Locus 6161

Sequence ID	X_DroMel_CAF1
Location	15,724,767 – 15,724,967
Length	200
Max. P	0.993868

overview

Window 5

Location	15,724,767 – 15,724,887
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.00
Mean single sequence MFE	-43.09
Consensus MFE	-35.95
Energy contribution	-36.35
Covariance contribution	0.40
Combinations/Pair	1.21
Mean z-score	-2.39
Structure conservation index	0.83
SVM decision value	2.43
SVM RNA-class probability	0.993868
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15724767 120 - 22224390
AUUGUUGUGGCUGCAAGUUGUCUUCGAGUGUGGGGUUCCAAACUUUAAGGCGUGCAGCGACUUUUGAUUGCCUGAUGUUCCUGCAUCGGGCGAUGGAUACCAAUGGCUUUUGCUGCCUUU
((((..((.((((((...((((((.((((.(((....))).)))).)))))))))))).))..((.((((((((((((....)))))))))))).))...))))(((.......)))... ( -48.80)
>DroSec_CAF1 8198 120 - 1
AUUGUUGUGGCUGGCAGUUGUCUUCGAGUGUGGGGUUCCAAACUUCAAGGCGUGCAUCGACUUCUGAUUGCCUGAUGUUCCUGCAUCGGGCGAUGGAUACCAAUGGCUUUUGCUGCCUUU
............((((((.(((((.((((.(((....))).)))).)))))..((.......(((.((((((((((((....)))))))))))))))........))....))))))... ( -42.96)
>DroSim_CAF1 8151 120 - 1
AUUGUUGUGGCUGGCAGUUGUCUUCGAGUGUGGGGUUCCAAACUUCAAGGCGUGCAUCGACUUCUGAUUGCCUGAUGUUCCUGCAUCGGGCGAUGGAUACCAAUGGUUUUUGCUGCCUUU
............((((((.(((((.((((.(((....))).)))).)))))...(((.(...(((.((((((((((((....)))))))))))))))...).)))......))))))... ( -42.30)
>DroEre_CAF1 8859 120 - 1
AUUGUUAUGGUUUGCAGUAGUGUUCGAGUGUGGUUUUCCAAAUUUCAGGGCGUGCAGUGACUUUUGAUUGCCUGAUGUACCUGCAUCGGGCGAUGGGUACCAAUGGUUUUUGCUGCCUUU
(((((........))))).......(((..(((....)))...)))((((((.((((.((((.(((((((((((((((....))))))))))))......))).)))).)))))))))). ( -38.80)
>DroYak_CAF1 7807 120 - 1
AUUGUUGUGACUCGCAGUUGUCUUCAAGUGUGGGGUCCCAAAUUUCAAGGCGUGCAGUGACUUUUGAUUGCCGGAUGCGCCAGCGUCGGGCGAUGGAUACCAAUGGCUUUUGCUGCCCUU
...((((.(.((((((.(((....))).))))))((((((((..(((..(....)..)))..))))((((((.(((((....))))).)))))))))).)))))(((.......)))... ( -42.60)
>consensus
AUUGUUGUGGCUGGCAGUUGUCUUCGAGUGUGGGGUUCCAAACUUCAAGGCGUGCAGCGACUUUUGAUUGCCUGAUGUUCCUGCAUCGGGCGAUGGAUACCAAUGGCUUUUGCUGCCUUU
............((((((.(((((.((((.(((....))).)))).)))))..((........((.((((((((((((....)))))))))))).))........))....))))))... (-35.95 = -36.35 +   0.40)

alignment

secondary structure

dotplot

Window 6

Location	15,724,847 – 15,724,967
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.75
Mean single sequence MFE	-30.70
Consensus MFE	-28.06
Energy contribution	-27.50
Covariance contribution	-0.56
Combinations/Pair	1.16
Mean z-score	-1.11
Structure conservation index	0.91
SVM decision value	0.04
SVM RNA-class probability	0.553246
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15724847 120 + 22224390
UGGAACCCCACACUCGAAGACAACUUGCAGCCACAACAAUCGACGCAUGUCUGUUCUGAACAAGUUGUUCAUGACGAACAUCACUGAUAUUCUGGCCACCGGCGCAGUUGCCGAUUCCAU
(((((........................((((.....((((..(.((((.((((.(((((.....))))).)))).)))))..))))....))))...(((((....))))).))))). ( -28.50)
>DroSec_CAF1 8278 120 + 1
UGGAACCCCACACUCGAAGACAACUGCCAGCCACAACAAUCGACGCAUGUCUGUUCUGAACAAGUUGUUCAUGACGAACAUCACUGAUAUUCUGGCCACCGGCGCAGUUGCCGAUUCCAU
(((((........(((..(.((((((((.((((.....((((..(.((((.((((.(((((.....))))).)))).)))))..))))....)))).....).)))))))))))))))). ( -30.60)
>DroSim_CAF1 8231 120 + 1
UGGAACCCCACACUCGAAGACAACUGCCAGCCACAACAAUCGACGCAUGUCUGUUCUGAACAAGUUGUUCAUGACGAACAUCACUGAUAUUCUGGCCACCGGCGCAGUUGCCGAUUCCAU
(((((........(((..(.((((((((.((((.....((((..(.((((.((((.(((((.....))))).)))).)))))..))))....)))).....).)))))))))))))))). ( -30.60)
>DroEre_CAF1 8939 120 + 1
UGGAAAACCACACUCGAACACUACUGCAAACCAUAACAAUCGACGCAUGUCCGUGCUGAACAAGUUGUUCAUGACGAACAUCACCGAUAUUCUGGCCACCGGCGCAGUUGCCGAUUCCAU
(((((........(((......(((((...........((((..(.((((.(((..(((((.....)))))..))).)))))..))))......(((...))))))))...)))))))). ( -28.10)
>DroYak_CAF1 7887 120 + 1
UGGGACCCCACACUUGAAGACAACUGCGAGUCACAACAAUCGACGCAUGUCCGUUCUGAACAAGUUGUUCAUGACGAACAUCACCGAUAUUCUGGCCACCGGCGCAGUGGCCGAUUCUAU
(((....))).................(((((......((((..(.((((.((((.(((((.....))))).)))).)))))..)))).....((((((.......)))))))))))... ( -35.70)
>consensus
UGGAACCCCACACUCGAAGACAACUGCCAGCCACAACAAUCGACGCAUGUCUGUUCUGAACAAGUUGUUCAUGACGAACAUCACUGAUAUUCUGGCCACCGGCGCAGUUGCCGAUUCCAU
(((((........................((((.....((((..(.((((.((((.(((((.....))))).)))).)))))..))))....))))...((((......)))).))))). (-28.06 = -27.50 +  -0.56)

alignment

secondary structure

dotplot

Window 7

Location	15,724,847 – 15,724,967
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.75
Mean single sequence MFE	-44.44
Consensus MFE	-34.96
Energy contribution	-37.04
Covariance contribution	2.08
Combinations/Pair	1.05
Mean z-score	-2.36
Structure conservation index	0.79
SVM decision value	1.41
SVM RNA-class probability	0.951463
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15724847 120 - 22224390
AUGGAAUCGGCAACUGCGCCGGUGGCCAGAAUAUCAGUGAUGUUCGUCAUGAACAACUUGUUCAGAACAGACAUGCGUCGAUUGUUGUGGCUGCAAGUUGUCUUCGAGUGUGGGGUUCCA
.((((((((((((((......(..((((.((((((..((((((..((..(((((.....)))))..))..)))).))..)).)))).))))..).))))))).(((....)))))))))) ( -43.50)
>DroSec_CAF1 8278 120 - 1
AUGGAAUCGGCAACUGCGCCGGUGGCCAGAAUAUCAGUGAUGUUCGUCAUGAACAACUUGUUCAGAACAGACAUGCGUCGAUUGUUGUGGCUGGCAGUUGUCUUCGAGUGUGGGGUUCCA
.((((((((((((((((.(....(((((.((((((..((((((..((..(((((.....)))))..))..)))).))..)).)))).))))))))))))))).(((....)))))))))) ( -45.30)
>DroSim_CAF1 8231 120 - 1
AUGGAAUCGGCAACUGCGCCGGUGGCCAGAAUAUCAGUGAUGUUCGUCAUGAACAACUUGUUCAGAACAGACAUGCGUCGAUUGUUGUGGCUGGCAGUUGUCUUCGAGUGUGGGGUUCCA
.((((((((((((((((.(....(((((.((((((..((((((..((..(((((.....)))))..))..)))).))..)).)))).))))))))))))))).(((....)))))))))) ( -45.30)
>DroEre_CAF1 8939 120 - 1
AUGGAAUCGGCAACUGCGCCGGUGGCCAGAAUAUCGGUGAUGUUCGUCAUGAACAACUUGUUCAGCACGGACAUGCGUCGAUUGUUAUGGUUUGCAGUAGUGUUCGAGUGUGGUUUUCCA
.(((((.(.(((...((((..(..((((.(((((((..(((((((((..(((((.....)))))..)))))))).)..))).)))).))).)..)....)))).....))).)..))))) ( -40.50)
>DroYak_CAF1 7887 120 - 1
AUAGAAUCGGCCACUGCGCCGGUGGCCAGAAUAUCGGUGAUGUUCGUCAUGAACAACUUGUUCAGAACGGACAUGCGUCGAUUGUUGUGACUCGCAGUUGUCUUCAAGUGUGGGGUCCCA
........((((((((...))))))))(.(((((((..(((((((((..(((((.....)))))..)))))))).)..))).)))).)..((((((.(((....))).))))))...... ( -47.60)
>consensus
AUGGAAUCGGCAACUGCGCCGGUGGCCAGAAUAUCAGUGAUGUUCGUCAUGAACAACUUGUUCAGAACAGACAUGCGUCGAUUGUUGUGGCUGGCAGUUGUCUUCGAGUGUGGGGUUCCA
.((((((((((((((((.....((((((.((((....((((((..(((.(((((.....))))).....)))..))))))..)))).))))))))))))))).(((....)))))))))) (-34.96 = -37.04 +   2.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:04 2006