Locus 3730

Sequence ID	3L_DroMel_CAF1
Location	10,796,906 – 10,796,996
Length	90
Max. P	0.959812

overview

Window 4

Location	10,796,906 – 10,796,996
Length	90
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	85.73
Mean single sequence MFE	-20.36
Consensus MFE	-15.70
Energy contribution	-15.54
Covariance contribution	-0.16
Combinations/Pair	1.07
Mean z-score	-2.18
Structure conservation index	0.77
SVM decision value	1.16
SVM RNA-class probability	0.924790
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10796906 90 + 23771897
CCUCUCCCUCUUUCCCAUUUGGGUUUCCCCCAAACCAUCG------------------CCCUGUUGUUGCUGGAAAUUAUAGCAUGUCCUUUUCGGACUAAGGACAUC
.................((((((.....))))))......------------------.........(((((.......)))))(((((((........))))))).. ( -18.70)
>DroSec_CAF1 6074 96 + 1
CCUCUCCCUCUUUCCCAUUUGGGUUUCCCCCA-ACCAUCGCCCC-----------ACGCCCUGUUGUUGCUGGAAAUUAUAGUAUGUCCUUUUCGGACUAAGGACAUC
.............(((....)))(((((..((-((((..((...-----------..))..))..))))..))))).......((((((((........)))))))). ( -20.50)
>DroSim_CAF1 7701 96 + 1
CCUCUCCCUCUUUCCCAUUUGGGUUUCCCCCA-ACCAUCGCCCC-----------ACGCCCUGUUGUUGCUGGAAAUUAUAGCAUGUCCUUUUCGGACUAAGGACAUC
.............(((....)))(((((..((-((((..((...-----------..))..))..))))..))))).......((((((((........)))))))). ( -20.60)
>DroEre_CAF1 7638 90 + 1
CCUCUCCCUCUUUCCCAUUCGGGUUUCCCCAC-ACC---CC--------------ACGCCCUGUUGUUGCUGGAAAUUAUAGCAUGUCCUUUUCGGACUAAGGACAUC
....................((((........-)))---).--------------............(((((.......)))))(((((((........))))))).. ( -16.90)
>DroYak_CAF1 6151 104 + 1
UCUCUCACUCUUUCCCAUUUGGGUUACCACCC-ACC---CCCCCACACCCAGCGUACACCCUGUUGUUGCUGGAAAUUAUAGCAUGUCCUUUUCGGACUAAGGACAUC
...................(((((....))))-)..---.........((((((.(((......)))))))))..........((((((((........)))))))). ( -25.10)
>consensus
CCUCUCCCUCUUUCCCAUUUGGGUUUCCCCCA_ACCAUCGCCCC___________ACGCCCUGUUGUUGCUGGAAAUUAUAGCAUGUCCUUUUCGGACUAAGGACAUC
.............(((....)))............................................(((((.......)))))(((((((........))))))).. (-15.70 = -15.54 +  -0.16)

alignment

secondary structure

dotplot

Window 5

Location	10,796,906 – 10,796,996
Length	90
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	85.73
Mean single sequence MFE	-29.60
Consensus MFE	-20.80
Energy contribution	-21.28
Covariance contribution	0.48
Combinations/Pair	1.05
Mean z-score	-2.81
Structure conservation index	0.70
SVM decision value	1.51
SVM RNA-class probability	0.959812
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10796906 90 - 23771897
GAUGUCCUUAGUCCGAAAAGGACAUGCUAUAAUUUCCAGCAACAACAGGG------------------CGAUGGUUUGGGGGAAACCCAAAUGGGAAAGAGGGAGAGG
..(.(((((.((((.....)))).........(((((.((.........)------------------)....(((((((.....))))))).))))).))))).).. ( -26.60)
>DroSec_CAF1 6074 96 - 1
GAUGUCCUUAGUCCGAAAAGGACAUACUAUAAUUUCCAGCAACAACAGGGCGU-----------GGGGCGAUGGU-UGGGGGAAACCCAAAUGGGAAAGAGGGAGAGG
..(.(((((.((((.....)))).........((((((....((((....((.-----------....))...))-))(((....)))...))))))..))))).).. ( -31.10)
>DroSim_CAF1 7701 96 - 1
GAUGUCCUUAGUCCGAAAAGGACAUGCUAUAAUUUCCAGCAACAACAGGGCGU-----------GGGGCGAUGGU-UGGGGGAAACCCAAAUGGGAAAGAGGGAGAGG
..(.(((((.((((.....)))).........((((((....((((....((.-----------....))...))-))(((....)))...))))))..))))).).. ( -31.10)
>DroEre_CAF1 7638 90 - 1
GAUGUCCUUAGUCCGAAAAGGACAUGCUAUAAUUUCCAGCAACAACAGGGCGU--------------GG---GGU-GUGGGGAAACCCGAAUGGGAAAGAGGGAGAGG
..(.(((((.((((.....)))).........(((((((((.(..((.....)--------------).---.))-))(((....)))...))))))..))))).).. ( -27.40)
>DroYak_CAF1 6151 104 - 1
GAUGUCCUUAGUCCGAAAAGGACAUGCUAUAAUUUCCAGCAACAACAGGGUGUACGCUGGGUGUGGGGG---GGU-GGGUGGUAACCCAAAUGGGAAAGAGUGAGAGA
.((((((((........))))))))(((((.((..((.(((....(((.(....).)))..)))..)).---.))-..)))))..(((....)))............. ( -31.80)
>consensus
GAUGUCCUUAGUCCGAAAAGGACAUGCUAUAAUUUCCAGCAACAACAGGGCGU___________GGGGCGAUGGU_UGGGGGAAACCCAAAUGGGAAAGAGGGAGAGG
..(.(((((.((((.....)))).........((((((((.........))...........................(((....)))...))))))..))))).).. (-20.80 = -21.28 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:21 2006