Locus 1745

Sequence ID	2L_DroMel_CAF1
Location	4,772,614 – 4,772,704
Length	90
Max. P	0.992543

overview

Window 1

Location	4,772,614 – 4,772,704
Length	90
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	80.19
Mean single sequence MFE	-25.92
Consensus MFE	-15.24
Energy contribution	-17.96
Covariance contribution	2.72
Combinations/Pair	1.05
Mean z-score	-2.93
Structure conservation index	0.59
SVM decision value	2.34
SVM RNA-class probability	0.992543
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4772614 90 + 22407834
UGUGUGUGAAGCCGGU-----------UCCACUGGGCACACUGUAAACCAAAAUGAAAAUUGCAAUUGCAAUUGCAAUAAAAUGGCUAAACGCACUUGAGC
.((((((..(((((((-----------(.((.((....)).))..)))).........((((((((....)))))))).....))))..))))))...... ( -27.00)
>DroSec_CAF1 220931 90 + 1
UGUGCGUGGAGCCGUC-----------UCCACUGGGCACACUGUAAACCAAAAUGAAAAUUGCAAUUGCAAUUGCAAUAAAAUGGCUAAACGCACUUGAGC
.((((((..((((((.-----------.....(((............)))........((((((((....))))))))...))))))..))))))...... ( -28.00)
>DroSim_CAF1 197886 90 + 1
UGUGCGUGGAGCCGGC-----------UCCACUGGGCACACUGUAAACCAAAAUGAAAAUUGCAAUUGCAAUUGCAAUAAAAUGGCUAAACGCACUUGAGC
.((((((..(((((((-----------((....)))).....................((((((((....))))))))....)))))..))))))...... ( -29.70)
>DroEre_CAF1 209628 88 + 1
------UGGAGCCGGUUCCACGGCUCCUCCACU-GGCAGAUUGUAAACCAAAAUGAAAAUUGCA------AUUGCAAUAAAAUGGCUAAACGCACUUGAGC
------.(((((((......))))))).....(-(((..(((((((.....(((....)))...------.)))))))......))))............. ( -23.80)
>DroYak_CAF1 207995 88 + 1
------UGAAGCCGAACCGAACUGCCUUCCACU-GGCAGAUUCUAAACCAAAAUGAAAAUUGCA------AUUGCAAUAAAAUGGCUAAACGCACUUGAGC
------...(((((....((((((((.......-))))).)))...............(((((.------...)))))....))))).............. ( -21.10)
>consensus
UGUG_GUGGAGCCGGC___________UCCACUGGGCACACUGUAAACCAAAAUGAAAAUUGCAAUUGCAAUUGCAAUAAAAUGGCUAAACGCACUUGAGC
.((((((..(((((....................((...........)).........((((((((....))))))))....)))))..))))))...... (-15.24 = -17.96 +   2.72)

alignment

secondary structure

dotplot

Window 2

Location	4,772,614 – 4,772,704
Length	90
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	80.19
Mean single sequence MFE	-27.08
Consensus MFE	-15.60
Energy contribution	-16.40
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.57
Structure conservation index	0.58
SVM decision value	1.63
SVM RNA-class probability	0.968725
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4772614 90 - 22407834
GCUCAAGUGCGUUUAGCCAUUUUAUUGCAAUUGCAAUUGCAAUUUUCAUUUUGGUUUACAGUGUGCCCAGUGGA-----------ACCGGCUUCACACACA
......(((.((..((((.....((((((((....)))))))).........(((((.((.((....)).))))-----------)))))))..)).))). ( -26.30)
>DroSec_CAF1 220931 90 - 1
GCUCAAGUGCGUUUAGCCAUUUUAUUGCAAUUGCAAUUGCAAUUUUCAUUUUGGUUUACAGUGUGCCCAGUGGA-----------GACGGCUCCACGCACA
......((((((..((((......(((((((....)))))))((((((((..(((.........))).))))))-----------)).))))..)))))). ( -29.80)
>DroSim_CAF1 197886 90 - 1
GCUCAAGUGCGUUUAGCCAUUUUAUUGCAAUUGCAAUUGCAAUUUUCAUUUUGGUUUACAGUGUGCCCAGUGGA-----------GCCGGCUCCACGCACA
......((((((..((((.....((((((((....)))))))).........(((((.((.((....)).))))-----------)))))))..)))))). ( -31.10)
>DroEre_CAF1 209628 88 - 1
GCUCAAGUGCGUUUAGCCAUUUUAUUGCAAU------UGCAAUUUUCAUUUUGGUUUACAAUCUGCC-AGUGGAGGAGCCGUGGAACCGGCUCCA------
((......))......((((...(((((...------.)))))........((((.........)))-))))).(((((((......))))))).------ ( -25.80)
>DroYak_CAF1 207995 88 - 1
GCUCAAGUGCGUUUAGCCAUUUUAUUGCAAU------UGCAAUUUUCAUUUUGGUUUAGAAUCUGCC-AGUGGAAGGCAGUUCGGUUCGGCUUCA------
((......))((..((((.....(((((...------.)))))...............(((.(((((-.......))))))))))))..))....------ ( -22.40)
>consensus
GCUCAAGUGCGUUUAGCCAUUUUAUUGCAAUUGCAAUUGCAAUUUUCAUUUUGGUUUACAGUGUGCCCAGUGGA___________ACCGGCUCCAC_CACA
((......))....((((.....((((((((....)))))))).(((((...(((.........)))..)))))..............))))......... (-15.60 = -16.40 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:04 2006