Locus 3489

Sequence ID X_DroMel_CAF1
Location 9,381,942 – 9,382,033
Length 91
Max. P 0.999621
window5702 window5703

overview

Window 2

Location 9,381,942 – 9,382,033
Length 91
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 77.85
Mean single sequence MFE -23.18
Consensus MFE -21.59
Energy contribution -21.27
Covariance contribution -0.33
Combinations/Pair 1.12
Mean z-score -0.92
Structure conservation index 0.93
SVM decision value 1.60
SVM RNA-class probability 0.966487
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9381942 91 + 22224390
AAAAAAUAAUUCAAAAA-U-------------------------AAGCGCUAUUUUUGUGCCCGCCAUCGUACUGACAGGCCAAAGUUCAUGAGACAGGGCAAAGGGGUCAGCAGCC
.................-.-------------------------..(((((((((((.((((((((.((.....))..)))....(((.....))).))))).)))))).))).)). ( -20.00)
>DroSec_CAF1 12150 91 + 1
AAAAAAUAAGACAAAGA-U-------------------------AGGCGCUAUUUUUGUGCCCGCCAUCGUACUGACAGGCCAAAGUUCAUGAGACAGGGCAAAGGGGUCAGCAGCC
.................-.-------------------------.((((((((((((.((((((((.((.....))..)))....(((.....))).))))).)))))).))).))) ( -22.50)
>DroYak_CAF1 11774 117 + 1
AAAUAAUAAUUGAAAAAAUAUGAAACAUUAAUUGAAAUACCUAAGGGCGCUAUUCUUGUGCCCGUCAUCGUACCGACAGGCCAAAGUUCAUGAGACAGGGCAAAGGGGUCAGCAGCC
......(((((((..............)))))))...........((((((((((((.((((((((.((((...(((........))).))))))).))))).)))))).))).))) ( -27.04)
>consensus
AAAAAAUAAUUCAAAAA_U_________________________AGGCGCUAUUUUUGUGCCCGCCAUCGUACUGACAGGCCAAAGUUCAUGAGACAGGGCAAAGGGGUCAGCAGCC
.............................................((((((((((((.((((((((.(((...)))..)))....(((.....))).))))).)))))).))).))) (-21.59 = -21.27 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 9,381,942 – 9,382,033
Length 91
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 77.85
Mean single sequence MFE -22.83
Consensus MFE -23.71
Energy contribution -22.83
Covariance contribution -0.88
Combinations/Pair 1.19
Mean z-score -0.54
Structure conservation index 1.04
SVM decision value 3.80
SVM RNA-class probability 0.999621
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9381942 91 - 22224390
GGCUGCUGACCCCUUUGCCCUGUCUCAUGAACUUUGGCCUGUCAGUACGAUGGCGGGCACAAAAAUAGCGCUU-------------------------A-UUUUUGAAUUAUUUUUU
(((.((((..............((....))..((((((((((((......)))))))).))))..))))))).-------------------------.-................. ( -21.30)
>DroSec_CAF1 12150 91 - 1
GGCUGCUGACCCCUUUGCCCUGUCUCAUGAACUUUGGCCUGUCAGUACGAUGGCGGGCACAAAAAUAGCGCCU-------------------------A-UCUUUGUCUUAUUUUUU
(((.((((..............((....))..((((((((((((......)))))))).))))..))))))).-------------------------.-................. ( -24.10)
>DroYak_CAF1 11774 117 - 1
GGCUGCUGACCCCUUUGCCCUGUCUCAUGAACUUUGGCCUGUCGGUACGAUGACGGGCACAAGAAUAGCGCCCUUAGGUAUUUCAAUUAAUGUUUCAUAUUUUUUCAAUUAUUAUUU
(((.((((..............((....))..((((((((((((......)))))))).))))..)))))))............................................. ( -23.10)
>consensus
GGCUGCUGACCCCUUUGCCCUGUCUCAUGAACUUUGGCCUGUCAGUACGAUGGCGGGCACAAAAAUAGCGCCU_________________________A_UUUUUGAAUUAUUUUUU
(((.((((..............((....))..((((((((((((......)))))))).))))..)))))))............................................. (-23.71 = -22.83 +  -0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:33 2006