Locus 2866

Sequence ID X_DroMel_CAF1
Location 7,672,395 – 7,672,508
Length 113
Max. P 0.999974
window4699 window4700

overview

Window 9

Location 7,672,395 – 7,672,508
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 71.53
Mean single sequence MFE -35.85
Consensus MFE -22.01
Energy contribution -23.07
Covariance contribution 1.06
Combinations/Pair 1.04
Mean z-score -3.32
Structure conservation index 0.61
SVM decision value 5.10
SVM RNA-class probability 0.999974
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7672395 113 + 22224390
GAGAGUGG-CGCAUGGUGCAGUGGC------AGUAGCAGUGAAAGGACGAAAGUCCUGGCACAAAGGGCAGGCGGUAAAAACAUUGCCAAGGUCUGGACAAAUGGACAAAGGGGCGUUCA
(((.((.(-(((.((.(((....))------).)))).(((..(((((....)))))..))).....)).((((((......))))))...(((((......)))))......)).))). ( -36.80)
>DroSec_CAF1 86488 113 + 1
GAGAGUGGCCGCAUGGGGCAGUGGC------AGUAGCAGUGAAAGGACGAAAGUCCUGCCACAAAG-GCAGGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
.......(((((........)))))------....((.(((..(((((....)))))..)))....-))................................................... ( -24.40)
>DroSim_CAF1 65271 113 + 1
GAGAGUGG-CGCAUGGGGCAGUGGC------AGUAGCAGUGAAAGGACGAAAGUCCUGCCACAAAGGGCAGGCGGCAAAAACACUGCCAAGGUCUGGACAAAUGGACAAAGGGGCGUUCA
..(((((.-(.(....(((((((..------.((.((......(((((....)))))(((......)))..)).)).....)))))))...(((((......)))))...).).))))). ( -40.80)
>DroYak_CAF1 87288 119 + 1
GAGAGUGC-AGCAUGGGGCAGUGGCAGUGGCAGUGGCAGUGAAAGGACGAAAGUCCUGCCACAAAGGGCAGGCGGGAAAAACACUGCCAAGGUCUGGACAAAUGGACAAAUGGACACAUG
....((.(-(...(.((((..((((((((...((((((......((((....)))))))))).....(....)........))))))))..)))).).....)).))..(((....))). ( -41.40)
>consensus
GAGAGUGG_CGCAUGGGGCAGUGGC______AGUAGCAGUGAAAGGACGAAAGUCCUGCCACAAAGGGCAGGCGG_AAAAACACUGCCAAGGUCUGGACAAAUGGACAAAGGGGCGUUCA
..........((........((.((.......)).)).(((..(((((....)))))..))).....)).(((((........)))))...(((((......)))))............. (-22.01 = -23.07 +   1.06)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 0

Location 7,672,395 – 7,672,508
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 71.53
Mean single sequence MFE -24.52
Consensus MFE -13.68
Energy contribution -15.93
Covariance contribution 2.25
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.56
SVM decision value 0.36
SVM RNA-class probability 0.706501
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7672395 113 - 22224390
UGAACGCCCCUUUGUCCAUUUGUCCAGACCUUGGCAAUGUUUUUACCGCCUGCCCUUUGUGCCAGGACUUUCGUCCUUUCACUGCUACU------GCCACUGCACCAUGCG-CCACUCUC
.....(((..((((..(....)..))))....)))...........(((.(((.....(((..(((((....)))))..))).((....------))....)))....)))-........ ( -20.40)
>DroSec_CAF1 86488 113 - 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCCUGC-CUUUGUGGCAGGACUUUCGUCCUUUCACUGCUACU------GCCACUGCCCCAUGCGGCCACUCUC
...............................................(((.((-...((.((((((((....)))).......((....------))...)))).)).)))))....... ( -18.70)
>DroSim_CAF1 65271 113 - 1
UGAACGCCCCUUUGUCCAUUUGUCCAGACCUUGGCAGUGUUUUUGCCGCCUGCCCUUUGUGGCAGGACUUUCGUCCUUUCACUGCUACU------GCCACUGCCCCAUGCG-CCACUCUC
....(((...((((..(....)..))))....(((((((....((((((.........))))))((((....)))).......((....------)))))))))....)))-........ ( -29.40)
>DroYak_CAF1 87288 119 - 1
CAUGUGUCCAUUUGUCCAUUUGUCCAGACCUUGGCAGUGUUUUUCCCGCCUGCCCUUUGUGGCAGGACUUUCGUCCUUUCACUGCCACUGCCACUGCCACUGCCCCAUGCU-GCACUCUC
...(((..(....)..)))..((.(((.....(((((((...................((((((((((....))))......)))))).((....))))))))).....))-).)).... ( -29.60)
>consensus
UGAACGCCCCUUUGUCCAUUUGUCCAGACCUUGGCAGUGUUUUU_CCGCCUGCCCUUUGUGGCAGGACUUUCGUCCUUUCACUGCUACU______GCCACUGCCCCAUGCG_CCACUCUC
................................(((((((............((.....(((..(((((....)))))..))).))............)))))))................ (-13.68 = -15.93 +   2.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:24 2006