Locus 3551

Sequence ID	2R_DroMel_CAF1
Location	11,865,423 – 11,865,540
Length	117
Max. P	0.654404

overview

Window 8

Location	11,865,423 – 11,865,515
Length	92
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	80.00
Mean single sequence MFE	-27.24
Consensus MFE	-23.14
Energy contribution	-22.94
Covariance contribution	-0.20
Combinations/Pair	1.09
Mean z-score	-1.38
Structure conservation index	0.85
SVM decision value	0.23
SVM RNA-class probability	0.646454
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11865423 92 + 20766785
UGUGCUCCA-------------UCG--CU----CCACCUAUGUGCUAUCUUUCGAAUCACGGAUGAUGGCUCCUGUGGCAUGUAAUGAGUUUUCCAUUGCCCCGCACACGG
(((((....-------------...--..----((((....(.((((((.((((.....)))).)))))).)..))))...((((((.......))))))...)))))... ( -25.70)
>DroSec_CAF1 5992 98 + 1
CGUGCUCCA-------AGUUCUCCU--CU----CCCACUAUGUGCUAUCUUUCGAAUCCCGGAUGAUGGCUCCUGUGGCAUGUAAUGAGUUUUCCAUUGCCCCGCACACGG
.((((....-------.........--..----.((((...(.((((((.((((.....)))).)))))).)..))))...((((((.......))))))...)))).... ( -27.60)
>DroSim_CAF1 5389 105 + 1
CGUGCUCCAAGAUCCAAGCUCUCCU--CU----CCCACUAUGUGCUAUCUUUCGAAUCCCGGAUGAUGGCUCCUGUGGCAUGUAAUGAGUUUUCCAUUGCCCCGCACACGG
.((((..(((.....((((((....--(.----.((((...(.((((((.((((.....)))).)))))).)..))))...)....))))))....)))....)))).... ( -28.80)
>DroEre_CAF1 5922 105 + 1
CCUGAUCCC------CUGCUCCCCUUGCUCCUGCCUUCUAUGUGCUAUCUUCCAAAUGCCGGAUGAUGGCUCUUGUGGCAUGUAAUGAGUUUUCCAUUGCCCCGCACACGG
.........------.....((...(((...((((..(...(.((((((.(((.......))).)))))).)..).)))).((((((.......))))))...)))...)) ( -24.50)
>DroYak_CAF1 5918 95 + 1
CCG---------------C-CUCUCUGCUCCUGGCUCCUAUCUGCUAUCUUCCGAAUCCCGGAUGAUGGCUCCUGUGGCAUGUAAUGAGUUUUCCAUUGCCCCGCACACGG
..(---------------(-(...........)))........((((((.((((.....)))).))))))..(((((((..((((((.......))))))...)).))))) ( -29.60)
>consensus
CGUGCUCCA________GCUCUCCU__CU____CCCACUAUGUGCUAUCUUUCGAAUCCCGGAUGAUGGCUCCUGUGGCAUGUAAUGAGUUUUCCAUUGCCCCGCACACGG
...........................................((((((.((((.....)))).))))))..(((((((..((((((.......))))))...)).))))) (-23.14 = -22.94 +  -0.20)

alignment

secondary structure

dotplot

Window 9

Location	11,865,444 – 11,865,540
Length	96
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	80.85
Mean single sequence MFE	-27.70
Consensus MFE	-18.71
Energy contribution	-19.41
Covariance contribution	0.70
Combinations/Pair	1.26
Mean z-score	-1.53
Structure conservation index	0.68
SVM decision value	0.25
SVM RNA-class probability	0.654404
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11865444 96 + 20766785
UGUGCUAUCUUUCGAAUCACGGAUGAUGGCUCCUGUGGCAUGUAAUGAGUUUUCCAUUGCCCCGC---ACACGGUGCAU------CAGGUUACCC---------GUACCUACAU
(((((((((.((((.....)))).))))))..(((((((..((((((.......))))))...))---.))))).))).------.((((.....---------..)))).... ( -26.80)
>DroSec_CAF1 6019 96 + 1
UGUGCUAUCUUUCGAAUCCCGGAUGAUGGCUCCUGUGGCAUGUAAUGAGUUUUCCAUUGCCCCGC---ACACGGUGCAU------CAGGUAACCC---------GUACCUACAU
(((((((((.((((.....)))).))))))..(((((((..((((((.......))))))...))---.))))).))).------.(((((....---------.))))).... ( -28.30)
>DroSim_CAF1 5423 96 + 1
UGUGCUAUCUUUCGAAUCCCGGAUGAUGGCUCCUGUGGCAUGUAAUGAGUUUUCCAUUGCCCCGC---ACACGGUGCAU------CAGGUUACCC---------GUACCUACAU
(((((((((.((((.....)))).))))))..(((((((..((((((.......))))))...))---.))))).))).------.((((.....---------..)))).... ( -27.20)
>DroEre_CAF1 5956 96 + 1
UGUGCUAUCUUCCAAAUGCCGGAUGAUGGCUCUUGUGGCAUGUAAUGAGUUUUCCAUUGCCCCGC---ACACGGUGCAU------CAGGUUUCCU---------GCACCUACAU
.(.((((((.(((.......))).)))))).).(((((...((((((.......)))))).))))---)...((((((.------..((...)))---------)))))..... ( -30.20)
>DroYak_CAF1 5942 96 + 1
UCUGCUAUCUUCCGAAUCCCGGAUGAUGGCUCCUGUGGCAUGUAAUGAGUUUUCCAUUGCCCCGC---ACACGGUGCAU------CAGGUUUCCU---------GUACCUACAU
...((((((.((((.....)))).))))))...(((((...((((((.......)))))).))))---)...((((((.------..((...)))---------)))))..... ( -30.50)
>DroAna_CAF1 5667 104 + 1
----------CCUGGUUUCUGGCUCCUGGUUCCUGUGGCAUGUAAUGAGUUUUCCAUUGCCUUCCAUUACACGCUGCAUCUGCGUCAGGUUACCCCGUUUUCCAAUACCCCUGU
----------..(((....(((..(((((..(.((..((.(((((((.................))))))).))..))...)..))))).....)))....))).......... ( -23.23)
>consensus
UGUGCUAUCUUCCGAAUCCCGGAUGAUGGCUCCUGUGGCAUGUAAUGAGUUUUCCAUUGCCCCGC___ACACGGUGCAU______CAGGUUACCC_________GUACCUACAU
...((((((.((((.....)))).))))))....((((...((((((.......)))))).)))).......(((((..........((....)).........)))))..... (-18.71 = -19.41 +   0.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:14 2006