUAUGCUUCAUUUAGACCGCGUUCAGCAGUCAGUGGGCUCUAUUUGCCCUUUCGCAAGAGCCCCAGCUCC
.(((...((-((((.....))))))..(((.......(((.((.....)).))).(.(((((((...(((......))))))))))))))))) ( -27.70)
>DroYak_CAF1 1742 92 + 1
CGUAACCAA-UUACUAAUCGUAGUCAUACUUCGUUUAGACCGCGUUUAGCAGUCAGUGGGCAUUAUUUGCCCUUUCACAGGAGCCCCAGCUCC
.((.((..(-((.((((.((..(((............)))..)).)))).)))..))(((((.....)))))....)).(((((....))))) ( -24.80)
>consensus
CAAAACCCA_UUACUAAUUGUAGUUACACCUCAUACAGACCGCAUUCAGCAGUCAGUGGGCUUUAUUUGCCCUUUCAAAGGAGCCGAAGCUCC
.....................................(((.((.....)).)))...((((.......)))).......(((((....))))) (-16.34 = -16.57 +   0.22)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,704,752 – 7,704,844
Length 92
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 77.83
Mean single sequence MFE -31.82
Consensus MFE -23.28
Energy contribution -22.62
Covariance contribution -0.66
Combinations/Pair 1.52
Mean z-score -2.63
Structure conservation index 0.73
SVM decision value 1.87
SVM RNA-class probability 0.980945
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7704752 92 - 27905053
GGAGCCUCGGCUCCUUUGAAAGGGCAAACAAAGCCCACUGACUGCUGAAUGCGGUCUAAAUGAGGUGUAACUACAAUUAGUAA-UGGGCUUUG
(((((....)))))..............(((((((((..((((((.....))))))(((.((((......)).)).)))....-))))))))) ( -33.80)
>DroPse_CAF1 48609 93 - 1
GCAGCUGUGGCUCCCGCGAAAGAACGAAUAACGCCCACUGGCUGCUGAAGGCGGUCUGUGCGGGAGGGGAUUCGAAUUAGUCAAUCAAUUCGG
..........(((((((....(..((.....))..)((.((((((.....)))))).)))))))))......((((((........)))))). ( -27.60)
>DroSec_CAF1 1694 92 - 1
GGAGCGUCGGCUCCUUUGAAAGGGCAAACAAAGCCCACUGACUGCUAAAUGCGGUCUGUAUGAAGUGUAACUACAAUUAGUAA-UGGGCUUUA
(((((....))))).......((((.......))))((.((((((.....)))))).)).((((((.((((((....))))..-)).)))))) ( -31.50)
>DroSim_CAF1 1690 92 - 1
GGAGCGUCGGCUCCUUUGAAAGGGCAAACAAAGCCCACUGACUGCUAAAUGCGGUCUGUAUGAGGUGUAGCUACAAUAAGUAA-UGGGCUUUA
(((((....))))).......((((.......))))((.((((((.....)))))).)).((((((.((..(((.....))).-)).)))))) ( -32.10)
>DroEre_CAF1 1777 92 - 1
GGAGCUGGGGCUCUUGCGAAAGGGCAAAUAGAGCCCACUGACUGCUGAACGCGGUCUAAAUGAAGCAUAACUACAAUUAGUAA-UUGGUUCCA
((((((.((((((((((......)))...)))))))...((((((.....)))))).............((((....))))..-..)))))). ( -33.00)
>DroYak_CAF1 1742 92 - 1
GGAGCUGGGGCUCCUGUGAAAGGGCAAAUAAUGCCCACUGACUGCUAAACGCGGUCUAAACGAAGUAUGACUACGAUUAGUAA-UUGGUUACG
(((((....))))).((((..(((((.....))))).(..(.((((((.((..(((............)))..)).)))))).-)..))))). ( -32.90)
>consensus
GGAGCUGCGGCUCCUGUGAAAGGGCAAACAAAGCCCACUGACUGCUAAAUGCGGUCUAAAUGAAGUGUAACUACAAUUAGUAA_UGGGCUUUA
(((((....))))).......((((.......))))...((((((.....))))))....((((((.((((((....))))...)).)))))) (-23.28 = -22.62 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,704,780 – 7,704,884
Length 104
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 77.95
Mean single sequence MFE -37.23
Consensus MFE -24.55
Energy contribution -24.92
Covariance contribution 0.37
Combinations/Pair 1.33
Mean z-score -1.57
Structure conservation index 0.66
SVM decision value 0.67
SVM RNA-class probability 0.817676
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7704780 104 - 27905053
CGAGAAUCAUUGGUAGCUCGCUCCUUGGCCAGUCGUUGCUGGAGCCUCGGCUCCUUUGAAAGGGCAAACAAAGCCCACUGACUGCUGAAUGCGGUCUAAAUGAG
......(((((..(((..(((...(..((.((((......(((((....))))).......((((.......))))...))))))..)..)))..)))))))). ( -36.90)
>DroVir_CAF1 5716 104 - 1
UGAGAUUCAGCCGCAGCACGCUCAUGGGCGAUACGUCGUUGUAGCAGCUGAUUGAGCGACAGGAGAUACAAAGCCCACUGACUGCUGAAGGCGGUCUGCAGGGA
((((((...(((.(((((.(.((((((((.....(((.((((....(((.....))).))))..))).....))))).)))))))))..))).)))).)).... ( -33.70)
>DroSec_CAF1 1722 104 - 1
CGAGAAUCAUUGGUAGCUCGCUCCUUGGCCAGUCGUUUCUGGAGCGUCGGCUCCUUUGAAAGGGCAAACAAAGCCCACUGACUGCUAAAUGCGGUCUGUAUGAA
......(((..((.((((((((((..(((.....)))...))))))..))))))..)))..((((.......))))((.((((((.....)))))).))..... ( -39.20)
>DroSim_CAF1 1718 104 - 1
CGAGAAUCAUUGGUAGCUCGCUCCUUGGCCAGUCGUUUCUGGAGCGUCGGCUCCUUUGAAAGGGCAAACAAAGCCCACUGACUGCUAAAUGCGGUCUGUAUGAG
......(((..((.((((((((((..(((.....)))...))))))..))))))..)))..((((.......))))((.((((((.....)))))).))..... ( -39.20)
>DroYak_CAF1 1770 104 - 1
CGAGAAUCAUUGGUGGCUCGCUCUUUGGCCAGCCGUUUCUGGAGCUGGGGCUCCUGUGAAAGGGCAAAUAAUGCCCACUGACUGCUAAACGCGGUCUAAACGAA
((((..((((.((.(.((((((((.(((....))).....))))).))).).)).))))..(((((.....))))).))((((((.....))))))....)).. ( -38.20)
>DroAna_CAF1 1434 104 - 1
UGGGAGCCAUGAGAAGCGCGCUCUCGGGCCAGCCGUUUCUGGAGCAGCUGAUUCUGGGACAGCACAAACAAUGCCCACUGGCUGCUAAAGGCAGUCUAGUGGAA
......(((.((..(((..((((((((.....))).....))))).)))..)).)))....(((.......)))(((((((((((.....)))).))))))).. ( -36.20)
>consensus
CGAGAAUCAUUGGUAGCUCGCUCCUUGGCCAGUCGUUUCUGGAGCAGCGGCUCCUGUGAAAGGGCAAACAAAGCCCACUGACUGCUAAAUGCGGUCUAAAUGAA
......(((..((.((((.(((((..(((.....)))...)))))...))))))..)))..((((.......))))...((((((.....))))))........ (-24.55 = -24.92 +   0.37)

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 10:46:55 2006