Locus 2474

Sequence ID	3R_DroMel_CAF1
Location	6,806,394 – 6,806,608
Length	214
Max. P	0.581773

overview

Window 4

Location	6,806,394 – 6,806,502
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.68
Mean single sequence MFE	-34.92
Consensus MFE	-18.74
Energy contribution	-18.55
Covariance contribution	-0.19
Combinations/Pair	1.22
Mean z-score	-2.31
Structure conservation index	0.54
SVM decision value	0.10
SVM RNA-class probability	0.581773
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6806394 108 - 27905053
CGUGCGACCCACUCGAGGCGUCAGGUGUUGGCGCAAUGAUUUUCCAUUUUACGCCUGAAAGUCAUGCGCUAAUUUUCUCGUC---CUUG-----GGUUG---GCGCCCCCACUCGCUCC-
...(((.((.((((((((((..(((.(((((((((.((((((((............)))))))))))))))))..))))).)---))))-----))).)---)))).............- ( -40.70)
>DroSec_CAF1 64667 107 - 1
CGUGCGACCCACUCGAGGCGUCAGGUGUUGGCGCAAUGAUUUUCCAUUUUACGCCUGAAAGUCAUGCGCUAAUUUUCUCGUC---CUUG-----GGUUC---GCGCC-CCACUCGCUUC-
.((((((...((((((((((..(((.(((((((((.((((((((............)))))))))))))))))..))))).)---))))-----)))))---)))).-...........- ( -41.30)
>DroSim_CAF1 70226 107 - 1
CGUGCGACCCACUCGAGGCGUCAGGUGUUGGCGCAAUGAUUUUCCAUUUUACGCCUGAAAGUCAUGCGCUAAUUUUCUCGUC---CUUG-----GGUUC---GCGCC-CCACUCGCUCC-
.((((((...((((((((((..(((.(((((((((.((((((((............)))))))))))))))))..))))).)---))))-----)))))---)))).-...........- ( -41.30)
>DroEre_CAF1 50410 107 - 1
CGUGCGACACACUCGAGGCGUCAGGUGUUGCCGCAAUGAUUUUCAAUUUUACGCCUGAAAGUCAUGCGCUAAUUUUCUCGUC---CUUG-----GGCUC---GCGCC-CCACUCGCCCC-
.((((((....(((((((((..(((.((((.((((.(((((((((..........))))))))))))).))))..))))).)---))))-----)).))---)))).-...........- ( -34.70)
>DroYak_CAF1 63268 107 - 1
CGUGCGACCCACUUGAGGCGUCAGGUGUUGCCGCAAUGAUUUUCAAUUUUACGCCUGAAAGUCAUGCGCUAAUUUUCUCGUC---CUUG-----GAUUC---GCACC-GCACUUGCCCC-
.(((((((((......)).))).(((((.((.(((.(((((((((..........))))))))))))))..........(((---....-----)))..---)))))-)))).......- ( -33.20)
>DroAna_CAF1 22517 106 - 1
CGAGUA-------------CCCAGGUGUUGCUGCAAUGAUUUUCAAUUUUAUGCCUGAAAGUCAUGCGCUAAUUUUACCAUUUUCCUCUGUCCAAGUUCUAAGUUCC-CCAAGCUUUUUC
.(((..-------------....((((..((.(((.(((((((((..........))))))))))))))......))))......)))............(((((..-...))))).... ( -18.30)
>consensus
CGUGCGACCCACUCGAGGCGUCAGGUGUUGCCGCAAUGAUUUUCAAUUUUACGCCUGAAAGUCAUGCGCUAAUUUUCUCGUC___CUUG_____GGUUC___GCGCC_CCACUCGCUCC_
.(((((((((......)).))).((.((((.((((.((((((((............)))))))))))).))))....)).......................)))).............. (-18.74 = -18.55 +  -0.19)

alignment

secondary structure

dotplot

Window 5

Location	6,806,502 – 6,806,608
Length	106
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	87.78
Mean single sequence MFE	-29.18
Consensus MFE	-18.46
Energy contribution	-20.34
Covariance contribution	1.88
Combinations/Pair	1.07
Mean z-score	-2.38
Structure conservation index	0.63
SVM decision value	-0.03
SVM RNA-class probability	0.518868
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6806502 106 - 27905053
GUGGAGUCGUGCAGCUGGAGCUUAAGGUUGUGCUGU------------AGCUGAAACGGAAACGGAAGCGGGCAAGCAGUUAAAGUAAGCUGAAAUCAUAAACGAAAAUCACGUAAUG
((((..((((.(((((...((((...(((.((((..------------.(((....((....))..))).))))))).....)))).))))).........))))...))))...... ( -28.90)
>DroSec_CAF1 64774 106 - 1
GUGGAGUCGUGCAGCUGGAGCUUGAGCUCGAGCUGA------------AGCUGAAACGGAAACGGAAGCGGGCAAGCAGUUAAAGUAAGCAGAAAUCAUAAACGAAAAUCACGUAAUG
((((..((((.(((((.((((....)))).))))).------------.(((....((....))...((......))..........)))...........))))...))))...... ( -33.20)
>DroSim_CAF1 70333 106 - 1
GUGGAGUCGUGCAGCUGGAGCUUGAGCUUGAGCUGG------------AGCUGAAACGGAAACGGAAGCGGGCAAGCAGUUAAAGUAAGCAGAAAUCAUAAACGAAAAUCACGUAAUG
((((..((((.(((((.((((....)))).)))))(------------(.(((...((....))...((......))............)))...))....))))...))))...... ( -32.20)
>DroEre_CAF1 50517 103 - 1
GUUGAGUCGUGCAGCUGGAACUGCAG---GAGCUGG------------AGUUGAAACGGAAGCGGAAGCGGGAAAGCAGUUAAAGUAAGCUGAAAUCAUAAACGAAAAUCACGUAAUG
..(((.((((.(((((..((((((..---...(((.------------........)))..((....))......))))))......))))).........))))...)))....... ( -25.70)
>DroYak_CAF1 63375 115 - 1
GUGGAGUCGUGCACCUGGAGCUGCAG---GAACUGGAGGAGCUGAGAGAGUCGAAACGGAAACGGAAGCGGGCAAGCAGUUAAAGUAAGCUGAAAUCAUAAACGAAAAUCACGUAAUG
((((..((((((.((((......)))---).(((.....(((((...(..(((...((....))....))).)...)))))..)))..))((....))...))))...))))...... ( -25.90)
>consensus
GUGGAGUCGUGCAGCUGGAGCUUCAG_U_GAGCUGG____________AGCUGAAACGGAAACGGAAGCGGGCAAGCAGUUAAAGUAAGCUGAAAUCAUAAACGAAAAUCACGUAAUG
((((..((((.(((((.((.(....).)).)))))..............(((....((....))..)))((.....(((((......)))))...))....))))...))))...... (-18.46 = -20.34 +   1.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:18 2006