Locus 5103

Sequence ID	2R_DroMel_CAF1
Location	16,599,870 – 16,600,011
Length	141
Max. P	0.950543

overview

Window 8

Location	16,599,870 – 16,599,971
Length	101
Sequences	4
Columns	101
Reading direction	reverse
Mean pairwise identity	94.72
Mean single sequence MFE	-26.38
Consensus MFE	-24.82
Energy contribution	-25.44
Covariance contribution	0.62
Combinations/Pair	1.06
Mean z-score	-2.05
Structure conservation index	0.94
SVM decision value	1.40
SVM RNA-class probability	0.950543
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16599870 101 - 20766785
AGUUCCGUUCACAUACAUAUAUCGCGGCGGUUGUACUUAUAUAUUUGUAUUAUUUUUAAGUUUAUAAGUAGAAAUGCCGUCGCGAUUCCAAGGCGCCGCGU
.((.((((......))....((((((((((((.((((((((.(((((.........))))).)))))))).)...))))))))))).....)).))..... ( -29.80)
>DroSec_CAF1 7092 101 - 1
AGUUCCGUUCACAUACAUAUAUCUUGGCGGUAGUACUUAUAUAUUUGUAUUAUUUUUAAGUUUAUAAGUAGAAAUGCCGUCGCGAUUCCAAGGCGCCGCGU
.((.((((......))....(((.((((((((.((((((((.(((((.........))))).))))))))....)))))))).))).....)).))..... ( -23.10)
>DroSim_CAF1 7121 101 - 1
AGUUCCGUUCACAUACAUAUAUCUUGGCGGUAGUACUUAUAUAUUUGUAUUAUUUUUAAGUUUAUAAGUAGAAAUGCCGUCGCGAUUCCAAGGCGCCGCGC
.((.((((......))....(((.((((((((.((((((((.(((((.........))))).))))))))....)))))))).))).....)).))..... ( -23.10)
>DroYak_CAF1 7103 97 - 1
AGUUCCGUUCGCA----UAUAUCGUGGCGGUUGUACUUAUAUAUUUGUAUUAUUUUUAAGUUUAUAAGUAGAAAUGCCGUCGCGAUUCCAAGACGCCGCGU
.((..((((....----...((((((((((((.((((((((.(((((.........))))).)))))))).)...))))))))))).....))))..)).. ( -29.50)
>consensus
AGUUCCGUUCACAUACAUAUAUCGUGGCGGUAGUACUUAUAUAUUUGUAUUAUUUUUAAGUUUAUAAGUAGAAAUGCCGUCGCGAUUCCAAGGCGCCGCGU
.((..((((...........((((((((((((.((((((((.(((((.........))))).))))))))....)))))))))))).....))))..)).. (-24.82 = -25.44 +   0.62)

alignment

secondary structure

dotplot

Window 9

Location	16,599,891 – 16,600,011
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.58
Mean single sequence MFE	-26.67
Consensus MFE	-22.70
Energy contribution	-23.51
Covariance contribution	0.81
Combinations/Pair	1.03
Mean z-score	-1.67
Structure conservation index	0.85
SVM decision value	0.17
SVM RNA-class probability	0.618450
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16599891 120 - 20766785
UAGGAACUCAAAACAUUGGGCACUUUAUGGUCAUUAUUCAAGUUCCGUUCACAUACAUAUAUCGCGGCGGUUGUACUUAUAUAUUUGUAUUAUUUUUAAGUUUAUAAGUAGAAAUGCCGU
..((((((........(((.((.....)).))).......)))))).................((((((.((.((((((((.(((((.........))))).)))))))).)).)))))) ( -29.56)
>DroSec_CAF1 7113 120 - 1
CAGGAACUCAAAACAUUGGGCACUUUGUGGUCAUUAUUCAAGUUCCGUUCACAUACAUAUAUCUUGGCGGUAGUACUUAUAUAUUUGUAUUAUUUUUAAGUUUAUAAGUAGAAAUGCCGU
..((((((........(((.(((...))).))).......))))))....................((((((.((((((((.(((((.........))))).))))))))....)))))) ( -27.16)
>DroSim_CAF1 7142 120 - 1
CAGGAACUCAAAACAUUGGGCACUUUGUGGUCAUUAUUCAAGUUCCGUUCACAUACAUAUAUCUUGGCGGUAGUACUUAUAUAUUUGUAUUAUUUUUAAGUUUAUAAGUAGAAAUGCCGU
..((((((........(((.(((...))).))).......))))))....................((((((.((((((((.(((((.........))))).))))))))....)))))) ( -27.16)
>DroYak_CAF1 7124 116 - 1
CAAGAACUCAAAACAUUGGGCACUUUAUAGUCAUUAUUCAAGUUCCGUUCGCA----UAUAUCGUGGCGGUUGUACUUAUAUAUUUGUAUUAUUUUUAAGUUUAUAAGUAGAAAUGCCGU
...((((.(((....)))((.((((.((((...))))..)))).))))))...----........((((.((.((((((((.(((((.........))))).)))))))).)).)))).. ( -22.80)
>consensus
CAGGAACUCAAAACAUUGGGCACUUUAUGGUCAUUAUUCAAGUUCCGUUCACAUACAUAUAUCGUGGCGGUAGUACUUAUAUAUUUGUAUUAUUUUUAAGUUUAUAAGUAGAAAUGCCGU
..((((((........(((.((.....)).))).......))))))..................(((((.((.((((((((.(((((.........))))).)))))))).)).))))). (-22.70 = -23.51 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:36 2006