Locus 7158

Sequence ID	X_DroMel_CAF1
Location	17,970,157 – 17,970,260
Length	103
Max. P	0.923467

overview

Window 8

Location	17,970,157 – 17,970,260
Length	103
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.94
Mean single sequence MFE	-35.10
Consensus MFE	-21.62
Energy contribution	-25.75
Covariance contribution	4.12
Combinations/Pair	1.14
Mean z-score	-2.06
Structure conservation index	0.62
SVM decision value	0.51
SVM RNA-class probability	0.763929
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17970157 103 + 22224390
-AUUUGGCUUUCACUGCAAAUCGCAGC---GCUAACGAAAGUCGAAACAAACAUGUUC------------CUGCUAGGAAGGCCUGACUGUA-GAGCAAUCAAAGGUGACUGCUUGCCUA
-.((((((((((.((((.....)))).---(....))))))))))).......(((((------------.(((((((....))))...)))-))))).....(((..(....)..))). ( -26.60)
>DroSec_CAF1 896 107 + 1
AGAUUGGCUUUCACUGCAAAUCGCAGCAGUGCUAACGAAAGCCGAAGCAAGCAUGUUC------------CUGCUAGGCAGGCCUGACUGUA-GAGCAAUCAAAGGUGACUGCUUGCCUA
...(((((((((.((((.....))))..((....))))))))))).(((((((.((((------------(((((..((((......)))).-.)))......))).))))))))))... ( -41.50)
>DroSim_CAF1 246 107 + 1
AGAUUGGCUUUCACUGCAAAUCGCAGCAGUGCUAACGAAAGCCGAAGCAAACAUGUUC------------CUGCUAGGCAGGCCUGACUGUA-GAGCAAUCAAAGGUGACUGCUUGCCUA
...(((((((((.((((.....))))..((....)))))))))))((((.........------------.))))((((((((.(((.((..-...)).))).((....)))))))))). ( -38.00)
>DroEre_CAF1 993 118 + 1
UGACUGGCUUUCACUGCAAUCCGCA--AGCACCAACGAAUGCGGAAGUAAACAUACUCUUUGCAAGGUUUGUGCUAGGGAGGCCUGACUGUAUGAGCAACUAAAGGUGACUGCUUGCCCA
.....(((((((..(((.....)))--(((((.(((...((((((((((....)))).))))))..))).)))))..)))))))........((.((((....((....))..)))).)) ( -34.30)
>consensus
AGAUUGGCUUUCACUGCAAAUCGCAGCAGUGCUAACGAAAGCCGAAGCAAACAUGUUC____________CUGCUAGGCAGGCCUGACUGUA_GAGCAAUCAAAGGUGACUGCUUGCCUA
...(((((((((.((((.....))))..(......))))))))))((((....)))).................(((((((((.(((.(((....))).))).((....))))))))))) (-21.62 = -25.75 +   4.12)

alignment

secondary structure

dotplot

Window 9

Location	17,970,157 – 17,970,260
Length	103
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.94
Mean single sequence MFE	-36.00
Consensus MFE	-23.91
Energy contribution	-24.47
Covariance contribution	0.56
Combinations/Pair	1.16
Mean z-score	-2.25
Structure conservation index	0.66
SVM decision value	1.15
SVM RNA-class probability	0.923467
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17970157 103 - 22224390
UAGGCAAGCAGUCACCUUUGAUUGCUC-UACAGUCAGGCCUUCCUAGCAG------------GAACAUGUUUGUUUCGACUUUCGUUAGC---GCUGCGAUUUGCAGUGAAAGCCAAAU-
..(((.((((((((....)))))))).-...(((((((....)))....(------------(((((....))))))))))........(---(((((.....))))))...)))....- ( -32.60)
>DroSec_CAF1 896 107 - 1
UAGGCAAGCAGUCACCUUUGAUUGCUC-UACAGUCAGGCCUGCCUAGCAG------------GAACAUGCUUGCUUCGGCUUUCGUUAGCACUGCUGCGAUUUGCAGUGAAAGCCAAUCU
.(((((((((......((((((((...-..))))))))(((((...))))------------)....))))))))).((((((((....)(((((........))))))))))))..... ( -41.70)
>DroSim_CAF1 246 107 - 1
UAGGCAAGCAGUCACCUUUGAUUGCUC-UACAGUCAGGCCUGCCUAGCAG------------GAACAUGUUUGCUUCGGCUUUCGUUAGCACUGCUGCGAUUUGCAGUGAAAGCCAAUCU
.(((((((((......((((((((...-..))))))))(((((...))))------------)....))))))))).((((((((....)(((((........))))))))))))..... ( -39.30)
>DroEre_CAF1 993 118 - 1
UGGGCAAGCAGUCACCUUUAGUUGCUCAUACAGUCAGGCCUCCCUAGCACAAACCUUGCAAAGAGUAUGUUUACUUCCGCAUUCGUUGGUGCU--UGCGGAUUGCAGUGAAAGCCAGUCA
..(((.(((((.(.......)))))).......(((.((.((((.(((((.(((..(((...(((((....)))))..)))...))).)))))--.).)))..))..)))..)))..... ( -30.40)
>consensus
UAGGCAAGCAGUCACCUUUGAUUGCUC_UACAGUCAGGCCUGCCUAGCAG____________GAACAUGUUUGCUUCGGCUUUCGUUAGCACUGCUGCGAUUUGCAGUGAAAGCCAAUCU
((((((((((((((....))))))))......(..(((....)))..)...................))))))....((((((((....)...(((((.....))))))))))))..... (-23.91 = -24.47 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:32 2006