Locus 2399

Sequence ID	3R_DroMel_CAF1
Location	6,749,537 – 6,749,737
Length	200
Max. P	0.685080

overview

Window 6

Location	6,749,537 – 6,749,657
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.47
Mean single sequence MFE	-23.10
Consensus MFE	-19.61
Energy contribution	-20.37
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-1.67
Structure conservation index	0.85
SVM decision value	0.32
SVM RNA-class probability	0.685080
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6749537 120 - 27905053
GGCCCCAAAAACCACACUUCCGCGUCCCUUAGCCACGCACACAGACGCCAGUGAGUGUCAUAUGUAAAUUCUCCCCUGACGCCAUUGACAAAGACACUUCACUGCAUCCCCAACCCUGCA
.((..................(((((.....((...)).....)))))(((((((((((...(((.(((((......))....))).)))..))))).)))))).............)). ( -22.80)
>DroSec_CAF1 13778 120 - 1
GGCCCCAAAACCCACACUCCCCCCACCCUUAGCCACGCACACAGAUGCCAGUGAGUGUCAUAUGUAAAUUCUCCCCUGACGCCAUUGACAAAGACACUUCACUGCAUCCCCUAGCCUGCA
(((............................((...)).....(((((.((((((((((...(((.(((((......))....))).)))..))))).)))))))))).....))).... ( -24.20)
>DroSim_CAF1 18106 120 - 1
GGCCCCAAAACCCACACUUCCCCCACCCUUAGCCACGCACACAGAUGCCAGUGAGUGUCAUAUGUAAAUUCUCCCCUGACGCCAUUGACAAAGACACUUCACUGCAUCCCCUAGCCUGCA
(((............................((...)).....(((((.((((((((((...(((.(((((......))....))).)))..))))).)))))))))).....))).... ( -24.20)
>DroYak_CAF1 9957 119 - 1
GACCCCAAAACCCGUACUUCCC-CUCCCUUGGCCACGCACACAAAUGCCAGUGAGUGUCAUAUGUAAAUUCUCCCCUGACGCCAUUGACAAAGACACUUCACUGCAUCCCCUGCCCUGCA
......................-........((...(((.....((((.((((((((((...(((.(((((......))....))).)))..))))).)))))))))....)))...)). ( -21.20)
>consensus
GGCCCCAAAACCCACACUUCCCCCACCCUUAGCCACGCACACAGAUGCCAGUGAGUGUCAUAUGUAAAUUCUCCCCUGACGCCAUUGACAAAGACACUUCACUGCAUCCCCUACCCUGCA
(((............................)))..(((....(((((.((((((((((...(((.(((((......))....))).)))..))))).))))))))))........))). (-19.61 = -20.37 +   0.75)

alignment

secondary structure

dotplot

Window 7

Location	6,749,617 – 6,749,737
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	90.34
Mean single sequence MFE	-30.20
Consensus MFE	-19.38
Energy contribution	-19.16
Covariance contribution	-0.22
Combinations/Pair	1.05
Mean z-score	-3.27
Structure conservation index	0.64
SVM decision value	0.04
SVM RNA-class probability	0.553551
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6749617 120 - 27905053
AAAAAUAACACAAAGGCUUGUUCGUGUGAGUGUAUGUGUGUAUGUGUGUGCACAAAAGAGCACUAAAUACAUACAUUCCAGGCCCCAAAAACCACACUUCCGCGUCCCUUAGCCACGCAC
..............((((.(..((((..(((((((((((((((....((((........))))...))))))))))....((.........)))))))..))))..)...))))...... ( -36.60)
>DroSec_CAF1 13858 110 - 1
AAAAAUAACACAAAGGCUUGUUCGUGUGAGUGUGU----------GUGUGCACAAAAGAGCACUAAAUACACACAUUCCAGGCCCCAAAACCCACACUCCCCCCACCCUUAGCCACGCAC
..............((((.....(((.((((((((----------((((((........)))).....))))))))))..((........))...........)))....))))...... ( -25.40)
>DroSim_CAF1 18186 112 - 1
AAAAAUAACACAAAGGCUUGUUCGUGUGAGUGUGU--------GUGUGUGCACAAAAGAGCACUAAAUACACACAUUCCAGGCCCCAAAACCCACACUUCCCCCACCCUUAGCCACGCAC
..............((((.....(((.((((((((--------((((((((........))))...))))))))))))..((........))...........)))....))))...... ( -28.60)
>consensus
AAAAAUAACACAAAGGCUUGUUCGUGUGAGUGUGU________GUGUGUGCACAAAAGAGCACUAAAUACACACAUUCCAGGCCCCAAAACCCACACUUCCCCCACCCUUAGCCACGCAC
..............((((((...(((((.((((..............((((........))))...)))).)))))..)))))).................................... (-19.38 = -19.16 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:38 2006