Locus 2536

Sequence ID	2L_DroMel_CAF1
Location	7,010,603 – 7,010,789
Length	186
Max. P	0.679471

overview

Window 5

Location	7,010,603 – 7,010,695
Length	92
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	79.44
Mean single sequence MFE	-22.48
Consensus MFE	-14.02
Energy contribution	-14.05
Covariance contribution	0.03
Combinations/Pair	1.32
Mean z-score	-1.62
Structure conservation index	0.62
SVM decision value	0.30
SVM RNA-class probability	0.679471
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7010603 92 - 22407834
----------GUGCGAAUGUUUGAAAACAGCAAGCA-ACCCAAAAUCA-AGGGAGGGUAAAAACCCACCUCC-GACUUCACAUGUCCU----CGGCAAUUAAACGAAAU
----------.(((...((((((.......))))))-.(((.......-.))).((((....))))......-(((.......)))..----..)))............ ( -18.00)
>DroSec_CAF1 31523 92 - 1
----------GUGCGAAUGUUUGAAAACAGUUAGCAAACCCAAAAUCA-AGGGAGGGUAA-AACCCACCUCC-GACUUCACAUGUCCU----GGGCAAUUAAACGAAAU
----------.(((...((((....))))....)))..((((......-..(((((....-......)))))-(((.......))).)----))).............. ( -20.60)
>DroSim_CAF1 31320 92 - 1
----------GUGCGAAUGUUUGAAAACAGUUAGCAAACCCAAAAUCA-AGGGAGGGUAA-AACCCACCUCC-GACUUCACAUGUCCU----GGGCAAUUAAACGAAAU
----------.(((...((((....))))....)))..((((......-..(((((....-......)))))-(((.......))).)----))).............. ( -20.60)
>DroEre_CAF1 31557 91 - 1
----------UCGCGAAUGUUUGAAAACAGUAAGCA-ACCCAACAUCA-GGGGAGGGUAA-AACCCACCUCC-GACUUCACAUGUCCU----GCACAAUUAAAUGAAAU
----------..((...((((....))))....)).-........(((-((((.(((...-..))).)).))-(((.......)))..----...........)))... ( -17.50)
>DroYak_CAF1 31476 91 - 1
----------UUGCGAAUGUUUGAAAACAGUAAGCA-GCCCAAAAUCA-GAGGAGGGUAA-AACCCACCUUC-GACUUCACAUGUCCU----GGGCAAUUAAACGAAAU
----------.(((...((((....))))....)))-(((((......-((((.(((...-..))).)))).-(((.......))).)----))))............. ( -25.40)
>DroPer_CAF1 50279 104 - 1
UUCUUCGAUGUAGUAAAUAUUUGUAAGCAGCAA-CA-G-GCGGCAGCAGGAGGAGGGUAA-AACCCUGCCUCAGA-GGCACAUGUGCCGUCGGUGCAAUUAGCUGAAAU
..........((((.(((...((....))(((.-..-(-((((((((..((((((((...-..)))).))))...-.)).....)))))))..))).))).)))).... ( -32.80)
>consensus
__________GUGCGAAUGUUUGAAAACAGUAAGCA_ACCCAAAAUCA_AGGGAGGGUAA_AACCCACCUCC_GACUUCACAUGUCCU____GGGCAAUUAAACGAAAU
.................(((((((..........................(((.((((....)))).)))............(((((.....))))).))))))).... (-14.02 = -14.05 +   0.03)

alignment

secondary structure

dotplot

Window 6

Location	7,010,695 – 7,010,789
Length	94
Sequences	4
Columns	94
Reading direction	forward
Mean pairwise identity	92.20
Mean single sequence MFE	-23.90
Consensus MFE	-18.70
Energy contribution	-17.95
Covariance contribution	-0.75
Combinations/Pair	1.20
Mean z-score	-1.57
Structure conservation index	0.78
SVM decision value	-0.05
SVM RNA-class probability	0.508377
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7010695 94 + 22407834
GCAACGGAAGCGGUGGCCGAACGAAAGACUCAAGCAACGAACUUGCUAAAAGGGUUGGCUAACAAAGUAGAGAGCACCAUAAAAGUGGGAUUGU
((..((....)).(((((((.(....).(((.(((((.....)))))....))))))))))............)).((((....))))...... ( -21.30)
>DroSec_CAF1 31615 94 + 1
GCAACGGAAGCGUUGGCCGAACGAAAGACUCAAGCAACGAACUUGCUAAAAGGGUUCGCCAACAAAGUAGAGAGCACCAUAAAAGUGGGAUUGU
((..(....).((((((.((((((.....)).(((((.....)))))......))))))))))..........)).((((....))))...... ( -24.40)
>DroSim_CAF1 31412 94 + 1
GCAACGGAAGCGUUGGCCGAACGAAAGACUCAAGCAACGAACUUGCUAAAAGGGUUCGCCAACAAAGUAGAGAGCACCAUAAAAGUGGGAUUGU
((..(....).((((((.((((((.....)).(((((.....)))))......))))))))))..........)).((((....))))...... ( -24.40)
>DroYak_CAF1 31567 94 + 1
GCAGCGGAAGCGCUGGUCAAACGAAAGACUGAAGCAACGAACUUGCUAAAAGGGUUCGCCAACAAUGCAUGGAUGACCAUAAAAGUGGGAUUGC
.(((((....))))).(((..(....)..))).((((....((..((.....((((..(((........)))..)))).....))..)).)))) ( -25.50)
>consensus
GCAACGGAAGCGUUGGCCGAACGAAAGACUCAAGCAACGAACUUGCUAAAAGGGUUCGCCAACAAAGUAGAGAGCACCAUAAAAGUGGGAUUGU
.(((((....)))))......(....).(((.(((((.....))))).....((....)).........)))....((((....))))...... (-18.70 = -17.95 +  -0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:13 2006