Locus 4922

Sequence ID	X_DroMel_CAF1
Location	12,823,796 – 12,823,907
Length	111
Max. P	0.893848

overview

Window 7

Location	12,823,796 – 12,823,907
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.54
Mean single sequence MFE	-26.91
Consensus MFE	-20.97
Energy contribution	-20.93
Covariance contribution	-0.04
Combinations/Pair	1.16
Mean z-score	-1.88
Structure conservation index	0.78
SVM decision value	0.75
SVM RNA-class probability	0.840278
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12823796 111 + 22224390
AAAUUCAACUCCCCAAGUGAUUUUUACUUCAAAGCCAAAGCUGCUGUAAACUUUCUACUCUCCAGGGUAUUUUUGCGAAAAAUUUCCUGGAAAUUUU---------CGGGGAAAAGCUGU
.........(((((.(((((..(((((.....(((....)))...)))))...)).))).(((((((.(((((.....))))).)))))))......---------.)))))........ ( -27.90)
>DroSec_CAF1 21858 111 + 1
AAAUUCAAUUCCCCAAGUGAUUUUUACUUCAAAGCCAAAGCUGCUGUAAACUUUCUACUCUCCAGGGUAUUUUUGCGAAACAUUUCCUGGAAAUUUU---------GGGGAAAAAGCUGU
........((((((((((((..(((((.....(((....)))...)))))...)).))..(((((((.................)))))))....))---------))))))........ ( -27.13)
>DroSim_CAF1 31611 111 + 1
AAAUUCAACUCCCCAAGUGAUUUUUACUUCAAAGCCAAAGCUGCUGUAAACUUUAUACUCUCCAGGGUAUUUUUGCGAAACAUUUCCUGGAAAUUUU---------GGGGGAAAAGCUGU
.........(((((((((((..(((((.....(((....)))...)))))..))))....(((((((.................)))))))....))---------)))))......... ( -26.63)
>DroEre_CAF1 30183 111 + 1
AAAUUCCACUCCCCAAGUGGUUUUUACUUCAAAGCCAAAGCUGAUGUAAACUUUCUAUUCUCCAGGGUAUUUUUGCGAAACAUUUCCUUGAAAUUUU---------GGGGGGAAAACUGU
........((((((((((((((((......)))))))(((..(((((........(((((....)))))..........)))))..))).....)))---------))))))........ ( -24.37)
>DroYak_CAF1 30486 120 + 1
AAAUUCAACUCCCCAAGUGAUUUUUACUUCAAAGCCAAAGCUGAUGUAAACUUUCUGCUCUCCAGGGUAUUUUUGCGAAACAUUUCCUGGAAAUUUUUGUUUGGUUAGGGGAAUAGCUGU
.........(((((((((((...))))))...(((((((((.((.........)).))..(((((((.................)))))))........))))))).)))))........ ( -28.53)
>consensus
AAAUUCAACUCCCCAAGUGAUUUUUACUUCAAAGCCAAAGCUGCUGUAAACUUUCUACUCUCCAGGGUAUUUUUGCGAAACAUUUCCUGGAAAUUUU_________GGGGGAAAAGCUGU
.........(((((.(((((..(((((.....(((....)))...)))))...)).))).(((((((.................)))))))................)))))........ (-20.97 = -20.93 +  -0.04)

alignment

secondary structure

dotplot

Window 8

Location	12,823,796 – 12,823,907
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.54
Mean single sequence MFE	-28.24
Consensus MFE	-21.70
Energy contribution	-21.82
Covariance contribution	0.12
Combinations/Pair	1.11
Mean z-score	-2.12
Structure conservation index	0.77
SVM decision value	0.98
SVM RNA-class probability	0.893848
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12823796 111 - 22224390
ACAGCUUUUCCCCG---------AAAAUUUCCAGGAAAUUUUUCGCAAAAAUACCCUGGAGAGUAGAAAGUUUACAGCAGCUUUGGCUUUGAAGUAAAAAUCACUUGGGGAGUUGAAUUU
.((((...((((((---------(...((((((((..(((((.....)))))..))))))))...((...(((((..((((....))..))..)))))..))..)))))))))))..... ( -31.30)
>DroSec_CAF1 21858 111 - 1
ACAGCUUUUUCCCC---------AAAAUUUCCAGGAAAUGUUUCGCAAAAAUACCCUGGAGAGUAGAAAGUUUACAGCAGCUUUGGCUUUGAAGUAAAAAUCACUUGGGGAAUUGAAUUU
........((((((---------((..((((((((...(((((.....))))).))))))))...((...(((((..((((....))..))..)))))..))..))))))))........ ( -28.40)
>DroSim_CAF1 31611 111 - 1
ACAGCUUUUCCCCC---------AAAAUUUCCAGGAAAUGUUUCGCAAAAAUACCCUGGAGAGUAUAAAGUUUACAGCAGCUUUGGCUUUGAAGUAAAAAUCACUUGGGGAGUUGAAUUU
.(((((....((((---------((..((((((((...(((((.....))))).))))))))........(((((..((((....))..))..)))))......)))))))))))..... ( -28.40)
>DroEre_CAF1 30183 111 - 1
ACAGUUUUCCCCCC---------AAAAUUUCAAGGAAAUGUUUCGCAAAAAUACCCUGGAGAAUAGAAAGUUUACAUCAGCUUUGGCUUUGAAGUAAAAACCACUUGGGGAGUGGAAUUU
..(((((..(((((---------((..((((.(((...(((((.....))))).))).))))........(((((.(((((....))..))).)))))......)))))).)..))))). ( -23.30)
>DroYak_CAF1 30486 120 - 1
ACAGCUAUUCCCCUAACCAAACAAAAAUUUCCAGGAAAUGUUUCGCAAAAAUACCCUGGAGAGCAGAAAGUUUACAUCAGCUUUGGCUUUGAAGUAAAAAUCACUUGGGGAGUUGAAUUU
.((((...(((((..............((((((((...(((((.....))))).))))))))...((...(((((.(((((....))..))).)))))..))....)))))))))..... ( -29.80)
>consensus
ACAGCUUUUCCCCC_________AAAAUUUCCAGGAAAUGUUUCGCAAAAAUACCCUGGAGAGUAGAAAGUUUACAGCAGCUUUGGCUUUGAAGUAAAAAUCACUUGGGGAGUUGAAUUU
....(..((((((..............((((((((...(((((.....))))).))))))))........(((((...(((....))).....)))))........))))))..)..... (-21.70 = -21.82 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:08 2006