Locus 8241

Sequence ID	3L_DroMel_CAF1
Location	21,651,888 – 21,652,058
Length	170
Max. P	0.655809

overview

Window 5

Location	21,651,888 – 21,651,984
Length	96
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	81.21
Mean single sequence MFE	-24.12
Consensus MFE	-17.25
Energy contribution	-17.53
Covariance contribution	0.28
Combinations/Pair	1.16
Mean z-score	-1.17
Structure conservation index	0.72
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21651888 96 - 23771897
GAGCCAAGU----UCUUCUCCCACUCCCACCAAGUGGGCGUUGCUUUCGAUUAUUAUCGAUUAUUCAGCAGGCCCGGCAACCAUAAAUCUGUGCACC----CCA----------
(.(((....----......((((((.......)))))).((((...(((((....))))).....)))).))).)((....((((....))))....----)).---------- ( -23.00)
>DroSec_CAF1 28624 100 - 1
GAGCCCUGUUCGUUCAUCUCCCACUCCCACCAAGUGGGUGUUGCUUUCGAUUAUUAUCGAUUAUUCAGCAGGCCCGGCAACCAUAAAUCAGUGCACC----CCA----------
(.(((..............((((((.......))))))(((((...(((((....))))).....)))))))).)((....(((......)))....----)).---------- ( -22.10)
>DroSim_CAF1 33059 100 - 1
GAGCCCUGUUCGUUCAUCUCCCACUCCCACCAAGUGGGUGUUGCUUUCGAUUAUUAUCGAUUAUUCAGCAGGCCCGGCAACCAUAAAUCAGUGCACC----CCA----------
(.(((..............((((((.......))))))(((((...(((((....))))).....)))))))).)((....(((......)))....----)).---------- ( -22.10)
>DroEre_CAF1 27700 95 - 1
-GGCCCUGCUCGCUUAUCUCCCACUC----CAAGUGGGUGUUGCUAUCGGUUAUUAUCGAUUAUUCAGCAGUCCCGGCACCCAUGAAUCAGUACACC----CCA----------
-((..(((((.((....(.(((((..----...))))).)..)).((((((....)))))).....)))))..))......................----...---------- ( -24.40)
>DroYak_CAF1 36919 96 - 1
AGGCCCAGUUCGUUUAUCUCCCACUC----CAAGUGGGUGUUGCUAUCGAUUAUUAUCGAUUAUUCAGCAGUCCCGGCAACCAUAAAUCAGUGCCCC----CCA----------
.((..(.............(((((..----...)))))(((((..((((((....))))))....))))))..))((((............))))..----...---------- ( -23.10)
>DroAna_CAF1 25937 105 - 1
GAGGUCUGC-CGCU----UCCCCCU----CCAAGUGGGUGUUGCUAUCGAUUAUUAUCGAUUAUUCCGCGGGCCUGGCAGCCAUAAAUCAGUGCACCAAGCCCACCAUCCCCCA
..(((...(-((((----(......----..))))))(((..(..((((((....))))))..)..)))((((.(((..(((........).)).))).)))))))........ ( -30.00)
>consensus
GAGCCCUGUUCGUUCAUCUCCCACUC___CCAAGUGGGUGUUGCUAUCGAUUAUUAUCGAUUAUUCAGCAGGCCCGGCAACCAUAAAUCAGUGCACC____CCA__________
..(((..............((((((.......))))))(((((...(((((....))))).....))))).....))).................................... (-17.25 = -17.53 +   0.28)

alignment

secondary structure

dotplot

Window 6

Location	21,651,949 – 21,652,058
Length	109
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	81.92
Mean single sequence MFE	-35.46
Consensus MFE	-20.86
Energy contribution	-22.53
Covariance contribution	1.67
Combinations/Pair	1.14
Mean z-score	-2.24
Structure conservation index	0.59
SVM decision value	0.26
SVM RNA-class probability	0.655809
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21651949 109 + 23771897
GCCCACUUGGUGGGAGUGGGAGAAGA----ACUUGGCUCCGACACU---CGAGCACUGCCAUGUAUGAAAAUUAAAUUAUAAAAUGCCAUGCAAGUGGGGCGGUGGC-CAGGAGUAU
.(((((((.....)))))))......----.((((((..((.....---))..(((((((...(((((........))))).....((((....)))))))))))))-))))..... ( -36.80)
>DroSec_CAF1 28685 113 + 1
ACCCACUUGGUGGGAGUGGGAGAUGAACGAACAGGGCUCCGACACU---CGAGCACAGCCACAUAUGAAAAUUAAAUUAUAAAAUGCCAUGCAAGUGGGGCGGUGGC-CAGGAGUAU
.....(((((((((.((.((((.((......))...)))).)).))---)...(((.(((...(((((........))))).....((((....))))))).)))))-))))..... ( -33.40)
>DroSim_CAF1 33120 113 + 1
ACCCACUUGGUGGGAGUGGGAGAUGAACGAACAGGGCUCCGACACU---CGAGCACAGCCACAUAUGAAAAUUAAAUUAUAAAAUGCCAUGCAUAUGGGGCGGUGGC-CAGGAGUAU
.....(((((((((.((.((((.((......))...)))).)).))---)...(((.(((.((((((........(((....)))......)))))).))).)))))-))))..... ( -34.64)
>DroEre_CAF1 27761 108 + 1
ACCCACUUG----GAGUGGGAGAUAAGCGAGCAGGGCC-CGGCAUG---CGGGCACUGCAGCAUAUGAAAAUUAAAUUAUAAAAUGCCAUGCAAGUGGGGCGGUGGC-CAGGAGUAU
..(((((((----..((((.(.....((..((((.(((-((.....---))))).)))).)).(((((........)))))...).)))).)))))))(((....))-)........ ( -40.60)
>DroYak_CAF1 36980 112 + 1
ACCCACUUG----GAGUGGGAGAUAAACGAACUGGGCCUCGACAUUCGUCGGCCACUGCCACAUAUGAAAAUUAAAUUAUAAAAUGCCAUGCAAGUGGGGCGGUGGC-CAGGAGUAU
.(((((...----..))))).................((((((....)))((((((((((...(((((........))))).....((((....)))))))))))))-)..)))... ( -40.70)
>DroAna_CAF1 26012 103 + 1
ACCCACUUGG----AGGGGGA----AGCG-GCAGACCUCGAACAUC---UCAACACU--CGCAUAUGAAAAUUAAAUUAUAAAAUGCUUUACAAGUGGGGCGGUGGCCCAGGAAUAU
.(((((((((----((.((((----..((-(......)))....))---))....))--)((((((((........)))))...)))....))))))((((....)))).))..... ( -26.60)
>consensus
ACCCACUUGG___GAGUGGGAGAUGAACGAACAGGGCUCCGACACU___CGAGCACUGCCACAUAUGAAAAUUAAAUUAUAAAAUGCCAUGCAAGUGGGGCGGUGGC_CAGGAGUAU
.(((((((.....)))))))...............((((((........)...(((((((...(((((........))))).....((((....))))))))))).....))))).. (-20.86 = -22.53 +   1.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:15 2006