Locus 5347

Sequence ID 3L_DroMel_CAF1
Location 14,762,117 – 14,762,244
Length 127
Max. P 0.999909
window8452 window8453 window8454 window8455

overview

Window 2

Location 14,762,117 – 14,762,216
Length 99
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 78.77
Mean single sequence MFE -52.32
Consensus MFE -38.61
Energy contribution -41.05
Covariance contribution 2.44
Combinations/Pair 1.22
Mean z-score -2.43
Structure conservation index 0.74
SVM decision value 2.34
SVM RNA-class probability 0.992627
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14762117 99 + 23771897
AUGGCCGC------UGCCGUCGGAGGAAAGUCUGGAAAUGGCCCUGGACCAGGAACCGGC---GGAGGACCCGGUCCUGGUCCAGGCCCACCUCCACACUACGGCGGC
...(((((------((((......))..(((.((((..(((.((((((((((((.((((.---(.....))))))))))))))))).)))..)))).))).))))))) ( -59.50)
>DroEre_CAF1 4897 105 + 1
AUGGCCGCUGCAGCUGCCGUUGGAGGAAAGUCUGGAAAUGGCUCUGGACCAGGAACCGGC---GGAGGUCCCGGUCCUGGCCCAGGCCCACCUCCACACUACGGCGGC
...(((((((((((....))))......(((.((((..(((..((((.((((((.((((.---.......)))))))))).))))..)))..)))).))).))))))) ( -52.00)
>DroYak_CAF1 4901 105 + 1
AUGGCCGCUGCAGCUGCCGUCGGCGGAAAGUCUGGAAAUGGCCCUGGACCAGGAACCGGC---GGAGGUCCCGGUCCUGGCCCAGGCCCACCUCCACACUACGGCGGC
...(((((((...(((((...)))))..(((.((((..(((.(((((.((((((.((((.---.......)))))))))).))))).)))..)))).))).))))))) ( -57.70)
>DroAna_CAF1 4558 99 + 1
AUGGCGGCC---GCCGCAGUGGGCGGAAAGAUCGGCAACGGCCCGGGACCAGGAGCAGGACCGGGAGGACCCG------GCUCAGGACCGCCCCCGCACUUUGGUAGU
..(((....---)))((.(.((((((......((....))((((.......)).)).(..(((((....))))------)..)....))))))).))........... ( -40.10)
>consensus
AUGGCCGCU___GCUGCCGUCGGAGGAAAGUCUGGAAAUGGCCCUGGACCAGGAACCGGC___GGAGGACCCGGUCCUGGCCCAGGCCCACCUCCACACUACGGCGGC
...(((((((...((((.....))))..(((.((((..(((.(((((.((((((.((((...........)))))))))).))))).)))..)))).))).))))))) (-38.61 = -41.05 +   2.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,762,117 – 14,762,216
Length 99
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 78.77
Mean single sequence MFE -59.35
Consensus MFE -43.66
Energy contribution -46.98
Covariance contribution 3.31
Combinations/Pair 1.09
Mean z-score -3.97
Structure conservation index 0.74
SVM decision value 4.49
SVM RNA-class probability 0.999909
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14762117 99 - 23771897
GCCGCCGUAGUGUGGAGGUGGGCCUGGACCAGGACCGGGUCCUCC---GCCGGUUCCUGGUCCAGGGCCAUUUCCAGACUUUCCUCCGACGGCA------GCGGCCAU
((.((((((((.(((((((((.((((((((((((((((.......---.)))).)))))))))))).))))))))).)))........))))).------))...... ( -64.60)
>DroEre_CAF1 4897 105 - 1
GCCGCCGUAGUGUGGAGGUGGGCCUGGGCCAGGACCGGGACCUCC---GCCGGUUCCUGGUCCAGAGCCAUUUCCAGACUUUCCUCCAACGGCAGCUGCAGCGGCCAU
(((((((((((.(((((((((..(((((((((((((((.......---.)))).)))))))))))..))))))))).)))........))))).((....)))))... ( -61.40)
>DroYak_CAF1 4901 105 - 1
GCCGCCGUAGUGUGGAGGUGGGCCUGGGCCAGGACCGGGACCUCC---GCCGGUUCCUGGUCCAGGGCCAUUUCCAGACUUUCCGCCGACGGCAGCUGCAGCGGCCAU
(((((.(((((.(((((((((.((((((((((((((((.......---.)))).)))))))))))).)))))))))........(((...))).))))).)))))... ( -69.40)
>DroAna_CAF1 4558 99 - 1
ACUACCAAAGUGCGGGGGCGGUCCUGAGC------CGGGUCCUCCCGGUCCUGCUCCUGGUCCCGGGCCGUUGCCGAUCUUUCCGCCCACUGCGGC---GGCCGCCAU
...........((((((((((....((..------(((..(..(((((..((......))..)))))..)...))).))...)))))).))))(((---....))).. ( -42.00)
>consensus
GCCGCCGUAGUGUGGAGGUGGGCCUGGGCCAGGACCGGGACCUCC___GCCGGUUCCUGGUCCAGGGCCAUUUCCAGACUUUCCGCCGACGGCAGC___AGCGGCCAU
(((((...(((.(((((((((.((((((((((((((((...........)))).)))))))))))).))))))))).)))....((.....)).......)))))... (-43.66 = -46.98 +   3.31)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,762,140 – 14,762,244
Length 104
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 74.47
Mean single sequence MFE -52.00
Consensus MFE -32.35
Energy contribution -33.35
Covariance contribution 1.00
Combinations/Pair 1.26
Mean z-score -1.90
Structure conservation index 0.62
SVM decision value 1.09
SVM RNA-class probability 0.913919
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14762140 104 + 23771897
GUCUGGAAAUGGCCCUGGACCAGGAACCGGC---GGAGGACCCGGUCCUGGUCCAGGCCCACCUCCACACUACGGCGGCGGC------------GGUGGUGGUGGCGGACACAUGGGAA
(((((....(((.((((((((((((.((((.---(.....))))))))))))))))).)))...(((((((((.((....))------------.))))).)))))))))......... ( -59.00)
>DroEre_CAF1 4926 101 + 1
GUCUGGAAAUGGCUCUGGACCAGGAACCGGC---GGAGGUCCCGGUCCUGGCCCAGGCCCACCUCCACACUACGGCGGCGGA---------------GGUAGUGGCGGACAUAUGGGUA
(((((.....(((.((((.((((((.((((.---.......)))))))))).))))))).((((((.(.(....).)..)))---------------))).....)))))......... ( -48.80)
>DroYak_CAF1 4930 101 + 1
GUCUGGAAAUGGCCCUGGACCAGGAACCGGC---GGAGGUCCCGGUCCUGGCCCAGGCCCACCUCCACACUACGGCGGCGGA---------------GGCGGUGGGGGACAUAUGGGCA
((((.....(((.(((((.((((((.((((.---.......)))))))))).))))).)))(((((((.((.((....)).)---------------)...)))))))......)))). ( -49.80)
>DroAna_CAF1 4584 113 + 1
GAUCGGCAACGGCCCGGGACCAGGAGCAGGACCGGGAGGACCCG------GCUCAGGACCGCCCCCGCACUUUGGUAGUGGAGGGGGAGGAGGAGGCGGCGGCGGCGGGCAUAUGGGCA
...((....))(((((.(.((....((....((....)).((((------.(((....((.(((((.((((.....))))..))))).))..))).))).)))....)))...))))). ( -50.40)
>consensus
GUCUGGAAAUGGCCCUGGACCAGGAACCGGC___GGAGGACCCGGUCCUGGCCCAGGCCCACCUCCACACUACGGCGGCGGA_______________GGCGGUGGCGGACAUAUGGGCA
(((((((..(((.(((((.((((((.((((...........)))))))))).))))).)))..)))...((((.((......................)).)))).))))......... (-32.35 = -33.35 +   1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,762,140 – 14,762,244
Length 104
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 74.47
Mean single sequence MFE -51.27
Consensus MFE -37.81
Energy contribution -39.88
Covariance contribution 2.06
Combinations/Pair 1.11
Mean z-score -2.84
Structure conservation index 0.74
SVM decision value 4.23
SVM RNA-class probability 0.999844
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14762140 104 - 23771897
UUCCCAUGUGUCCGCCACCACCACC------------GCCGCCGCCGUAGUGUGGAGGUGGGCCUGGACCAGGACCGGGUCCUCC---GCCGGUUCCUGGUCCAGGGCCAUUUCCAGAC
.........(((......(((.((.------------((....)).)).)))(((((((((.((((((((((((((((.......---.)))).)))))))))))).)))))))))))) ( -55.70)
>DroEre_CAF1 4926 101 - 1
UACCCAUAUGUCCGCCACUACC---------------UCCGCCGCCGUAGUGUGGAGGUGGGCCUGGGCCAGGACCGGGACCUCC---GCCGGUUCCUGGUCCAGAGCCAUUUCCAGAC
.........(((......((((---------------((((((......).)))))))))((((((((((((((((((.......---.)))).))))))))))).))).......))) ( -51.70)
>DroYak_CAF1 4930 101 - 1
UGCCCAUAUGUCCCCCACCGCC---------------UCCGCCGCCGUAGUGUGGAGGUGGGCCUGGGCCAGGACCGGGACCUCC---GCCGGUUCCUGGUCCAGGGCCAUUUCCAGAC
.((((............(((((---------------((((((......).))))))))))...((((((((((((((.......---.)))).))))))))))))))........... ( -54.60)
>DroAna_CAF1 4584 113 - 1
UGCCCAUAUGCCCGCCGCCGCCGCCUCCUCCUCCCCCUCCACUACCAAAGUGCGGGGGCGGUCCUGAGC------CGGGUCCUCCCGGUCCUGCUCCUGGUCCCGGGCCGUUGCCGAUC
.........(((((..((((..((.....((.(((((..((((.....)))).))))).))....(..(------((((....)))))..).))...))))..)))))........... ( -43.10)
>consensus
UGCCCAUAUGUCCGCCACCACC_______________UCCGCCGCCGUAGUGUGGAGGUGGGCCUGGGCCAGGACCGGGACCUCC___GCCGGUUCCUGGUCCAGGGCCAUUUCCAGAC
.................................................((.(((((((((.((((((((((((((((...........)))).)))))))))))).))))))))).)) (-37.81 = -39.88 +   2.06)

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 11:47:57 2006