Locus 4055

Sequence ID	3R_DroMel_CAF1
Location	11,046,812 – 11,046,972
Length	160
Max. P	0.897909

overview

Window 7

Location	11,046,812 – 11,046,932
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.78
Mean single sequence MFE	-39.79
Consensus MFE	-37.96
Energy contribution	-37.52
Covariance contribution	-0.44
Combinations/Pair	1.06
Mean z-score	-1.71
Structure conservation index	0.95
SVM decision value	0.32
SVM RNA-class probability	0.685979
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11046812 120 + 27905053
CUACAGCACCGAGUCGCAUGCCAAGGACCACGAAAACUUUAUCAAUGUGGCAAGGACGCGAAAGCGAAGGGCUAAAGCCCUGCACGACUUUGAGCGGCACGACGACGAUGAGUUGGGAUU
...((((.(...(((((.((((.....(((((.............)))))(((((.(((....))).(((((....)))))......)))))...)))).).))))...).))))..... ( -40.02)
>DroSec_CAF1 9582 120 + 1
CUACAGCACCGAGUCGCAUGCCAAGGACCACGAAAACUUUAUCAAUGUGGCAAGGACGCGAAAGCGAAGGGCUAAAGCCUUGCACGACUUUGAGCGGCACGACGACGAUGAGUUGGGAUU
...((((.(...(((((.((((.....(((((.............)))))(((((.(((....))).(((((....)))))......)))))...)))).).))))...).))))..... ( -37.32)
>DroSim_CAF1 9600 120 + 1
CUACAGCACAGAGUCGCAUGCCAAGGACCACGAAAACUUUAUCAAUGUGGCAAGGACGCGAAAGCGUAGGGCUAAAGCCUUGCACGACUUUGAGCGGCACGACGAUGAUGAGUUGGGAUU
...((((.((..(((((.((((.....(((((.............)))))(((((..((....))(((((((....)))))))....)))))...)))).).))))..)).))))..... ( -42.02)
>consensus
CUACAGCACCGAGUCGCAUGCCAAGGACCACGAAAACUUUAUCAAUGUGGCAAGGACGCGAAAGCGAAGGGCUAAAGCCUUGCACGACUUUGAGCGGCACGACGACGAUGAGUUGGGAUU
...((((.(...(((((.((((.....(((((.............)))))(((((.(((....))).(((((....)))))......)))))...)))).).))))...).))))..... (-37.96 = -37.52 +  -0.44)

alignment

secondary structure

dotplot

Window 8

Location	11,046,852 – 11,046,972
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.22
Mean single sequence MFE	-37.70
Consensus MFE	-35.89
Energy contribution	-35.67
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-2.16
Structure conservation index	0.95
SVM decision value	1.00
SVM RNA-class probability	0.897909
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11046852 120 + 27905053
AUCAAUGUGGCAAGGACGCGAAAGCGAAGGGCUAAAGCCCUGCACGACUUUGAGCGGCACGACGACGAUGAGUUGGGAUUUCGGCGGAACGACAUCAUAACAAUCAUCAGUCAAAAAGAC
.....(((.((((((.(((....))).(((((....)))))......))))..)).)))....((((((((((((.(((.(((......))).))).))))..))))).)))........ ( -38.80)
>DroSec_CAF1 9622 120 + 1
AUCAAUGUGGCAAGGACGCGAAAGCGAAGGGCUAAAGCCUUGCACGACUUUGAGCGGCACGACGACGAUGAGUUGGGAUUUCGACGGAACGACAUCAUUACAAUCAUCAGUCAAAAAGAC
.....(((.((((((.(((....))).(((((....)))))......))))..)).)))....((((((((.(((.(((.(((......))).)))....)))))))).)))........ ( -34.30)
>DroSim_CAF1 9640 120 + 1
AUCAAUGUGGCAAGGACGCGAAAGCGUAGGGCUAAAGCCUUGCACGACUUUGAGCGGCACGACGAUGAUGAGUUGGGAUUUCGGCGGAACGACAUCAUUACAAUCAUCAGUCAAAAAGAC
.....(((.((((((..((....))(((((((....)))))))....))))..)).))).(((((((((..((...(((.(((......))).)))...)).)))))).)))........ ( -40.00)
>consensus
AUCAAUGUGGCAAGGACGCGAAAGCGAAGGGCUAAAGCCUUGCACGACUUUGAGCGGCACGACGACGAUGAGUUGGGAUUUCGGCGGAACGACAUCAUUACAAUCAUCAGUCAAAAAGAC
.....(((.((((((.(((....))).(((((....)))))......))))..)).))).(((...(((((.(((.(((.(((......))).)))....)))))))).)))........ (-35.89 = -35.67 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:59 2006