Locus 8462

Sequence ID	3L_DroMel_CAF1
Location	22,268,446 – 22,268,644
Length	198
Max. P	0.974677

overview

Window 4

Location	22,268,446 – 22,268,564
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.38
Mean single sequence MFE	-41.42
Consensus MFE	-37.81
Energy contribution	-37.75
Covariance contribution	-0.06
Combinations/Pair	1.08
Mean z-score	-2.59
Structure conservation index	0.91
SVM decision value	1.73
SVM RNA-class probability	0.974677
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22268446 118 - 23771897
CACGUCACUUCGGUGGCAUGCAACGAGCGAGUUGUAGCAGCGCUUGUUGCAACUUUAUUUACCUUUACGUAUGACAUAACUUGUGAAUAGAGAUACAAACGGGGCUUGCACGUAU--GUG
...(((((....))))).(((((((((((.((....))..))))))))))).((((((((((..(((.(.....).)))...)))))))))).((((.(((..(....).))).)--))) ( -39.00)
>DroSec_CAF1 26748 118 - 1
CACGUCACUUCGGUGGCAUGCAACGAGCGAGUUGCAGCAGCGCUUGUUGCAACUUUAUUUACCUUUACGUGGGACAUAACUUGUAAAUAGAGAUACAAACGGGGGUUGCACGUGU--GUG
((((((((....))))).((((((......))))))(((((.((((((....((((((((.(((......)))(((.....))))))))))).....)))))).)))))..))).--... ( -43.10)
>DroSim_CAF1 17149 118 - 1
CACGUCACUUCGGUGGCAUGCAACGAGCGAGUUGCAGCAGCGCUUGUUGCAACUUUAUUUACCUUUACGUGGGACAUAACUUGUAAAUAGAGAUACAAACGGGGGUUGCACGUGU--GUG
((((((((....))))).((((((......))))))(((((.((((((....((((((((.(((......)))(((.....))))))))))).....)))))).)))))..))).--... ( -43.10)
>DroEre_CAF1 25701 120 - 1
CACGUCACUUCGGUGGCAUGCAACGAGCGAGUUACAGCAGCGUUUGUUGCAACUUUAUUUACCUUUAGGUGGGACAUAACUUGUAAAUAGAGAUACAAACGGGGGUUGCACGUGUGUGUG
...(((((....))))).(((((((((((.((....))..))))))))))).((((((((((....((((........))))))))))))))(((((.(((.........))).))))). ( -40.50)
>consensus
CACGUCACUUCGGUGGCAUGCAACGAGCGAGUUGCAGCAGCGCUUGUUGCAACUUUAUUUACCUUUACGUGGGACAUAACUUGUAAAUAGAGAUACAAACGGGGGUUGCACGUGU__GUG
((((((((....))))).((((((......))))))(((((.((((((....((((((((((..(((.(.....).)))...)))))))))).....)))))).)))))........))) (-37.81 = -37.75 +  -0.06)

alignment

secondary structure

dotplot

Window 5

Location	22,268,484 – 22,268,604
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.25
Mean single sequence MFE	-41.73
Consensus MFE	-38.06
Energy contribution	-38.25
Covariance contribution	0.19
Combinations/Pair	1.09
Mean z-score	-1.62
Structure conservation index	0.91
SVM decision value	0.20
SVM RNA-class probability	0.630370
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22268484 120 - 23771897
ACGGCAAACCACAAGCGCGCUUUGAGCAAAGGAGGGAGUGCACGUCACUUCGGUGGCAUGCAACGAGCGAGUUGUAGCAGCGCUUGUUGCAACUUUAUUUACCUUUACGUAUGACAUAAC
..((....)).((.(((.((.....))(((((..(((((....(((((....))))).(((((((((((.((....))..)))))))))))))))).....))))).))).))....... ( -38.70)
>DroSec_CAF1 26786 120 - 1
ACGGCAAACCACAAGCGCGCUUUGAGCGAAGGAGGGAGUGCACGUCACUUCGGUGGCAUGCAACGAGCGAGUUGCAGCAGCGCUUGUUGCAACUUUAUUUACCUUUACGUGGGACAUAAC
........((((..(.(((((((...(....)..))))))).)(((((....))))).(((((((((((.((....))..))))))))))).................))))........ ( -43.30)
>DroSim_CAF1 17187 120 - 1
ACGGCAAACCACAAGCGCGCUUUGAGCGAAGCAGGGAGUGCACGUCACUUCGGUGGCAUGCAACGAGCGAGUUGCAGCAGCGCUUGUUGCAACUUUAUUUACCUUUACGUGGGACAUAAC
...(((....(((((((((((((....)))))......(((..(((((....))))).((((((......))))))))))))))))))))...........(((......)))....... ( -45.00)
>DroEre_CAF1 25741 120 - 1
ACGGCAAACCACAAGCGCGCUUUGAGCGGAGGAGGGAGUGCACGUCACUUCGGUGGCAUGCAACGAGCGAGUUACAGCAGCGUUUGUUGCAACUUUAUUUACCUUUAGGUGGGACAUAAC
........((((...(((.......)))((((..(((((....(((((....))))).(((((((((((.((....))..)))))))))))))))).....))))...))))........ ( -39.90)
>consensus
ACGGCAAACCACAAGCGCGCUUUGAGCGAAGGAGGGAGUGCACGUCACUUCGGUGGCAUGCAACGAGCGAGUUGCAGCAGCGCUUGUUGCAACUUUAUUUACCUUUACGUGGGACAUAAC
........((((....((.......))(((((..(((((....(((((....))))).(((((((((((.((....))..)))))))))))))))).....)))))..))))........ (-38.06 = -38.25 +   0.19)

alignment

secondary structure

dotplot

Window 6

Location	22,268,524 – 22,268,644
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	97.92
Mean single sequence MFE	-38.35
Consensus MFE	-35.96
Energy contribution	-36.02
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-1.69
Structure conservation index	0.94
SVM decision value	0.11
SVM RNA-class probability	0.590675
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22268524 120 - 23771897
GAAAAUUCAUUUCAAUUAGUGAAAUGGUUUUGGGAUUUGUACGGCAAACCACAAGCGCGCUUUGAGCAAAGGAGGGAGUGCACGUCACUUCGGUGGCAUGCAACGAGCGAGUUGUAGCAG
......((((((((.....))))))))..(((((.((((.....)))))).)))(((((((((...(....)..)))))))..(((((....))))).((((((......)))))))).. ( -36.10)
>DroSec_CAF1 26826 120 - 1
GAAAAUUCAUUUCAAUUAGUGAAAUGGUUUUGGGAUUUGUACGGCAAACCACAAGCGCGCUUUGAGCGAAGGAGGGAGUGCACGUCACUUCGGUGGCAUGCAACGAGCGAGUUGCAGCAG
......((((((((.....))))))))..(((((.((((.....)))))).)))(((((((((...(....)..)))))))..(((((....))))).((((((......)))))))).. ( -40.80)
>DroSim_CAF1 17227 120 - 1
GAAAAUUCAUUUCAAUUAGUGAAAUGGUUUUGGGAUUUGUACGGCAAACCACAAGCGCGCUUUGAGCGAAGCAGGGAGUGCACGUCACUUCGGUGGCAUGCAACGAGCGAGUUGCAGCAG
......((((((((.....))))))))..(((((.((((.....)))))).)))(((((((((..((...))..)))))))..(((((....))))).((((((......)))))))).. ( -40.50)
>DroEre_CAF1 25781 120 - 1
GAAAAUUCAUUUCAAUUAGUGAAAUGGUUUUGGGAUUUGUACGGCAAACCACAAGCGCGCUUUGAGCGGAGGAGGGAGUGCACGUCACUUCGGUGGCAUGCAACGAGCGAGUUACAGCAG
......((((((((.....))))))))..(((..((((((.((.....((.(...(.(((.....))))..).))...((((.(((((....))))).)))).)).))))))..)))... ( -36.00)
>consensus
GAAAAUUCAUUUCAAUUAGUGAAAUGGUUUUGGGAUUUGUACGGCAAACCACAAGCGCGCUUUGAGCGAAGGAGGGAGUGCACGUCACUUCGGUGGCAUGCAACGAGCGAGUUGCAGCAG
......((((((((.....))))))))..(((((.((((.....)))))).)))(((((((((...........)))))))..(((((....))))).((((((......)))))))).. (-35.96 = -36.02 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:15:59 2006