Locus 6160

Sequence ID	X_DroMel_CAF1
Location	15,723,836 – 15,724,035
Length	199
Max. P	0.996829

overview

Window 2

Location	15,723,836 – 15,723,955
Length	119
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	92.18
Mean single sequence MFE	-28.34
Consensus MFE	-22.30
Energy contribution	-24.22
Covariance contribution	1.92
Combinations/Pair	1.11
Mean z-score	-2.17
Structure conservation index	0.79
SVM decision value	1.30
SVM RNA-class probability	0.939737
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15723836 119 - 22224390
GGUCGGUGCUGCUGAGCAAUAAAGGUAUUAAUUUAUGAAAUCAUUGUUGCGCAGCAAAAAUUGAUCAGAGGAAUAUGAAAAUAAUCGAAUCGAGACGGCACGUCUAAAAGGUGAGCUAA
(((((((..(((((.(((((((.(((.(((.....))).))).))))))).)))))...)))))))....((.(((....))).))..(((.(((((...)))))....)))....... ( -31.40)
>DroSec_CAF1 7378 115 - 1
GGUCGGUGCUGCUGAGCAAUAAAGGUAU----UUAUGAAAUCAUUGUUGCGCAGCAAAAAUUGAUCAGAGGAAUAUGAAAAUAAUCGAACCGAGACGGCACGUCUAAAAGGUAAGCUAA
(((((((..(((((.(((((((.(((..----.......))).))))))).)))))...)))))))....((.(((....))).))..(((.(((((...)))))....)))....... ( -32.80)
>DroSim_CAF1 7328 118 - 1
GGUC-GUGCUGCUGAGCAAUAAAGGUAUUAAUUUAUGAAAUCAUUGUUGCGCAGCAAAAAUUGAUCAGAGGAAUAUGAAAAUAAUCGAAUCGAGACGGCACGUCUAAAAGGUGAGCUAA
((.(-(((((((((.(((((((.(((.(((.....))).))).))))))).)))).....(((((..((....(((....))).))..)))))...)))))).)).............. ( -32.00)
>DroEre_CAF1 7715 119 - 1
GGUCAGUGCUGCUGAGCAACAAAUAUAUUCAUUUAUGAAAUCAUUGUUGCGCAGAAAGAAUUGAACACAGGAAUAUGAAAAUAAUCGAAUCGAAACGGCACGUCUAAAAGGUGAGCUAA
(.((((((((((((.(((((((.....((((....))))....))))))).)))................((.(((....))).)).........)))))).((.....))))).)... ( -25.00)
>DroYak_CAF1 6827 119 - 1
GGUCGGUGCUGCUCGGCAAUAAAAAUAUUAAUUUAUGAAAUCAUUGUUGCGCAGAAAGAAUUGAACACAGGAAUAUGAGAAUAAUCGAAUCGAAACGGCACGUCUAAAAGGUGAGCUAA
..(((((.((((.(((((((....(((......)))......))))))).))))................((.(((....))).))..)))))...(((.(..(.....)..).))).. ( -20.50)
>consensus
GGUCGGUGCUGCUGAGCAAUAAAGGUAUUAAUUUAUGAAAUCAUUGUUGCGCAGCAAAAAUUGAUCAGAGGAAUAUGAAAAUAAUCGAAUCGAGACGGCACGUCUAAAAGGUGAGCUAA
(((((((..(((((.(((((((.(((.(((.....))).))).))))))).)))))...)))))))....((.(((....))).))..(((.(((((...)))))....)))....... (-22.30 = -24.22 +   1.92)

alignment

secondary structure

dotplot

Window 3

Location	15,723,875 – 15,723,995
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.25
Mean single sequence MFE	-25.76
Consensus MFE	-22.92
Energy contribution	-24.44
Covariance contribution	1.52
Combinations/Pair	1.11
Mean z-score	-2.07
Structure conservation index	0.89
SVM decision value	2.75
SVM RNA-class probability	0.996829
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15723875 120 - 22224390
UAGGUAGUUCGUAAAAUUGUAAAUACAGUAAGUCGCAAAAGGUCGGUGCUGCUGAGCAAUAAAGGUAUUAAUUUAUGAAAUCAUUGUUGCGCAGCAAAAAUUGAUCAGAGGAAUAUGAAA
.......((((((..(((((....)))))...........(((((((..(((((.(((((((.(((.(((.....))).))).))))))).)))))...))))))).......)))))). ( -30.10)
>DroSec_CAF1 7417 116 - 1
UAAGUAGUUCGUAAAAUUGUAAAUACAGUAAGUCGCAAAAGGUCGGUGCUGCUGAGCAAUAAAGGUAU----UUAUGAAAUCAUUGUUGCGCAGCAAAAAUUGAUCAGAGGAAUAUGAAA
.......((((((..(((((....)))))...........(((((((..(((((.(((((((.(((..----.......))).))))))).)))))...))))))).......)))))). ( -28.90)
>DroSim_CAF1 7367 119 - 1
UAAGUAGUUCGUAAAAUUGUAAAUACAGUAAGUCGCAAAAGGUC-GUGCUGCUGAGCAAUAAAGGUAUUAAUUUAUGAAAUCAUUGUUGCGCAGCAAAAAUUGAUCAGAGGAAUAUGAAA
.......((((((..(((((....)))))...........((((-(...(((((.(((((((.(((.(((.....))).))).))))))).))))).....))))).......)))))). ( -26.80)
>DroEre_CAF1 7754 120 - 1
UAGAUAGUUCGUAAAAUUGUAAAUACAGUAAGUCGCAAAAGGUCAGUGCUGCUGAGCAACAAAUAUAUUCAUUUAUGAAAUCAUUGUUGCGCAGAAAGAAUUGAACACAGGAAUAUGAAA
.......((((((...((((.....(((((....((.....))...)))))(((.(((((((.....((((....))))....))))))).)))............))))...)))))). ( -23.30)
>DroYak_CAF1 6866 120 - 1
UUGGUAGUUCGUAAAAUUGUAAAUACAGUAAGUCGCAAAAGGUCGGUGCUGCUCGGCAAUAAAAAUAUUAAUUUAUGAAAUCAUUGUUGCGCAGAAAGAAUUGAACACAGGAAUAUGAGA
.......((((((..(((((....)))))...........(.(((((.((((.(((((((....(((......)))......))))))).)))).....))))).).......)))))). ( -19.70)
>consensus
UAGGUAGUUCGUAAAAUUGUAAAUACAGUAAGUCGCAAAAGGUCGGUGCUGCUGAGCAAUAAAGGUAUUAAUUUAUGAAAUCAUUGUUGCGCAGCAAAAAUUGAUCAGAGGAAUAUGAAA
.......((((((..(((((....)))))...........(((((((..(((((.(((((((.(((.(((.....))).))).))))))).)))))...))))))).......)))))). (-22.92 = -24.44 +   1.52)

alignment

secondary structure

dotplot

Window 4

Location	15,723,915 – 15,724,035
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.25
Mean single sequence MFE	-23.19
Consensus MFE	-21.54
Energy contribution	-21.74
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.39
Structure conservation index	0.93
SVM decision value	1.18
SVM RNA-class probability	0.926783
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15723915 120 + 22224390
UUUCAUAAAUUAAUACCUUUAUUGCUCAGCAGCACCGACCUUUUGCGACUUACUGUAUUUACAAUUUUACGAACUACCUAUGAAAAUUGUGACAAUGAUUUUAGUAGGUUAAAGGUCUUU
......................((((....))))..(((((((...((((((((((((((((((((((...(......)...))))))))))..)))....))))))))))))))))... ( -23.10)
>DroSec_CAF1 7457 116 + 1
UUUCAUAA----AUACCUUUAUUGCUCAGCAGCACCGACCUUUUGCGACUUACUGUAUUUACAAUUUUACGAACUACUUAUGAAAAUUGUGACAAUGAUUUUAGUAGGUUAAAGGUCUUU
........----..........((((....))))..(((((((...((((((((((((((((((((((...((....))...))))))))))..)))....))))))))))))))))... ( -23.50)
>DroSim_CAF1 7407 119 + 1
UUUCAUAAAUUAAUACCUUUAUUGCUCAGCAGCAC-GACCUUUUGCGACUUACUGUAUUUACAAUUUUACGAACUACUUAUGAAAAUUGUGACAAUGAUUUUAGUAGGUUAAAGGUCUUU
......................((((....)))).-(((((((...((((((((((((((((((((((...((....))...))))))))))..)))....))))))))))))))))... ( -23.50)
>DroEre_CAF1 7794 120 + 1
UUUCAUAAAUGAAUAUAUUUGUUGCUCAGCAGCACUGACCUUUUGCGACUUACUGUAUUUACAAUUUUACGAACUAUCUAUGAAAAUUGCGACAAUGAUUUUAGUAGGUUAAAGGUCUUU
.((((....))))......((((((...))))))..(((((((...(((((((((...((((((((((..((....))....)))))))......)))...))))))))))))))))... ( -23.90)
>DroYak_CAF1 6906 120 + 1
UUUCAUAAAUUAAUAUUUUUAUUGCCGAGCAGCACCGACCUUUUGCGACUUACUGUAUUUACAAUUUUACGAACUACCAAUGAAAAUUGUGACAAUGAUUUUAGUAGGUUAAAGGUCUUU
......................(((......)))..(((((((...((((((((((((((((((((((..............))))))))))..)))....))))))))))))))))... ( -21.94)
>consensus
UUUCAUAAAUUAAUACCUUUAUUGCUCAGCAGCACCGACCUUUUGCGACUUACUGUAUUUACAAUUUUACGAACUACCUAUGAAAAUUGUGACAAUGAUUUUAGUAGGUUAAAGGUCUUU
......................(((......)))..(((((((...((((((((((((((((((((((..............))))))))))..)))....))))))))))))))))... (-21.54 = -21.74 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:01 2006