Locus 2267

Sequence ID	X_DroMel_CAF1
Location	6,146,457 – 6,146,642
Length	185
Max. P	0.844625

overview

Window 8

Location	6,146,457 – 6,146,570
Length	113
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	89.40
Mean single sequence MFE	-25.35
Consensus MFE	-24.18
Energy contribution	-24.25
Covariance contribution	0.06
Combinations/Pair	1.15
Mean z-score	-1.54
Structure conservation index	0.95
SVM decision value	0.76
SVM RNA-class probability	0.844625
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6146457 113 + 22224390
AAUUUUUUUACUUUAUUCCAUUGGUUUGUGUUCUUCACACGGGCACGGUCACACUUUCACCUAGCGAUGGCAUUUCGUCCCAAUUCAACGCCUAUCGAUGUGCCAAUCGUUAC
...................((((((((((((.....)))))))).))))............((((((((((((.(((..................))).))))).))))))). ( -24.97)
>DroSec_CAF1 1891 111 + 1
AAUUU-UUUACUUUAUUCCAUUGGUUUGUGUUCUUCACACGCGCACGGUCACACUUUCACCUAGCGAUGGCACCUCGUCCC-AUUCAACGCCUAUCGAUGUGCCAAUCGUUAC
.....-.............((((((.(((((.....))))).)).))))............((((((((((((.(((....-.............))).))))).))))))). ( -23.73)
>DroEre_CAF1 1875 109 + 1
AAUU--UUUACUUUAUUCCAUUGGUUUGUGUUCUUCACAUGCGCACGGUCACACUAUCCCCUAGCGGUGGCACGCCGUGC--ACCCAGCGCCUAUCGAUGUGCCAAUCGUUAC
....--.............((((((.((((.....)))).))(((((((..((((..........))))....)))))))--.....((((........))))))))...... ( -24.40)
>DroYak_CAF1 1905 107 + 1
AAUU--UUUACUUUAUUCCAUUGGUUUGUGUUCCUCACACGCGCACGGUCACACUA--CCCUAGCGGUGGCACAUCGUCU--ACCCAGCGCCUAUCGAUGUGCCAAUCGUUAC
....--................(((.((((..((............)).))))..)--)).((((((((((((((((...--.............))))))))).))))))). ( -28.29)
>consensus
AAUU__UUUACUUUAUUCCAUUGGUUUGUGUUCUUCACACGCGCACGGUCACACUAUCACCUAGCGAUGGCACAUCGUCC__ACCCAACGCCUAUCGAUGUGCCAAUCGUUAC
...................(((((..(((((.....)))))..).))))............((((((((((((((((..................))))))))).))))))). (-24.18 = -24.25 +   0.06)

alignment

secondary structure

dotplot

Window 9

Location	6,146,530 – 6,146,642
Length	112
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	77.70
Mean single sequence MFE	-29.52
Consensus MFE	-19.97
Energy contribution	-21.16
Covariance contribution	1.19
Combinations/Pair	1.12
Mean z-score	-1.78
Structure conservation index	0.68
SVM decision value	0.61
SVM RNA-class probability	0.798737
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6146530 112 + 22224390
UUCGUCCCAAUUCAACGCCUAUCGAUGUGCCAAUCGUUACGUGACGUU----GGCGCAGGUCGUACUUAACGUUACGUCACGUAACGGAAAAGCGUUAAUUCAAAUUGCACUUAUU
.............(((((...(((((......)))((((((((((((.----((((.(((.....)))..)))))))))))))))).))...)))))................... ( -30.70)
>DroSec_CAF1 1963 107 + 1
CUCGUCCC-AUUCAACGCCUAUCGAUGUGCCAAUCGUUACGUGACGUU----GGCGCAGGUCGUAUUUAACGUUACGUUACGUAACGGAAAAGCGUUAAUUCAAA----AUUUUUG
........-....(((((....(((((((((((.((((....))))))----))))))..)))..(((..(((((((...)))))))..))))))))........----....... ( -30.40)
>DroEre_CAF1 1946 103 + 1
GCCGUGC--ACCCAGCGCCUAUCGAUGUGCCAAUCGUUACGUGACGUUGUAUGACGCUGGUCAUAUUUAA----------CGUAACGGAAAAGCGUUACUUCAAAUUA-AAUUAAU
...((((--.....)))).....(((((.....(((((((((......(((((((....)))))))...)----------))))))))....)))))...........-....... ( -26.30)
>DroYak_CAF1 1974 102 + 1
AUCGUCU--ACCCAGCGCCUAUCGAUGUGCCAAUCGUUACGUGACGUU----GACGCAGGUCUUAUUUAACGUUACGUAACGUAACGGAUAAGCGUUAUUUUAAAUGG--------
.......--....(((((.(((((((......)))(((((((((((((----((............)))))))))))))))......)))).)))))...........-------- ( -30.70)
>consensus
AUCGUCC__ACCCAACGCCUAUCGAUGUGCCAAUCGUUACGUGACGUU____GACGCAGGUCGUAUUUAACGUUACGU_ACGUAACGGAAAAGCGUUAAUUCAAAUUG_A_UUAUU
.............(((((...(((((......)))((((((((((((.....(((....)))............)))))))))))).))...)))))................... (-19.97 = -21.16 +   1.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:08 2006