Locus 1702

Sequence ID	2R_DroMel_CAF1
Location	6,436,746 – 6,436,912
Length	166
Max. P	0.961289

overview

Window 2

Location	6,436,746 – 6,436,842
Length	96
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	84.16
Mean single sequence MFE	-22.64
Consensus MFE	-12.94
Energy contribution	-14.02
Covariance contribution	1.08
Combinations/Pair	1.04
Mean z-score	-2.53
Structure conservation index	0.57
SVM decision value	0.48
SVM RNA-class probability	0.753209
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6436746 96 - 20766785
AAAUAGCUGGAAACAUGAAGUGCAAUAUACAUAUAUGUAUGUAUGUACGGCA-GCAACAUCGAGUGCAACUUGCUCUCAUCGCCCAUCAAGGCAGCA
.....((((....).....((((((((((((....))))))).)))))))).-((......(((.((.....)).)))...(((......))).)). ( -28.70)
>DroSec_CAF1 12559 79 - 1
AAAUAGCUGGAAACAUGAAGUGCAAUAUA--------UAUGU---------A-GCAACAUCGAGUGCAACUUGCUCUCAUCGCCCAUCAAGGCAGCA
.....((((....)..((..(((.(((..--------..)))---------.-)))...))(((.((.....)).)))...(((......)))))). ( -17.70)
>DroSim_CAF1 11022 88 - 1
AAAUAGCUGGAAACAUGAAGUGCAAUAUA--------UAUGUAUGAACGGCA-GCAACAUCGAGUGCAACUUGCUCUCAUCGCCCAUCAAGGCAGCA
.....((((....).....(((((.....--------..)))))....))).-((......(((.((.....)).)))...(((......))).)). ( -20.00)
>DroEre_CAF1 11080 79 - 1
AAAUAGCUGGAAACAUGAAGUGCAAUAUA--------CA----------GCAGGCAACAUGCAGUGCAACUUGCACUCAUCGCCCAUCAAGGCAGCA
.....((((....)((((.((((((..((--------(.----------((((....).))).)))....)))))))))).(((......)))))). ( -24.00)
>DroYak_CAF1 11253 88 - 1
AAAUAGCUGGCAACAUGAAGUGCAAUAUA--------CACAGCUACAGAGCA-GCAACAUCCAGUGCAACUUGCACUCAUCGCCCAUCAAGGCAGCA
.....((((....)((((.((((((....--------....(((....))).-(((........)))...)))))))))).(((......)))))). ( -22.80)
>consensus
AAAUAGCUGGAAACAUGAAGUGCAAUAUA________UAUGU_U__A__GCA_GCAACAUCGAGUGCAACUUGCUCUCAUCGCCCAUCAAGGCAGCA
.....((((....)((((.(.(((((((((......)))))............(((........)))...)))).))))).(((......)))))). (-12.94 = -14.02 +   1.08)

alignment

secondary structure

dotplot

Window 3

Location	6,436,764 – 6,436,872
Length	108
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	82.85
Mean single sequence MFE	-20.56
Consensus MFE	-10.72
Energy contribution	-11.12
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.66
Structure conservation index	0.52
SVM decision value	0.76
SVM RNA-class probability	0.842355
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6436764 108 - 20766785
CAUCAAAAACUACG-AG--AAAAAUAACCAGUUAAAUAGCUGGAAACAUGAAGUGCAAUAUACAUAUAUGUAUGUAUGUACGGCA-GCAACAUCGAGUGCAACUUGCUCUCA
.............(-(.--........((((((....)))))).....((..((((((((((((....))))))).)))))..))-......))(((.((.....)).))). ( -25.80)
>DroSec_CAF1 12577 90 - 1
CAUCAAAAACUACGA----AAAAAUAACCAGUUAAAUAGCUGGAAACAUGAAGUGCAAUAUA--------UAUGU---------A-GCAACAUCGAGUGCAACUUGCUCUCA
...............----........((((((....))))))......((..(((.(((..--------..)))---------.-)))...))(((.((.....)).))). ( -16.50)
>DroSim_CAF1 11040 101 - 1
CAUCAAAAACUACAGAG--AAAAAUAACCAGUUAAAUAGCUGGAAACAUGAAGUGCAAUAUA--------UAUGUAUGAACGGCA-GCAACAUCGAGUGCAACUUGCUCUCA
..............(((--(.......((((((....)))))).......(((((((.....--------.((((.((.......-.))))))....))).))))..)))). ( -17.80)
>DroEre_CAF1 11098 93 - 1
CAUCAAAAGCAACG-AGCAAAAAAUAACCAGUUAAAUAGCUGGAAACAUGAAGUGCAAUAUA--------CA----------GCAGGCAACAUGCAGUGCAACUUGCACUCA
..(((...((....-.)).........((((((....)))))).....)))(((((((..((--------(.----------((((....).))).)))....))))))).. ( -22.90)
>DroYak_CAF1 11271 100 - 1
CAUCAAAAACUACG-AG--AAAAAUAACCAGUUAAAUAGCUGGCAACAUGAAGUGCAAUAUA--------CACAGCUACAGAGCA-GCAACAUCCAGUGCAACUUGCACUCA
..............-..--........((((((....)))))).....(((.((((((....--------....(((....))).-(((........)))...))))))))) ( -19.80)
>consensus
CAUCAAAAACUACG_AG__AAAAAUAACCAGUUAAAUAGCUGGAAACAUGAAGUGCAAUAUA________UAUGU_U__A__GCA_GCAACAUCGAGUGCAACUUGCUCUCA
...........................((((((....))))))...................................................(((.((.....)).))). (-10.72 = -11.12 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	6,436,802 – 6,436,912
Length	110
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	90.07
Mean single sequence MFE	-16.36
Consensus MFE	-14.46
Energy contribution	-14.42
Covariance contribution	-0.04
Combinations/Pair	1.05
Mean z-score	-1.73
Structure conservation index	0.88
SVM decision value	1.52
SVM RNA-class probability	0.961289
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6436802 110 - 20766785
GAUACUUCGAAAAGUUUCCAAAUGAAUGGUACUAUGAAAACAUCAAAAACUACG-AG--AAAAAUAACCAGUUAAAUAGCUGGAAACAUGAAGUGCAAUAUACAUAUAUGUAU
(.(((((((...(((..(((......))).))).....................-..--........((((((....)))))).....))))))))...(((((....))))) ( -17.70)
>DroSec_CAF1 12606 101 - 1
GAUACUUCGAAAAGUUUCCAAAUGAAUGGUACUAUGAAAACAUCAAAAACUACGA----AAAAAUAACCAGUUAAAUAGCUGGAAACAUGAAGUGCAAUAUA--------UAU
(.(((((((...(((..(((......))).)))......................----........((((((....)))))).....))))))))......--------... ( -16.60)
>DroSim_CAF1 11078 103 - 1
GAUACUUCGAAAAGUUUCCAAAUGAAUGGUACUAUGAAAACAUCAAAAACUACAGAG--AAAAAUAACCAGUUAAAUAGCUGGAAACAUGAAGUGCAAUAUA--------UAU
(.(((((((...(((..(((......))).)))........................--........((((((....)))))).....))))))))......--------... ( -16.60)
>DroEre_CAF1 11128 103 - 1
GGUAUUUCGAAAAGUUUCCAAAUGAAUGGCACUAUGAAAACAUCAAAAGCAACG-AGCAAAAAAUAACCAGUUAAAUAGCUGGAAACAUGAAGUGCAAUAUA--------CA-
.((((((((....(((((((..((..((((....(((.....)))...((....-.))............))))..))..))))))).))))))))......--------..- ( -18.80)
>DroYak_CAF1 11309 101 - 1
GAUAUUUCGAA-ACUUUCCAAAUGAAUGGUACUAUGAAAACAUCAAAAACUACG-AG--AAAAAUAACCAGUUAAAUAGCUGGCAACAUGAAGUGCAAUAUA--------CAC
..(((((.((.-....)).)))))....(((((.(((.....))).........-..--........((((((....))))))........)))))......--------... ( -12.10)
>consensus
GAUACUUCGAAAAGUUUCCAAAUGAAUGGUACUAUGAAAACAUCAAAAACUACG_AG__AAAAAUAACCAGUUAAAUAGCUGGAAACAUGAAGUGCAAUAUA________UAU
(.(((((((...(((..(((......))).)))..................................((((((....)))))).....))))))))................. (-14.46 = -14.42 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:10 2006