Locus 3273

Sequence ID	2R_DroMel_CAF1
Location	11,183,769 – 11,183,903
Length	134
Max. P	0.903370

overview

Window 8

Location	11,183,769 – 11,183,877
Length	108
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	80.11
Mean single sequence MFE	-23.98
Consensus MFE	-15.05
Energy contribution	-14.92
Covariance contribution	-0.14
Combinations/Pair	1.27
Mean z-score	-1.67
Structure conservation index	0.63
SVM decision value	0.29
SVM RNA-class probability	0.670630
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11183769 108 - 20766785
AUACAGAUG-----GAGUAAUUGGCAUGUUAAUUACAGGCUAGUUAUGACUCGUAUGGCAACAAUUAAAGUUAAUUAACAUUCGAAA-ACAA-ACUG--CAAA-AAGCCGUCUAAAUC
....(((((-----(.(((((((((.(((.....))).)))))))))...(((..((....))......(((....)))...)))..-....-....--....-...))))))..... ( -22.00)
>DroPse_CAF1 98361 108 - 1
ACAAAGGCG-----CAGUAAUUGGCAUGUUAAUUGCAGGCUAGUUAUGACUCGUAUGGCAACAAUUAAAGUUAAUUAACAUUCGAUC-ACAA-ACUG--CAAA-CAGUCGCCAGAGUG
.....((((-----..((.(((((.(((((((((((..((.(((....))).)).((....))......).))))))))))))))).-))..-((((--....-))))))))...... ( -24.60)
>DroWil_CAF1 145342 103 - 1
AUAAAGACAACGACAAAUAAUUGGCAUGUUAAUUAUAGGAUAGUUAUGACUCGAAUGGCAACAAUUAAAGUUAAUUAACAUUCGAAU-GUUGCUCUGUC--------------GGCUU
.....((((.(((((.((((((((....)))))))).((((.(((((((((..((((....).)))..)))))..))))))))...)-))))...))))--------------..... ( -21.00)
>DroYak_CAF1 98395 109 - 1
AUACAGAUG-----AAGUAAUUGGCAUGUUAAUUACGGGCUAGUUAUGACUCGUAUGGCAACAAUUAAAGUUAAUUAACAUUCGAAA-ACAA-ACUG--CAAAAAAGCCGUCUAAAUG
....(((((-----..((..((((.(((((((((((((((.......).))))).((....)).........)))))))))))))..-))..-...(--(......)))))))..... ( -20.50)
>DroAna_CAF1 105925 108 - 1
AGCCAUGCG-----GUGUAAUUGGCAUGUUAAUUACAGGCUAGUUAUGACUCGUAUGGCAACAAUUAAAGUUAAUUAACAUUCGCAAAUCAA-ACUG---AAA-AAGUCGCCCGAGUG
.((((((((-----(((((((((((.(((.....))).))))))))).)).))))))))...................((((((........-(((.---...-.)))....)))))) ( -31.20)
>DroPer_CAF1 98136 108 - 1
ACAAAGGCG-----CAGUAAUUGGCAUGUUAAUUGCAGGCUAGUUAUGACUCGUAUGGCAACAAUUAAAGUUAAUUAACAUUCGAUC-ACAA-ACUG--CAAA-CAGUCGCCAGAGUG
.....((((-----..((.(((((.(((((((((((..((.(((....))).)).((....))......).))))))))))))))).-))..-((((--....-))))))))...... ( -24.60)
>consensus
AUAAAGACG_____AAGUAAUUGGCAUGUUAAUUACAGGCUAGUUAUGACUCGUAUGGCAACAAUUAAAGUUAAUUAACAUUCGAAA_ACAA_ACUG__CAAA_AAGUCGCCAGAGUG
.....((((.......(((((((((.(((.....))).)))))))))((((....((....)).....))))....................................))))...... (-15.05 = -14.92 +  -0.14)

alignment

secondary structure

dotplot

Window 9

Location	11,183,802 – 11,183,903
Length	101
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	75.86
Mean single sequence MFE	-19.23
Consensus MFE	-13.23
Energy contribution	-12.90
Covariance contribution	-0.33
Combinations/Pair	1.17
Mean z-score	-1.52
Structure conservation index	0.69
SVM decision value	1.03
SVM RNA-class probability	0.903370
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11183802 101 - 20766785
ACACUCGCACACUC-GCUGGCUUACA-UAUACAGAUG-----GAGUAAUUGGCAUGUUAAUUACAGGCUAGUUAUGACUCGUAUGGCAACAAUUAAAGUUAAUUAACA
......((......-))((((((...-.((((.((.(-----..(((((((((.(((.....))).)))))))))..)))))))(....).....))))))....... ( -21.00)
>DroPse_CAF1 98394 86 - 1
ACAU--GUACA---------------GCACAAAGGCG-----CAGUAAUUGGCAUGUUAAUUGCAGGCUAGUUAUGACUCGUAUGGCAACAAUUAAAGUUAAUUAACA
....--.....---------------((.((...(((-----..(((((((((.(((.....))).)))))))))....))).))))..................... ( -17.00)
>DroSim_CAF1 97389 98 - 1
ACACUCGCACACUCCGCC-----ACACUAUACAGAUG-----GAGUAAUUGGCAUGUUAAUUACAGGCUAGUUAUGACUCGUAUGGCAACAAUUAAAGUUAAUUAACA
...............(((-----(.....(((.((.(-----..(((((((((.(((.....))).)))))))))..))))))))))..................... ( -20.00)
>DroWil_CAF1 145365 87 - 1
----------ACUC-----------ACUAUAAAGACAACGACAAAUAAUUGGCAUGUUAAUUAUAGGAUAGUUAUGACUCGAAUGGCAACAAUUAAAGUUAAUUAACA
----------..((-----------.((((((.((((....(((....)))...))))..))))))))..(((((((((..((((....).)))..)))))..)))). ( -13.30)
>DroAna_CAF1 105958 92 - 1
---------CACUC-ACUCAUAUGUA-UAGCCAUGCG-----GUGUAAUUGGCAUGUUAAUUACAGGCUAGUUAUGACUCGUAUGGCAACAAUUAAAGUUAAUUAACA
---------.....-...........-..((((((((-----(((((((((((.(((.....))).))))))))).)).))))))))..................... ( -27.10)
>DroPer_CAF1 98169 86 - 1
ACAU--GUACA---------------GCACAAAGGCG-----CAGUAAUUGGCAUGUUAAUUGCAGGCUAGUUAUGACUCGUAUGGCAACAAUUAAAGUUAAUUAACA
....--.....---------------((.((...(((-----..(((((((((.(((.....))).)))))))))....))).))))..................... ( -17.00)
>consensus
ACA___G_ACACUC___________A_UAUAAAGACG_____GAGUAAUUGGCAUGUUAAUUACAGGCUAGUUAUGACUCGUAUGGCAACAAUUAAAGUUAAUUAACA
............................................(((((((((.(((.....))).)))))))))((((....((....)).....))))........ (-13.23 = -12.90 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:37 2006