Locus 8291

Sequence ID 3R_DroMel_CAF1
Location 22,149,301 – 22,149,541
Length 240
Max. P 0.977558
window13368 window13369 window13370 window13371

overview

Window 8

Location 22,149,301 – 22,149,421
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.42
Mean single sequence MFE -31.27
Consensus MFE -27.74
Energy contribution -28.80
Covariance contribution 1.06
Combinations/Pair 1.03
Mean z-score -1.90
Structure conservation index 0.89
SVM decision value 0.67
SVM RNA-class probability 0.817094
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22149301 120 - 27905053
GGCAAAUUAUACCUUCUUCAAAGCUUUAAAGACCUUUUAAGGCACUUCGGCCCCAGGGGAGGAGGGCAAGAAAGUUGUUCAAUCGAAACGACAAUUAAUUGGCUAAAAUAAAUAUUCACG
(((.(((((..((((((((...(((((((((...))))))))).......((....)))))))))).......(((((((....).))))))...))))).)))................ ( -28.90)
>DroSec_CAF1 79752 120 - 1
GGCAAAUUAUGACCUCUUCAGAGCUUUAAAGACCUUUUAAGGCACUUCGGCCCCAGGGGAGGAGGGCAAGAAAGUUGUUCAAUAGAAACGACAAUUAAUUGGCUAAAAUAAAUAUUCACG
(((.(((((((.(((((((...(((((((((...))))))))).......((....))))))))).)).....(((((((....).))))))...))))).)))................ ( -29.70)
>DroSim_CAF1 74227 120 - 1
GGCAAAUUAUGCCCUCUUCAGAGCUUUAAAGACCUUUUAAGUCACUUCGGCCCCAGGGGAGGAGGGCAAGAAAGUUGUUCAAUCGAAACGACAAUUAAUUGGCUAAAAUAAAUAUUCACG
(((.(((((((((((((((...........(((.......))).......((....)))))))))))).....(((((((....).))))))...))))).)))................ ( -32.00)
>DroYak_CAF1 72666 120 - 1
GGCAAAUUAUGGCCUCUUCAAAGCUUUAAAGGCCUUUUAAGGCUCUUCGCCCCCAGGGGAGAAGGGCAAGAAAGUUGUUCAAUCGAAACGACAAUUAAUUGGCUAAAAUAAAUAUUCACG
(((........)))................((((..((((.(((((((.(((....))).)))))))......(((((((....).))))))..))))..))))................ ( -34.50)
>consensus
GGCAAAUUAUGCCCUCUUCAAAGCUUUAAAGACCUUUUAAGGCACUUCGGCCCCAGGGGAGGAGGGCAAGAAAGUUGUUCAAUCGAAACGACAAUUAAUUGGCUAAAAUAAAUAUUCACG
(((.(((((((((((((((...(((((((((...))))))))).......((....)))))))))))).....(((((((....).))))))...))))).)))................ (-27.74 = -28.80 +   1.06)

alignment

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secondary structure

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dotplot

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Window 9

Location 22,149,381 – 22,149,501
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.58
Mean single sequence MFE -30.47
Consensus MFE -28.84
Energy contribution -29.28
Covariance contribution 0.44
Combinations/Pair 1.08
Mean z-score -2.25
Structure conservation index 0.95
SVM decision value 1.77
SVM RNA-class probability 0.976303
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22149381 120 + 27905053
UUAAAAGGUCUUUAAAGCUUUGAAGAAGGUAUAAUUUGCCCUGUGUCUGCUAUUGCCAUUCACGAAUAUGAAUGAAAAAUUUUGGCCCCGCCAGGAGAAAAGCAAUAAAAGCCUUUAAAU
...(((((.((((...((...((....((((.....)))).....)).))((((((((((((......)))))).....(((((((...))))))).....))))))))))))))).... ( -29.20)
>DroSec_CAF1 79832 120 + 1
UUAAAAGGUCUUUAAAGCUCUGAAGAGGUCAUAAUUUGCCCAGUGUCUGCUAUUGCCAUUCACGAAUAUGAAUGAAAAAUGUUGGCCCCGCCAGGAGAAAAGCAAUAAAAGCCUUUAAAU
...(((((.((((...((...((...((.((.....)).))....)).))((((((((((((......)))))).....(.(((((...))))).).....))))))))))))))).... ( -26.20)
>DroSim_CAF1 74307 120 + 1
UUAAAAGGUCUUUAAAGCUCUGAAGAGGGCAUAAUUUGCCCAGUGUCUGCUAUUGCCAUUCACGAAUAUGAAUGAAAAAUUCUGGCCCCGCCAGGAGAAAAGCAAUAAAAGCCUUUAAAU
...(((((.((((...((...((...(((((.....)))))....)).))((((((((((((......)))))).....(((((((...))))))).....))))))))))))))).... ( -37.20)
>DroYak_CAF1 72746 120 + 1
UUAAAAGGCCUUUAAAGCUUUGAAGAGGCCAUAAUUUGCCCAGUGUCUGCUAUUGCCAUUCACGAAUAUGAAUGAAAUUUUUUGGCCCCGCCAGGAGGAAAGCAAUAAAAGCUUUUAAAU
(((((((((((((..........)))))))..............(.((..((((((((((((......))))))...(((((((((...)))))))))...))))))..))))))))).. ( -29.30)
>consensus
UUAAAAGGUCUUUAAAGCUCUGAAGAGGGCAUAAUUUGCCCAGUGUCUGCUAUUGCCAUUCACGAAUAUGAAUGAAAAAUUUUGGCCCCGCCAGGAGAAAAGCAAUAAAAGCCUUUAAAU
...(((((.((((...((...((...(((((.....)))))....)).))((((((((((((......)))))).....(((((((...))))))).....))))))))))))))).... (-28.84 = -29.28 +   0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 22,149,381 – 22,149,501
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.58
Mean single sequence MFE -30.50
Consensus MFE -25.23
Energy contribution -25.35
Covariance contribution 0.12
Combinations/Pair 1.09
Mean z-score -2.28
Structure conservation index 0.83
SVM decision value 0.76
SVM RNA-class probability 0.842699
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22149381 120 - 27905053
AUUUAAAGGCUUUUAUUGCUUUUCUCCUGGCGGGGCCAAAAUUUUUCAUUCAUAUUCGUGAAUGGCAAUAGCAGACACAGGGCAAAUUAUACCUUCUUCAAAGCUUUAAAGACCUUUUAA
....(((((..((((..(((((..(((....)))(((.........(((((((....)))))))((....))........)))................)))))..))))..)))))... ( -25.80)
>DroSec_CAF1 79832 120 - 1
AUUUAAAGGCUUUUAUUGCUUUUCUCCUGGCGGGGCCAACAUUUUUCAUUCAUAUUCGUGAAUGGCAAUAGCAGACACUGGGCAAAUUAUGACCUCUUCAGAGCUUUAAAGACCUUUUAA
....(((((..((((..(((......((((.((((.((........(((((((....)))))))((..(((......))).))......)).)))).)))))))..))))..)))))... ( -26.90)
>DroSim_CAF1 74307 120 - 1
AUUUAAAGGCUUUUAUUGCUUUUCUCCUGGCGGGGCCAGAAUUUUUCAUUCAUAUUCGUGAAUGGCAAUAGCAGACACUGGGCAAAUUAUGCCCUCUUCAGAGCUUUAAAGACCUUUUAA
.....((((((((((((((.......(((((...))))).......(((((((....)))))))))))))...((....(((((.....)))))...))))))))))............. ( -33.80)
>DroYak_CAF1 72746 120 - 1
AUUUAAAAGCUUUUAUUGCUUUCCUCCUGGCGGGGCCAAAAAAUUUCAUUCAUAUUCGUGAAUGGCAAUAGCAGACACUGGGCAAAUUAUGGCCUCUUCAAAGCUUUAAAGGCCUUUUAA
..(((((((((((((..(((((((....)).(((((((........(((((((....)))))))((..(((......))).))......)))))))...)))))..)))))).))))))) ( -35.50)
>consensus
AUUUAAAGGCUUUUAUUGCUUUUCUCCUGGCGGGGCCAAAAUUUUUCAUUCAUAUUCGUGAAUGGCAAUAGCAGACACUGGGCAAAUUAUGCCCUCUUCAAAGCUUUAAAGACCUUUUAA
.....((((((((((((((........((((...))))........(((((((....)))))))))))))...((....(((((.....)))))...))))))))))............. (-25.23 = -25.35 +   0.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 22,149,421 – 22,149,541
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 97.08
Mean single sequence MFE -32.35
Consensus MFE -30.95
Energy contribution -30.82
Covariance contribution -0.13
Combinations/Pair 1.06
Mean z-score -2.78
Structure conservation index 0.96
SVM decision value 1.79
SVM RNA-class probability 0.977558
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22149421 120 + 27905053
CUGUGUCUGCUAUUGCCAUUCACGAAUAUGAAUGAAAAAUUUUGGCCCCGCCAGGAGAAAAGCAAUAAAAGCCUUUAAAUAUUUACACACUCAGCCAGAAAAGAGCAAACAAGCGGGCGC
..(((((((((.((((((((((......)))))).....(((((((.((....))..(((.((.......)).))).................)))))))....))))...))))))))) ( -30.50)
>DroSec_CAF1 79872 120 + 1
CAGUGUCUGCUAUUGCCAUUCACGAAUAUGAAUGAAAAAUGUUGGCCCCGCCAGGAGAAAAGCAAUAAAAGCCUUUAAAUAUUUACACACUCAGCCAGAAAAGAGCAAACAAGCGGGCGC
..((((((((((((((((((((......)))))).....(.(((((...))))).).....))))))...((((((.......................)))).))......)))))))) ( -28.60)
>DroSim_CAF1 74347 120 + 1
CAGUGUCUGCUAUUGCCAUUCACGAAUAUGAAUGAAAAAUUCUGGCCCCGCCAGGAGAAAAGCAAUAAAAGCCUUUAAAUAUUUACACACUCAGCCAGAAAAGAGCAAACAAGCGGGCGC
..(((((((((.((((((((((......)))))).....(((((((.((....))..(((.((.......)).))).................)))))))....))))...))))))))) ( -33.30)
>DroYak_CAF1 72786 120 + 1
CAGUGUCUGCUAUUGCCAUUCACGAAUAUGAAUGAAAUUUUUUGGCCCCGCCAGGAGGAAAGCAAUAAAAGCUUUUAAAUAUUUACACACUCAGCCAGAAAAGAGCAAACAAGCGGGCGC
..(((((((((.((((((((((......))))))...(((((((((.((....))..((((((.......)))))).................)))))))))..))))...))))))))) ( -37.00)
>consensus
CAGUGUCUGCUAUUGCCAUUCACGAAUAUGAAUGAAAAAUUUUGGCCCCGCCAGGAGAAAAGCAAUAAAAGCCUUUAAAUAUUUACACACUCAGCCAGAAAAGAGCAAACAAGCGGGCGC
..(((((((((.((((((((((......)))))).....(((((((.((....))..(((.((.......)).))).................)))))))....))))...))))))))) (-30.95 = -30.82 +  -0.13)

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 13:08:04 2006