Locus 4562

Sequence ID	3R_DroMel_CAF1
Location	12,066,208 – 12,066,430
Length	222
Max. P	0.932393

overview

Window 9

Location	12,066,208 – 12,066,310
Length	102
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.50
Mean single sequence MFE	-25.36
Consensus MFE	-20.06
Energy contribution	-21.06
Covariance contribution	1.00
Combinations/Pair	1.07
Mean z-score	-2.04
Structure conservation index	0.79
SVM decision value	1.04
SVM RNA-class probability	0.904437
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12066208 102 + 27905053
CCAUUA------------------UAACAGUAGGGUUUCCUUCAACCAUCUGGUACAGUCAUCCCUUCCCCGCGAGAUACAUAGUACCCGGGGACCCAUUAUACCGCCGUUGAUAACCAA
......------------------.........((((....(((((....(((((.(((.......((((((.(.(.(((...)))))))))))...))).)))))..))))).)))).. ( -21.20)
>DroSec_CAF1 2807 120 + 1
CCAUUAUAUUAUCCAAAUAUUCCAUAACAGUACGGUUGCCUUCAACCAUCUGGUACAGUCAUCCCUUCCCCGCGAGAUACAUAGUACCCGGGGACCCAUUGUACCGCCGUUGAUAACCAA
.................................(((((...(((((....(((((((((.......((((((.(.(.(((...)))))))))))...)))))))))..)))))))))).. ( -27.60)
>DroSim_CAF1 3238 120 + 1
CCAUUAUAUUAUCCAACUAUUCCAUAACAGUAAGGUUUCCUUCAACCAUCUGGUACAGUCAUCCCUUCCCCGCGAGAUACAUAGUACCCGGGGACCCAUUGUACCGCCGUUGAUAACCAA
.................................((((....(((((....(((((((((.......((((((.(.(.(((...)))))))))))...)))))))))..))))).)))).. ( -27.40)
>DroEre_CAF1 4776 119 + 1
CA-UUAUAUUGUCCAACUACUCCAUAACAGUAAGGCUUCCCUCUACCAUCUGGUACAGUCGUCCCUUCCCCACGAUAUACAUGGUACCCGGGGACUCAUUGUGCCACAGUUGAUAACCAA
..-.....(((((.((((...........((((((....))).)))....(((((((((.((((((...(((.(.....).))).....))))))..))))))))).))))))))).... ( -29.20)
>DroYak_CAF1 4854 120 + 1
CCUUUAGAUUGUCCAACUACUCCAUAACAGUAAGGCUUCUCUCUACCAUCUGGUACAGUCAUCCCUUCCCCGCGAGAUACAUAGUACCCGUGGACCCAUUGUACCACAGUUGAUAACCAA
......(.(((((.((((........(((((((((.....((.((((....)))).)).....))))..(((((.(.(((...))).))))))....))))).....))))))))).).. ( -21.42)
>consensus
CCAUUAUAUUAUCCAACUACUCCAUAACAGUAAGGUUUCCUUCAACCAUCUGGUACAGUCAUCCCUUCCCCGCGAGAUACAUAGUACCCGGGGACCCAUUGUACCGCCGUUGAUAACCAA
.................................((((....(((((....(((((((((.......((((((.(..((.....))..)))))))...)))))))))..))))).)))).. (-20.06 = -21.06 +   1.00)

alignment

secondary structure

dotplot

Window 0

Location	12,066,310 – 12,066,430
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-33.39
Consensus MFE	-31.82
Energy contribution	-32.02
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.53
Structure conservation index	0.95
SVM decision value	1.22
SVM RNA-class probability	0.932393
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12066310 120 + 27905053
UAGCGAUAGCCUCGACCAGUUGCAUGUCCGUCAUCAGCUGGACGAGAACUCGAACUACCUUUGUACCCCUGUCGAUGGGGAAUAAAAAAUAAACCCCAAUCUCGUUCGCCUCGAAGUAAU
..((((.........(((((((.(((.....))))))))))((((((..((((..(((....)))......))))(((((.............))))).))))))))))........... ( -32.82)
>DroSec_CAF1 2927 120 + 1
UAGCGAUAGCCUCGACCAGUUGCAUGUCCGUCAUCAGCUGGACGAGAACCCGAACUACCUUUGUACCCCUGUCGAUGGGGAAUAAAAAAUAAACCCCAAUCUCGUUCGCCUCGAAGUAAU
..((((....((((.(((((((.(((.....)))))))))).)))).............(((((.((((.......)))).)))))...................))))........... ( -32.30)
>DroSim_CAF1 3358 120 + 1
UAGCGAUAGCCUCGACCAGUUGCAUGUCCGUCAUCAGCUGGACGAGAACCCGAACUACCUUUGUACCCCUGUCGAUGGGGAAUAAAAAAUAAACCCCAAUCUCGUUCGCCUCGAAGUAAU
..((((....((((.(((((((.(((.....)))))))))).)))).............(((((.((((.......)))).)))))...................))))........... ( -32.30)
>DroEre_CAF1 4895 120 + 1
UAGCGAUAGCCUCGACCAGUUGCAUGUCGGUCAUCAGCUGGACGAGAACCCGAACUACCUUUGUACCCCUGUCGAUGGGGAAUAAAAAAUAAACCCCAAUCUCGUUCGCCUCGAAGUAAU
..((((....((((.(((((((.(((.....)))))))))).)))).............(((((.((((.......)))).)))))...................))))........... ( -32.30)
>DroYak_CAF1 4974 120 + 1
UAGCGAUGGCCUCGACCAGUUGCAUGUCCGUCAUCAGCUGGACGAGAACCCGAACUACCUUUGGACCCCUGUCGAUGGGGAAUAAAAAAUAAACCCCAAUCUCGUUCGCCUCAAAGUAAU
....((.(((((((.(((((((.(((.....)))))))))).)))).....((((........(((....)))(((((((.............)))).)))..)))))))))........ ( -37.22)
>consensus
UAGCGAUAGCCUCGACCAGUUGCAUGUCCGUCAUCAGCUGGACGAGAACCCGAACUACCUUUGUACCCCUGUCGAUGGGGAAUAAAAAAUAAACCCCAAUCUCGUUCGCCUCGAAGUAAU
..((((....((((.(((((((.(((.....)))))))))).)))).............(((((.((((.......)))).)))))...................))))........... (-31.82 = -32.02 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:33 2006