Locus 1276

Sequence ID	2R_DroMel_CAF1
Location	5,008,710 – 5,008,800
Length	90
Max. P	0.981108

overview

Window 1

Location	5,008,710 – 5,008,800
Length	90
Sequences	6
Columns	90
Reading direction	forward
Mean pairwise identity	94.22
Mean single sequence MFE	-25.05
Consensus MFE	-23.25
Energy contribution	-22.95
Covariance contribution	-0.30
Combinations/Pair	1.12
Mean z-score	-1.61
Structure conservation index	0.93
SVM decision value	1.81
SVM RNA-class probability	0.978291
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5008710 90 + 20766785
UGGCCAUUCGACCACUUGGUCUCUGCCAAUUGUCCAUGACGAACGAUCCGUUUUGGCUUUUACCUGUUACAUGGCCACGGCAUGCGCACA
(((((((..((((....))))...((((((((((...)))))(((...))).))))).............)))))))..((....))... ( -24.80)
>DroPse_CAF1 63920 90 + 1
UGGCCAUUCGACCACUUGGUCUCUGCCAAUUGUCCAUGACGAACGAUCCGUUUUGGCUUUUACCUGUUACAUGGACACGGCAAACAUACA
..(((....((((....)))).........((((((((..(((((...)))))((((........)))))))))))).)))......... ( -25.50)
>DroEre_CAF1 58025 90 + 1
UGGCCAUUCGACCACUUGGUCUCUGCCAAUUGUCCAUGACGAACGAUCCGUUUUGGCUUUUACCUGUUACAUGGACGCGGCAUGCGCACA
((((.....((((....))))...))))...(((((((..(((((...)))))((((........)))))))))))(((.....)))... ( -27.00)
>DroYak_CAF1 67874 90 + 1
UGGCCAUUCGACCACUUGGUCUCUGCCAAUUGUCCAUGACGAACGAUCCGUUUUGGCUUUUACCUGUUACAUGGACGCGGCAUGCGCACA
((((.....((((....))))...))))...(((((((..(((((...)))))((((........)))))))))))(((.....)))... ( -27.00)
>DroAna_CAF1 63554 90 + 1
UGGCUAUUCGACCACUUGGUCUCUGCCAAUUGCCCAUGACGAACGAUCCGUUUUGGCUUUUACCUGUUACAUGGACACAGUGCCCAUACA
((((.....((((....))))...))))...(((...((((.......))))..))).............((((.(.....).))))... ( -20.50)
>DroPer_CAF1 64105 90 + 1
UGGCCAUUCGACCACUUGGUCUCUGCCAAUUGUCCAUGACGAACGAUCCGUUUUGGCUUUUACCUGUUACAUGGACACGGCAAACAUACA
..(((....((((....)))).........((((((((..(((((...)))))((((........)))))))))))).)))......... ( -25.50)
>consensus
UGGCCAUUCGACCACUUGGUCUCUGCCAAUUGUCCAUGACGAACGAUCCGUUUUGGCUUUUACCUGUUACAUGGACACGGCAUGCACACA
..(((....((((....)))).........((((((((..(((((...)))))((((........)))))))))))).)))......... (-23.25 = -22.95 +  -0.30)

alignment

secondary structure

dotplot

Window 2

Location	5,008,710 – 5,008,800
Length	90
Sequences	6
Columns	90
Reading direction	reverse
Mean pairwise identity	94.22
Mean single sequence MFE	-29.08
Consensus MFE	-26.02
Energy contribution	-25.22
Covariance contribution	-0.80
Combinations/Pair	1.19
Mean z-score	-1.99
Structure conservation index	0.89
SVM decision value	1.88
SVM RNA-class probability	0.981108
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5008710 90 - 20766785
UGUGCGCAUGCCGUGGCCAUGUAACAGGUAAAAGCCAAAACGGAUCGUUCGUCAUGGACAAUUGGCAGAGACCAAGUGGUCGAAUGGCCA
(((..((((((....).))))).)))(((....))).....((.((((((((((........))))...((((....)))))))))))). ( -28.40)
>DroPse_CAF1 63920 90 - 1
UGUAUGUUUGCCGUGUCCAUGUAACAGGUAAAAGCCAAAACGGAUCGUUCGUCAUGGACAAUUGGCAGAGACCAAGUGGUCGAAUGGCCA
......((((((.((((((((.....(((....)))...(((((...)))))))))))))...))))))((((....))))......... ( -30.00)
>DroEre_CAF1 58025 90 - 1
UGUGCGCAUGCCGCGUCCAUGUAACAGGUAAAAGCCAAAACGGAUCGUUCGUCAUGGACAAUUGGCAGAGACCAAGUGGUCGAAUGGCCA
...(((.....)))(((((((.....(((....)))...(((((...))))))))))))...((((...((((....)))).....)))) ( -29.10)
>DroYak_CAF1 67874 90 - 1
UGUGCGCAUGCCGCGUCCAUGUAACAGGUAAAAGCCAAAACGGAUCGUUCGUCAUGGACAAUUGGCAGAGACCAAGUGGUCGAAUGGCCA
...(((.....)))(((((((.....(((....)))...(((((...))))))))))))...((((...((((....)))).....)))) ( -29.10)
>DroAna_CAF1 63554 90 - 1
UGUAUGGGCACUGUGUCCAUGUAACAGGUAAAAGCCAAAACGGAUCGUUCGUCAUGGGCAAUUGGCAGAGACCAAGUGGUCGAAUAGCCA
......(((.(((((((((((.....(((....)))...(((((...)))))))))))).....)))).((((....)))).....))). ( -27.90)
>DroPer_CAF1 64105 90 - 1
UGUAUGUUUGCCGUGUCCAUGUAACAGGUAAAAGCCAAAACGGAUCGUUCGUCAUGGACAAUUGGCAGAGACCAAGUGGUCGAAUGGCCA
......((((((.((((((((.....(((....)))...(((((...)))))))))))))...))))))((((....))))......... ( -30.00)
>consensus
UGUACGCAUGCCGUGUCCAUGUAACAGGUAAAAGCCAAAACGGAUCGUUCGUCAUGGACAAUUGGCAGAGACCAAGUGGUCGAAUGGCCA
...(((.....)))(((((((.....(((....)))...(((((...))))))))))))...((((...((((....)))).....)))) (-26.02 = -25.22 +  -0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:45 2006