Locus 1734

Sequence ID	2L_DroMel_CAF1
Location	4,755,984 – 4,756,135
Length	151
Max. P	0.757327

overview

Window 5

Location	4,755,984 – 4,756,095
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.12
Mean single sequence MFE	-23.19
Consensus MFE	-14.81
Energy contribution	-15.87
Covariance contribution	1.06
Combinations/Pair	1.09
Mean z-score	-1.58
Structure conservation index	0.64
SVM decision value	0.24
SVM RNA-class probability	0.650435
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4755984 111 + 22407834
GCUUUUAAUAAACCGAUGAGGCAUGCUUUA----AAAAAAGGAAAAUGUGGCGAAGCCAUUUAAGGCAUCCAAACUGUUUGUUUAU----AUAUAACGGACA-ACCGCAAAAACCAUCGA
.............(((((.((.((((((((----(............(((((...))))))))))))))))....((((((((...----....))))))))-...........))))). ( -26.70)
>DroPse_CAF1 223081 102 + 1
-----AAGUUAACUUUUCAGGCAUCCC--A----AAAAUAUA-CACUGUGGUAUGGCCGUUUAAGGCAUCCGAACUGUUUGUUUAU------AUAACGGACAAACCGCAAAAACCAUCGA
-----..............((....))--.----........-...((((((...(((......)))........((((((((...------..)))))))).))))))........... ( -19.50)
>DroSim_CAF1 181191 114 + 1
GCUUUUAAUAAAACGAUGAGGCAUGCUUUACAAAAAAAAAGG-AAAUGUGGCGAAGCCAUUUAAGGCAUCCAAACUGUUUGUUUAU----AUAUAACGGACA-ACCGCAAAAACCAUCGA
.............(((((.((.((((((((............-....(((((...))))).))))))))))....((((((((...----....))))))))-...........))))). ( -25.33)
>DroEre_CAF1 192994 113 + 1
GCUUUUAAUAAAACGACGAGGCAUGCCUUU----AAA-AAGG-AAAUGUGGCGAAGCCAUUUAAGGCAUCCAAACUGUUUGUUUAUACAUAUAUAACGGACA-GCCGCAAAAACCAUCGA
.............(((.((((....)))).----...-..((-...((((((((.(((......))).)).....(((((((((((....))).))))))))-))))))....)).))). ( -27.90)
>DroYak_CAF1 190967 110 + 1
GGUUUUAAUAAAACGAUGAGGCAUGCCCUA----AAAAAAGA-AAAUGUGGCAAAGCCAGUUAAGGCAUCCAAACUGUUUGUUUAU----AUAUAACGGCCA-ACCGCAAAAACCAUCGA
((((((....(((((.(..((.(((((((.----.....)).-.....((((...)))).....)))))))..).)))))......----......(((...-.)))..))))))..... ( -21.50)
>DroPer_CAF1 230806 102 + 1
-----AAGUUAACUUUUCAGGCAUCCC--A----AAAAUAUA-CACUGUGGUAUGGCCGUUUAAGGGAUCCGAACUGUUUGUUUAU------AUAACGGACAAACCGCAAAAACCAUCGA
-----..........(((.((.(((((--(----((..((((-(......)))))....)))..)))))))))).((((((((...------..)))))))).................. ( -18.20)
>consensus
GCUUUUAAUAAAACGAUGAGGCAUGCCUUA____AAAAAAGA_AAAUGUGGCAAAGCCAUUUAAGGCAUCCAAACUGUUUGUUUAU____AUAUAACGGACA_ACCGCAAAAACCAUCGA
.............(((((.((....))...................(((((....(((......)))........((((((((...........))))))))..))))).....))))). (-14.81 = -15.87 +   1.06)

alignment

secondary structure

dotplot

Window 6

Location	4,756,020 – 4,756,135
Length	115
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	87.69
Mean single sequence MFE	-30.35
Consensus MFE	-24.33
Energy contribution	-24.42
Covariance contribution	0.08
Combinations/Pair	1.13
Mean z-score	-2.44
Structure conservation index	0.80
SVM decision value	0.49
SVM RNA-class probability	0.757327
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4756020 115 + 22407834
GGAAAAUGUGGCGAAGCCAUUUAAGGCAUCCAAACUGUUUGUUUAU----AUAUAACGGACA-ACCGCAAAAACCAUCGAAUUUGGCAAAAUGUCAGAAUGCGGUUUUUGCCACCAAACU
.......(((((((((((......))).........(((((((...----....)))))))(-((((((....(....)..((((((.....)))))).)))))))))))))))...... ( -32.60)
>DroPse_CAF1 223110 113 + 1
UA-CACUGUGGUAUGGCCGUUUAAGGCAUCCGAACUGUUUGUUUAU------AUAACGGACAAACCGCAAAAACCAUCGAAUUUGGCAAAAUGUCAGAAUGCGGUUUUUGCCACUAAACU
..-....((((((..(((......))).........(((((((...------..)))))))((((((((....(....)..((((((.....)))))).)))))))).))))))...... ( -31.00)
>DroEre_CAF1 193029 118 + 1
GG-AAAUGUGGCGAAGCCAUUUAAGGCAUCCAAACUGUUUGUUUAUACAUAUAUAACGGACA-GCCGCAAAAACCAUCGAAUUUGGCAAAAUGUCAGAAUGCGGUUUUUGCCACCAAACU
((-......(((((.(((......))).)).....(((((((((((....))).))))))))-)))(((((((((......((((((.....))))))....)))))))))..))..... ( -34.00)
>DroYak_CAF1 191003 114 + 1
GA-AAAUGUGGCAAAGCCAGUUAAGGCAUCCAAACUGUUUGUUUAU----AUAUAACGGCCA-ACCGCAAAAACCAUCGAAUUUGGCAAAAUGUCAGAAUGCGGUUUUUGCCACCAAACU
..-....(((((((((((.(((((((((..(.....)..)))))..----...))))))).(-((((((....(....)..((((((.....)))))).)))))))))))))))...... ( -31.30)
>DroAna_CAF1 203146 112 + 1
AU-AACAUUGGCGUAGCCAUUUAAGACUUACAAACUGUUUGUUUAU------AUAACGGACG-ACCACAAAAACCAUCGAAUUUGGCAAAAUGUCAGAAUGCGGUUUUUGCCACUAAGUU
..-.....((((...)))).....((((((.....((((((((...------..))))))))-....((((((((......((((((.....))))))....))))))))....)))))) ( -24.10)
>DroPer_CAF1 230835 113 + 1
UA-CACUGUGGUAUGGCCGUUUAAGGGAUCCGAACUGUUUGUUUAU------AUAACGGACAAACCGCAAAAACCAUCGAAUUUGGCAAAAUGUCAGAAUGCGGUUUUUGCCACUAAACU
..-....((((((.((((((....((....((...((((((((...------..))))))))...))......))......((((((.....))))))..))))))..))))))...... ( -29.10)
>consensus
GA_AAAUGUGGCAAAGCCAUUUAAGGCAUCCAAACUGUUUGUUUAU______AUAACGGACA_ACCGCAAAAACCAUCGAAUUUGGCAAAAUGUCAGAAUGCGGUUUUUGCCACCAAACU
.......((((((..(((......)))........((((((((...........)))))))).((((((....(....)..((((((.....)))))).))))))...))))))...... (-24.33 = -24.42 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:48 2006