Locus 8804

Sequence ID 3R_DroMel_CAF1
Location 23,532,780 – 23,532,990
Length 210
Max. P 0.932257
window14136 window14137 window14138

overview

Window 6

Location 23,532,780 – 23,532,900
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.33
Mean single sequence MFE -33.94
Consensus MFE -30.24
Energy contribution -31.13
Covariance contribution 0.89
Combinations/Pair 1.07
Mean z-score -1.79
Structure conservation index 0.89
SVM decision value 0.12
SVM RNA-class probability 0.595207
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23532780 120 - 27905053
AAAGCCGCUUGAGAAAACAAGCGUCCCAAAUUUCUUUCUAUUCUUUCUGCCUGUCUCUUUCACUCAUUUCGACAGAUGUCAGCUGUUUCAGCUGCUGGCGGCGUUGCCAGAUAGGCGUCA
.....((((((......)))))).........................((((((((.....................((((((.((....)).))))))(((...))))))))))).... ( -33.60)
>DroSim_CAF1 567 120 - 1
AAAGCCGCUUGAGAAAACAAGCGUCCCAAAUUUCUUUCUAUUCUUUCUGCCUGUCUCUUUCACUAAUUUCAACAGAUGUCAGCUGUUUCAGCUGCCGACGACGCUGCCAGAUAGGCGGCA
...((((((((........((((((....................((((..((................)).))))((.((((((...)))))).))..))))))......)))))))). ( -31.63)
>DroYak_CAF1 605 120 - 1
AAAGCCGCUUAAGAAAGCAAGCGUCCCAAAUUUCUUUCUUUUCUUUCUGCCUGUCUCUUUCACUCAUUUCGUCAGAUGUCAGCUGUUUCAGCUGCUGGCGGCGUUGCCAGAUGGGCGGCA
...(((....(((((((.((..........)).)))))))........((((((((..............(((((....((((((...)))))))))))(((...)))))))))))))). ( -36.60)
>consensus
AAAGCCGCUUGAGAAAACAAGCGUCCCAAAUUUCUUUCUAUUCUUUCUGCCUGUCUCUUUCACUCAUUUCGACAGAUGUCAGCUGUUUCAGCUGCUGGCGGCGUUGCCAGAUAGGCGGCA
...((((((((......)))))..........................((((((((.....................((((((.((....)).))))))(((...)))))))))))))). (-30.24 = -31.13 +   0.89)

alignment

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secondary structure

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dotplot

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Window 7

Location 23,532,860 – 23,532,980
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.61
Mean single sequence MFE -33.53
Consensus MFE -30.95
Energy contribution -31.40
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -1.54
Structure conservation index 0.92
SVM decision value -0.05
SVM RNA-class probability 0.507320
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23532860 120 + 27905053
UAGAAAGAAAUUUGGGACGCUUGUUUUCUCAAGCGGCUUUAUUAAAUUUCUAAUCCCAGCAAGAGGUGGAAAUGCUGCCAUCCACGGGUCUCUUUAAGGGCUUCUUGUGCCCUUACUUUG
...(((((.((((((((.(((((......)))))(((..((((..((((((..........))))))...))))..))).))).))))).)))))((((((.......))))))...... ( -35.20)
>DroSim_CAF1 647 120 + 1
UAGAAAGAAAUUUGGGACGCUUGUUUUCUCAAGCGGCUUUAUUAAAUUUCUAAUCCCAGCAAAAGGUGGAAAUGCUGCCAUCCACGGGUCUCUUUAAGGGCUUCGUGUGCCCUUACUUUG
...(((((.((((((((((((((......))))))(((..((((......))))...)))....((..(.....)..)).))).))))).)))))((((((.......))))))...... ( -35.00)
>DroYak_CAF1 685 120 + 1
AAGAAAGAAAUUUGGGACGCUUGCUUUCUUAAGCGGCUUUAAUAAACAUCUAAUCCCAGCAAAAGGUGGAAAUGCUUCCAUCCACGGGUCUCUUUAAGGGCUUUCUGUGCCCGUACUUUG
...((((......((((((((.((((....))))((..(((.........)))..)))))....(((((((....))))))).....))))).....((((.......))))...)))). ( -30.40)
>consensus
UAGAAAGAAAUUUGGGACGCUUGUUUUCUCAAGCGGCUUUAUUAAAUUUCUAAUCCCAGCAAAAGGUGGAAAUGCUGCCAUCCACGGGUCUCUUUAAGGGCUUCCUGUGCCCUUACUUUG
...(((((.((((((((((((((......))))))(((..((((......))))...)))....((..(.....)..)).))).))))).)))))((((((.......))))))...... (-30.95 = -31.40 +   0.45)

alignment

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secondary structure

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dotplot

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Window 8

Location 23,532,900 – 23,532,990
Length 90
Sequences 3
Columns 90
Reading direction reverse
Mean pairwise identity 93.70
Mean single sequence MFE -27.97
Consensus MFE -27.67
Energy contribution -28.00
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.99
SVM decision value 1.22
SVM RNA-class probability 0.932257
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23532900 90 - 27905053
UCCUGGCCGUCAAAGUAAGGGCACAAGAAGCCCUUAAAGAGACCCGUGGAUGGCAGCAUUUCCACCUCUUGCUGGGAUUAGAAAUUUAAU
(((..((........(((((((.......)))))))(((((....(((((..........))))))))))))..)))............. ( -29.00)
>DroSim_CAF1 687 90 - 1
UCCUGGCCGUCAAAGUAAGGGCACACGAAGCCCUUAAAGAGACCCGUGGAUGGCAGCAUUUCCACCUUUUGCUGGGAUUAGAAAUUUAAU
(((..((.(((....(((((((.......)))))))....)))..(((((..........))))).....))..)))............. ( -29.00)
>DroYak_CAF1 725 90 - 1
UCCUGGCCGUCAAAGUACGGGCACAGAAAGCCCUUAAAGAGACCCGUGGAUGGAAGCAUUUCCACCUUUUGCUGGGAUUAGAUGUUUAUU
(((..((.(((....((.((((.......)))).))....)))..(((((((....))..))))).....))..)))............. ( -25.90)
>consensus
UCCUGGCCGUCAAAGUAAGGGCACAAGAAGCCCUUAAAGAGACCCGUGGAUGGCAGCAUUUCCACCUUUUGCUGGGAUUAGAAAUUUAAU
(((..((.(((....(((((((.......)))))))....)))..(((((..........))))).....))..)))............. (-27.67 = -28.00 +   0.33)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:20:07 2006