Locus 3013

Sequence ID 2R_DroMel_CAF1
Location 10,398,989 – 10,399,088
Length 99
Max. P 0.991146
window4970 window4971

overview

Window 0

Location 10,398,989 – 10,399,088
Length 99
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 76.82
Mean single sequence MFE -20.30
Consensus MFE -13.04
Energy contribution -14.85
Covariance contribution 1.81
Combinations/Pair 1.10
Mean z-score -2.41
Structure conservation index 0.64
SVM decision value 2.25
SVM RNA-class probability 0.991146
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10398989 99 + 20766785
AACUUGGAGAGCUUUAUAUACUACAUAUAAUUGCAAUGCAACAAGCAUUACACUUCAUCCAAAAGCUUUCCCAUGAGAUCUAAGGU---UUUUUUUUUAAUU
..(((((((((((((.((((.....))))..((.(((((.....))))).)).........))))))))))...))).........---............. ( -17.60)
>DroSim_CAF1 11373 95 + 1
AACUUGGAGAGCUUUAUGUACU----AUAAUUGCUAAGCAACAUGCAUUAGACGUUAUCCAAAAGCUUUCCCAUGAAAUCUAAGGU---UUUUUUUUUAAUU
.....((((((((((.((....----(((((..((((((.....)).))))..))))).))))))))))))...(((((.....))---))).......... ( -18.60)
>DroEre_CAF1 9967 94 + 1
UACCAGGAGAGCUAUGUAUACU----AUAUUUGCAUUACAAAAUGAAUUGCACUGUAGUCAAAAGCUUUCCUAUGAGAUCGAAGU----UUUUUUUGUAAUU
....(((((((((......(((----(((..((((.............)))).))))))....))))))))).......(((((.----...)))))..... ( -19.52)
>DroYak_CAF1 11369 98 + 1
UACUUGGAGAGCUUUGUAUACU----AUAACUGCAUUACACUUUGUAUUGCACUGUAGCCAAAAGCUUUCCUAUGAGAAUUAAUUCUUUUUUUUUUCUAAUU
.....((((((((((.....((----(((..((((.(((.....))).)))).)))))...))))))))))...(((((..((.....))..)))))..... ( -25.50)
>consensus
AACUUGGAGAGCUUUAUAUACU____AUAAUUGCAAUACAACAUGCAUUACACUGUAGCCAAAAGCUUUCCCAUGAGAUCUAAGGU___UUUUUUUUUAAUU
.....((((((((((.(((.......)))..((((((((.....)))))))).........))))))))))............................... (-13.04 = -14.85 +   1.81)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 1

Location 10,398,989 – 10,399,088
Length 99
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 76.82
Mean single sequence MFE -17.91
Consensus MFE -12.06
Energy contribution -13.62
Covariance contribution 1.56
Combinations/Pair 1.15
Mean z-score -1.54
Structure conservation index 0.67
SVM decision value 0.04
SVM RNA-class probability 0.553716
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10398989 99 - 20766785
AAUUAAAAAAAAA---ACCUUAGAUCUCAUGGGAAAGCUUUUGGAUGAAGUGUAAUGCUUGUUGCAUUGCAAUUAUAUGUAGUAUAUAAAGCUCUCCAAGUU
.............---...............(((.((((((...(((...((((((((.....))))))))...........)))..)))))).)))..... ( -19.74)
>DroSim_CAF1 11373 95 - 1
AAUUAAAAAAAAA---ACCUUAGAUUUCAUGGGAAAGCUUUUGGAUAACGUCUAAUGCAUGUUGCUUAGCAAUUAU----AGUACAUAAAGCUCUCCAAGUU
.............---...............(((.((((((((.((((...((((.((.....))))))...))))----....)).)))))).)))..... ( -15.30)
>DroEre_CAF1 9967 94 - 1
AAUUACAAAAAAA----ACUUCGAUCUCAUAGGAAAGCUUUUGACUACAGUGCAAUUCAUUUUGUAAUGCAAAUAU----AGUAUACAUAGCUCUCCUGGUA
.............----............(((((.((((....((((...((((...(.....)...))))....)----)))......)))).)))))... ( -16.60)
>DroYak_CAF1 11369 98 - 1
AAUUAGAAAAAAAAAAGAAUUAAUUCUCAUAGGAAAGCUUUUGGCUACAGUGCAAUACAAAGUGUAAUGCAGUUAU----AGUAUACAAAGCUCUCCAAGUA
...............................(((.((((((..((((.((((((.(((.....))).)))).)).)----)))....)))))).)))..... ( -20.00)
>consensus
AAUUAAAAAAAAA___AACUUAGAUCUCAUAGGAAAGCUUUUGGAUAAAGUGCAAUGCAUGUUGCAAUGCAAUUAU____AGUAUACAAAGCUCUCCAAGUA
...............................(((.((((((..(((....((((((((.....)))))))).........)))....)))))).)))..... (-12.06 = -13.62 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:13 2006