Locus 5491

Sequence ID	2R_DroMel_CAF1
Location	17,650,325 – 17,650,485
Length	160
Max. P	0.990407

overview

Window 9

Location	17,650,325 – 17,650,445
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-33.48
Consensus MFE	-31.22
Energy contribution	-31.82
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.68
Structure conservation index	0.93
SVM decision value	1.49
SVM RNA-class probability	0.958827
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17650325 120 + 20766785
UUUCUGACUGCGAGUGACAUUAUUACUGUCACACUGUGUCGCCCGAUGCAGCUUCUCUGCCUUUUAUAAUGCAUUUAUGCUGCAAUUUGUUUGAAUUAGCGGCUCGCGGGCACCAACUUG
.......((((((((((((.......)))))).....(((((.....(((((.....(((.((....)).))).....)))))(((((....))))).)))))))))))........... ( -34.50)
>DroSec_CAF1 3925 120 + 1
UUUCUGACUGCGAGUGACAUUAUUACUGUCACACUGUGUCGCCCGAUGCAGCUCCUCUGCCUUUUAUAAUGCAUUUAUGCUGCAAUUUGUUUGAAUUAGCGGCUCGCGGGCCCCAACUUG
.......((((((((((((.......)))))).....(((((.....(((((.....(((.((....)).))).....)))))(((((....))))).)))))))))))........... ( -34.50)
>DroSim_CAF1 9844 120 + 1
UUUCUGACUGCGAGUGACAUUAUUACUGUCACACUGUGUCGCCCGAUGCAGCUCCUCUGCCUUUUAUAAUGCAUUUAUGCUGCAAUUUGUUUGAAUUAGCGGCUCGCGGGCCCCAACUUG
.......((((((((((((.......)))))).....(((((.....(((((.....(((.((....)).))).....)))))(((((....))))).)))))))))))........... ( -34.50)
>DroEre_CAF1 3988 119 + 1
UUUCUGACUGCCAGUGACAUUAUUACUGUCACACUGUGUCGCCCGAUGCUGCUCCUCUGCCUUUUAUAAUGCAUUUAUGCUGCAAUUUGUUUGAAUUAGCGGCUCGCG-GCCCCAACUUG
.....(((.....((((((.......)))))).....)))((((((.((((((.....((.((....)).))(((((.((........)).))))).))))))))).)-))......... ( -29.40)
>DroYak_CAF1 15260 120 + 1
UUUCUGACUGCGAGUGACAUUAUUACUGUCACACUGUGUCGCCCGAUGCAGCUCCUCUGCCUUUUAUAAUGCAUUUAUGCUGCAAUUUGUUUGAAUUAGCGGCUCGCGGGCCCCAACUUG
.......((((((((((((.......)))))).....(((((.....(((((.....(((.((....)).))).....)))))(((((....))))).)))))))))))........... ( -34.50)
>consensus
UUUCUGACUGCGAGUGACAUUAUUACUGUCACACUGUGUCGCCCGAUGCAGCUCCUCUGCCUUUUAUAAUGCAUUUAUGCUGCAAUUUGUUUGAAUUAGCGGCUCGCGGGCCCCAACUUG
.......((((((((((((.......)))))).....(((((.....(((((.....(((.((....)).))).....)))))(((((....))))).)))))))))))........... (-31.22 = -31.82 +   0.60)

alignment

secondary structure

dotplot

Window 0

Location	17,650,325 – 17,650,445
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-33.40
Consensus MFE	-31.38
Energy contribution	-31.98
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.69
Structure conservation index	0.94
SVM decision value	1.60
SVM RNA-class probability	0.966571
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17650325 120 - 20766785
CAAGUUGGUGCCCGCGAGCCGCUAAUUCAAACAAAUUGCAGCAUAAAUGCAUUAUAAAAGGCAGAGAAGCUGCAUCGGGCGACACAGUGUGACAGUAAUAAUGUCACUCGCAGUCAGAAA
.........(((((((...)))..............((((((.....(((..........))).....))))))..))))(((...(.((((((.......)))))).)...)))..... ( -34.60)
>DroSec_CAF1 3925 120 - 1
CAAGUUGGGGCCCGCGAGCCGCUAAUUCAAACAAAUUGCAGCAUAAAUGCAUUAUAAAAGGCAGAGGAGCUGCAUCGGGCGACACAGUGUGACAGUAAUAAUGUCACUCGCAGUCAGAAA
.........(((((((...)))..............((((((.....(((..........))).....))))))..))))(((...(.((((((.......)))))).)...)))..... ( -34.60)
>DroSim_CAF1 9844 120 - 1
CAAGUUGGGGCCCGCGAGCCGCUAAUUCAAACAAAUUGCAGCAUAAAUGCAUUAUAAAAGGCAGAGGAGCUGCAUCGGGCGACACAGUGUGACAGUAAUAAUGUCACUCGCAGUCAGAAA
.........(((((((...)))..............((((((.....(((..........))).....))))))..))))(((...(.((((((.......)))))).)...)))..... ( -34.60)
>DroEre_CAF1 3988 119 - 1
CAAGUUGGGGC-CGCGAGCCGCUAAUUCAAACAAAUUGCAGCAUAAAUGCAUUAUAAAAGGCAGAGGAGCAGCAUCGGGCGACACAGUGUGACAGUAAUAAUGUCACUGGCAGUCAGAAA
.........((-(.(((((.(((..((.........((((.......))))............))..))).)).))))))(((.....((((((.......)))))).....)))..... ( -28.60)
>DroYak_CAF1 15260 120 - 1
CAAGUUGGGGCCCGCGAGCCGCUAAUUCAAACAAAUUGCAGCAUAAAUGCAUUAUAAAAGGCAGAGGAGCUGCAUCGGGCGACACAGUGUGACAGUAAUAAUGUCACUCGCAGUCAGAAA
.........(((((((...)))..............((((((.....(((..........))).....))))))..))))(((...(.((((((.......)))))).)...)))..... ( -34.60)
>consensus
CAAGUUGGGGCCCGCGAGCCGCUAAUUCAAACAAAUUGCAGCAUAAAUGCAUUAUAAAAGGCAGAGGAGCUGCAUCGGGCGACACAGUGUGACAGUAAUAAUGUCACUCGCAGUCAGAAA
.........(((((((...)))..............((((((.....(((..........))).....))))))..))))(((...(.((((((.......)))))).)...)))..... (-31.38 = -31.98 +   0.60)

alignment

secondary structure

dotplot

Window 1

Location	17,650,365 – 17,650,485
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.00
Mean single sequence MFE	-40.98
Consensus MFE	-34.16
Energy contribution	-35.40
Covariance contribution	1.24
Combinations/Pair	1.03
Mean z-score	-2.37
Structure conservation index	0.83
SVM decision value	2.21
SVM RNA-class probability	0.990407
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17650365 120 - 20766785
UCCAAGUUGCUCCGUAGGCUCCAUCCACUCCAAUCUGAGGCAAGUUGGUGCCCGCGAGCCGCUAAUUCAAACAAAUUGCAGCAUAAAUGCAUUAUAAAAGGCAGAGAAGCUGCAUCGGGC
(((.(((.((((.(..(((.(((....(((......)))......))).)))..))))).))).............((((((.....(((..........))).....))))))..))). ( -36.20)
>DroSec_CAF1 3965 120 - 1
UCCAAGUAGCUCCGUAGGCUCCAUCCACUCCAAUCUGAGGCAAGUUGGGGCCCGCGAGCCGCUAAUUCAAACAAAUUGCAGCAUAAAUGCAUUAUAAAAGGCAGAGGAGCUGCAUCGGGC
(((..(((((((((..(((((((....(((......)))......)))))))..)..(((((.((((......)))))).(((....))).........)))...))))))))...))). ( -43.10)
>DroSim_CAF1 9884 120 - 1
UCCAAGUAGCUCCGUAGGCUCCAUCCACUCCAAUCUGAGGCAAGUUGGGGCCCGCGAGCCGCUAAUUCAAACAAAUUGCAGCAUAAAUGCAUUAUAAAAGGCAGAGGAGCUGCAUCGGGC
(((..(((((((((..(((((((....(((......)))......)))))))..)..(((((.((((......)))))).(((....))).........)))...))))))))...))). ( -43.10)
>DroEre_CAF1 4028 119 - 1
UCCAAGUAGCUCCGUUGGCUCGAUCCACUCCAAUCCGUGGCAAGUUGGGGC-CGCGAGCCGCUAAUUCAAACAAAUUGCAGCAUAAAUGCAUUAUAAAAGGCAGAGGAGCAGCAUCGGGC
.................((((((((..((((....((((((........))-)))).(((((.((((......)))))).(((....))).........)))...))))..).))))))) ( -35.20)
>DroYak_CAF1 15300 120 - 1
UCCAAGCAGCUCCAUCGGCUCCAGCCACUCCGAUCCGCGGCAAGUUGGGGCCCGCGAGCCGCUAAUUCAAACAAAUUGCAGCAUAAAUGCAUUAUAAAAGGCAGAGGAGCUGCAUCGGGC
(((..((((((((.(((((((((((....(((.....)))...))))))))).....(((((.((((......)))))).(((....))).........))).))))))))))...))). ( -47.30)
>consensus
UCCAAGUAGCUCCGUAGGCUCCAUCCACUCCAAUCUGAGGCAAGUUGGGGCCCGCGAGCCGCUAAUUCAAACAAAUUGCAGCAUAAAUGCAUUAUAAAAGGCAGAGGAGCUGCAUCGGGC
(((..((((((((((.(((((((...(((((.......))..)))))))))).))..(((((.((((......)))))).(((....))).........)))...))))))))...))). (-34.16 = -35.40 +   1.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:12 2006