Locus 4110

Sequence ID 3R_DroMel_CAF1
Location 11,213,171 – 11,213,315
Length 144
Max. P 0.997489
window6580 window6581 window6582 window6583

overview

Window 0

Location 11,213,171 – 11,213,275
Length 104
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 78.21
Mean single sequence MFE -26.22
Consensus MFE -19.61
Energy contribution -19.17
Covariance contribution -0.44
Combinations/Pair 1.10
Mean z-score -2.15
Structure conservation index 0.75
SVM decision value 1.93
SVM RNA-class probability 0.983126
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11213171 104 + 27905053
UGGCAUCCUUUGA---------AGCACCAUCCAACCCCAAGAUCAA-----AUACUAAUGCCAGUGAACCGUCUUUAAACAAGAUGCACACAUGUCAUGUUGUUUUUAGACGAUUUAC
((((((..(((((---------....................))))-----).....))))))(((((.(((((..((((((.(((.((....))))).))))))..))))).))))) ( -26.65)
>DroEre_CAF1 20363 108 + 1
UGGCAUCCUCAAACGAAGGAUUGGCACCAUCCAACCCGAAGAUCGU-----AUAAUAUGGCGAGUGAACCGUCCUUAAACAAGAUGCA-----GCCAUGUUGUUUUUGGACGAUUUAC
.(.(((......((((.((.((((......)))).)).....))))-----.....))).)..(((((.(((((..((((((.(((..-----..))).))))))..))))).))))) ( -29.70)
>DroYak_CAF1 15862 104 + 1
UGGCAUCCUGAAA---------AGCACCACCCAACCCAAUGAUCAUAAUAUAUAUUAUUGCGAGUGAACCGUCUUUAAACAAGAUGCA-----GCCAUGUUGUUUUUGGACGAUUUAC
(((....((....---------))..))).....(.(((((((.(((...)))))))))).).(((((.(((((..((((((.(((..-----..))).))))))..))))).))))) ( -22.30)
>consensus
UGGCAUCCUCAAA_________AGCACCAUCCAACCCAAAGAUCAU_____AUAAUAUUGCGAGUGAACCGUCUUUAAACAAGAUGCA_____GCCAUGUUGUUUUUGGACGAUUUAC
...............................................................(((((.(((((..((((((.((((......).))).))))))..))))).))))) (-19.61 = -19.17 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,213,171 – 11,213,275
Length 104
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 78.21
Mean single sequence MFE -29.47
Consensus MFE -20.07
Energy contribution -19.74
Covariance contribution -0.33
Combinations/Pair 1.10
Mean z-score -1.73
Structure conservation index 0.68
SVM decision value 0.67
SVM RNA-class probability 0.817927
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11213171 104 - 27905053
GUAAAUCGUCUAAAAACAACAUGACAUGUGUGCAUCUUGUUUAAAGACGGUUCACUGGCAUUAGUAU-----UUGAUCUUGGGGUUGGAUGGUGCU---------UCAAAGGAUGCCA
((.((((((((..((((((.(((((....)).))).))))))..)))))))).)).(((((((.(((-----(..(((....)))..)))).).((---------....)))))))). ( -30.70)
>DroEre_CAF1 20363 108 - 1
GUAAAUCGUCCAAAAACAACAUGGC-----UGCAUCUUGUUUAAGGACGGUUCACUCGCCAUAUUAU-----ACGAUCUUCGGGUUGGAUGGUGCCAAUCCUUCGUUUGAGGAUGCCA
((.((((((((..((((((.(((..-----..))).))))))..)))))))).)).((((((.....-----.(((((....))))).))))))...((((((.....)))))).... ( -35.70)
>DroYak_CAF1 15862 104 - 1
GUAAAUCGUCCAAAAACAACAUGGC-----UGCAUCUUGUUUAAAGACGGUUCACUCGCAAUAAUAUAUAUUAUGAUCAUUGGGUUGGGUGGUGCU---------UUUCAGGAUGCCA
.......(.(((.........))))-----.((((((((...((((((.(..((((((..(((((....)))))......)))).))..).)).))---------)).)))))))).. ( -22.00)
>consensus
GUAAAUCGUCCAAAAACAACAUGGC_____UGCAUCUUGUUUAAAGACGGUUCACUCGCAAUAAUAU_____AUGAUCUUCGGGUUGGAUGGUGCU_________UUUAAGGAUGCCA
((.((((((((..((((((.(((.........))).))))))..)))))))).))..................(((((....)))))..(((((((..............)).))))) (-20.07 = -19.74 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,213,200 – 11,213,315
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.18
Mean single sequence MFE -27.50
Consensus MFE -25.39
Energy contribution -25.17
Covariance contribution -0.22
Combinations/Pair 1.12
Mean z-score -3.43
Structure conservation index 0.92
SVM decision value 2.87
SVM RNA-class probability 0.997489
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11213200 115 + 27905053
AAGAUCAA-----AUACUAAUGCCAGUGAACCGUCUUUAAACAAGAUGCACACAUGUCAUGUUGUUUUUAGACGAUUUACUCCGGUUUCCAUUUACCAUUUCCACUCACUAUUUAACUUU
........-----...........(((((..(((((..((((((.(((.((....))))).))))))..))))).........(((........)))........))))).......... ( -24.80)
>DroEre_CAF1 20401 108 + 1
AAGAUCGU-----AUAAUAUGGCGAGUGAACCGUCCUUAAACAAGAUGCA-----GCCAUGUUGUUUUUGGACGAUUUACUUCGGUUCG--AAUACCAUUUCCGCUCACUAUCUAAUUUU
........-----.....((((.(((((((((((((..((((((.(((..-----..))).))))))..))))((......)))))))(--((......))).)))).))))........ ( -30.70)
>DroYak_CAF1 15891 113 + 1
AUGAUCAUAAUAUAUAUUAUUGCGAGUGAACCGUCUUUAAACAAGAUGCA-----GCCAUGUUGUUUUUGGACGAUUUACUCCGGUUCU--UAUACCAUUUCCACUCACUAUCUAAUUUU
............((((..((((.(((((((.(((((..((((((.(((..-----..))).))))))..))))).)))))))))))...--))))......................... ( -27.00)
>consensus
AAGAUCAU_____AUAAUAUUGCGAGUGAACCGUCUUUAAACAAGAUGCA_____GCCAUGUUGUUUUUGGACGAUUUACUCCGGUUCC__UAUACCAUUUCCACUCACUAUCUAAUUUU
.......................(((((((.(((((..((((((.((((......).))).))))))..))))).))))))).(((........)))....................... (-25.39 = -25.17 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,213,200 – 11,213,315
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.18
Mean single sequence MFE -27.90
Consensus MFE -23.35
Energy contribution -24.13
Covariance contribution 0.78
Combinations/Pair 1.04
Mean z-score -2.50
Structure conservation index 0.84
SVM decision value 1.81
SVM RNA-class probability 0.978271
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11213200 115 - 27905053
AAAGUUAAAUAGUGAGUGGAAAUGGUAAAUGGAAACCGGAGUAAAUCGUCUAAAAACAACAUGACAUGUGUGCAUCUUGUUUAAAGACGGUUCACUGGCAUUAGUAU-----UUGAUCUU
...((((((((.(((((.....((((........)))).(((.((((((((..((((((.(((((....)).))).))))))..)))))))).))).)).))).)))-----)))))... ( -28.50)
>DroEre_CAF1 20401 108 - 1
AAAAUUAGAUAGUGAGCGGAAAUGGUAUU--CGAACCGAAGUAAAUCGUCCAAAAACAACAUGGC-----UGCAUCUUGUUUAAGGACGGUUCACUCGCCAUAUUAU-----ACGAUCUU
...........(((.(((....((((...--...)))).(((.((((((((..((((((.(((..-----..))).))))))..)))))))).))))))))).....-----........ ( -27.60)
>DroYak_CAF1 15891 113 - 1
AAAAUUAGAUAGUGAGUGGAAAUGGUAUA--AGAACCGGAGUAAAUCGUCCAAAAACAACAUGGC-----UGCAUCUUGUUUAAAGACGGUUCACUCGCAAUAAUAUAUAUUAUGAUCAU
.......(((.(((((((((..((((...--...)))).......(((((...((((((.(((..-----..))).))))))...)))))))))))))).(((((....))))).))).. ( -27.60)
>consensus
AAAAUUAGAUAGUGAGUGGAAAUGGUAUA__AGAACCGGAGUAAAUCGUCCAAAAACAACAUGGC_____UGCAUCUUGUUUAAAGACGGUUCACUCGCAAUAAUAU_____AUGAUCUU
...........(((((((((..((((........)))).......((((((..((((((.(((.........))).))))))..)))))))))))))))..................... (-23.35 = -24.13 +   0.78)

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 11:18:24 2006