Locus 2311

Sequence ID 3L_DroMel_CAF1
Location 6,506,554 – 6,506,704
Length 150
Max. P 0.894056
window3567 window3568

overview

Window 7

Location 6,506,554 – 6,506,664
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.27
Mean single sequence MFE -26.30
Consensus MFE -19.34
Energy contribution -19.90
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -1.91
Structure conservation index 0.74
SVM decision value 0.39
SVM RNA-class probability 0.717867
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6506554 110 - 23771897
UAGAACGCCCAGGA--------UCCCAGGUCCUGGCAGGCUGGCAAAACUUUUGCACUGCCAAAACAAAAUAUUUAGAUAGCAAACGAACAUAUAUAUACACGCCAGGCUAA--ACACAC
......(((.((((--------(.....)))))))).(((..((((.....))))...))).................((((...((..............))....)))).--...... ( -23.94)
>DroSec_CAF1 1876 110 - 1
UGGAACGCCCAGGA--------UCCCAGGUCCUGGCAGGCUGGCAAAAGUUUUGCACUGCCAAAACAAAAUAUUUAGAUAGCAAACGAACACAUAUAUACACGGCAGGCCAA--ACACAC
(((...((((((((--------(.....))))))((.(((..((((.....))))...))).........(((....)))))....................)))...))).--...... ( -26.50)
>DroSim_CAF1 1869 110 - 1
UGGAACGCCCAGGA--------UCCCAGGUCCUGGCAGGCUGGCAAAACUUUUGCACUGCCAAAACAAAAUAUUUAGAUAGCAAACGAACACAUAUAUACACGGCAGGCCAA--ACACAC
(((...((((((((--------(.....))))))((.(((..((((.....))))...))).........(((....)))))....................)))...))).--...... ( -26.50)
>DroEre_CAF1 1822 110 - 1
UGGAACGCCCAGGAUCCCAGGAUCCCAGGUCCUGGCAGGCUGGCAAAACUUUUGCACUGCCAAAACAAAAUAUUUAGAUAGCAAACGAACACAUACACAU----------AUAUACACAC
.((...(((..(((((....)))))..)))))((((((....((((.....)))).))))))......................................----------.......... ( -25.40)
>DroYak_CAF1 1794 112 - 1
UGGAACGCCCAGGA--------UCCCAGGUCCUGGCAGGCUGGCAAAACUUUUGCACUGCCAAAACAAAAUAUUUAGAUAGCAAACGAACACAUAUAUGCACGGCAGGCCAAACACACAC
......(((.((((--------(.....)))))))).(((..((((.....)))).(((((.........(((....)))(((..............)))..)))))))).......... ( -29.14)
>consensus
UGGAACGCCCAGGA________UCCCAGGUCCUGGCAGGCUGGCAAAACUUUUGCACUGCCAAAACAAAAUAUUUAGAUAGCAAACGAACACAUAUAUACACGGCAGGCCAA__ACACAC
(((...(((..(((((....)))))..)))..((((((....((((.....)))).))))))..............................................)))......... (-19.34 = -19.90 +   0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,506,592 – 6,506,704
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.88
Mean single sequence MFE -31.36
Consensus MFE -26.94
Energy contribution -27.22
Covariance contribution 0.28
Combinations/Pair 1.03
Mean z-score -1.55
Structure conservation index 0.86
SVM decision value 0.98
SVM RNA-class probability 0.894056
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6506592 112 + 23771897
UAUCUAAAUAUUUUGUUUUGGCAGUGCAAAAGUUUUGCCAGCCUGCCAGGACCUGGGA--------UCCUGGGCGUUCUACAACCACACGGGCCAGCCCCCACAUUUUUGUAAUGCAAAA
....................(((.(((((((((...((..((((((((((((....).--------))))))(.(((....))))...)))))..))......))))))))).))).... ( -29.20)
>DroSec_CAF1 1914 112 + 1
UAUCUAAAUAUUUUGUUUUGGCAGUGCAAAACUUUUGCCAGCCUGCCAGGACCUGGGA--------UCCUGGGCGUUCCACAAGCACACGGCCCAGCCCCCAAAUUUUUUUAAUGCAAAA
..............((((((((((.((((.....))))....)))))))))).((((.--------..((((((................))))))..)))).................. ( -31.79)
>DroSim_CAF1 1907 112 + 1
UAUCUAAAUAUUUUGUUUUGGCAGUGCAAAAGUUUUGCCAGCCUGCCAGGACCUGGGA--------UCCUGGGCGUUCCACAAGCACACGGCCCAGCCCCCACAUUUUUGUAAUGCAAAA
..............((((((((((.((((.....))))....)))))))))).((((.--------..((((((................))))))..))))...(((((.....))))) ( -32.59)
>DroEre_CAF1 1852 120 + 1
UAUCUAAAUAUUUUGUUUUGGCAGUGCAAAAGUUUUGCCAGCCUGCCAGGACCUGGGAUCCUGGGAUCCUGGGCGUUCCACAACCACACGGCCCACCCCCCACAUUUUUGUAAUGCAAAA
..............((((((((((.((((.....))))....))))))))))(..(((((....)))))..)(((((..((((......((........))......))))))))).... ( -33.70)
>DroYak_CAF1 1834 108 + 1
UAUCUAAAUAUUUUGUUUUGGCAGUGCAAAAGUUUUGCCAGCCUGCCAGGACCUGGGA--------UCCUGGGCGUUCCACAACCACACGGCCGAG----CACAUUUUUGUAAUGCAAAA
....................(((.(((((((((..((((.(((..(((((((....).--------))))))(.(((....))))....))).).)----)).))))))))).))).... ( -29.50)
>consensus
UAUCUAAAUAUUUUGUUUUGGCAGUGCAAAAGUUUUGCCAGCCUGCCAGGACCUGGGA________UCCUGGGCGUUCCACAACCACACGGCCCAGCCCCCACAUUUUUGUAAUGCAAAA
..............((((((((((.((((.....))))....))))))))))(..(((((....)))))..)(((((............((........))(((....)))))))).... (-26.94 = -27.22 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:15 2006