Locus 5632

Sequence ID 3R_DroMel_CAF1
Location 14,826,292 – 14,826,452
Length 160
Max. P 0.999999
window9179 window9180 window9181 window9182

overview

Window 9

Location 14,826,292 – 14,826,412
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.64
Mean single sequence MFE -37.87
Consensus MFE -33.50
Energy contribution -33.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.88
SVM decision value 0.55
SVM RNA-class probability 0.778410
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14826292 120 + 27905053
UCCGCACCUUUGGCUGGGUGGCUGUUCAGCGGGCAAAGUGUUGCCAAAUGUUUGCAGCAUUUCCUGUUGUCUACGGGGCGUUGUCGCUGCAAAGUUUUGGUCUUUUAACUUUUAGCACGU
.((.(((((......)))))(((....)))))(((((((...((((((..((((((((((.((((((.....))))))....)).))))))))..))))))......)))))..)).... ( -39.20)
>DroSec_CAF1 4476 116 + 1
UCCGCACCUUUGGCU----GGCUGUUCAGCGGGCAAAGUGUUGCCAAAUGUUUGCAGCAUUUCCUGUUGUCUACGGGGCGUUGUCGCUGCAAAGUUUUGGUCUUUUAACUUUUAGCACGU
...(((((((((.((----.(((....))).))))))).)).((((((..((((((((((.((((((.....))))))....)).))))))))..)))))).............)).... ( -37.90)
>DroSim_CAF1 4592 116 + 1
UCCGCACCUUUGGCU----GGCUGUUCAGCGGGCAAAGUGUUGCCAAAUGUUUGCAGCAUUUCCUGUUGUCUACGGGGCGUUGUCGCUGCAAAGUUUUGGUCNNNNNNNNNNNNNNNNNN
...((((.((((.((----.(((....))).)))))))))).((((((..((((((((((.((((((.....))))))....)).))))))))..))))))................... ( -36.50)
>consensus
UCCGCACCUUUGGCU____GGCUGUUCAGCGGGCAAAGUGUUGCCAAAUGUUUGCAGCAUUUCCUGUUGUCUACGGGGCGUUGUCGCUGCAAAGUUUUGGUCUUUUAACUUUUAGCACGU
...((((.((((.((.....(((....))))).)))))))).((((((..((((((((((.((((((.....))))))....)).))))))))..))))))................... (-33.50 = -33.50 +   0.00)

alignment

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secondary structure

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Window 0

Location 14,826,292 – 14,826,412
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 87.64
Mean single sequence MFE -29.53
Consensus MFE -23.95
Energy contribution -23.95
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.78
Structure conservation index 0.81
SVM decision value 0.00
SVM RNA-class probability 0.534151
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14826292 120 - 27905053
ACGUGCUAAAAGUUAAAAGACCAAAACUUUGCAGCGACAACGCCCCGUAGACAACAGGAAAUGCUGCAAACAUUUGGCAACACUUUGCCCGCUGAACAGCCACCCAGCCAAAGGUGCGGA
.((..(............(.(((((..(((((((((......((..((.....)).))...)))))))))..))))))....(((((...((((..........))))))))))..)).. ( -30.00)
>DroSec_CAF1 4476 116 - 1
ACGUGCUAAAAGUUAAAAGACCAAAACUUUGCAGCGACAACGCCCCGUAGACAACAGGAAAUGCUGCAAACAUUUGGCAACACUUUGCCCGCUGAACAGCC----AGCCAAAGGUGCGGA
.((..(............(.(((((..(((((((((......((..((.....)).))...)))))))))..))))))....(((((...((((......)----)))))))))..)).. ( -31.10)
>DroSim_CAF1 4592 116 - 1
NNNNNNNNNNNNNNNNNNGACCAAAACUUUGCAGCGACAACGCCCCGUAGACAACAGGAAAUGCUGCAAACAUUUGGCAACACUUUGCCCGCUGAACAGCC----AGCCAAAGGUGCGGA
....................(((((..(((((((((......((..((.....)).))...)))))))))..)))))(..((((((....((((......)----)))..))))))..). ( -27.50)
>consensus
ACGUGCUAAAAGUUAAAAGACCAAAACUUUGCAGCGACAACGCCCCGUAGACAACAGGAAAUGCUGCAAACAUUUGGCAACACUUUGCCCGCUGAACAGCC____AGCCAAAGGUGCGGA
..................(.(((((..(((((((((......((..((.....)).))...)))))))))..))))))..........((((......((......)).......)))). (-23.95 = -23.95 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,826,332 – 14,826,452
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 67.50
Mean single sequence MFE -29.33
Consensus MFE -23.80
Energy contribution -23.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.24
Structure conservation index 0.81
SVM decision value 5.69
SVM RNA-class probability 0.999992
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14826332 120 + 27905053
UUGCCAAAUGUUUGCAGCAUUUCCUGUUGUCUACGGGGCGUUGUCGCUGCAAAGUUUUGGUCUUUUAACUUUUAGCACGUGUCAGUAAAGAAAAAAUGCAAAAGUUGUUCGGUAUAAAAU
..((((((..((((((((((.((((((.....))))))....)).))))))))..))))))....((((((((.(((....((......)).....)))))))))))............. ( -32.10)
>DroSec_CAF1 4512 120 + 1
UUGCCAAAUGUUUGCAGCAUUUCCUGUUGUCUACGGGGCGUUGUCGCUGCAAAGUUUUGGUCUUUUAACUUUUAGCACGUGUCAGUAAAGAAAAAAUGCAAAAGUUGUUCGGCAUAAAAU
..((((((..((((((((((.((((((.....))))))....)).))))))))..))))))....((((((((.(((....((......)).....)))))))))))............. ( -32.10)
>DroSim_CAF1 4628 120 + 1
UUGCCAAAUGUUUGCAGCAUUUCCUGUUGUCUACGGGGCGUUGUCGCUGCAAAGUUUUGGUCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
..((((((..((((((((((.((((((.....))))))....)).))))))))..))))))........................................................... ( -23.80)
>consensus
UUGCCAAAUGUUUGCAGCAUUUCCUGUUGUCUACGGGGCGUUGUCGCUGCAAAGUUUUGGUCUUUUAACUUUUAGCACGUGUCAGUAAAGAAAAAAUGCAAAAGUUGUUCGG_AUAAAAU
..((((((..((((((((((.((((((.....))))))....)).))))))))..))))))........................................................... (-23.80 = -23.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,826,332 – 14,826,452
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 67.50
Mean single sequence MFE -23.77
Consensus MFE -17.03
Energy contribution -17.03
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.64
Structure conservation index 0.72
SVM decision value 6.55
SVM RNA-class probability 0.999999
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14826332 120 - 27905053
AUUUUAUACCGAACAACUUUUGCAUUUUUUCUUUACUGACACGUGCUAAAAGUUAAAAGACCAAAACUUUGCAGCGACAACGCCCCGUAGACAACAGGAAAUGCUGCAAACAUUUGGCAA
..............(((((((((((....((......))...)))).)))))))....(.(((((..(((((((((......((..((.....)).))...)))))))))..)))))).. ( -25.60)
>DroSec_CAF1 4512 120 - 1
AUUUUAUGCCGAACAACUUUUGCAUUUUUUCUUUACUGACACGUGCUAAAAGUUAAAAGACCAAAACUUUGCAGCGACAACGCCCCGUAGACAACAGGAAAUGCUGCAAACAUUUGGCAA
......(((((((.(((((((((((....((......))...)))).))))))).............(((((((((......((..((.....)).))...)))))))))..))))))). ( -28.80)
>DroSim_CAF1 4628 120 - 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGACCAAAACUUUGCAGCGACAACGCCCCGUAGACAACAGGAAAUGCUGCAAACAUUUGGCAA
..........................................................(.(((((..(((((((((......((..((.....)).))...)))))))))..)))))).. ( -16.90)
>consensus
AUUUUAU_CCGAACAACUUUUGCAUUUUUUCUUUACUGACACGUGCUAAAAGUUAAAAGACCAAAACUUUGCAGCGACAACGCCCCGUAGACAACAGGAAAUGCUGCAAACAUUUGGCAA
..........................................................(.(((((..(((((((((......((..((.....)).))...)))))))))..)))))).. (-17.03 = -17.03 +   0.00)

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 11:59:57 2006