Locus 1183

Sequence ID	2L_DroMel_CAF1
Location	3,224,132 – 3,224,225
Length	93
Max. P	0.987473

overview

Window 9

Location	3,224,132 – 3,224,225
Length	93
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	69.88
Mean single sequence MFE	-31.84
Consensus MFE	-15.36
Energy contribution	-15.25
Covariance contribution	-0.11
Combinations/Pair	1.32
Mean z-score	-1.86
Structure conservation index	0.48
SVM decision value	1.03
SVM RNA-class probability	0.902897
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3224132 93 + 22407834
CCUGGGUGGCUGGGUG--UUGGACCCUCGGUUAUUAUGCUGAUUGUGUUGACACACUCGCCAUCCCAAGUAUGUCCACAUAU--ACC----------------GAUAUAG-------UAU
..((((((((.(((((--(..(((..(((((......)))))..)).)..)))).)).)))).)))).(((((....)))))--...----------------.......-------... ( -30.60)
>DroSec_CAF1 58173 99 + 1
CCUGGGUGGCUGGGUG--UUGGACCCUCGGUUAUUAUGCUGAUUGUGUUGACACACUCGCCAUCCCAAGUAUGCCCACAUAU--AGC-------------AUGGCUAUGGGU----AUAU
..((((((((.(((((--(..(((..(((((......)))))..)).)..)))).)).)))).)))).(((((((((....(--(((-------------...)))))))))----)))) ( -40.20)
>DroSim_CAF1 56677 92 + 1
CCUGGGUGGCUGGGUG--UUGGACCCUCGGUUAUUAUGCUGAUUGUGUUGACACACUCGCCAUUCCAAGUAUGUCCAC----------------------AUGGCUAUGGGU----AUAU
..((((((((.(((((--(..(((..(((((......)))))..)).)..)))).)).)))).)))).((((..(((.----------------------.......)))..----)))) ( -31.00)
>DroEre_CAF1 54765 117 + 1
CCAGGGUGGCUGGGUG--UUGGACCCUCAGUUAUUAUGCUGAUUGUGUUGACACACUCGCCCUCCCAAGUUUGUCCAGAUAUACAGCCAGCAUAUAUAGCAUAG-UAUAGGUACAUGUAU
....(.((((((..((--((((((..(((((......))))).((((....)))).................))))).)))..)))))).).......((((.(-((....))))))).. ( -32.50)
>DroYak_CAF1 53515 104 + 1
CCUGGGCGGCUGGGUG--UUGGACCCUCAGUUAUUAUGCUGAUUGUGUUGACACACUCGGCCACCCAACUUUGCCCACAAAU--AGCC-------AUAGUAUAG-UAU----ACUUGUAU
..((((.(((((((((--((.((((.(((((......)))))..).))).).)))))))))).))))(((.(((........--....-------...))).))-)..----........ ( -32.66)
>DroPer_CAF1 68205 94 + 1
CUUGGAGGUCACGGCCAUAUGUACUCUAGGUUAUUAUGCUGAUUGUGUUGACACACUGUGCGUCUGUUGUUUGUACUU----------------------UCGGUGCUGACC----UUAG
....(((((((((((...((((((.....((((..((((.....)))))))).....))))))..)))))..((((..----------------------...)))).))))----)).. ( -24.10)
>consensus
CCUGGGUGGCUGGGUG__UUGGACCCUCGGUUAUUAUGCUGAUUGUGUUGACACACUCGCCAUCCCAAGUAUGUCCACAUAU__AGC_____________AUGG_UAUGGGU____AUAU
...(((.(((.(((((....(.((..(((((......)))))..)).).....)))))))).)))....................................................... (-15.36 = -15.25 +  -0.11)

alignment

secondary structure

dotplot

Window 0

Location	3,224,132 – 3,224,225
Length	93
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	69.88
Mean single sequence MFE	-29.42
Consensus MFE	-13.96
Energy contribution	-14.35
Covariance contribution	0.39
Combinations/Pair	1.25
Mean z-score	-2.30
Structure conservation index	0.47
SVM decision value	2.08
SVM RNA-class probability	0.987473
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3224132 93 - 22407834
AUA-------CUAUAUC----------------GGU--AUAUGUGGACAUACUUGGGAUGGCGAGUGUGUCAACACAAUCAGCAUAAUAACCGAGGGUCCAA--CACCCAGCCACCCAGG
...-------((((((.----------------...--..)))))).....((((((.((((((.((((....)))).))..............((((....--.)))).)))))))))) ( -29.80)
>DroSec_CAF1 58173 99 - 1
AUAU----ACCCAUAGCCAU-------------GCU--AUAUGUGGGCAUACUUGGGAUGGCGAGUGUGUCAACACAAUCAGCAUAAUAACCGAGGGUCCAA--CACCCAGCCACCCAGG
.(((----.((((((.....-------------...--...)))))).)))((((((.((((((.((((....)))).))..............((((....--.)))).)))))))))) ( -34.20)
>DroSim_CAF1 56677 92 - 1
AUAU----ACCCAUAGCCAU----------------------GUGGACAUACUUGGAAUGGCGAGUGUGUCAACACAAUCAGCAUAAUAACCGAGGGUCCAA--CACCCAGCCACCCAGG
....----..(((((....)----------------------)))).....(((((..((((((.((((....)))).))..............((((....--.)))).)))).))))) ( -26.90)
>DroEre_CAF1 54765 117 - 1
AUACAUGUACCUAUA-CUAUGCUAUAUAUGCUGGCUGUAUAUCUGGACAAACUUGGGAGGGCGAGUGUGUCAACACAAUCAGCAUAAUAACUGAGGGUCCAA--CACCCAGCCACCCUGG
.....(((.((((((-(...((((.......)))).)))))...)))))...(..((..(((..((((....))))..((((........))))((((....--.)))).)))..))..) ( -31.70)
>DroYak_CAF1 53515 104 - 1
AUACAAGU----AUA-CUAUACUAU-------GGCU--AUUUGUGGGCAAAGUUGGGUGGCCGAGUGUGUCAACACAAUCAGCAUAAUAACUGAGGGUCCAA--CACCCAGCCGCCCAGG
..((((((----(..-(........-------)..)--))))))((((...(((((((((((..((((....))))..((((........)))).)))....--)))))))).))))... ( -35.30)
>DroPer_CAF1 68205 94 - 1
CUAA----GGUCAGCACCGA----------------------AAGUACAAACAACAGACGCACAGUGUGUCAACACAAUCAGCAUAAUAACCUAGAGUACAUAUGGCCGUGACCUCCAAG
...(----(((((...(((.----------------------..((((........(((((.....))))).......((((.........)).))))))...)))...))))))..... ( -18.60)
>consensus
AUAC____ACCCAUA_CCAU_____________GCU__AUAUGUGGACAAACUUGGGAUGGCGAGUGUGUCAACACAAUCAGCAUAAUAACCGAGGGUCCAA__CACCCAGCCACCCAGG
...........................................(((((...(((((....((...((((....))))....)).......))))).)))))................... (-13.96 = -14.35 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:43 2006