Locus 5309

Sequence ID	X_DroMel_CAF1
Location	13,876,804 – 13,877,002
Length	198
Max. P	0.891923

overview

Window 1

Location	13,876,804 – 13,876,922
Length	118
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	88.48
Mean single sequence MFE	-27.33
Consensus MFE	-20.78
Energy contribution	-20.67
Covariance contribution	-0.11
Combinations/Pair	1.07
Mean z-score	-2.23
Structure conservation index	0.76
SVM decision value	0.22
SVM RNA-class probability	0.640161
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13876804 118 + 22224390
ACAGAGAAUUCAUUUUAUUCAUGAGGAAAUCCUUUUGAAUUCCUUAUUUUCUUGUGCUUAAAACUUGGUGAAACUGCAAUUGCACCUUUCU--GUUGCGUUUUCUUAGCCAAUUUUCGCA
(((((((((.......(((((.((((....)))).))))).....)))))).)))((..((((.(((((((((.((((((...........--)))))).))))...))))))))).)). ( -26.50)
>DroSec_CAF1 26097 116 + 1
ACAGAGAA--CAUUCUAUUCACGAGGAUAUCCUUUUGAAUCCCUGAUUUUCUUGUGCUUAAAACUUGGCGAAACUGCAAUUGCACCUUUGU--GUGGCAUUUUCUUAGCCAUUUUUCGCA
((((((((--((....(((((.((((....)))).)))))...)).))))).)))((..((((..((((((((.(((....((((....))--)).))).))))...))))))))..)). ( -27.90)
>DroEre_CAF1 20901 116 + 1
A-AGAAAA--CAUUCUAUUCAUGAGGAUAUCCUUUUGAAUCCCUGAUUUUCCUGUGCUGCAAACUUGGCGAAACUGCAAUUGCACCUUUGUGUGUGGCAUUUUCUUAGCCA-UUUUCGCU
.-.(((((--((....(((((.((((....)))).)))))...)).))))).......((.((..((((((((.(((...(((((....)))))..))).))))...))))-..)).)). ( -27.60)
>consensus
ACAGAGAA__CAUUCUAUUCAUGAGGAUAUCCUUUUGAAUCCCUGAUUUUCUUGUGCUUAAAACUUGGCGAAACUGCAAUUGCACCUUUGU__GUGGCAUUUUCUUAGCCA_UUUUCGCA
...(((((........(((((.((((....)))).)))))......)))))................((((((.(((....)))..........((((.........))))..)))))). (-20.78 = -20.67 +  -0.11)

alignment

secondary structure

dotplot

Window 2

Location	13,876,884 – 13,877,002
Length	118
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	93.00
Mean single sequence MFE	-29.70
Consensus MFE	-24.73
Energy contribution	-26.40
Covariance contribution	1.67
Combinations/Pair	1.00
Mean z-score	-2.94
Structure conservation index	0.83
SVM decision value	0.97
SVM RNA-class probability	0.891923
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13876884 118 - 22224390
AGCACAUGAAUCGCUUUAUGCGAAAGGGCAUAAAAUGAAUUAAACACGACCAGCUCAAGGUCAAAUCGACAAAGGCGCUUUGCGAAAAUUGGCUAAGAAAACGCAAC--AGAAAGGUGCA
.((((.(((.(((.(((((((......))))))).))).)))..........((((..((((((.(((.(((((...))))))))...))))))..))....))...--......)))). ( -27.20)
>DroSec_CAF1 26175 117 - 1
AGCACAUGAAUCGCUUUAUGCGAAAGGGCAUAAAAUGAAUUAAACACGACCAGCUCAAGGUCAAAUCGACAAAGGAGCU-UGCGAAAAAUGGCUAAGAAAAUGCCAC--ACAAAGGUGCA
.((((.....(((((((((((......))))))).................(((((...(((.....)))....)))))-.))))....((((.........)))).--......)))). ( -33.00)
>DroEre_CAF1 20978 118 - 1
AACACAUGAAUCGCUUUAUGCGAAAGGGCACAACAUGAAUUAAACACGACCAGCUCAAGGUCAAAUCGACAAAGGAGCU-AGCGAAAA-UGGCUAAGAAAAUGCCACACACAAAGGUGCA
..........((((.....))))....((((...............((.(.(((((...(((.....)))....)))))-.)))....-((((.........)))).........)))). ( -28.90)
>consensus
AGCACAUGAAUCGCUUUAUGCGAAAGGGCAUAAAAUGAAUUAAACACGACCAGCUCAAGGUCAAAUCGACAAAGGAGCU_UGCGAAAA_UGGCUAAGAAAAUGCCAC__ACAAAGGUGCA
.((((.(((.(((.(((((((......))))))).))).)))....((...(((((...(((.....)))....)))))...)).....((((.........)))).........)))). (-24.73 = -26.40 +   1.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:32 2006