Locus 3211

Sequence ID	2R_DroMel_CAF1
Location	10,962,279 – 10,962,380
Length	101
Max. P	0.942306

overview

Window 0

Location	10,962,279 – 10,962,380
Length	101
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	95.84
Mean single sequence MFE	-24.24
Consensus MFE	-22.17
Energy contribution	-22.06
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-1.26
Structure conservation index	0.91
SVM decision value	0.71
SVM RNA-class probability	0.829865
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10962279 101 + 20766785
UUGGCAAGGUCAGAGUGGUGAUUCAUUUUGCACAUUCC-----GCAUGCAAAUUGAAUUAAAGCAAUCUUAAUUACAUCGGAGUGAAUUAAGCUGUGCUCAGGAAA
((((((....(((.((..(((((((.((((((......-----...)))))).)))))))..))...(((((((.(((....)))))))))))))))).))).... ( -23.80)
>DroSec_CAF1 74617 101 + 1
UUGGCAAGGUCAGAGUGGUGAUUCAUUUUGCACAUUCC-----GCAUGCAAAUUGAAUUAAAGCAAUCUUAAUUACAUCGGAGUGAAUUAAGCUGUGCUCAGGAAA
((((((....(((.((..(((((((.((((((......-----...)))))).)))))))..))...(((((((.(((....)))))))))))))))).))).... ( -23.80)
>DroSim_CAF1 76908 101 + 1
UUGGCAAGGUCAGAGUGGUGAUUCAUUUUGCACAUUCC-----GCAUGCAAAUUGAAUUAAAGCAAUCUUAAUUACAUCGGAGUGAAUUAAGCUGUGCUCAGGAAA
((((((....(((.((..(((((((.((((((......-----...)))))).)))))))..))...(((((((.(((....)))))))))))))))).))).... ( -23.80)
>DroEre_CAF1 76951 101 + 1
UUGGCAAGGUCAGAGUGGUGAUUCAUUUUGCACAUUCC-----GCAUGCAAAUUGAAUUAAAGCAAUCUUAAUUACAUCGAAGUGAAUUAAGCUGUGCUCAGGAAA
((((((....(((.((..(((((((.((((((......-----...)))))).)))))))..))...(((((((.(((....)))))))))))))))).))).... ( -23.80)
>DroYak_CAF1 78074 101 + 1
UUGGCAAGGUCAGAGUGGUGAUUCAUUUUGCACAUUCC-----GCAUGCAAAUUGAAUUAAAGCAAUCUUAAUUACAUCGAAGUGAAUUAAGCUGUGCUCAGGAAA
((((((....(((.((..(((((((.((((((......-----...)))))).)))))))..))...(((((((.(((....)))))))))))))))).))).... ( -23.80)
>DroAna_CAF1 75029 106 + 1
UUGGCAAGGUCAGAUCGGUGAUUCAUUUUGCACAUUCCAUUCAGCAUGCAAAUUGAAUUAAAGCAAUCUUAAUUACAUCGAAGUGAAUUGAGCUGUGCUCCGAAAG
(((((...))))).(((((((((((.((((((..............)))))).))))))).((((..(((((((.(((....))))))))))...))))))))... ( -26.44)
>consensus
UUGGCAAGGUCAGAGUGGUGAUUCAUUUUGCACAUUCC_____GCAUGCAAAUUGAAUUAAAGCAAUCUUAAUUACAUCGAAGUGAAUUAAGCUGUGCUCAGGAAA
..((((....(((.((..(((((((.((((((..............)))))).)))))))..))...(((((((.(((....)))))))))))))))))....... (-22.17 = -22.06 +  -0.11)

alignment

secondary structure

dotplot

Window 1

Location	10,962,279 – 10,962,380
Length	101
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	95.84
Mean single sequence MFE	-20.71
Consensus MFE	-19.30
Energy contribution	-19.47
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.36
Structure conservation index	0.93
SVM decision value	1.33
SVM RNA-class probability	0.942306
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10962279 101 - 20766785
UUUCCUGAGCACAGCUUAAUUCACUCCGAUGUAAUUAAGAUUGCUUUAAUUCAAUUUGCAUGC-----GGAAUGUGCAAAAUGAAUCACCACUCUGACCUUGCCAA
......(((((...(((((((.((......)))))))))..)))))..(((((.(((((((..-----.....))))))).))))).................... ( -20.60)
>DroSec_CAF1 74617 101 - 1
UUUCCUGAGCACAGCUUAAUUCACUCCGAUGUAAUUAAGAUUGCUUUAAUUCAAUUUGCAUGC-----GGAAUGUGCAAAAUGAAUCACCACUCUGACCUUGCCAA
......(((((...(((((((.((......)))))))))..)))))..(((((.(((((((..-----.....))))))).))))).................... ( -20.60)
>DroSim_CAF1 76908 101 - 1
UUUCCUGAGCACAGCUUAAUUCACUCCGAUGUAAUUAAGAUUGCUUUAAUUCAAUUUGCAUGC-----GGAAUGUGCAAAAUGAAUCACCACUCUGACCUUGCCAA
......(((((...(((((((.((......)))))))))..)))))..(((((.(((((((..-----.....))))))).))))).................... ( -20.60)
>DroEre_CAF1 76951 101 - 1
UUUCCUGAGCACAGCUUAAUUCACUUCGAUGUAAUUAAGAUUGCUUUAAUUCAAUUUGCAUGC-----GGAAUGUGCAAAAUGAAUCACCACUCUGACCUUGCCAA
......(((((...(((((((.((......)))))))))..)))))..(((((.(((((((..-----.....))))))).))))).................... ( -20.60)
>DroYak_CAF1 78074 101 - 1
UUUCCUGAGCACAGCUUAAUUCACUUCGAUGUAAUUAAGAUUGCUUUAAUUCAAUUUGCAUGC-----GGAAUGUGCAAAAUGAAUCACCACUCUGACCUUGCCAA
......(((((...(((((((.((......)))))))))..)))))..(((((.(((((((..-----.....))))))).))))).................... ( -20.60)
>DroAna_CAF1 75029 106 - 1
CUUUCGGAGCACAGCUCAAUUCACUUCGAUGUAAUUAAGAUUGCUUUAAUUCAAUUUGCAUGCUGAAUGGAAUGUGCAAAAUGAAUCACCGAUCUGACCUUGCCAA
...((((((..............)))))).((((...((((((.....(((((.(((((((.((....))...))))))).)))))...))))))....))))... ( -21.24)
>consensus
UUUCCUGAGCACAGCUUAAUUCACUCCGAUGUAAUUAAGAUUGCUUUAAUUCAAUUUGCAUGC_____GGAAUGUGCAAAAUGAAUCACCACUCUGACCUUGCCAA
......(((((...(((((((.((......)))))))))..)))))..(((((.(((((((............))))))).))))).................... (-19.30 = -19.47 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:09 2006