Locus 4040

Sequence ID	2R_DroMel_CAF1
Location	13,338,030 – 13,338,217
Length	187
Max. P	0.959905

overview

Window 9

Location	13,338,030 – 13,338,149
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	79.35
Mean single sequence MFE	-24.23
Consensus MFE	-12.12
Energy contribution	-12.50
Covariance contribution	0.38
Combinations/Pair	1.08
Mean z-score	-3.08
Structure conservation index	0.50
SVM decision value	1.51
SVM RNA-class probability	0.959905
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13338030 119 - 20766785
CUUCCUUAACUUGAACUGUCCAUAACUAAGACGGCUUAUUCAUAGAAGGUGGGUUCUCCGAAUCUCACUCUCAUGACUAAAUCAUAUU-GUAUACAUAUAUACAUAUUUAUAUAUUUCUA
...........(((.(((((.........))))).(((.((((.((..((((((((...))))).)))..)))))).))).)))...(-(((((.((((....)))).))))))...... ( -19.60)
>DroSec_CAF1 37429 118 - 1
CUUCCUUAACUCGAACUGUCCAUAACUAAGACGGCUUAUUCAUGGGA-GUGGGUUCUCCGAAUCUCACUCUCAUGACUAAAUCAUAUU-AUAUAUGUAUAUACAUAUUUAUAUGUUUCUA
...............(((((.........))))).(((.((((((((-((((((((...))))).))))))))))).)))..(((((.-..((((((....))))))..)))))...... ( -31.30)
>DroSim_CAF1 39293 111 - 1
CUUCCUUAACUCGAACUGUCCAUAACUAAGACGGCUUAUUCAUAGGA-GUGGGUUCUUCGAAUCUCACUCUCAUGACUAAAUCAUAUU-AUAUAUGUAU-------UAUAUAUGUUUCUA
............((.(((((.........))))).(((.((((..((-((((((((...))))).)))))..)))).))).))....(-(((((((...-------))))))))...... ( -22.00)
>DroYak_CAF1 38867 92 - 1
CUUUCUUAACGCGAACUGUCCAUAACUGAGAUGGCUUAUUCAUAAGA-GUGCCUUCUCCGAAU--CACUCUCAUGACUAAGUCAUACUCGUAUAU-------------------------
...........................(((((((((((.((((.(((-(((..(((...))).--)))))).)))).)))))))).)))......------------------------- ( -24.00)
>consensus
CUUCCUUAACUCGAACUGUCCAUAACUAAGACGGCUUAUUCAUAGGA_GUGGGUUCUCCGAAUCUCACUCUCAUGACUAAAUCAUAUU_AUAUAUGUAU_______UUUAUAUGUUUCUA
............((.(((((.........))))).(((.((((.(((.((((((((...))))).)))))).)))).))).))..................................... (-12.12 = -12.50 +   0.38)

alignment

secondary structure

dotplot

Window 0

Location	13,338,109 – 13,338,217
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	96.11
Mean single sequence MFE	-30.36
Consensus MFE	-29.02
Energy contribution	-28.70
Covariance contribution	-0.32
Combinations/Pair	1.08
Mean z-score	-1.38
Structure conservation index	0.96
SVM decision value	1.25
SVM RNA-class probability	0.935582
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13338109 108 - 20766785
ACAGGGCGUUGCAGCUGCGGCGGCAUGGCAAUAUUAAAAAAUAGCUGCACUUGCUGCAUAACGUCGGACUUCCUUAACUUGAACUGUCCAUAACUAAGACGGCUUAUU
....(((((((((((((((((.((...))..((((....))))))))))...))))))..)))))((....))......(((.(((((.........))))).))).. ( -29.30)
>DroSec_CAF1 37507 108 - 1
ACAGGGCGUUGCAGCUGCGGCGGCAUAGCAAUAUUAAAAAAUAGCUGCACUUGCUGCAUAACGUCGGACUUCCUUAACUCGAACUGUCCAUAACUAAGACGGCUUAUU
..(((.(((((((((((((((.((...))..((((....))))))))))...)))))........(((((((........)))..))))........)))).)))... ( -29.20)
>DroSim_CAF1 39364 108 - 1
ACAGGGCGUUGCAGCUGCGGCGGCAUAGCAAUAUUAAAAAAUAGCUGCACUUGCUGCAUAACGUCGGACUUCCUUAACUCGAACUGUCCAUAACUAAGACGGCUUAUU
..(((.(((((((((((((((.((...))..((((....))))))))))...)))))........(((((((........)))..))))........)))).)))... ( -29.20)
>DroEre_CAF1 38295 108 - 1
ACAGGGCGUUGCAGCUGCGGCGGCAUAGUAAUAUUAAAAAAUAGCUGCACUUGCUGCAUAACGUCGGGCUUUCUUAACUCCAACUGUCCAUAACUAAGAUGGCUUAUU
....(((((((((((....(((((...................)))))....))))))..)))))(((((.(((((..................))))).)))))... ( -30.68)
>DroYak_CAF1 38919 108 - 1
ACAGGGCGUUGCAGCUGCGGCGGCAUGGCAAUAUUAAAAAAUAGCUGCACUUGCUGCAUAACGUCGGACUUUCUUAACGCGAACUGUCCAUAACUGAGAUGGCUUAUU
.((((((((((((((((((((.((...))..((((....))))))))))...))))))..)))))((((.(((.......)))..))))....)))............ ( -33.40)
>consensus
ACAGGGCGUUGCAGCUGCGGCGGCAUAGCAAUAUUAAAAAAUAGCUGCACUUGCUGCAUAACGUCGGACUUCCUUAACUCGAACUGUCCAUAACUAAGACGGCUUAUU
....(((((((((((....(((((...................)))))....))))))..)))))((((................)))).....((((....)))).. (-29.02 = -28.70 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:14 2006