Locus 8111

Sequence ID	X_DroMel_CAF1
Location	20,179,858 – 20,180,015
Length	157
Max. P	0.797976

overview

Window 0

Location	20,179,858 – 20,179,978
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.97
Mean single sequence MFE	-39.20
Consensus MFE	-36.99
Energy contribution	-36.42
Covariance contribution	-0.56
Combinations/Pair	1.09
Mean z-score	-1.72
Structure conservation index	0.94
SVM decision value	0.61
SVM RNA-class probability	0.797976
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20179858 120 - 22224390
CCGCCACACCAGACGGAGAAACCACUUUUCAGGGUCAGGAGGCAAUCCAUUGGAUUGGCCUUGUGUACAACAGAGCCGGGGCCAAUUACUCAAUGUGAUGGAUGACCCAACGAACGCUUA
(((.(......).))).((((.....)))).((((((.....(.(((((((((((((((((((.((........)))))))))))))...))))).))).).))))))............ ( -36.60)
>DroSec_CAF1 1521 120 - 1
CCACCACACCAGACGGAGAAACCACUUUUCAGGGUCAGGAGGCAAUCCAUUGGAUUGGCCUUGUGUACAACAGAGCCGGGGCCAAUUACUCAAUGUGAUGGAUGACCCACCGAACGCUUA
.............(((.((((.....)))).((((((.....(.(((((((((((((((((((.((........)))))))))))))...))))).))).).)))))).)))........ ( -38.40)
>DroSim_CAF1 944 120 - 1
CCACCACACCAGACGGAGAAACCACUUUUCAGGGUCAGGAGGCAAUCCAUUGGAUUGGCCUUGUGUACAACAGAGCCGGGGCCAAUUACUCAAUGUGAUGGAUGACCCAGCGAACGCUUA
...............(((((.....))))).((((((.....(.(((((((((((((((((((.((........)))))))))))))...))))).))).).))))))(((....))).. ( -37.00)
>DroYak_CAF1 1513 120 - 1
CCAACACACCAGACGGGAAAACCACUUUUCAGGGUCAGGAGCCAAUCCAUUGGAUUGGCCUUGUGCACAACAGGGCCGGGGCCAAUUACUCAAUGUGAUGGAUGACCCACCGAAUGCUUA
.........((..((((((((....))))).((((((....(((.((((((((((((((((((.((........)))))))))))))...))))).))))).)))))).)))..)).... ( -44.80)
>consensus
CCACCACACCAGACGGAGAAACCACUUUUCAGGGUCAGGAGGCAAUCCAUUGGAUUGGCCUUGUGUACAACAGAGCCGGGGCCAAUUACUCAAUGUGAUGGAUGACCCACCGAACGCUUA
.............(((((((.....))))).((((((.......(((((((((((((((((((.((........)))))))))))))...))))).)))...))))))..))........ (-36.99 = -36.42 +  -0.56)

alignment

secondary structure

dotplot

Window 1

Location	20,179,898 – 20,180,015
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.84
Mean single sequence MFE	-36.67
Consensus MFE	-28.65
Energy contribution	-29.77
Covariance contribution	1.13
Combinations/Pair	1.10
Mean z-score	-1.57
Structure conservation index	0.78
SVM decision value	-0.01
SVM RNA-class probability	0.530242
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20179898 117 + 22224390
CCCGGCUCUGUUGUACACAAGGCCAAUCCAAUGGAUUGCCUCCUGACCCUGAAAAGUGGUUUCUCCGUCUGGUGUGGCGGUCUC-UUCGCCACAAGAUUGGUUUCCAACUAUU--GUAAA
...(((..(((.....)))..))).......((((..(((....((((((....)).)))).....((((..((((((((....-.)))))))))))).))).))))......--..... ( -36.40)
>DroSec_CAF1 1561 117 + 1
CCCGGCUCUGUUGUACACAAGGCCAAUCCAAUGGAUUGCCUCCUGACCCUGAAAAGUGGUUUCUCCGUCUGGUGUGGUGGUCUC-UUCGCCACAGGAUUGCUUUCCAACUAUU--GUAUA
...(((..(((.....)))..))).......((((..((.((((((((((....)).))))............(((((((....-.)))))))))))..))..))))......--..... ( -36.40)
>DroSim_CAF1 984 117 + 1
CCCGGCUCUGUUGUACACAAGGCCAAUCCAAUGGAUUGCCUCCUGACCCUGAAAAGUGGUUUCUCCGUCUGGUGUGGUGGUCUC-UUCGCCACAGGAUUGCUUUCCAACUAUU--GUAUA
...(((..(((.....)))..))).......((((..((.((((((((((....)).))))............(((((((....-.)))))))))))..))..))))......--..... ( -36.40)
>DroYak_CAF1 1553 120 + 1
CCCGGCCCUGUUGUGCACAAGGCCAAUCCAAUGGAUUGGCUCCUGACCCUGAAAAGUGGUUUUCCCGUCUGGUGUGUUGGUUCCUUUCGCCACAAGAUCGGAUUCCAACUAUUUUGUGCA
.............((((((((((((((((...)))))))))((.(((...(((((....)))))..))).))...(((((.(((..((.......))..)))..)))))....))))))) ( -37.50)
>consensus
CCCGGCUCUGUUGUACACAAGGCCAAUCCAAUGGAUUGCCUCCUGACCCUGAAAAGUGGUUUCUCCGUCUGGUGUGGUGGUCUC_UUCGCCACAAGAUUGCUUUCCAACUAUU__GUAUA
...((((.(((.....))).)))).......((((.........((((((....)).)))).....((((..((((((((......)))))))))))).....))))............. (-28.65 = -29.77 +   1.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:55:40 2006