Locus 6622

Sequence ID	3R_DroMel_CAF1
Location	17,423,365 – 17,423,482
Length	117
Max. P	0.998736

overview

Window 1

Location	17,423,365 – 17,423,462
Length	97
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	93.21
Mean single sequence MFE	-24.84
Consensus MFE	-23.50
Energy contribution	-23.90
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.95
Structure conservation index	0.95
SVM decision value	3.21
SVM RNA-class probability	0.998736
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17423365 97 + 27905053
AAAA-------UAAAAUAGCAACUACAGCGGCAGCCGGGUCAUUAUGCGCAUGUGUCGCCCAUUAUCGUAUAAUGUCGCCGGCGAUCUCCAA---ACAAUACAUCCA
....-------.......((..(....)..)).((((((.(((((((((...(((.....)))...))))))))).).))))).........---............ ( -25.90)
>DroSec_CAF1 27298 104 + 1
AAAAUAAAAAAUAAAAUAGCAACUACAGCGGCAGCCGGGUCAUUAUGCGCAUGUGUCGCCCAUUAUCGUAUAAUGUCGCCGGCGAUCUCCAA---AGAAUACAUCCA
..................((..(....)..)).((((((.(((((((((...(((.....)))...))))))))).).))))).........---............ ( -25.90)
>DroSim_CAF1 24744 104 + 1
AAAAUAAAAAAUAAAAUAGCAACUACAGCGGCAGCCGGGUCAUUAUGCGCAUGUGUCGCCCAUUAUCGUAUAAUGUCGCCGGCGAUCUCCAA---ACAAUACAUCCA
..................((..(....)..)).((((((.(((((((((...(((.....)))...))))))))).).))))).........---............ ( -25.90)
>DroEre_CAF1 27057 100 + 1
AAAA-------UAAAAUAGCAACUACAGCGGCAGGCGGGUCAUUAUGCGCAUGUGUCGCCCAUUAUAGUAUAAUGUCGCCGGCGAUCUCCACACCACAAUACAUCCA
....-------.......((.......)).((.(((((..((((((((....(((.....)))....))))))))))))).))........................ ( -20.60)
>DroYak_CAF1 25098 97 + 1
AAAA-------UAAAAUAGCAACUACAGCGGCAGCCGGGUCAUUAUGCGCAUGUGUCGCCCAUUAUCGUAUAAUGUCGCCGGCGAUCUCCAA---ACAAUACAUCCA
....-------.......((..(....)..)).((((((.(((((((((...(((.....)))...))))))))).).))))).........---............ ( -25.90)
>consensus
AAAA_______UAAAAUAGCAACUACAGCGGCAGCCGGGUCAUUAUGCGCAUGUGUCGCCCAUUAUCGUAUAAUGUCGCCGGCGAUCUCCAA___ACAAUACAUCCA
..................((..(....)..)).((((((.(((((((((...(((.....)))...))))))))).).)))))........................ (-23.50 = -23.90 +   0.40)

alignment

secondary structure

dotplot

Window 2

Location	17,423,389 – 17,423,482
Length	93
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	92.72
Mean single sequence MFE	-25.00
Consensus MFE	-23.10
Energy contribution	-23.70
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.01
Structure conservation index	0.92
SVM decision value	3.08
SVM RNA-class probability	0.998362
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17423389 93 + 27905053
CAGCCGGGUCAUUAUGCGCAUGUGUCGCCCAUUAUCGUAUAAUGUCGCCGGCGAUCUCCAA---ACAAUACAUCCACUGCAGUUACUAUGCAAA-----CC
..((((((.(((((((((...(((.....)))...))))))))).).))))).........---.............((((.......))))..-----.. ( -27.00)
>DroSec_CAF1 27329 93 + 1
CAGCCGGGUCAUUAUGCGCAUGUGUCGCCCAUUAUCGUAUAAUGUCGCCGGCGAUCUCCAA---AGAAUACAUCCACUGCAGUUACUAUGCACA-----CU
..((((((.(((((((((...(((.....)))...))))))))).).))))).........---.............((((.......))))..-----.. ( -26.70)
>DroSim_CAF1 24775 93 + 1
CAGCCGGGUCAUUAUGCGCAUGUGUCGCCCAUUAUCGUAUAAUGUCGCCGGCGAUCUCCAA---ACAAUACAUCCACUGCAGUUACUAUGCACA-----CU
..((((((.(((((((((...(((.....)))...))))))))).).))))).........---.............((((.......))))..-----.. ( -26.70)
>DroEre_CAF1 27081 96 + 1
CAGGCGGGUCAUUAUGCGCAUGUGUCGCCCAUUAUAGUAUAAUGUCGCCGGCGAUCUCCACACCACAAUACAUCCACUUCAGUUACUAUGCAUA-----AU
..(((((..((((((((....(((.....)))....)))))))))))))((.(.......).))..............................-----.. ( -17.80)
>DroYak_CAF1 25122 98 + 1
CAGCCGGGUCAUUAUGCGCAUGUGUCGCCCAUUAUCGUAUAAUGUCGCCGGCGAUCUCCAA---ACAAUACAUCCACUGCAGUUACUAUGCAUACCACUAU
..((((((.(((((((((...(((.....)))...))))))))).).))))).........---.............((((.......))))......... ( -26.80)
>consensus
CAGCCGGGUCAUUAUGCGCAUGUGUCGCCCAUUAUCGUAUAAUGUCGCCGGCGAUCUCCAA___ACAAUACAUCCACUGCAGUUACUAUGCACA_____CU
..((((((.(((((((((...(((.....)))...))))))))).).))))).........................((((.......))))......... (-23.10 = -23.70 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:08 2006