Locus 112

Sequence ID	2L_DroMel_CAF1
Location	372,626 – 372,729
Length	103
Max. P	0.969749

overview

Window 5

Location	372,626 – 372,729
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.71
Mean single sequence MFE	-13.92
Consensus MFE	-10.36
Energy contribution	-10.56
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.60
Structure conservation index	0.74
SVM decision value	0.06
SVM RNA-class probability	0.562982
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 372626 103 + 22407834
UUUAUUAAACGACCGCACCAAGCCACAAAUGGCGAAAAAUAAAUCGCUUUUCACUCUACACAAUCUUUAGCCUUCAUUCCAUCCUCCUUCCGAAAACGGAAAA-----------------
..........((..((.....((((....))))(((((.........))))).................))..))............(((((....)))))..----------------- ( -14.50)
>DroSec_CAF1 40287 103 + 1
UUUAUUAAACGACCGCACCAAGCCACAAAUGGCGAAAAAUAAAUCGCUUUUCACUCUACACAAUCUUUGCCCUCCAUUCCAUCCUCCUUCCGAAAACGGAAAA-----------------
..........((..(((....((((....))))(((((.........)))))...............)))..)).............(((((....)))))..----------------- ( -14.00)
>DroSim_CAF1 40957 103 + 1
UUUAUUAAACGACCGCACCAAGCCACAAAUGGCGAAAAAUAAAUCGCUUUUCACUCUACACAAUCUUUGCCCUCCAUUCCAUCCUCCUUCCGAAAACGGAAAA-----------------
..........((..(((....((((....))))(((((.........)))))...............)))..)).............(((((....)))))..----------------- ( -14.00)
>DroEre_CAF1 46851 103 + 1
UUUAUUAAACGACCGCACCAAGCCACAAAUGGCGAAAAAUAAAUCGCUUUUCACUCUACACAAUCUUAACUCGCCUUUCCAACCUCCUUCCGAAAUCGGAAAA-----------------
..............((.....((((....))))(((((.........)))))....................)).............(((((....)))))..----------------- ( -14.20)
>DroYak_CAF1 41483 120 + 1
UUUAUUAAACGACCGCACCAAGCCACAAAUGGCGAAAAAUAAAUCGCUUUUCACUCUACACAAUCUUAACUCGCCACUUCAUCCUCCUUCCGAAAACGAAAAAAGAAGUUGAAUGUUGCA
..............(((.((..(.((....(((((........)))))...............((((...(((....(((...........)))..)))...)))).)).)..)).))). ( -12.90)
>consensus
UUUAUUAAACGACCGCACCAAGCCACAAAUGGCGAAAAAUAAAUCGCUUUUCACUCUACACAAUCUUUACCCUCCAUUCCAUCCUCCUUCCGAAAACGGAAAA_________________
..............((.....((((....))))((........))))........................................(((((....)))))................... (-10.36 = -10.56 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	372,626 – 372,729
Length	103
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.71
Mean single sequence MFE	-27.68
Consensus MFE	-26.70
Energy contribution	-25.90
Covariance contribution	-0.80
Combinations/Pair	1.12
Mean z-score	-1.64
Structure conservation index	0.96
SVM decision value	1.65
SVM RNA-class probability	0.969749
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 372626 103 - 22407834
-----------------UUUUCCGUUUUCGGAAGGAGGAUGGAAUGAAGGCUAAAGAUUGUGUAGAGUGAAAAGCGAUUUAUUUUUCGCCAUUUGUGGCUUGGUGCGGUCGUUUAAUAAA
-----------------..((((((((((.....))))))))))...........(((((..(.((((.(...((((........))))......).)))).)..))))).......... ( -26.40)
>DroSec_CAF1 40287 103 - 1
-----------------UUUUCCGUUUUCGGAAGGAGGAUGGAAUGGAGGGCAAAGAUUGUGUAGAGUGAAAAGCGAUUUAUUUUUCGCCAUUUGUGGCUUGGUGCGGUCGUUUAAUAAA
-----------------..((((((((((.....))))))))))...........(((((..(.((((.(...((((........))))......).)))).)..))))).......... ( -26.40)
>DroSim_CAF1 40957 103 - 1
-----------------UUUUCCGUUUUCGGAAGGAGGAUGGAAUGGAGGGCAAAGAUUGUGUAGAGUGAAAAGCGAUUUAUUUUUCGCCAUUUGUGGCUUGGUGCGGUCGUUUAAUAAA
-----------------..((((((((((.....))))))))))...........(((((..(.((((.(...((((........))))......).)))).)..))))).......... ( -26.40)
>DroEre_CAF1 46851 103 - 1
-----------------UUUUCCGAUUUCGGAAGGAGGUUGGAAAGGCGAGUUAAGAUUGUGUAGAGUGAAAAGCGAUUUAUUUUUCGCCAUUUGUGGCUUGGUGCGGUCGUUUAAUAAA
-----------------((((((((((((.....)))))))))))).........(((((..(.((((.(...((((........))))......).)))).)..))))).......... ( -27.90)
>DroYak_CAF1 41483 120 - 1
UGCAACAUUCAACUUCUUUUUUCGUUUUCGGAAGGAGGAUGAAGUGGCGAGUUAAGAUUGUGUAGAGUGAAAAGCGAUUUAUUUUUCGCCAUUUGUGGCUUGGUGCGGUCGUUUAAUAAA
.((.((.((((..(((((((((((....))))))))))))))))).)).......(((((..(.((((.(...((((........))))......).)))).)..))))).......... ( -31.30)
>consensus
_________________UUUUCCGUUUUCGGAAGGAGGAUGGAAUGGAGGGUAAAGAUUGUGUAGAGUGAAAAGCGAUUUAUUUUUCGCCAUUUGUGGCUUGGUGCGGUCGUUUAAUAAA
...................((((((((((.....))))))))))...........(((((..(.((((.(...((((........))))......).)))).)..))))).......... (-26.70 = -25.90 +  -0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:26:09 2006