Locus 6659

Sequence ID X_DroMel_CAF1
Location 16,614,962 – 16,615,158
Length 196
Max. P 0.955892
window10873 window10874 window10875 window10876 window10877

overview

Window 3

Location 16,614,962 – 16,615,067
Length 105
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 84.98
Mean single sequence MFE -21.85
Consensus MFE -17.45
Energy contribution -17.07
Covariance contribution -0.38
Combinations/Pair 1.11
Mean z-score -1.66
Structure conservation index 0.80
SVM decision value 0.38
SVM RNA-class probability 0.711605
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16614962 105 - 22224390
GUUUGACGGCCCAUUACGUCACCAUCACCAUCAUCGCGAUGCUGAGCGUAGAACGCGCCAAAAUCUAAGCAUGCAGCAAAAAGAAAAAA---AUCCAAAAGCAAACAU
(((((.((((..............(((.((((.....)))).)))(((.....)))))).........((.....))............---........)))))).. ( -20.60)
>DroSim_CAF1 25183 108 - 1
GUUUGACGGCCCAUUACGUCACCAUCACCAUCAUCGCGAUGCUGAGCGUAGAACGCGCCAAAAUCUAAGCAUGCAGCAAAAAAAAAAAAAUAAUCCAAAAGCAAACAU
(((((.((((..............(((.((((.....)))).)))(((.....)))))).........((.....)).......................)))))).. ( -20.60)
>DroEre_CAF1 27169 100 - 1
GUUUGGCGGC-CAUUACGUCACC------AUCGUCGCGAUGCUGAGCGUAGAACACGCCAAAAUCUAAGCAUGCAGCGAAAAUAAAGAG-AAACCCAAGAUCAAACAA
.(((((((..-..((((((((.(------((((...))))).))).)))))....)))))))......((.....))............-.................. ( -23.40)
>DroYak_CAF1 28854 97 - 1
GUUUGACGGCCCAUUACGUCACC------AGCAGCGCGAUGCUGAGCGUAGAACGCGCCAAAAUCUAAGCAUGCAGCUAAAAAAA-----AACACCAAAAGCAAACAU
(((((.(((((..((((((...(------((((......))))).))))))...).)))........(((.....))).......-----..........)))))).. ( -22.80)
>consensus
GUUUGACGGCCCAUUACGUCACC______AUCAUCGCGAUGCUGAGCGUAGAACGCGCCAAAAUCUAAGCAUGCAGCAAAAAAAAAAAA_AAAUCCAAAAGCAAACAU
((((((((........))))...............((.(((((..((((.....)))).........)))))))............................)))).. (-17.45 = -17.07 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,614,999 – 16,615,100
Length 101
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 79.62
Mean single sequence MFE -32.89
Consensus MFE -17.16
Energy contribution -17.52
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -2.51
Structure conservation index 0.52
SVM decision value 1.46
SVM RNA-class probability 0.955892
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16614999 101 + 22224390
UUAGAUUUUGGCGCGUUCUACGCUCAGCAUCGCGAUGAUGGUGA--UGGUGACGUAAUGGGCCGUCAAACAGGUUGGCCAAAAUAACAAAAUAACGGCC-------AAAA
.....(((((((.((((.((((.(((.((((((.......))))--)).)))))))...(((((.(......).))))).............)))))))-------)))) ( -34.90)
>DroSim_CAF1 25223 101 + 1
UUAGAUUUUGGCGCGUUCUACGCUCAGCAUCGCGAUGAUGGUGA--UGGUGACGUAAUGGGCCGUCAAACAGGUUGGCCGAAAUAACAAAAUAACGGCC-------AAAA
......(((((((.((((((((.(((.((((((.......))))--)).)))))))..)))))))))))....(((((((..............)))))-------)).. ( -36.34)
>DroEre_CAF1 27208 94 + 1
UUAGAUUUUGGCGUGUUCUACGCUCAGCAUCGCGACGAU--------GGUGACGUAAUG-GCCGCCAAACAGGUUGCCCAAAAUUACAAAAUAGCGGCC-------AAAA
......(((((((.(((.((((.(((.(((((...))))--------).)))))))..)-)))))))))..((((((................))))))-------.... ( -31.09)
>DroYak_CAF1 28889 95 + 1
UUAGAUUUUGGCGCGUUCUACGCUCAGCAUCGCGCUGCU--------GGUGACGUAAUGGGCCGUCAAACAGGUUGGCCAAAAUAACAAAAUAACGGCC-------AAAA
.....(((((((.((((...(((.(((((......))))--------))))..((.((.(((((.(......).)))))...)).)).....)))))))-------)))) ( -29.80)
>DroAna_CAF1 36771 96 + 1
U----UUUUGGCGCGUUCUCAGAUCAGCAUCUCCGAGAUUGAGGCCCGAUGACGUAAUGGGCCGCCAAACAGGUUGCC----------AAAUAACGGCCGGGCCAGAAAG
(----(((((((.(..((((((((....))))..))))(((.(((((.((......)))))))..)))...(((((..----------......)))))).)))))))). ( -32.30)
>consensus
UUAGAUUUUGGCGCGUUCUACGCUCAGCAUCGCGAUGAU_G_G____GGUGACGUAAUGGGCCGUCAAACAGGUUGGCCAAAAUAACAAAAUAACGGCC_______AAAA
......(((((((.((((((((.(((.(...................).)))))))..)))))))))))..(((((..................)))))........... (-17.16 = -17.52 +   0.36)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,614,999 – 16,615,100
Length 101
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 79.62
Mean single sequence MFE -29.96
Consensus MFE -16.66
Energy contribution -16.18
Covariance contribution -0.48
Combinations/Pair 1.20
Mean z-score -2.12
Structure conservation index 0.56
SVM decision value 0.73
SVM RNA-class probability 0.834567
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16614999 101 - 22224390
UUUU-------GGCCGUUAUUUUGUUAUUUUGGCCAACCUGUUUGACGGCCCAUUACGUCACCA--UCACCAUCAUCGCGAUGCUGAGCGUAGAACGCGCCAAAAUCUAA
((((-------(((((((.............((((............))))..((((((((.((--((.(.......).)))).))).))))))))).)))))))..... ( -28.10)
>DroSim_CAF1 25223 101 - 1
UUUU-------GGCCGUUAUUUUGUUAUUUCGGCCAACCUGUUUGACGGCCCAUUACGUCACCA--UCACCAUCAUCGCGAUGCUGAGCGUAGAACGCGCCAAAAUCUAA
((((-------(((((((.............((((............))))..((((((((.((--((.(.......).)))).))).))))))))).)))))))..... ( -28.40)
>DroEre_CAF1 27208 94 - 1
UUUU-------GGCCGCUAUUUUGUAAUUUUGGGCAACCUGUUUGGCGGC-CAUUACGUCACC--------AUCGUCGCGAUGCUGAGCGUAGAACACGCCAAAAUCUAA
...(-------((((((((......(((...((....)).))))))))))-))((((((((.(--------((((...))))).))).)))))................. ( -30.00)
>DroYak_CAF1 28889 95 - 1
UUUU-------GGCCGUUAUUUUGUUAUUUUGGCCAACCUGUUUGACGGCCCAUUACGUCACC--------AGCAGCGCGAUGCUGAGCGUAGAACGCGCCAAAAUCUAA
((((-------(((((((.............((((............))))..((((((...(--------((((......))))).)))))))))).)))))))..... ( -29.80)
>DroAna_CAF1 36771 96 - 1
CUUUCUGGCCCGGCCGUUAUUU----------GGCAACCUGUUUGGCGGCCCAUUACGUCAUCGGGCCUCAAUCUCGGAGAUGCUGAUCUGAGAACGCGCCAAAA----A
......((((((((((.....)----------)))........(((((........))))).))))))....(((((((........)))))))...........----. ( -33.50)
>consensus
UUUU_______GGCCGUUAUUUUGUUAUUUUGGCCAACCUGUUUGACGGCCCAUUACGUCACC____C_C_AUCAUCGCGAUGCUGAGCGUAGAACGCGCCAAAAUCUAA
...........(((((((.........................(((((........)))))...............(((........)))...)))).)))......... (-16.66 = -16.18 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,615,067 – 16,615,158
Length 91
Sequences 4
Columns 91
Reading direction forward
Mean pairwise identity 89.65
Mean single sequence MFE -20.35
Consensus MFE -13.98
Energy contribution -14.22
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.63
Structure conservation index 0.69
SVM decision value 0.49
SVM RNA-class probability 0.755542
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16615067 91 + 22224390
AGGUUGGCCAAAAUAACAAAAUAACGGCCAAAAAGCCAUUAGACUUUUAGCCAGAUUGAAAGCCAGCCAGCCAGCCCUUCCCACACAACUU
.(((((((.................(((......)))....(.(((((((.....))))))).).)))))))................... ( -20.60)
>DroSim_CAF1 25291 91 + 1
AGGUUGGCCGAAAUAACAAAAUAACGGCCAAAAAGCCAUUAGACUUUUAGCCAGAAUGAAAGCCAACCAGCCAGCCCUUCCCACACAACUU
.(((((((.(...............(((......)))....(.((((((.......)))))).)...).)))))))............... ( -19.80)
>DroEre_CAF1 27269 86 + 1
AGGUUGCCCAAAAUUACAAAAUAGCGGCCAAAAAGCCAUUAGGCUUUUAGCCAGGUCGAA-----GCCAGCCAGCCCUUCCCACACAAAUG
.(((((...................(((..(((((((....))))))).))).(((....-----)))...)))))............... ( -21.10)
>DroYak_CAF1 28951 86 + 1
AGGUUGGCCAAAAUAACAAAAUAACGGCCAAAAAGCCAUUAGACUUUUAGCCAGCUUGAA-----GCCAGCCAGCCCUUCCCACACAAAUU
.(((((((.................(((......)))....(.((((.((....)).)))-----).).)))))))............... ( -19.90)
>consensus
AGGUUGGCCAAAAUAACAAAAUAACGGCCAAAAAGCCAUUAGACUUUUAGCCAGAUUGAA_____GCCAGCCAGCCCUUCCCACACAAAUU
.(((((((.................(((..(((((........))))).))).....(.........).)))))))............... (-13.98 = -14.22 +   0.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,615,067 – 16,615,158
Length 91
Sequences 4
Columns 91
Reading direction reverse
Mean pairwise identity 89.65
Mean single sequence MFE -28.25
Consensus MFE -22.84
Energy contribution -22.72
Covariance contribution -0.12
Combinations/Pair 1.09
Mean z-score -2.26
Structure conservation index 0.81
SVM decision value 1.21
SVM RNA-class probability 0.931404
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16615067 91 - 22224390
AAGUUGUGUGGGAAGGGCUGGCUGGCUGGCUUUCAAUCUGGCUAAAAGUCUAAUGGCUUUUUGGCCGUUAUUUUGUUAUUUUGGCCAACCU
.........(((((((.(..(....)..))))))....(((((((((..(((((((((....))))))))....)...))))))))).)). ( -28.70)
>DroSim_CAF1 25291 91 - 1
AAGUUGUGUGGGAAGGGCUGGCUGGUUGGCUUUCAUUCUGGCUAAAAGUCUAAUGGCUUUUUGGCCGUUAUUUUGUUAUUUCGGCCAACCU
..((((.((.((((..((.((((..((((((........)))))).))))((((((((....))))))))....))..)))).)))))).. ( -30.80)
>DroEre_CAF1 27269 86 - 1
CAUUUGUGUGGGAAGGGCUGGCUGGC-----UUCGACCUGGCUAAAAGCCUAAUGGCUUUUUGGCCGCUAUUUUGUAAUUUUGGGCAACCU
.........(((..(((((....)))-----.))..)))(((((((((((....))).))))))))................((....)). ( -25.80)
>DroYak_CAF1 28951 86 - 1
AAUUUGUGUGGGAAGGGCUGGCUGGC-----UUCAAGCUGGCUAAAAGUCUAAUGGCUUUUUGGCCGUUAUUUUGUUAUUUUGGCCAACCU
.........(((...(((..(((...-----....)))..)))(((((((....)))))))((((((..((......))..)))))).))) ( -27.70)
>consensus
AAGUUGUGUGGGAAGGGCUGGCUGGC_____UUCAAUCUGGCUAAAAGUCUAAUGGCUUUUUGGCCGUUAUUUUGUUAUUUUGGCCAACCU
..............(((.(((((((.............((((((((((((....))).))))))))).............))))))).))) (-22.84 = -22.72 +  -0.12)

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 12:19:25 2006