Locus 345

Sequence ID 2L_DroMel_CAF1
Location 1,046,061 – 1,046,248
Length 187
Max. P 0.981284
window546 window547 window548

overview

Window 6

Location 1,046,061 – 1,046,154
Length 93
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 72.45
Mean single sequence MFE -28.24
Consensus MFE -16.70
Energy contribution -17.92
Covariance contribution 1.22
Combinations/Pair 1.14
Mean z-score -1.89
Structure conservation index 0.59
SVM decision value 1.29
SVM RNA-class probability 0.940584
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1046061 93 + 22407834
GUCCGUGAAUGGGUCACCAUAUCG---CCCUGACAUUAUUAUGCCAGCUUUCCGCUGGUCUAU------------------------UUGUGGGUGUGACAUGACCAUUCAAGCUUUUUG
((...(((((((.(((......((---(((..(((....((.((((((.....)))))).)).------------------------.)))))))).....)))))))))).))...... ( -29.70)
>DroSec_CAF1 28268 93 + 1
GUCCGUGAAUGGGUCACCAUAUCC---CCCUGACAUUAUUAUGCCAGCUUUCUGCUGGUCUAU------------------------UUGUGGGUGUGACAUGACCAUUCAAUCUUUUUG
.....(((((((.(((.(((((((---.....(((....((.((((((.....)))))).)).------------------------.))))))))))...))))))))))......... ( -28.80)
>DroSim_CAF1 20060 93 + 1
GUCCGCGAAUGGGUCACCAUAUCC---CCCUGACAUUAUUAUGCCAGCUUUCUGCUGGUCUAU------------------------UUGUGGGUGCGACAUGACCAUUAAAUCUUUUUG
.(((((((((((((((........---...))))........((((((.....))))))))))------------------------))))))).......................... ( -25.20)
>DroEre_CAF1 25544 72 + 1
-----GUAGUGGGUCACCAUAUCU------------------CCCAGCUUUUCGCUGGUCUGA------------------------UUGUGGGUGUGAAAUUACCAUUCAAGCU-UUGG
-----(((((....((((..(((.------------------.(((((.....)))))...))------------------------)....))))....)))))..........-.... ( -19.40)
>DroYak_CAF1 27603 120 + 1
GUCCGUGAAUGGGUCACCACCUCUUUUCCGUGACAUUAUUAUGCCAGCUUUCCGCUGGUCUGCUGGUGGGAUUGUGGGUUUGUGGGUUUGUGGGUGUGAAAUUACCAUUCAAGCUCUUUG
(((((.(((.((((....))))...))))).)))........(((.((.((((((..(....)..))))))..)).)))....(((((((..((((......))))...))))))).... ( -38.10)
>consensus
GUCCGUGAAUGGGUCACCAUAUCC___CCCUGACAUUAUUAUGCCAGCUUUCCGCUGGUCUAU________________________UUGUGGGUGUGACAUGACCAUUCAAGCUUUUUG
.....(((((((.....(((((((.........(((....)))(((((.....))))).................................)))))))......)))))))......... (-16.70 = -17.92 +   1.22) 

alignment

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secondary structure

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dotplot

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Window 7

Location 1,046,061 – 1,046,154
Length 93
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.45
Mean single sequence MFE -23.12
Consensus MFE -17.46
Energy contribution -19.46
Covariance contribution 2.00
Combinations/Pair 1.14
Mean z-score -1.61
Structure conservation index 0.76
SVM decision value 1.88
SVM RNA-class probability 0.981284
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1046061 93 - 22407834
CAAAAAGCUUGAAUGGUCAUGUCACACCCACAA------------------------AUAGACCAGCGGAAAGCUGGCAUAAUAAUGUCAGGG---CGAUAUGGUGACCCAUUCACGGAC
.......(.((((((((((((((...((((((.------------------------.((..(((((.....)))))..))....)))..)))---.)))))))....))))))).)... ( -26.40)
>DroSec_CAF1 28268 93 - 1
CAAAAAGAUUGAAUGGUCAUGUCACACCCACAA------------------------AUAGACCAGCAGAAAGCUGGCAUAAUAAUGUCAGGG---GGAUAUGGUGACCCAUUCACGGAC
.........((((((((((((((...((((((.------------------------.((..(((((.....)))))..))....)))..)))---.)))))))....)))))))..... ( -27.70)
>DroSim_CAF1 20060 93 - 1
CAAAAAGAUUUAAUGGUCAUGUCGCACCCACAA------------------------AUAGACCAGCAGAAAGCUGGCAUAAUAAUGUCAGGG---GGAUAUGGUGACCCAUUCGCGGAC
......((((....))))...((((.((((((.------------------------.((..(((((.....)))))..))....)))..)))---((((..(....)..)))))))).. ( -22.40)
>DroEre_CAF1 25544 72 - 1
CCAA-AGCUUGAAUGGUAAUUUCACACCCACAA------------------------UCAGACCAGCGAAAAGCUGGG------------------AGAUAUGGUGACCCACUAC-----
....-....((((.......))))((((....(------------------------((...(((((.....))))).------------------.)))..)))).........----- ( -16.10)
>DroYak_CAF1 27603 120 - 1
CAAAGAGCUUGAAUGGUAAUUUCACACCCACAAACCCACAAACCCACAAUCCCACCAGCAGACCAGCGGAAAGCUGGCAUAAUAAUGUCACGGAAAAGAGGUGGUGACCCAUUCACGGAC
.......(.(((((((.....(((((((.......((.................((.((......))))...(.((((((....)))))))))......))).)))).))))))).)... ( -23.02)
>consensus
CAAAAAGCUUGAAUGGUCAUGUCACACCCACAA________________________AUAGACCAGCGGAAAGCUGGCAUAAUAAUGUCAGGG___AGAUAUGGUGACCCAUUCACGGAC
.........(((((((....(((((.....................................(((((.....))))).......(((((........))))).))))))))))))..... (-17.46 = -19.46 +   2.00) 

alignment

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secondary structure

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dotplot

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Window 8

Location 1,046,154 – 1,046,248
Length 94
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 75.89
Mean single sequence MFE -24.16
Consensus MFE -17.40
Energy contribution -18.36
Covariance contribution 0.96
Combinations/Pair 1.23
Mean z-score -1.34
Structure conservation index 0.72
SVM decision value 0.37
SVM RNA-class probability 0.707798
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1046154 94 + 22407834
UCUCAGGUCAACGAGGUGCCUCGAAUUGUUAUUCAGUUGACCAGACC------------------UUAACUGCAGGCAAAUAAAUCAUGUUUGCAAAUGCCCAUUUAUGGGA
(((((((((((((((....)))((((....)))).))))))).....------------------......(((.(((((((.....)))))))...))).......))))) ( -30.80)
>DroSec_CAF1 28361 92 + 1
UCUCAGGUCAACGAGGUGCCUCGAAUUGGAACUCAGUUGACCAGACC------------------UUAUCUGCAGUCAAAUAAAUCAUGAUUGCAAUUGCCCAUUUCUGU--
.....((((((((((...((.......))..))).))))))).....------------------.....((((((((.........))))))))...............-- ( -25.80)
>DroSim_CAF1 20153 92 + 1
UCUCAGGCCAGCGAGGUGCCUCGAAUUGGGACUCAGUUGACCAGACC------------------UUAUCUGCAGUCAAAUAAAUCAUGAUUGCAAUUGCCCAUUUCUGU--
.....(((((((..(((.((.......)).)))..))))........------------------.....((((((((.........))))))))...))).........-- ( -23.00)
>DroEre_CAF1 25616 97 + 1
UCCCAGGUAAACGAGGUGCCUCGAAUUAUAAUUCAGUUGGC---------------AAGAUAUGUGUAUCUGCGGUCAAAUAUCUCAUGCUCGCAAUUGCCCAAUUAGGUGA
.....(((((.((((....))))............((.(((---------------(((((((.((.((.....)))).))))))..)))).))..)))))........... ( -21.50)
>DroYak_CAF1 27723 112 + 1
UCUCAGCUUAACGAGGUGCCUCGAAUUAUAAUUCAGUUGGCCAGACCAUAAUAGCCAAGAUAUGUUUACCUGCAGUCAAAUAUAUCAUGUUCGCAAUUGCCCAAUUACGUGA
.....((.....(((....)))((((..........(((((.(........).)))))(((((((((..(....)..)))))))))..)))))).................. ( -19.70)
>consensus
UCUCAGGUCAACGAGGUGCCUCGAAUUGUAAUUCAGUUGACCAGACC__________________UUAUCUGCAGUCAAAUAAAUCAUGAUUGCAAUUGCCCAUUUAUGUGA
.....((((((((((....)))((((....)))).)))))))............................((((((((.........))))))))................. (-17.40 = -18.36 +   0.96) 

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 09:33:34 2006