Locus 2347

Sequence ID	X_DroMel_CAF1
Location	6,271,874 – 6,272,025
Length	151
Max. P	0.961812

overview

Window 9

Location	6,271,874 – 6,271,987
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.61
Mean single sequence MFE	-26.85
Consensus MFE	-21.66
Energy contribution	-21.22
Covariance contribution	-0.44
Combinations/Pair	1.12
Mean z-score	-2.00
Structure conservation index	0.81
SVM decision value	1.24
SVM RNA-class probability	0.935310
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6271874 113 + 22224390
GCAUUGCACAACAUUGAACAUCAUGCUCGGCUCAUUACAGAAAGCCCCGUUUCAUGGCCAACAAAAUGUUGGC-------CAGGUAAUAAUUCAAAUUGAUGACCGACAUUCGAUCGCAU
....(((.....(((((.....(((.((((.((((((..((((......)))).((((((((.....))))))-------))...............)))))))))))))))))).))). ( -28.90)
>DroSec_CAF1 14204 113 + 1
GCAUUGCACAACAUUGAACAUCAUGCUCGGCUCAUUACAAAAAGCCCCGUUUCAUGGCCAACAAAAUGUUGGC-------CAGGUAAUAAUUCAAAUUGAUGACCGACAUUCGAUCGCAU
....(((.....(((((.....(((.((((.((((((...........(((...((((((((.....))))))-------))...))).........)))))))))))))))))).))). ( -26.85)
>DroSim_CAF1 15752 113 + 1
GCAUUGCACAACAUUGAACAUCAUGCUCGGCUCAUUACAAAAAGCCCCGUUUCAUGGCCAACAAAAUGUUGGC-------CAGGUAAUAAUUCAAAUUGAUGACCGACAUUCGAUCGCAU
....(((.....(((((.....(((.((((.((((((...........(((...((((((((.....))))))-------))...))).........)))))))))))))))))).))). ( -26.85)
>DroEre_CAF1 3215 113 + 1
ACAUUGCACAACAUUGAACAUCAUGCUCGGCUCAUUACAAAAAGCACUGUUUCAUGGCCAACAAAAUGUUGGC-------CAGGUAAUAAUUCAAAUUGAUGACCGACAUUCGAUCGCAU
....(((.....(((((.....(((.((((.((((((..........((((...((((((((.....))))))-------))...))))........)))))))))))))))))).))). ( -27.97)
>DroYak_CAF1 11367 120 + 1
AUAUUGCACAACAUUGAACAUCAUGCUCGGCUCAUUACGAAAAAUCCCGUUUCAUGGCCAACAAAAUGUUGGUACAGGUACAGGUUAUAAUUCAAAUUCAUGACCGACAUUCGAUCGCAU
....(((.(((((((((.(.....).))(((.(((.(((........)))...)))))).....)))))))......((...(((((((((....))).)))))).))........))). ( -23.70)
>consensus
GCAUUGCACAACAUUGAACAUCAUGCUCGGCUCAUUACAAAAAGCCCCGUUUCAUGGCCAACAAAAUGUUGGC_______CAGGUAAUAAUUCAAAUUGAUGACCGACAUUCGAUCGCAU
....(((.....(((((.....(((.((((.((((((((..((((...))))..))((((((.....))))))........................)))))))))))))))))).))). (-21.66 = -21.22 +  -0.44)

alignment

secondary structure

dotplot

Window 0

Location	6,271,874 – 6,271,987
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.61
Mean single sequence MFE	-34.16
Consensus MFE	-27.58
Energy contribution	-28.22
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-2.16
Structure conservation index	0.81
SVM decision value	1.53
SVM RNA-class probability	0.961812
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6271874 113 - 22224390
AUGCGAUCGAAUGUCGGUCAUCAAUUUGAAUUAUUACCUG-------GCCAACAUUUUGUUGGCCAUGAAACGGGGCUUUCUGUAAUGAGCCGAGCAUGAUGUUCAAUGUUGUGCAAUGC
.((((((((.....)))))..((((((((((.(((((.((-------((((((.....)))))))).)......(((((........))))).....)))))))))).)))).))).... ( -36.30)
>DroSec_CAF1 14204 113 - 1
AUGCGAUCGAAUGUCGGUCAUCAAUUUGAAUUAUUACCUG-------GCCAACAUUUUGUUGGCCAUGAAACGGGGCUUUUUGUAAUGAGCCGAGCAUGAUGUUCAAUGUUGUGCAAUGC
.((((((((.....)))))..((((((((((.(((((.((-------((((((.....)))))))).)......(((((........))))).....)))))))))).)))).))).... ( -36.30)
>DroSim_CAF1 15752 113 - 1
AUGCGAUCGAAUGUCGGUCAUCAAUUUGAAUUAUUACCUG-------GCCAACAUUUUGUUGGCCAUGAAACGGGGCUUUUUGUAAUGAGCCGAGCAUGAUGUUCAAUGUUGUGCAAUGC
.((((((((.....)))))..((((((((((.(((((.((-------((((((.....)))))))).)......(((((........))))).....)))))))))).)))).))).... ( -36.30)
>DroEre_CAF1 3215 113 - 1
AUGCGAUCGAAUGUCGGUCAUCAAUUUGAAUUAUUACCUG-------GCCAACAUUUUGUUGGCCAUGAAACAGUGCUUUUUGUAAUGAGCCGAGCAUGAUGUUCAAUGUUGUGCAAUGU
.((((((((.....)))))..((((((((((.(((.(.((-------((((((.....)))))))).).....((((((...((.....)).))))))))))))))).)))).))).... ( -33.20)
>DroYak_CAF1 11367 120 - 1
AUGCGAUCGAAUGUCGGUCAUGAAUUUGAAUUAUAACCUGUACCUGUACCAACAUUUUGUUGGCCAUGAAACGGGAUUUUUCGUAAUGAGCCGAGCAUGAUGUUCAAUGUUGUGCAAUAU
.((((((((.....))))).............(((((..(((....))).((((((.((((((((((...(((((....))))).))).))).)))).))))))....)))))))).... ( -28.70)
>consensus
AUGCGAUCGAAUGUCGGUCAUCAAUUUGAAUUAUUACCUG_______GCCAACAUUUUGUUGGCCAUGAAACGGGGCUUUUUGUAAUGAGCCGAGCAUGAUGUUCAAUGUUGUGCAAUGC
.((((((((.....)))))..((((((((((................((((((.....))))))((((......(((((........)))))...))))..)))))).)))).))).... (-27.58 = -28.22 +   0.64)

alignment

secondary structure

dotplot

Window 1

Location	6,271,914 – 6,272,025
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.36
Mean single sequence MFE	-37.08
Consensus MFE	-26.90
Energy contribution	-27.14
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.99
Structure conservation index	0.73
SVM decision value	0.19
SVM RNA-class probability	0.627845
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6271914 111 - 22224390
GGACAAGUGAGCCUGAUUGGGGCUACCGCAAA--UUCGGGAUGCGAUCGAAUGUCGGUCAUCAAUUUGAAUUAUUACCUG-------GCCAACAUUUUGUUGGCCAUGAAACGGGGCUUU
........((((((((((((.((..(((....--..)))...))(((((.....))))).))))))..........(.((-------((((((.....)))))))).).....)))))). ( -36.30)
>DroSec_CAF1 14244 111 - 1
GGACAAGUGAGCCUGAUUGGGGCUCCCGCAAA--UUCGGGAUGCGAUCGAAUGUCGGUCAUCAAUUUGAAUUAUUACCUG-------GCCAACAUUUUGUUGGCCAUGAAACGGGGCUUU
........((((((((((((.(((((((....--..))))).))(((((.....))))).))))))..........(.((-------((((((.....)))))))).).....)))))). ( -40.80)
>DroSim_CAF1 15792 111 - 1
GGACAAGUGAGCCUGAUUGGGGCUCCCGCAAA--UUCGGGAUGCGAUCGAAUGUCGGUCAUCAAUUUGAAUUAUUACCUG-------GCCAACAUUUUGUUGGCCAUGAAACGGGGCUUU
........((((((((((((.(((((((....--..))))).))(((((.....))))).))))))..........(.((-------((((((.....)))))))).).....)))))). ( -40.80)
>DroEre_CAF1 3255 111 - 1
AGACAAGUGAGCCUGAUUGUGCCUCCCGCAAG--CUCGGGAUGCGAUCGAAUGUCGGUCAUCAAUUUGAAUUAUUACCUG-------GCCAACAUUUUGUUGGCCAUGAAACAGUGCUUU
........(((((((((((.((.(((((....--..))))).))(((((.....)))))..))))...........(.((-------((((((.....)))))))).)...))).)))). ( -38.20)
>DroYak_CAF1 11407 120 - 1
GGACAAGUGAGCCUGAUUGUGCCAGCCGCAAAAUUUCGGGAUGCGAUCGAAUGUCGGUCAUGAAUUUGAAUUAUAACCUGUACCUGUACCAACAUUUUGUUGGCCAUGAAACGGGAUUUU
...((((((..(((((...(((.....))).....)))))...)(((((.....)))))....)))))........(((((..(....(((((.....)))))....)..)))))..... ( -29.30)
>consensus
GGACAAGUGAGCCUGAUUGGGGCUCCCGCAAA__UUCGGGAUGCGAUCGAAUGUCGGUCAUCAAUUUGAAUUAUUACCUG_______GCCAACAUUUUGUUGGCCAUGAAACGGGGCUUU
...((((((..((((((((.(.....).)))....)))))...)(((((.....)))))....)))))........((((.......((((((.....)))))).......))))..... (-26.90 = -27.14 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:22 2006