Locus 5484

Sequence ID 3R_DroMel_CAF1
Location 14,459,158 – 14,459,310
Length 152
Max. P 0.797535
window8945 window8946 window8947

overview

Window 5

Location 14,459,158 – 14,459,278
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.42
Mean single sequence MFE -38.84
Consensus MFE -34.95
Energy contribution -35.45
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.90
SVM decision value 0.61
SVM RNA-class probability 0.797535
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14459158 120 + 27905053
UAAUGCCCUGCGUCAGGGUAUAAAGAGUAGCCAUAAAAAGAUUUAAUUUUUUCGGUGUUUUUUGGACAACAACGGCGGAUGGGAGUGCGUCGUCAUGGGGCACACCCCUUUGCCACGUCA
..((((((((...))))))))...((((.((((.(((((.((..((....))..)).)))))))).).))...((((((.(((.((((.((.....)).)))).))).))))))...)). ( -39.30)
>DroSec_CAF1 16509 119 + 1
CAAUGCCCUGCUUCAGGGUAUAAAGAGUAGCCAUAAAAAGAUUUAAUU-UUUCGGUGUUUUUUGGACACCAACGGCGGAUGGGAGUGCGUCGUCAUGGGGCACACCCCUUUGCCACGUCA
..((((((((...))))))))..................(((......-....((((((.....))))))...((((((.(((.((((.((.....)).)))).))).))))))..))). ( -42.00)
>DroSim_CAF1 17124 119 + 1
CAAUGCCCUGCGUCAGGGUAUAAAGAGUAGCCAUAAAAAGAUUUAAUU-UUUCGGUGUUUUUUGGACACCAACGGCGGAUGGGAGUGCGUCGUCAUGGGGCACACCCCUUUGCCACGUCA
..((((((((...))))))))..................(((......-....((((((.....))))))...((((((.(((.((((.((.....)).)))).))).))))))..))). ( -42.00)
>DroYak_CAF1 19038 117 + 1
UAUUGCCCUGCGUCAGAGUA--AAAAAUAGCCAUAAAAAGAUUUAAUU-UUUCUGUGUUUUUUGGGGACCAACGGCGGAUGGGAGUGCGUCGUCAUGGGGCACACCCCUUUGCCACGUCA
.....(((.(((.(((((..--..........................-.)))))))).....)))(((....((((((.(((.((((.((.....)).)))).))).))))))..))). ( -32.05)
>consensus
CAAUGCCCUGCGUCAGGGUAUAAAGAGUAGCCAUAAAAAGAUUUAAUU_UUUCGGUGUUUUUUGGACACCAACGGCGGAUGGGAGUGCGUCGUCAUGGGGCACACCCCUUUGCCACGUCA
..((((((((...)))))))).........(((.(((((.((..((....))..)).))))))))........((((((.(((.((((.((.....)).)))).))).))))))...... (-34.95 = -35.45 +   0.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,459,198 – 14,459,310
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.45
Mean single sequence MFE -40.35
Consensus MFE -31.20
Energy contribution -31.57
Covariance contribution 0.37
Combinations/Pair 1.07
Mean z-score -1.54
Structure conservation index 0.77
SVM decision value 0.18
SVM RNA-class probability 0.623405
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14459198 112 + 27905053
AUUUAAUUUUUUCGGUGUUUUUUGGACAACAACGGCGGAUGGGAGUGCGUCGUCAUGGGGCACACCCCUUUGCCACGUCAGGCGUUGUGGCUAGCUGGUUGUC--------UGUCUGUCC
.......................((((((((((((((((.(((.((((.((.....)).)))).))).)))((((((........))))))..))).))))).--------))))).... ( -36.30)
>DroSec_CAF1 16549 119 + 1
AUUUAAUU-UUUCGGUGUUUUUUGGACACCAACGGCGGAUGGGAGUGCGUCGUCAUGGGGCACACCCCUUUGCCACGUCAGGCGUUGUGGCUAGCUGGUUGUCUGUCUGUCUGACUGUCC
........-....((((((.....))))))...((((((.(((.((((.((.....)).)))).))).))))))..((((((((....(((..((.....))..)))))))))))..... ( -44.60)
>DroSim_CAF1 17164 116 + 1
AUUUAAUU-UUUCGGUGUUUUUUGGACACCAACGGCGGAUGGGAGUGCGUCGUCAUGGGGCACACCCCUUUGCCACGUCAGGCGUUGUGGCUAGCUGG---UCUGUCUGUCUGCCUGUCC
........-....((((((.....))))))...((((((.(((.((((.((.....)).)))).))).))))))..(.((((((....(((..((...---...))..))))))))).). ( -43.20)
>DroYak_CAF1 19076 103 + 1
AUUUAAUU-UUUCUGUGUUUUUUGGGGACCAACGGCGGAUGGGAGUGCGUCGUCAUGGGGCACACCCCUUUGCCACGUCAGGCGUUGUGGCUAGUUGGUUGUC----------------U
........-..............((.(((((((((((((.(((.((((.((.....)).)))).))).))))))......(((......))).))))))).))----------------. ( -37.30)
>consensus
AUUUAAUU_UUUCGGUGUUUUUUGGACACCAACGGCGGAUGGGAGUGCGUCGUCAUGGGGCACACCCCUUUGCCACGUCAGGCGUUGUGGCUAGCUGGUUGUC________UG_CUGUCC
.............((((((.....))))))..(((((((.(((.((((.((.....)).)))).))).)))((((((........))))))..))))....................... (-31.20 = -31.57 +   0.37)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,459,198 – 14,459,310
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.45
Mean single sequence MFE -31.62
Consensus MFE -24.81
Energy contribution -26.12
Covariance contribution 1.31
Combinations/Pair 1.04
Mean z-score -1.82
Structure conservation index 0.78
SVM decision value 0.61
SVM RNA-class probability 0.797405
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14459198 112 - 27905053
GGACAGACA--------GACAACCAGCUAGCCACAACGCCUGACGUGGCAAAGGGGUGUGCCCCAUGACGACGCACUCCCAUCCGCCGUUGUUGUCCAAAAAACACCGAAAAAAUUAAAU
(((((....--------.(((((..((..(((((..........)))))...(((((((((........).))))).)))....)).))))))))))....................... ( -31.20)
>DroSec_CAF1 16549 119 - 1
GGACAGUCAGACAGACAGACAACCAGCUAGCCACAACGCCUGACGUGGCAAAGGGGUGUGCCCCAUGACGACGCACUCCCAUCCGCCGUUGGUGUCCAAAAAACACCGAAA-AAUUAAAU
((((.(((.....))).....((((((..(((((..........)))))...(((((((((........).))))).))).......))))))))))..............-........ ( -36.20)
>DroSim_CAF1 17164 116 - 1
GGACAGGCAGACAGACAGA---CCAGCUAGCCACAACGCCUGACGUGGCAAAGGGGUGUGCCCCAUGACGACGCACUCCCAUCCGCCGUUGGUGUCCAAAAAACACCGAAA-AAUUAAAU
((((.(.....)......(---(((((..(((((..........)))))...(((((((((........).))))).))).......))))))))))..............-........ ( -32.60)
>DroYak_CAF1 19076 103 - 1
A----------------GACAACCAACUAGCCACAACGCCUGACGUGGCAAAGGGGUGUGCCCCAUGACGACGCACUCCCAUCCGCCGUUGGUCCCCAAAAAACACAGAAA-AAUUAAAU
.----------------....((((((..(((((..........)))))...(((((((((........).))))).))).......))))))..................-........ ( -26.50)
>consensus
GGACAG_CA________GACAACCAGCUAGCCACAACGCCUGACGUGGCAAAGGGGUGUGCCCCAUGACGACGCACUCCCAUCCGCCGUUGGUGUCCAAAAAACACCGAAA_AAUUAAAU
(((((.................(((((..(((((..........)))))...(((((((((........).))))).))).......))))))))))....................... (-24.81 = -26.12 +   1.31)

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 11:56:14 2006