Locus 1351

Sequence ID 2L_DroMel_CAF1
Location 3,582,949 – 3,583,042
Length 93
Max. P 0.985373
window2208 window2209

overview

Window 8

Location 3,582,949 – 3,583,042
Length 93
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 75.59
Mean single sequence MFE -18.92
Consensus MFE -12.32
Energy contribution -12.77
Covariance contribution 0.45
Combinations/Pair 1.25
Mean z-score -1.34
Structure conservation index 0.65
SVM decision value 0.47
SVM RNA-class probability 0.747070
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3582949 93 + 22407834
AUUUCCCAUAUACAUAGAUGUUUUUUUAAGUGCAAGGG-UAAAGGAGAAACCAGUCCCUCCUGCUCCUGGCUGCCCUAUCCUUGCCCUUCCUUU
...........................(((.(((((((-((.(((((..........)))))((.....)).....))))))))).)))..... ( -20.30)
>DroSec_CAF1 50671 92 + 1
CUUUCCAAUAUAAAU-GAUUUUUUUUUAAGUGCAAGGG-AAGAGGAGAAACCAGUCCCUCCUGCUCCUGGCUGCCCUAUCCUUGCCCUUCCUUU
...............-...........(((.(((((((-.(((((((..........)))))((.....))....)).))))))).)))..... ( -19.10)
>DroSim_CAF1 53380 91 + 1
CUUUCCAAUAUAACU-GAUUUU-UUUUAAGUGCAAGGG-AAGAGGAGAAACCAGUCCCUCCUGCUCCUGGCUGCCCUAUCCUUGCCCUUCCUUU
...............-......-....(((.(((((((-.(((((((..........)))))((.....))....)).))))))).)))..... ( -19.10)
>DroEre_CAF1 52662 77 + 1
---------------CUAUGUUUUUUUGAGUGCAAGGG-AGCAGGAGAAACCAGUCCCUCCUGCUCCUGGCUGCCCCAUCC-UGCCCUGCCUUU
---------------............(((.(((.(((-((((((((..........)))))))))))(((..........-.))).)))))). ( -27.70)
>DroYak_CAF1 53309 78 + 1
---------------AUUUGUUUUUUUCAGUGCAAGGG-AAAAGGAGAAACCAGUCCCUCCUGCUCCUGGCUGCCCUAUCCUUGCCCUGCCUUU
---------------............(((.(((((((-...(((((..........)))))((.....)).......))))))).)))..... ( -19.70)
>DroAna_CAF1 54841 74 + 1
--------------------UAUUUUCAAGUGCAGAGAAUAAAAGAGAAACCAGUCCCUCCUGCUCCUUCCUGUCCUAGCCCAUCUUGUCCUUU
--------------------......((((.((((.((....(((.((...(((......))).)))))....)))).))....))))...... (  -7.60)
>consensus
________________GAUGUUUUUUUAAGUGCAAGGG_AAAAGGAGAAACCAGUCCCUCCUGCUCCUGGCUGCCCUAUCCUUGCCCUUCCUUU
...........................(((.((((((.....(((((..........)))))((........)).....)))))).)))..... (-12.32 = -12.77 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 3,582,949 – 3,583,042
Length 93
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 75.59
Mean single sequence MFE -25.20
Consensus MFE -17.62
Energy contribution -18.07
Covariance contribution 0.45
Combinations/Pair 1.24
Mean z-score -2.22
Structure conservation index 0.70
SVM decision value 2.00
SVM RNA-class probability 0.985373
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3582949 93 - 22407834
AAAGGAAGGGCAAGGAUAGGGCAGCCAGGAGCAGGAGGGACUGGUUUCUCCUUUA-CCCUUGCACUUAAAAAAACAUCUAUGUAUAUGGGAAAU
.....(((.((((((..((((.((((((............)))))).).)))...-.)))))).))).........(((((....))))).... ( -23.00)
>DroSec_CAF1 50671 92 - 1
AAAGGAAGGGCAAGGAUAGGGCAGCCAGGAGCAGGAGGGACUGGUUUCUCCUCUU-CCCUUGCACUUAAAAAAAAAUC-AUUUAUAUUGGAAAG
.....(((.((((((...((....)).((((.(((((..(....)..))))))))-))))))).)))...........-............... ( -26.60)
>DroSim_CAF1 53380 91 - 1
AAAGGAAGGGCAAGGAUAGGGCAGCCAGGAGCAGGAGGGACUGGUUUCUCCUCUU-CCCUUGCACUUAAAA-AAAAUC-AGUUAUAUUGGAAAG
.....(((.((((((...((....)).((((.(((((..(....)..))))))))-))))))).)))....-......-............... ( -26.60)
>DroEre_CAF1 52662 77 - 1
AAAGGCAGGGCA-GGAUGGGGCAGCCAGGAGCAGGAGGGACUGGUUUCUCCUGCU-CCCUUGCACUCAAAAAAACAUAG---------------
....(.((.(((-((.(((.....)))((((((((((..(....)..))))))))-))))))).)))............--------------- ( -32.40)
>DroYak_CAF1 53309 78 - 1
AAAGGCAGGGCAAGGAUAGGGCAGCCAGGAGCAGGAGGGACUGGUUUCUCCUUUU-CCCUUGCACUGAAAAAAACAAAU---------------
.....(((.(((((....((....)).((((.(((((..(....)..))))).))-))))))).)))............--------------- ( -26.50)
>DroAna_CAF1 54841 74 - 1
AAAGGACAAGAUGGGCUAGGACAGGAAGGAGCAGGAGGGACUGGUUUCUCUUUUAUUCUCUGCACUUGAAAAUA--------------------
......((((....((..(((...((((((((((......)))....)))))))..)))..)).))))......-------------------- ( -16.10)
>consensus
AAAGGAAGGGCAAGGAUAGGGCAGCCAGGAGCAGGAGGGACUGGUUUCUCCUUUU_CCCUUGCACUUAAAAAAACAUC________________
.....(((.((((((.....((........))(((((..(....)..))))).....)))))).)))........................... (-17.62 = -18.07 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:22 2006