Locus 4569

Sequence ID	3R_DroMel_CAF1
Location	12,070,617 – 12,070,776
Length	159
Max. P	0.859896

overview

Window 2

Location	12,070,617 – 12,070,736
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.51
Mean single sequence MFE	-32.64
Consensus MFE	-26.62
Energy contribution	-27.02
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.78
Structure conservation index	0.82
SVM decision value	0.70
SVM RNA-class probability	0.825283
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12070617 119 + 27905053
ACAAACUUUUUGGCGUCGCCGUCGUCGUCAGCGUCAGCGUCAUUGCUCUGUUUACGUUUUCUCUUUCGUUGACGGCAGCGGAGCAGCUCGCAUUAAUU-UCUUAGUUCUUUCGACAGUAA
....(((..((((((.((....)).)))))).(((.(((...((((((((((..((((..(......)..))))..))))))))))..)))(((((..-..)))))......)))))).. ( -33.30)
>DroSec_CAF1 7157 113 + 1
ACAAACUUUUUGGCGUCGCCGUCG------GCGUCAGCGUCAUUGCUCUGUUUACGUUUUCUCUUUCGUUGACGGCAGCGGAGCAGCUCGCAUUAAUU-UCUUAGUUCUUUCGACAGUAA
...((((...((((((((....))------))))))(((...((((((((((..((((..(......)..))))..))))))))))..))).......-....))))............. ( -33.70)
>DroSim_CAF1 7593 113 + 1
ACAAACUUUUUGGCGUCGCCGUCG------GCGUCAGCGUCAUUGCUCUGUUUACGUUUUCUCUUUCGUUGACGGCAGCGGAGCAGCUCGCAUUAAUU-UCUUAGUUCUUUCUACAGUAA
...((((...((((((((....))------))))))(((...((((((((((..((((..(......)..))))..))))))))))..))).......-....))))............. ( -33.70)
>DroEre_CAF1 9183 114 + 1
ACAAACUUUUUGGCGUCGCUGUCC------GCGUCAGCGUCAUUGCUCUGUUUACGUUUUCUCUUUCGUUGACGGCAGCGGAGCACCUCGCAUUAAUUUUCUUAGUUCUUUCGACAGUAA
.................((((((.------......(((....(((((((((..((((..(......)..))))..)))))))))...)))(((((.....)))))......)))))).. ( -29.20)
>DroYak_CAF1 9275 113 + 1
ACAAACUUUUUGGCGUCGCCGUCG------GCGUCAGCGUCAUUGCUCUGUUUACGUUUUCUCUUUCCUUGACGGCAGCGGAGCAGUUCGCAUUAAUU-UCUUAGUUCUUUCGACAGUAA
...((((...((((((((....))------))))))(((..(((((((((((..((((............))))..))))))))))).))).......-....))))............. ( -33.30)
>consensus
ACAAACUUUUUGGCGUCGCCGUCG______GCGUCAGCGUCAUUGCUCUGUUUACGUUUUCUCUUUCGUUGACGGCAGCGGAGCAGCUCGCAUUAAUU_UCUUAGUUCUUUCGACAGUAA
...((((...((((((..............))))))(((...((((((((((..((((..(......)..))))..))))))))))..)))............))))............. (-26.62 = -27.02 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	12,070,657 – 12,070,776
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.35
Mean single sequence MFE	-28.60
Consensus MFE	-22.30
Energy contribution	-23.70
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-1.93
Structure conservation index	0.78
SVM decision value	0.82
SVM RNA-class probability	0.859896
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12070657 119 + 27905053
CAUUGCUCUGUUUACGUUUUCUCUUUCGUUGACGGCAGCGGAGCAGCUCGCAUUAAUU-UCUUAGUUCUUUCGACAGUAAGAAAAAGUUGUACUAUGCGUUUAGUUCAUGUUGAAUUUGC
..((((((((((..((((..(......)..))))..))))))))))..(((((..((.-.(((..(((((.(....).))))).)))..))...)))))...(((((.....)))))... ( -28.80)
>DroSec_CAF1 7191 119 + 1
CAUUGCUCUGUUUACGUUUUCUCUUUCGUUGACGGCAGCGGAGCAGCUCGCAUUAAUU-UCUUAGUUCUUUCGACAGUAAGAAAAAGUUUUACAAUGCGUUUAGUUCAUGCUAAAUUUGC
..((((((((((..((((..(......)..))))..))))))))))..((((((..((-(((((.(((....)).).)))))))..(.....)))))))((((((....))))))..... ( -30.70)
>DroSim_CAF1 7627 119 + 1
CAUUGCUCUGUUUACGUUUUCUCUUUCGUUGACGGCAGCGGAGCAGCUCGCAUUAAUU-UCUUAGUUCUUUCUACAGUAAGAAAAAGUUUUACAAUGCGUUUAGUUCAUGCUAAAUUUGC
..((((((((((..((((..(......)..))))..))))))))))..((((((....-...(((......)))..((((((.....))))))))))))((((((....))))))..... ( -30.30)
>DroEre_CAF1 9217 95 + 1
CAUUGCUCUGUUUACGUUUUCUCUUUCGUUGACGGCAGCGGAGCACCUCGCAUUAAUUUUCUUAGUUCUUUCGACAGUAAGAAAAAGUUGUUCAC-------------------------
...(((((((((..((((..(......)..))))..)))))))))....(((....((((((((.(((....)).).))))))))...)))....------------------------- ( -23.50)
>DroYak_CAF1 9309 119 + 1
CAUUGCUCUGUUUACGUUUUCUCUUUCCUUGACGGCAGCGGAGCAGUUCGCAUUAAUU-UCUUAGUUCUUUCGACAGUAAGAAAAAGUUGUACAAUGCGUUGAGUUCAUGCUGAAUUUUC
.(((((((((((..((((............))))..))))))))))).((((((.((.-.(((..(((((.(....).))))).)))..))..))))))..((((((.....)))))).. ( -29.70)
>consensus
CAUUGCUCUGUUUACGUUUUCUCUUUCGUUGACGGCAGCGGAGCAGCUCGCAUUAAUU_UCUUAGUUCUUUCGACAGUAAGAAAAAGUUGUACAAUGCGUUUAGUUCAUGCUAAAUUUGC
...(((((((((..((((..(......)..))))..)))))))))...((((((......(((..(((((.(....).))))).)))......))))))..................... (-22.30 = -23.70 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:57 2006