Locus 1233

Sequence ID X_DroMel_CAF1
Location 3,672,336 – 3,672,432
Length 96
Max. P 0.553628
window1987

overview

Window 7

Location 3,672,336 – 3,672,432
Length 96
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 68.33
Mean single sequence MFE -26.77
Consensus MFE -14.51
Energy contribution -16.65
Covariance contribution 2.14
Combinations/Pair 1.18
Mean z-score -1.32
Structure conservation index 0.54
SVM decision value 0.04
SVM RNA-class probability 0.553628
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3672336 96 + 22224390
AGGUGGCUAAUUAAUAACGAAUUUGAGCU---------GGAAUUCGAAUUGGCCGCAGAAGGGGCGCUACCCUGUGACCCCAAUCAAAAACCCGAGCUUAUUAGG
..((((((((((.....(((((((.....---------.)))))))))))))))))....(((((((......))).)))).........((..(.....)..)) ( -29.80)
>DroPse_CAF1 10060 73 + 1
UGGCCCCUAAUUAAUUACGAAUU---------------------CCA---CGUCACA-AGGGGGCGCGACCCUGCGACCUCAAUCC-------GAGCGUUUAAAG
..((((((........(((....---------------------...---)))....-.))))))(((....)))((((((.....-------))).)))..... ( -16.22)
>DroSec_CAF1 6549 105 + 1
AGGUGGCUAAUUAAUAAAGAAUUUGAGCUUCGAGCUUCGAGCUUCGAAUUGGCCGCAGAAGGGGCGCUACCCUGUGACCCCAAUCAAAAACCUGAGCUUAUUAGG
..((((((((((......((((((((((.....)).))))).))).))))))))))....(((((((......))).)))).........(((((.....))))) ( -35.10)
>DroEre_CAF1 10908 96 + 1
AGGCGGCUAAUUGAUUACGAUUCUGAGCU---------GGAAUUCGAAUUGGCCGCAGAAGGGGCGCUACCCUGUGACCCCAAUCGGCAGCCAGAGCUUAUCAAG
.(((((((((((.....(((((((.....---------)))).)))))))))))((.((.(((((((......))).))))..)).)).)))............. ( -32.90)
>DroYak_CAF1 6304 95 + 1
AGGUGGCUAAUUAAUUACGAAU-UGAACU---------GGAAUUCGUAUUGGCCGCAUAAGGGGCGCUACCCUGUGACCCCAAUCAGAAACCAGAGUUUAUCCAG
..((((((((.....(((((((-(.....---------..))))))))))))))))....(((((((......))).))))........................ ( -29.20)
>DroPer_CAF1 11852 73 + 1
UGGCCCCUAAUUAAUUACGGAUU---------------------CCU---CGUCACA-AGGGGGCGCGACCCUGCGACCUCAAUUC-------GAGCGUUUAAAG
..((((((........((((...---------------------..)---)))....-.))))))(((....)))((((((.....-------))).)))..... ( -17.42)
>consensus
AGGCGGCUAAUUAAUUACGAAUUUGAGCU_________GGAAUUCGAAUUGGCCGCAGAAGGGGCGCUACCCUGUGACCCCAAUCA_AAACC_GAGCUUAUAAAG
..((((((((((..................................))))))))))....(((((((......))).))))........................ (-14.51 = -16.65 +   2.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:37 2006