Locus 7377

Sequence ID X_DroMel_CAF1
Location 18,372,473 – 18,372,603
Length 130
Max. P 0.827130
window12091 window12092 window12093

overview

Window 1

Location 18,372,473 – 18,372,565
Length 92
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 95.14
Mean single sequence MFE -27.57
Consensus MFE -25.72
Energy contribution -25.72
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.79
Structure conservation index 0.93
SVM decision value 0.35
SVM RNA-class probability 0.701573
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18372473 92 + 22224390
GAGACAGAACGCUCUGGGCCAGUUUUGUGGGCAGUUUGCGGCCAGGCAAGCGA------AGCCUGGCAAAUUGAAAUCGAAAAAGAAAACUCGUUAAU
((((((((((((.....))..)))))))((.((((((...(((((((......------.)))))))))))))...))...........)))...... ( -27.30)
>DroSec_CAF1 17212 92 + 1
GAGACAGAACGCUCUGGGCCAGUUUUGUGGGCAGUUUGCGGACAGGCAAGCGA------AGCCUGGCAAAUUGAAAUCGAAAAAGAAAACUCGUUAAU
((((((((((((.....))..)))))))((.((((((((...(((((......------.)))))))))))))...))...........)))...... ( -26.60)
>DroYak_CAF1 16039 98 + 1
GAGACAGAACGCUCUGGGCCAGUUUUGUGGGCAGUUUGCGGCCAGGCAAGCGAAGCCGAAGCCUGGCAAAUUGAAAUCGAAAAAGAAAACUCGUUAAU
((((((((((((.....))..)))))))((.((((((...(((((((...((....))..)))))))))))))...))...........)))...... ( -28.80)
>consensus
GAGACAGAACGCUCUGGGCCAGUUUUGUGGGCAGUUUGCGGCCAGGCAAGCGA______AGCCUGGCAAAUUGAAAUCGAAAAAGAAAACUCGUUAAU
((((((((((((.....))..)))))))((.((((((((...(((((.............)))))))))))))...))...........)))...... (-25.72 = -25.72 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 18,372,513 – 18,372,603
Length 90
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 91.61
Mean single sequence MFE -23.91
Consensus MFE -19.32
Energy contribution -19.99
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.71
Structure conservation index 0.81
SVM decision value 0.70
SVM RNA-class probability 0.827130
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18372513 90 + 22224390
GCCAGGCAAGCGA------AGCCUGGCAAAUUGAAAUCGAAAAAGAAAACUCGUUAAUUAAAAAGUUAACAUGUG--GACCGGGUUCGAGAAUUAGAG
(((((((......------.)))))))...((((..(((((.......((..(((((((....)))))))..)).--.......)))))...)))).. ( -24.86)
>DroSec_CAF1 17252 90 + 1
GACAGGCAAGCGA------AGCCUGGCAAAUUGAAAUCGAAAAAGAAAACUCGUUAAUUAAAAAGUUAACAUGUG--GACCGGGUUCGAGAAUUAGAG
..(((((......------.))))).....((((..(((((.......((..(((((((....)))))))..)).--.......)))))...)))).. ( -18.26)
>DroYak_CAF1 16079 98 + 1
GCCAGGCAAGCGAAGCCGAAGCCUGGCAAAUUGAAAUCGAAAAAGAAAACUCGUUAAUUAAAAAGUUAACAUGUGGGGACCGGGUCCGAGAAUUGGUG
(((((((...((....))..)))))))..((..(..((......))...((((((((((....)))))))......((((...)))))))..)..)). ( -28.60)
>consensus
GCCAGGCAAGCGA______AGCCUGGCAAAUUGAAAUCGAAAAAGAAAACUCGUUAAUUAAAAAGUUAACAUGUG__GACCGGGUUCGAGAAUUAGAG
(((((((.............)))))))...(((((..((.....((....))(((((((....)))))))..........))..)))))......... (-19.32 = -19.99 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 18,372,513 – 18,372,603
Length 90
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 91.61
Mean single sequence MFE -19.27
Consensus MFE -16.01
Energy contribution -16.12
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -2.18
Structure conservation index 0.83
SVM decision value 0.31
SVM RNA-class probability 0.684565
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18372513 90 - 22224390
CUCUAAUUCUCGAACCCGGUC--CACAUGUUAACUUUUUAAUUAACGAGUUUUCUUUUUCGAUUUCAAUUUGCCAGGCU------UCGCUUGCCUGGC
.........(((((...((..--.((.((((((........)))))).))...))..))))).........(((((((.------......))))))) ( -20.70)
>DroSec_CAF1 17252 90 - 1
CUCUAAUUCUCGAACCCGGUC--CACAUGUUAACUUUUUAAUUAACGAGUUUUCUUUUUCGAUUUCAAUUUGCCAGGCU------UCGCUUGCCUGUC
.........(((((...((..--.((.((((((........)))))).))...))..)))))...........(((((.------......))))).. ( -14.90)
>DroYak_CAF1 16079 98 - 1
CACCAAUUCUCGGACCCGGUCCCCACAUGUUAACUUUUUAAUUAACGAGUUUUCUUUUUCGAUUUCAAUUUGCCAGGCUUCGGCUUCGCUUGCCUGGC
....((..(((((((...))))......(((((........))))))))..))..................(((((((...(((...))).))))))) ( -22.20)
>consensus
CUCUAAUUCUCGAACCCGGUC__CACAUGUUAACUUUUUAAUUAACGAGUUUUCUUUUUCGAUUUCAAUUUGCCAGGCU______UCGCUUGCCUGGC
.........(((((...((.....((.((((((........)))))).))...))..))))).........(((((((.............))))))) (-16.01 = -16.12 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:37:25 2006