Locus 824

Sequence ID	2R_DroMel_CAF1
Location	3,875,180 – 3,875,298
Length	118
Max. P	0.999583

overview

Window 0

Location	3,875,180 – 3,875,298
Length	118
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	80.43
Mean single sequence MFE	-25.90
Consensus MFE	-18.54
Energy contribution	-19.60
Covariance contribution	1.06
Combinations/Pair	1.08
Mean z-score	-1.92
Structure conservation index	0.72
SVM decision value	0.85
SVM RNA-class probability	0.866859
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3875180 118 + 20766785
UUUUUUGUUAGGAUCGGAUACCUGACUGCUAAAGCAAAUUAAUAGAAACAUCACUUUGUAUCUAUUACUUCGUUUUAAAAGCCAGACCCUCAACUUGCACUUUUACGUGUUUCGGUAG
............((((((...(((.((..((((((.((.(((((((.(((......))).))))))).)).))))))..)).)))...........((((......)))))))))).. ( -24.40)
>DroSec_CAF1 2152 117 + 1
UUU-UUAUUAAGAUAGGAGACCUGACCGCUAAAGCAAAUUAAUAGAAACAUAUAUUUGUAUCUAUUACUUUGUUUUAAAAGCCAGACCCUCAACUUGCACUUCUACGUGUAUCGUUAG
...-............(((..(((.(...(((((((((.(((((((.(((......))).))))))).)))))))))...).)))...)))(((.(((((......)))))..))).. ( -25.70)
>DroEre_CAF1 2365 116 + 1
UUG-UUGUACGGAUCGAAGACCUGACUUCUAAAGCAAAGUAAUAGAAACGC-AACUUGUAUCUAUUGCUUCGUUUUAAAAGGCAGACCCUCCGCUUCCAUUCUUUCAGAUUUAGUUAA
...-......(((.((.((..(((.(((.((((((.((((((((((.(((.-....))).)))))))))).)))))).))).)))...)).))..))).................... ( -27.70)
>DroYak_CAF1 2424 117 + 1
UUG-UUGCUAGGAUCGAAGACCUGACUUCUAAAGCAAAGUAAUAGAAACGCCAACUUGCAUCUAUUACUUCGUUUUAAAAGGCAGUCCCUCAACUUCCAUUUUUUCAGAUUUGUGUAU
...-......(((..((.(..(((.(((.((((((.((((((((((...((......)).)))))))))).)))))).))).)))..).))....))).................... ( -25.80)
>consensus
UUG_UUGUUAGGAUCGAAGACCUGACUGCUAAAGCAAAGUAAUAGAAACACCAACUUGUAUCUAUUACUUCGUUUUAAAAGCCAGACCCUCAACUUCCACUUUUACAGAUUUCGGUAG
.....................(((.(((.((((((.((((((((((.(((......))).)))))))))).)))))).))).)))................................. (-18.54 = -19.60 +   1.06)

alignment

secondary structure

dotplot

Window 1

Location	3,875,180 – 3,875,298
Length	118
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	80.43
Mean single sequence MFE	-33.00
Consensus MFE	-27.11
Energy contribution	-29.05
Covariance contribution	1.94
Combinations/Pair	1.10
Mean z-score	-3.43
Structure conservation index	0.82
SVM decision value	3.75
SVM RNA-class probability	0.999583
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3875180 118 - 20766785
CUACCGAAACACGUAAAAGUGCAAGUUGAGGGUCUGGCUUUUAAAACGAAGUAAUAGAUACAAAGUGAUGUUUCUAUUAAUUUGCUUUAGCAGUCAGGUAUCCGAUCCUAACAAAAAA
.........(((......)))...(((.(((((((((((.(((((.((((.(((((((.(((......))).))))))).)))).))))).)))))((...)))))))))))...... ( -29.80)
>DroSec_CAF1 2152 117 - 1
CUAACGAUACACGUAGAAGUGCAAGUUGAGGGUCUGGCUUUUAAAACAAAGUAAUAGAUACAAAUAUAUGUUUCUAUUAAUUUGCUUUAGCGGUCAGGUCUCCUAUCUUAAUAA-AAA
.....(((((((......)))......(..(..((((((.(((((.((((.(((((((.(((......))).))))))).)))).))))).))))))..)..))))).......-... ( -30.90)
>DroEre_CAF1 2365 116 - 1
UUAACUAAAUCUGAAAGAAUGGAAGCGGAGGGUCUGCCUUUUAAAACGAAGCAAUAGAUACAAGUU-GCGUUUCUAUUACUUUGCUUUAGAAGUCAGGUCUUCGAUCCGUACAA-CAA
................(.(((((....((((..(((.((((((((.(((((.((((((.((.....-..)).)))))).))))).)))))))).)))..))))..))))).)..-... ( -34.20)
>DroYak_CAF1 2424 117 - 1
AUACACAAAUCUGAAAAAAUGGAAGUUGAGGGACUGCCUUUUAAAACGAAGUAAUAGAUGCAAGUUGGCGUUUCUAUUACUUUGCUUUAGAAGUCAGGUCUUCGAUCCUAGCAA-CAA
....................(((..((((((..(((.((((((((.(((((((((((((((......)))..)))))))))))).)))))))).)))..)))))))))......-... ( -37.10)
>consensus
CUAACGAAACACGAAAAAAUGCAAGUUGAGGGUCUGCCUUUUAAAACGAAGUAAUAGAUACAAAUUGACGUUUCUAUUAAUUUGCUUUAGAAGUCAGGUCUCCGAUCCUAACAA_AAA
...........................((((..((((((((((((.((((((((((((.((........)).)))))))))))).))))))))))))..))))............... (-27.11 = -29.05 +   1.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:20 2006