Locus 1128

Sequence ID	2R_DroMel_CAF1
Location	4,517,940 – 4,518,060
Length	120
Max. P	0.739160

overview

Window 1

Location	4,517,940 – 4,518,031
Length	91
Sequences	5
Columns	91
Reading direction	forward
Mean pairwise identity	91.43
Mean single sequence MFE	-25.04
Consensus MFE	-20.60
Energy contribution	-21.12
Covariance contribution	0.52
Combinations/Pair	1.11
Mean z-score	-1.49
Structure conservation index	0.82
SVM decision value	0.44
SVM RNA-class probability	0.739160
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4517940 91 + 20766785
GAUAAGAAUUGCAUGGUGACUUCCUUGGCUUUUAAGUACGUUUUCCGAGAAACGUAUGGGAAGAAACUUCUAAGGAGCAGCACUUCUGGGG
....((((.(((..(....)((((((((((((...(((((((((....)))))))))..))))......))))))))..))).)))).... ( -25.00)
>DroSec_CAF1 52305 91 + 1
GAUAAGAAUUGCAUGGUGACUUCCUUGGCUUUUAAGUAUCUUUUCCCAGAAACGAAUGGGAAGAAACUUCUAAGGAGCAGCACUUCUGAGG
....((((.(((..(....)((((((((.....((((.(((..(((((........)))))))).))))))))))))..))).)))).... ( -26.80)
>DroSim_CAF1 51232 91 + 1
GAUAAGAAUUGCAUGGUGACUUCCUUGGCUUUUAAGUAUGUUUUCCCAGAAACGUAUGGGAAGAAACUUCUAAGGAGCAGCACUUCUAGGG
....((((.(((..(....)((((((((.....((((...((((((((........)))))))).))))))))))))..))).)))).... ( -27.60)
>DroEre_CAF1 51422 91 + 1
GAUAAGAAUUGCAUGGCGACUUCUUCGGCUUUUAAGUGUGUUUUCCCAGAAAUGUGUGGGAAGAAACUUCCAAGGAGCAACACUUCUGGGG
...(((((((((...)))).)))))...................(((((((.(((((.(((((...))))).....)).))).))))))). ( -23.20)
>DroYak_CAF1 53888 89 + 1
GAUAAGAAUUGCAUGGUGACUUCCGUGGCU--UAAGUAUGUUUUCCCAGAAAUUUAUGGGUAGAAACUUCUAAGGAGCAGCACUUCUGGGG
....((((.(((((((......)))).(((--(.((...(((((((((........))))..)))))..))...)))).))).)))).... ( -22.60)
>consensus
GAUAAGAAUUGCAUGGUGACUUCCUUGGCUUUUAAGUAUGUUUUCCCAGAAACGUAUGGGAAGAAACUUCUAAGGAGCAGCACUUCUGGGG
....((((.(((...((....(((((((.....((((...((((((((........)))))))).))))))))))))).))).)))).... (-20.60 = -21.12 +   0.52)

alignment

secondary structure

dotplot

Window 2

Location	4,517,961 – 4,518,060
Length	99
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	84.72
Mean single sequence MFE	-27.76
Consensus MFE	-19.82
Energy contribution	-19.58
Covariance contribution	-0.24
Combinations/Pair	1.17
Mean z-score	-1.78
Structure conservation index	0.71
SVM decision value	0.27
SVM RNA-class probability	0.659913
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4517961 99 + 20766785
UCCUUGGCUUUUAAGUACGUUUUCCGAGAAACGUAUGGGAAGAAACUUCUAAGGAGCAGCACUUCUGGGGAAAAACACUUUGCUCAUUUCAGGAAGGGA-----------
(((((.((((((..(((((((((....))))))))).(((((...))))).))))))........((((.(((.....))).)))).......))))).----------- ( -23.30)
>DroSec_CAF1 52326 99 + 1
UCCUUGGCUUUUAAGUAUCUUUUCCCAGAAACGAAUGGGAAGAAACUUCUAAGGAGCAGCACUUCUGAGGAAAAACACUUUACCCAUUUCAGAAAGGGA-----------
(((((.((((((.((....((((((((........)))))))).....)).)))))).....((((((((.(((....))).))....)))))))))))----------- ( -25.40)
>DroSim_CAF1 51253 99 + 1
UCCUUGGCUUUUAAGUAUGUUUUCCCAGAAACGUAUGGGAAGAAACUUCUAAGGAGCAGCACUUCUAGGGAAAAACACUUUGCCCAUUUCAGAAAGGGA-----------
(((((.((((((.((....((((((((........)))))))).....)).))))))..........(((.(((....))).)))........))))).----------- ( -25.70)
>DroEre_CAF1 51443 99 + 1
UCUUCGGCUUUUAAGUGUGUUUUCCCAGAAAUGUGUGGGAAGAAACUUCCAAGGAGCAACACUUCUGGGGAAAAACACUUUGCUUAUUUUGGGAGGGGA-----------
((((((((....((((((.(((((((((((.(((((.(((((...))))).....)).))).))))))))))).)))))).)))........)))))..----------- ( -35.00)
>DroYak_CAF1 53909 108 + 1
UCCGUGGCU--UAAGUAUGUUUUCCCAGAAAUUUAUGGGUAGAAACUUCUAAGGAGCAGCACUUCUGGGGAACAACACUUUGCUCAUUUUGGGAAGGGAAAUUUAGCUUU
.....((((--.((((.(.((((((((((.....(((((((((...((((.(((((.....)))))..))))......))))))))))))))))))).).)))))))).. ( -29.40)
>consensus
UCCUUGGCUUUUAAGUAUGUUUUCCCAGAAACGUAUGGGAAGAAACUUCUAAGGAGCAGCACUUCUGGGGAAAAACACUUUGCUCAUUUCAGGAAGGGA___________
((((((((....((((...((((((((........))))))))...((((.(((((.....))))).)))).....)))).)))..........)))))........... (-19.82 = -19.58 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:14 2006