Locus 4303

Sequence ID	2L_DroMel_CAF1
Location	12,305,196 – 12,305,294
Length	98
Max. P	0.775730

overview

Window 5

Location	12,305,196 – 12,305,294
Length	98
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	82.92
Mean single sequence MFE	-24.83
Consensus MFE	-18.49
Energy contribution	-18.63
Covariance contribution	0.14
Combinations/Pair	1.10
Mean z-score	-2.08
Structure conservation index	0.74
SVM decision value	0.50
SVM RNA-class probability	0.759446
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12305196 98 + 22407834
UGCU------GCUGAUGCAACAUCACAUGCAUUAAACC---CGCUCAUUGCUGUCAGCGUCACUCGCUCGUGAUGCGGUUAUUUUAGCAUCCUUUUUGCA-----------UCCUUUU
((((------(.(((((((........)))))))((((---.((.....)).....(((((((......)))))))))))....)))))...........-----------....... ( -25.90)
>DroSec_CAF1 127853 104 + 1
UGCUGCUGCUGCUGAUGCAACAUCACAUGCAUUAAACC---CGCUCAUUGCUGUCAGCGUCACUCGCUCGUGAUGCGGUUAUUUUAGCAUCCUUUUUGCA-----------UCCUUUU
.((....))....(((((((......((((....((((---.((.....)).....(((((((......)))))))))))......)))).....)))))-----------))..... ( -26.70)
>DroSim_CAF1 131521 104 + 1
UGCUGCUGCUGCUGAUGCAACAUCACAUGCAUUAAACC---CGCUCAUUGCUGUCAGCGUCACUCGCUCGUGAUGCGGUUAUUUUAGCAUCCUUUUUGCA-----------UCCUUUU
.((....))....(((((((......((((....((((---.((.....)).....(((((((......)))))))))))......)))).....)))))-----------))..... ( -26.70)
>DroEre_CAF1 125857 112 + 1
UUCUGCUG---CUGAUGCAACAUCACAUGCAUUAAACC---CGCUCAUUGCUGUCAGCGUCAUUCGCUCGUGAUGCGGUUAUUUUUGCAUCCUUUUUGCAUCCUUUUUGCAUCCUUUU
...(((..---..(((((((......(((((...((((---.((.....)).....(((((((......))))))))))).....))))).....)))))))......)))....... ( -28.00)
>DroYak_CAF1 132428 89 + 1
UUCUGCUG---CUG-UGCAACAUCACAUGCAUUAAACC---CGCUCAUUGCUGUCAGCGUCAUUCGCUCGUGAUGCGGUUAUUUUUGCA----------------------UCCUUUU
...(((((---(((-((......)))).)))...((((---.((.....)).....(((((((......)))))))))))......)))----------------------....... ( -21.20)
>DroAna_CAF1 116740 93 + 1
UUCUGCUG---CUGAUGCUGCAUCACAUGCAUUAACCCGCUCGCUCAUUGCUGUCAGCGUCACUCGUUCGUGAUGUGGUUAUUUUUUCG----------------------UCCUGUU
...(((((---.(((((...))))))).))).(((((.....((.....)).....(((((((......))))))))))))........----------------------....... ( -20.50)
>consensus
UGCUGCUG___CUGAUGCAACAUCACAUGCAUUAAACC___CGCUCAUUGCUGUCAGCGUCACUCGCUCGUGAUGCGGUUAUUUUAGCAUCCUUUUUGCA___________UCCUUUU
............(((((((........)))))))((((....((.....)).....(((((((......)))))))))))...................................... (-18.49 = -18.63 +   0.14)

alignment

secondary structure

dotplot

Window 6

Location	12,305,196 – 12,305,294
Length	98
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	82.92
Mean single sequence MFE	-27.62
Consensus MFE	-19.42
Energy contribution	-20.80
Covariance contribution	1.38
Combinations/Pair	1.00
Mean z-score	-2.38
Structure conservation index	0.70
SVM decision value	0.54
SVM RNA-class probability	0.775730
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12305196 98 - 22407834
AAAAGGA-----------UGCAAAAAGGAUGCUAAAAUAACCGCAUCACGAGCGAGUGACGCUGACAGCAAUGAGCG---GGUUUAAUGCAUGUGAUGUUGCAUCAGC------AGCA
.....((-----------(((((...(.((((........((((.((((......)))).((.....)).....)))---).......)))).)....)))))))...------.... ( -28.86)
>DroSec_CAF1 127853 104 - 1
AAAAGGA-----------UGCAAAAAGGAUGCUAAAAUAACCGCAUCACGAGCGAGUGACGCUGACAGCAAUGAGCG---GGUUUAAUGCAUGUGAUGUUGCAUCAGCAGCAGCAGCA
.....((-----------(((((...(.((((........((((.((((......)))).((.....)).....)))---).......)))).)....))))))).((....)).... ( -30.06)
>DroSim_CAF1 131521 104 - 1
AAAAGGA-----------UGCAAAAAGGAUGCUAAAAUAACCGCAUCACGAGCGAGUGACGCUGACAGCAAUGAGCG---GGUUUAAUGCAUGUGAUGUUGCAUCAGCAGCAGCAGCA
.....((-----------(((((...(.((((........((((.((((......)))).((.....)).....)))---).......)))).)....))))))).((....)).... ( -30.06)
>DroEre_CAF1 125857 112 - 1
AAAAGGAUGCAAAAAGGAUGCAAAAAGGAUGCAAAAAUAACCGCAUCACGAGCGAAUGACGCUGACAGCAAUGAGCG---GGUUUAAUGCAUGUGAUGUUGCAUCAG---CAGCAGAA
.......(((......(((((((...(.(((((.......((((......((((.....))))..((....)).)))---)......))))).)....)))))))..---..)))... ( -31.12)
>DroYak_CAF1 132428 89 - 1
AAAAGGA----------------------UGCAAAAAUAACCGCAUCACGAGCGAAUGACGCUGACAGCAAUGAGCG---GGUUUAAUGCAUGUGAUGUUGCA-CAG---CAGCAGAA
....(.(----------------------((((.......((((......((((.....))))..((....)).)))---)......))))).)..((((((.-..)---)))))... ( -23.42)
>DroAna_CAF1 116740 93 - 1
AACAGGA----------------------CGAAAAAAUAACCACAUCACGAACGAGUGACGCUGACAGCAAUGAGCGAGCGGGUUAAUGCAUGUGAUGCAGCAUCAG---CAGCAGAA
.......----------------------........(((((...((((......))))((((....((.....)).))))))))).(((.(((((((...))))).---)))))... ( -22.20)
>consensus
AAAAGGA___________UGCAAAAAGGAUGCAAAAAUAACCGCAUCACGAGCGAGUGACGCUGACAGCAAUGAGCG___GGUUUAAUGCAUGUGAUGUUGCAUCAG___CAGCAGAA
...........................(((((..........((((((((((((.....))))....(((.(((((.....))))).))).)))))))).)))))............. (-19.42 = -20.80 +   1.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:37 2006