Locus 5722

Sequence ID	2L_DroMel_CAF1
Location	16,280,962 – 16,281,072
Length	110
Max. P	0.998838

overview

Window 3

Location	16,280,962 – 16,281,072
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	94.27
Mean single sequence MFE	-27.32
Consensus MFE	-22.81
Energy contribution	-23.01
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-3.14
Structure conservation index	0.83
SVM decision value	3.25
SVM RNA-class probability	0.998838
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16280962 110 + 22407834
CACGCUCUUUUAUUUUAGCACCAACAACAAACAGACAGCAGCUGCUAAAACGCAGUUGUUAUACCGUCCACACUGGUGGCAAAAAUAACCGUGCCACCUUCGAAGUUUUA
...(((..........))).........((((.((((((((((((......))))))))).....)))......(((((((..........)))))))......)))).. ( -26.60)
>DroSec_CAF1 25245 110 + 1
CACGCUCUUUUAUUUUAGCACCAACAACAAACAGACAGCAGCUGCUAAAACGCAGUUGUUAUACCGUCCACACUGGUGGCAAAAAUAACCGUGCCACCUUCGAAGUUUUA
...(((..........))).........((((.((((((((((((......))))))))).....)))......(((((((..........)))))))......)))).. ( -26.60)
>DroSim_CAF1 20972 110 + 1
CACGCUCUUUUAUUUUAGCACCAACAACAAACAGACAGCAGCUGCUAAAACGCAGUUGUUAUACCGUCCACACUAGUGGCAAAAAUAACCGUGCCACCUUCGAAGUUUAA
...(((..........))).........((((.((((((((((((......))))))))).....))).......((((((..........)))))).......)))).. ( -23.70)
>DroEre_CAF1 21325 110 + 1
CACGCUCUUUUAUUUUAGCACCAACAACAAACGGACAGCAGCUGCUAAAACGCAGUUGUUAUACCGCCCACACUGGUGGCAAAAAUAACAGUGCCACCUUUGAAUUUUUA
...((.((.(((((((.((((((........(((..(((((((((......)))))))))...))).......)))).)).))))))).)).))................ ( -29.86)
>DroYak_CAF1 26374 106 + 1
CACGCUCUUUUAUUUUAGCACCAACAACAAACGGACAGCAGCUGCUAAAACGCAGUUGUUAUACCGCCCACACUGGUGGCAAAAAUAACAGUGCCAAAUUU----UAUUA
...((.((.(((((((.((((((........(((..(((((((((......)))))))))...))).......)))).)).))))))).)).)).......----..... ( -29.86)
>consensus
CACGCUCUUUUAUUUUAGCACCAACAACAAACAGACAGCAGCUGCUAAAACGCAGUUGUUAUACCGUCCACACUGGUGGCAAAAAUAACCGUGCCACCUUCGAAGUUUUA
...((.(..(((((((.((((((.............(((((((((......))))))))).............)))).)).)))))))..).))................ (-22.81 = -23.01 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	16,280,962 – 16,281,072
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	94.27
Mean single sequence MFE	-31.20
Consensus MFE	-30.88
Energy contribution	-30.24
Covariance contribution	-0.64
Combinations/Pair	1.10
Mean z-score	-1.40
Structure conservation index	0.99
SVM decision value	1.70
SVM RNA-class probability	0.972606
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16280962 110 - 22407834
UAAAACUUCGAAGGUGGCACGGUUAUUUUUGCCACCAGUGUGGACGGUAUAACAACUGCGUUUUAGCAGCUGCUGUCUGUUUGUUGUUGGUGCUAAAAUAAAAGAGCGUG
................((.(..(((((((.((.((((..(..(((((.(((.((.((((......)))).)).))))))))..)...)))))).)))))))..).))... ( -30.90)
>DroSec_CAF1 25245 110 - 1
UAAAACUUCGAAGGUGGCACGGUUAUUUUUGCCACCAGUGUGGACGGUAUAACAACUGCGUUUUAGCAGCUGCUGUCUGUUUGUUGUUGGUGCUAAAAUAAAAGAGCGUG
................((.(..(((((((.((.((((..(..(((((.(((.((.((((......)))).)).))))))))..)...)))))).)))))))..).))... ( -30.90)
>DroSim_CAF1 20972 110 - 1
UUAAACUUCGAAGGUGGCACGGUUAUUUUUGCCACUAGUGUGGACGGUAUAACAACUGCGUUUUAGCAGCUGCUGUCUGUUUGUUGUUGGUGCUAAAAUAAAAGAGCGUG
................((.(..(((((((.((.((((..(..(((((.(((.((.((((......)))).)).))))))))..)...)))))).)))))))..).))... ( -28.60)
>DroEre_CAF1 21325 110 - 1
UAAAAAUUCAAAGGUGGCACUGUUAUUUUUGCCACCAGUGUGGGCGGUAUAACAACUGCGUUUUAGCAGCUGCUGUCCGUUUGUUGUUGGUGCUAAAAUAAAAGAGCGUG
................((.((.(((((((.((.((((..(..(((((.(((.((.((((......)))).)).))))))))..)...)))))).))))))).)).))... ( -32.80)
>DroYak_CAF1 26374 106 - 1
UAAUA----AAAUUUGGCACUGUUAUUUUUGCCACCAGUGUGGGCGGUAUAACAACUGCGUUUUAGCAGCUGCUGUCCGUUUGUUGUUGGUGCUAAAAUAAAAGAGCGUG
.....----.......((.((.(((((((.((.((((..(..(((((.(((.((.((((......)))).)).))))))))..)...)))))).))))))).)).))... ( -32.80)
>consensus
UAAAACUUCGAAGGUGGCACGGUUAUUUUUGCCACCAGUGUGGACGGUAUAACAACUGCGUUUUAGCAGCUGCUGUCUGUUUGUUGUUGGUGCUAAAAUAAAAGAGCGUG
................((.(..(((((((.((.((((..(..(((((.(((.((.((((......)))).)).))))))))..)...)))))).)))))))..).))... (-30.88 = -30.24 +  -0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:03 2006