Locus 3705

Sequence ID	2L_DroMel_CAF1
Location	10,801,220 – 10,801,354
Length	134
Max. P	0.994364

overview

Window 9

Location	10,801,220 – 10,801,317
Length	97
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	69.50
Mean single sequence MFE	-31.22
Consensus MFE	-13.60
Energy contribution	-15.12
Covariance contribution	1.52
Combinations/Pair	1.06
Mean z-score	-2.42
Structure conservation index	0.44
SVM decision value	2.47
SVM RNA-class probability	0.994364
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10801220 97 + 22407834
---CCUCCCCUCACCACACCAACCCGCCGCCACGCCCCCUUAUGCACGCCCCGGCUUCGAACGGCGGCAAGUUCAAGUCGCAAUGUUAGGCUUGAACGGA
---...............((.....((((((..((........))..((....)).......))))))..(((((((((.........))))))))))). ( -32.60)
>DroPse_CAF1 36333 88 + 1
UUUGAUCUACUGUACAC-ACAUGCGG---CCGCA---CUGCAUGUGUGCCUCAGCGUCGAAUGGCA--AA--GCAAGUCCCAA-GAUGGGCUUGAGCAAU
((((((...(((..(((-((((((((---.....---)))))))))))...))).))))))..((.--..--.(((((((...-...))))))).))... ( -33.70)
>DroSec_CAF1 34821 94 + 1
---CCUCCCCUCACCACACCAGCCCG---CCACGCCCACUUAUGCACGCCCCGGCUUCGAACGGCGGCAAGUUCAAGUCGCAAUGUUAGGCUUGAACGGA
---...............((.(((.(---((..((........))..((....)).......))))))..(((((((((.........))))))))))). ( -28.70)
>DroSim_CAF1 40045 94 + 1
---CCUCCCCUCUUCAUCACAACCCG---CCACGCCCACCUAUGCACGCCCCGGCUUCGAACGGCGGCAAGUUCAAGUCGCAAUGUUAGGCUUGAACGGA
---..(((...............(((---((..((........))..((....)).......)))))...(((((((((.........)))))))))))) ( -27.40)
>DroPer_CAF1 36047 88 + 1
UUUGAUCUACUGUACAC-ACAUGCGG---CCGCA---CUGCAUGUGUGCCUCAGCGUCGAAUGGCA--AA--GCAAGUCCCAA-GAUGGGCUUGAGCAAU
((((((...(((..(((-((((((((---.....---)))))))))))...))).))))))..((.--..--.(((((((...-...))))))).))... ( -33.70)
>consensus
___CCUCCCCUCUACAC_ACAACCCG___CCACGCCCCCGUAUGCACGCCCCGGCUUCGAACGGCGGCAAGUUCAAGUCGCAAUGUUAGGCUUGAACGGA
..........................................(((.((((............))))))).(((((((((.........)))))))))... (-13.60 = -15.12 +   1.52)

alignment

secondary structure

dotplot

Window 0

Location	10,801,241 – 10,801,354
Length	113
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	82.53
Mean single sequence MFE	-40.97
Consensus MFE	-25.86
Energy contribution	-26.12
Covariance contribution	0.25
Combinations/Pair	1.14
Mean z-score	-1.95
Structure conservation index	0.63
SVM decision value	0.08
SVM RNA-class probability	0.575160
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10801241 113 + 22407834
CGCCGCCACGCCCCCUUAUGCACGCCCCGGCUUCGAACGGCGGCAAGUUCAAGUCGCAAUGUUAGGCUUGAACGGAAAUGGCGGCUUAGCUAGUUUCUAGACAGCUUUUGUUU--
.(((((((..((...........((((((........))).)))..(((((((((.........)))))))))))...)))))))..((((.(((....))))))).......-- ( -44.50)
>DroSec_CAF1 34842 110 + 1
CG---CCACGCCCACUUAUGCACGCCCCGGCUUCGAACGGCGGCAAGUUCAAGUCGCAAUGUUAGGCUUGAACGGAGUUGGCGGAUCAGCUAGUUUCUAGACAACUUUUGUUU--
((---(((.((((..........((((((........))).)))..(((((((((.........))))))))))).))))))).....(((((...)))).)...........-- ( -36.30)
>DroSim_CAF1 40066 110 + 1
CG---CCACGCCCACCUAUGCACGCCCCGGCUUCGAACGGCGGCAAGUUCAAGUCGCAAUGUUAGGCUUGAACGGAGUUGGCGGAUCAGCUAGUUUCUAGACAACUUUUGUUU--
((---(((.((((..........((((((........))).)))..(((((((((.........))))))))))).))))))).....(((((...)))).)...........-- ( -36.30)
>DroEre_CAF1 35672 106 + 1
CG---CCACGCC-CCUCAUGCACGCCCCAUCUUCGAACGGCGGCAAGUUCAAGUCGCAAUGUUAGGCUUGAACGGCGAUGGCGGGCUAGCGCCUUUCUAGCCAGCU---GUUU--
((---(((((((-.....(((.((((............))))))).(((((((((.........))))))))))))).)))))((((((.......))))))....---....-- ( -46.20)
>DroYak_CAF1 35956 109 + 1
CG---CCACGCCCCCUCAUGCACGCCCCGUCUUCGAACGGCGGCAAGUUCAAGUCGCAAUGUUAGGCUUGAACGGCGAUGGCGGAUCAGCUCAUUUCUAGCCAGCUUU-GUUU--
((---(((((((...........(((((((......)))).)))..(((((((((.........))))))))))))).)))))....((((...........))))..-....-- ( -40.70)
>DroAna_CAF1 34259 105 + 1
CG---CAGUG------CAUGCACGCUUUGGCUUCGUACGGCGGCAAGUUCAAGUCGCAAUGUUAGGCUUGAGCAGAGAUGGCCGAUCGGCCAUAUUGCGGCUAGCUUA-GUGCUG
..---(((..------(..((..((....)).......(((.(((((((((((((.........)))))))))....((((((....)))))).)))).))).))...-)..))) ( -41.80)
>consensus
CG___CCACGCCCCCUCAUGCACGCCCCGGCUUCGAACGGCGGCAAGUUCAAGUCGCAAUGUUAGGCUUGAACGGAGAUGGCGGAUCAGCUAGUUUCUAGACAGCUUU_GUUU__
........((((......(((.((((.((....))...))))))).(((((((((.........)))))))))......))))................................ (-25.86 = -26.12 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:04 2006