Locus 1223

Sequence ID	3L_DroMel_CAF1
Location	3,466,549 – 3,466,708
Length	159
Max. P	0.966725

overview

Window 3

Location	3,466,549 – 3,466,668
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.11
Mean single sequence MFE	-22.68
Consensus MFE	-17.86
Energy contribution	-19.36
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-2.59
Structure conservation index	0.79
SVM decision value	1.03
SVM RNA-class probability	0.902531
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3466549 119 + 23771897
AACUUUUUGGCCA-ACUCUUCAUCAUUUUGGCCUCUAAGAACACCCCGACGGCACUUUAACCGGUUCCAUUUUAAUUGUUACCGCCACCUUCCUUCCGCCCGGCAAAUGCUUUCCAAAUU
..(((...(((((-(............))))))...)))........((.((((........(((..((.......))..)))(((...............)))...)))).))...... ( -22.96)
>DroSec_CAF1 13716 116 + 1
AACUUUUUGGCCAAACUCUUCAUCAUUUUGGCCUCUAAGAAUACCCCGACGGCACUUUAACCGGUUCCAUUUUAAUUGUUACCGCCCCCU---UUCCGCCC-GCAAAUGCUUUCCAAAUU
..(((...(((((((...........)))))))...)))...........(((........((((..((.......))..))))......---....))).-((....)).......... ( -20.77)
>DroSim_CAF1 13839 117 + 1
AACUUUUUGGCCAAACUCUUCAUCAUUUUGGCCUCUAAGAACACCCCGACGGCACUUUAACCGGUUCCAUUUUAAUUGUUACCGCCCCCA---UUCUGCCCGGCAAAUGCUUUCCAAAUU
..(((...(((((((...........)))))))...)))......(((..((((.......((((..((.......))..))))......---...)))))))................. ( -23.69)
>DroYak_CAF1 14292 115 + 1
AACUUUUGGGCCA-ACUCUUCAUCAACUUGGCAUCUAAAAACACCCCGACGGCACUUUAACCGGUUCCAUUUUAAUUGUUACCGCCUUC----UUCCGUUCGGCAAAUGCUUUCCAAAUU
....(((((((((-(............))))).............(((((((.........((((..((.......))..)))).....----..))).))))..........))))).. ( -23.29)
>consensus
AACUUUUUGGCCA_ACUCUUCAUCAUUUUGGCCUCUAAGAACACCCCGACGGCACUUUAACCGGUUCCAUUUUAAUUGUUACCGCCCCCU___UUCCGCCCGGCAAAUGCUUUCCAAAUU
..(((...(((((((...........)))))))...)))........((.((((........(((..((.......))..)))(((...............)))...)))).))...... (-17.86 = -19.36 +   1.50)

alignment

secondary structure

dotplot

Window 4

Location	3,466,588 – 3,466,708
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.80
Mean single sequence MFE	-24.39
Consensus MFE	-23.09
Energy contribution	-23.34
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.15
Structure conservation index	0.95
SVM decision value	1.60
SVM RNA-class probability	0.966725
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3466588 120 + 23771897
ACACCCCGACGGCACUUUAACCGGUUCCAUUUUAAUUGUUACCGCCACCUUCCUUCCGCCCGGCAAAUGCUUUCCAAAUUAAUUAAUAGCAUUGUCUGUCUUUGGCAAUUUGCCACGCCC
..........(((........((((..((.......))..)))).................((((((((((................))))(((((.......)))))))))))..))). ( -24.79)
>DroSec_CAF1 13756 116 + 1
AUACCCCGACGGCACUUUAACCGGUUCCAUUUUAAUUGUUACCGCCCCCU---UUCCGCCC-GCAAAUGCUUUCCAAAUUAAUUAAUAGCAUUGUCUGUCUUUGGCAAUUUGCCACGCCC
.......(((((.((......((((..((.......))..))))......---........-...((((((................)))))))))))))..((((.....))))..... ( -21.99)
>DroSim_CAF1 13879 117 + 1
ACACCCCGACGGCACUUUAACCGGUUCCAUUUUAAUUGUUACCGCCCCCA---UUCUGCCCGGCAAAUGCUUUCCAAAUUAAUUAAUAGCAUUGUCUGUCUUUGGCAAUUUGCCACGCCC
.......(((((((.......((((..((.......))..))))......---...)))).(((((.((((................))))))))).)))..((((.....))))..... ( -25.98)
>DroYak_CAF1 14331 116 + 1
ACACCCCGACGGCACUUUAACCGGUUCCAUUUUAAUUGUUACCGCCUUC----UUCCGUUCGGCAAAUGCUUUCCAAAUUAAUUAAUAGCAUUGUCUGUCUUUGGCAAUUUGCCACGCCC
..........(((........((((..((.......))..)))).....----........((((((((((................))))(((((.......)))))))))))..))). ( -24.79)
>consensus
ACACCCCGACGGCACUUUAACCGGUUCCAUUUUAAUUGUUACCGCCCCCU___UUCCGCCCGGCAAAUGCUUUCCAAAUUAAUUAAUAGCAUUGUCUGUCUUUGGCAAUUUGCCACGCCC
..........(((........((((..((.......))..)))).................((((((((((................))))(((((.......)))))))))))..))). (-23.09 = -23.34 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:32 2006