Locus 6122

Sequence ID X_DroMel_CAF1
Location 15,686,243 – 15,686,391
Length 148
Max. P 0.999836
window9954 window9955 window9956

overview

Window 4

Location 15,686,243 – 15,686,351
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.32
Mean single sequence MFE -27.71
Consensus MFE -22.71
Energy contribution -22.31
Covariance contribution -0.40
Combinations/Pair 1.19
Mean z-score -1.79
Structure conservation index 0.82
SVM decision value 0.89
SVM RNA-class probability 0.875311
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15686243 108 + 22224390
--UCGUAUUUGUAUUUUG--UGUCUUCAAGUGAUUCAGU--------AAUUCACUGACUUAACUGCCCAUCCGAAUUCGAAAUGGGCAAGUUUCCAGGUCGCAUGUAAUCAGCACAAUCA
--.............(((--(((...((.((((((((((--------.....)))))((.((((((((((.((....))..)))))).))))...))))))).))......))))))... ( -27.00)
>DroSec_CAF1 1924 110 + 1
--UCGUAUUUGUAUUUUGUGUGUCUUCAAGUGAUUCAAU--------AAUUCACUGACUUAACUGCCCAUCCGAUUUCGAAAUGGGCAAGUUUCCAGGUCGUAUGUAAUCAGCACAAUCA
--.............((((((.....(((((((......--------...)))))(((((((((((((((.((....))..)))))).))))...)))))...))......))))))... ( -27.50)
>DroSim_CAF1 1799 110 + 1
--UCGUAUUUGUAUUUUGUGUGUCUUCAAGUGAUUCAAU--------AAUUCACUGACUUAACUGCCCAUCCGAUUUCGAAAUGGGCAAGUUUCCAGGUCGUAUGUAAUCAGCACAAUCA
--.............((((((.....(((((((......--------...)))))(((((((((((((((.((....))..)))))).))))...)))))...))......))))))... ( -27.50)
>DroEre_CAF1 3285 116 + 1
--UCGUAUUUGUAUUUUGUGCU--UCCAAGUGGUUCAGUAAUGAAGUAAUUCACUGACUUAACUGCCCAUCCGAUUUCGAAAUGGGCAAGUUUCCAGGUCGUAUGUAAUCAGUGCAUUCA
--..(((((.(.(((.(((((.--....(((((((((....)))).....)))))(((((((((((((((.((....))..)))))).))))...)))))))))).)))))))))..... ( -29.30)
>DroYak_CAF1 1789 120 + 1
UUUUGUAUUUGUAUUCUGUGUUUUUUCAAGUGAUUCAGUAAUGCAGUAAUUCACUGAUUUAACUGCCCAUCCGAUUUCGAAAUGGGCAAGUUUCCAGGUCGUAUGUAAUCAGUGCAAUCA
........((((((((((.(((.........))).))).))))))).....((((((((.((((((((((.((....))..)))))).))))..............))))))))...... ( -27.26)
>consensus
__UCGUAUUUGUAUUUUGUGUGUCUUCAAGUGAUUCAGU________AAUUCACUGACUUAACUGCCCAUCCGAUUUCGAAAUGGGCAAGUUUCCAGGUCGUAUGUAAUCAGCACAAUCA
................(((((.......(((((.................)))))(((((((((((((((.((....))..)))))).))))...)))))...........))))).... (-22.71 = -22.31 +  -0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 15,686,243 – 15,686,351
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.32
Mean single sequence MFE -26.33
Consensus MFE -24.00
Energy contribution -23.36
Covariance contribution -0.64
Combinations/Pair 1.15
Mean z-score -1.85
Structure conservation index 0.91
SVM decision value 1.78
SVM RNA-class probability 0.976742
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15686243 108 - 22224390
UGAUUGUGCUGAUUACAUGCGACCUGGAAACUUGCCCAUUUCGAAUUCGGAUGGGCAGUUAAGUCAGUGAAUU--------ACUGAAUCACUUGAAGACA--CAAAAUACAAAUACGA--
...(((((((..........(((..(....)(((((((((.((....)))))))))))....)))(((((...--------......)))))...)).))--))).............-- ( -26.10)
>DroSec_CAF1 1924 110 - 1
UGAUUGUGCUGAUUACAUACGACCUGGAAACUUGCCCAUUUCGAAAUCGGAUGGGCAGUUAAGUCAGUGAAUU--------AUUGAAUCACUUGAAGACACACAAAAUACAAAUACGA--
...(((((.((.........(((..(....)(((((((((.((....)))))))))))....)))(((((...--------......)))))......))))))).............-- ( -26.00)
>DroSim_CAF1 1799 110 - 1
UGAUUGUGCUGAUUACAUACGACCUGGAAACUUGCCCAUUUCGAAAUCGGAUGGGCAGUUAAGUCAGUGAAUU--------AUUGAAUCACUUGAAGACACACAAAAUACAAAUACGA--
...(((((.((.........(((..(....)(((((((((.((....)))))))))))....)))(((((...--------......)))))......))))))).............-- ( -26.00)
>DroEre_CAF1 3285 116 - 1
UGAAUGCACUGAUUACAUACGACCUGGAAACUUGCCCAUUUCGAAAUCGGAUGGGCAGUUAAGUCAGUGAAUUACUUCAUUACUGAACCACUUGGA--AGCACAAAAUACAAAUACGA--
..(((.((((((((...........(....)(((((((((.((....)))))))))))...)))))))).)))..((((....))))((....)).--....................-- ( -26.60)
>DroYak_CAF1 1789 120 - 1
UGAUUGCACUGAUUACAUACGACCUGGAAACUUGCCCAUUUCGAAAUCGGAUGGGCAGUUAAAUCAGUGAAUUACUGCAUUACUGAAUCACUUGAAAAAACACAGAAUACAAAUACAAAA
(((((.((((((((...........(....)(((((((((.((....)))))))))))...))))))))))))).((.(((.(((.................)))))).))......... ( -26.93)
>consensus
UGAUUGUGCUGAUUACAUACGACCUGGAAACUUGCCCAUUUCGAAAUCGGAUGGGCAGUUAAGUCAGUGAAUU________ACUGAAUCACUUGAAGACACACAAAAUACAAAUACGA__
......((((((((...........(....)(((((((((.((....)))))))))))...))))))))................................................... (-24.00 = -23.36 +  -0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 15,686,278 – 15,686,391
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.79
Mean single sequence MFE -33.76
Consensus MFE -33.88
Energy contribution -32.84
Covariance contribution -1.04
Combinations/Pair 1.17
Mean z-score -2.10
Structure conservation index 1.00
SVM decision value 4.21
SVM RNA-class probability 0.999836
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15686278 113 - 22224390
GCUCAAUGUUCCAUGGAAAUAGCAAAAUGGCAUUGGCAAUUGAUUGUGCUGAUUACAUGCGACCUGGAAACUUGCCCAUUUCGAAUUCGGAUGGGCAGUUAAGUCAGUGAAUU-------
((.(((((..((((............)))))))))))..........(((((((...........(....)(((((((((.((....)))))))))))...))))))).....------- ( -31.60)
>DroSec_CAF1 1961 113 - 1
GCUCGAUGCUCCAUGGAAAUAGCAAAAUGGCAUUGGCAAUUGAUUGUGCUGAUUACAUACGACCUGGAAACUUGCCCAUUUCGAAAUCGGAUGGGCAGUUAAGUCAGUGAAUU-------
((.(((((((.....(......).....)))))))))..........(((((((...........(....)(((((((((.((....)))))))))))...))))))).....------- ( -32.20)
>DroSim_CAF1 1836 113 - 1
GCUCGAUGCUCCAUGGAAAUAGCAAAAUGGCAUUGGCAAUUGAUUGUGCUGAUUACAUACGACCUGGAAACUUGCCCAUUUCGAAAUCGGAUGGGCAGUUAAGUCAGUGAAUU-------
((.(((((((.....(......).....)))))))))..........(((((((...........(....)(((((((((.((....)))))))))))...))))))).....------- ( -32.20)
>DroEre_CAF1 3321 120 - 1
GCCCAAUGCUCCAUGGAAAUAGCAAAAUGGCAUUGGCAAUUGAAUGCACUGAUUACAUACGACCUGGAAACUUGCCCAUUUCGAAAUCGGAUGGGCAGUUAAGUCAGUGAAUUACUUCAU
(((.((((((.....(......).....)))))))))...((((..((((((((...........(....)(((((((((.((....)))))))))))...))))))))......)))). ( -35.70)
>DroYak_CAF1 1829 120 - 1
GCUCAAUGCUCCAUGGAAAUAGCAAAAUGGCAUUGGCAAUUGAUUGCACUGAUUACAUACGACCUGGAAACUUGCCCAUUUCGAAAUCGGAUGGGCAGUUAAAUCAGUGAAUUACUGCAU
...(((((((.....(......).....)))))))(((..(((((.((((((((...........(....)(((((((((.((....)))))))))))...))))))))))))).))).. ( -37.10)
>consensus
GCUCAAUGCUCCAUGGAAAUAGCAAAAUGGCAUUGGCAAUUGAUUGUGCUGAUUACAUACGACCUGGAAACUUGCCCAUUUCGAAAUCGGAUGGGCAGUUAAGUCAGUGAAUU_______
((.(((((((.....(......).....))))))))).........((((((((...........(....)(((((((((.((....)))))))))))...))))))))........... (-33.88 = -32.84 +  -1.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:50 2006