Locus 7412

Sequence ID 3R_DroMel_CAF1
Location 19,720,531 – 19,720,679
Length 148
Max. P 0.894047
window11983 window11984

overview

Window 3

Location 19,720,531 – 19,720,644
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.56
Mean single sequence MFE -24.25
Consensus MFE -19.56
Energy contribution -20.19
Covariance contribution 0.63
Combinations/Pair 1.09
Mean z-score -1.59
Structure conservation index 0.81
SVM decision value 0.17
SVM RNA-class probability 0.615548
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19720531 113 + 27905053
AAGAAUACAAAACAACAAACUCCAAAGCUGAGGCCUGACACCUAACACUAAACUCUA--UACUCGUAUCGUCACAUAUGUAUGGAUAACUCUAUAUAUAUGGCCUGGCGGUAUGU-----
...................(((.......))).........................--....((((((((((((((((((((((....))))))))))))...)))))))))).----- ( -24.30)
>DroSec_CAF1 34140 113 + 1
AAGAAUACAAAACAACAAACUCCAAAGCUGAGGCCUGACACCUAACACUAAACUCUA--UACUCGUAUCGUCACAUAUGUAUGGAUAGCUCUAUAUGUAUGGCCUGGCGGUAUGU-----
...................(((.......))).........................--....((((((((((((((((((((((....))))))))))))...)))))))))).----- ( -23.30)
>DroSim_CAF1 39516 113 + 1
AAGAAUACAAAACAACAAACUCCAAAGCUGAGGCCUGACACCUAACACUAAACUCUA--UACUCGUUUCGUCACAUAUGUAUGGAUAGCUCUAUAUGUAUGGCCUGGCGGUUUGU-----
..............(((((((.....(((.(((((((((....(((...........--.....)))..)))).(((((((((((....))))))))))))))))))))))))))----- ( -26.49)
>DroYak_CAF1 34973 114 + 1
AAGAAUACAAAACAACAAACUCCAAAGCUGAGGCCUGACACCUAACACUAAACUCUAUGUACUCGUAUCGUCGCAUAUG----GAUA--UCUAUAUGUAUGGCCUGGCGGCAUCUCCUCC
..........................(((((((((.(((...((....)).....((((....))))..)))(((((((----(...--.))))))))..)))))..))))......... ( -22.90)
>consensus
AAGAAUACAAAACAACAAACUCCAAAGCUGAGGCCUGACACCUAACACUAAACUCUA__UACUCGUAUCGUCACAUAUGUAUGGAUAGCUCUAUAUGUAUGGCCUGGCGGUAUGU_____
..........................(((.(((((((((..............................)))).(((((((((((....)))))))))))))))))))............ (-19.56 = -20.19 +   0.63)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,720,571 – 19,720,679
Length 108
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.43
Mean single sequence MFE -24.76
Consensus MFE -20.91
Energy contribution -21.85
Covariance contribution 0.94
Combinations/Pair 1.12
Mean z-score -1.93
Structure conservation index 0.84
SVM decision value 0.98
SVM RNA-class probability 0.894047
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19720571 108 + 27905053
CCUAACACUAAACUCUA--UACUCGUAUCGUCACAUAUGUAUGGAUAACUCUAUAUAUAUGGCCUGGCGGUAUGU----------AUCCUCCUGCUGCCCACUACUUAUGCCCGAUAACG
.................--....(((((((...((((((((((((....))))))))))))....(((((((.(.----------.....).))))))).............)))).))) ( -26.30)
>DroSec_CAF1 34180 108 + 1
CCUAACACUAAACUCUA--UACUCGUAUCGUCACAUAUGUAUGGAUAGCUCUAUAUGUAUGGCCUGGCGGUAUGU----------AUCCUUCUGCUGCCCACUACUUAUGCCCGAUAACG
.................--....(((((((...((((((((((((....))))))))))))....(((((((.(.----------.....).))))))).............)))).))) ( -24.30)
>DroSim_CAF1 39556 108 + 1
CCUAACACUAAACUCUA--UACUCGUUUCGUCACAUAUGUAUGGAUAGCUCUAUAUGUAUGGCCUGGCGGUUUGU----------AUCCCCCUGCUGCCCACUACUUAUGCCCGAUAACG
.................--....(((((((...((((((((((((....))))))))))))....((((((..(.----------.....)..)))))).............))).)))) ( -23.10)
>DroYak_CAF1 35013 114 + 1
CCUAACACUAAACUCUAUGUACUCGUAUCGUCGCAUAUG----GAUA--UCUAUAUGUAUGGCCUGGCGGCAUCUCCUCCUUCUCCUCCUCCUGCCGCCCACUACUUAUGCCCGAUAACG
.......................(((((((..(((((((----(...--.))))))))..(((..(((((((....................)))))))..........))))))).))) ( -25.35)
>consensus
CCUAACACUAAACUCUA__UACUCGUAUCGUCACAUAUGUAUGGAUAGCUCUAUAUGUAUGGCCUGGCGGUAUGU__________AUCCUCCUGCUGCCCACUACUUAUGCCCGAUAACG
.......................(((((((...((((((((((((....))))))))))))....(((((((....................))))))).............)))).))) (-20.91 = -21.85 +   0.94)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:45:21 2006