Locus 8763

Sequence ID	3R_DroMel_CAF1
Location	23,396,583 – 23,396,716
Length	133
Max. P	0.989288

overview

Window 5

Location	23,396,583 – 23,396,676
Length	93
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	83.14
Mean single sequence MFE	-27.60
Consensus MFE	-16.56
Energy contribution	-18.76
Covariance contribution	2.20
Combinations/Pair	1.00
Mean z-score	-3.19
Structure conservation index	0.60
SVM decision value	1.82
SVM RNA-class probability	0.978525
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23396583 93 + 27905053
CGGUGGGAAAUUAAUUUCCCACGAUAAGCCGCCUCUUGCAAAUUGAAGAUGGGCAAGCUA--CGACUGCCCAAUCGAUAUUACUAUCGAAAUCAU
..((((((((....))))))))(((........((((........))))((((((.....--....)))))).((((((....)))))).))).. ( -27.00)
>DroSec_CAF1 11198 93 + 1
CGCUGGGAAAUUAAUUUCCCACCCAAAGCCGCCUCUUGCAAAUUGAAGAUGGGCAAGCUA--CGAUUGCCCAAUCGAUAUUCCUAUCGAAAUUAU
...(((((((....)))))))............((((........))))(((((((....--...))))))).((((((....))))))...... ( -24.20)
>DroSim_CAF1 11219 93 + 1
CGCUGGGAAAUUAAUUUCCCACCCAAAGCCACCUCUUGCAAAGUGAAGAUGGGCAAGCUA--CGACUGCCCAAUCGAUAUUUCUAUCAAAAUUAU
((((((((((....)))))).......((........))..))))..((((((((.....--....))))).)))((((....))))........ ( -22.10)
>DroEre_CAF1 14291 92 + 1
UGGGGGGAAAUUAAUUUCCCACCCAAAACCACC-CUCCCCAAUGGGAGGUGGCAAGGCUA--CGACUGCACAAUCGAUAUUCCUAUCGAACUUAU
((((((((((....)))))).))))...(((((-.((((....))))))))).(((((..--.....))....((((((....)))))).))).. ( -35.10)
>DroYak_CAF1 12127 94 + 1
UGGUGGGAAAUUAAUUUCCCACCCAACGCCACC-CGCCCAAAAUGGAAGUGGCAUAGCUAGAUGACUGCCCAAUCGAUAUUGCUAUCGAACUUAU
.(((((((((....)))))))))....(((((.-..((......))..)))))...((.((....))))....((((((....))))))...... ( -29.60)
>consensus
CGGUGGGAAAUUAAUUUCCCACCCAAAGCCACCUCUUGCAAAUUGAAGAUGGGCAAGCUA__CGACUGCCCAAUCGAUAUUCCUAUCGAAAUUAU
.(((((((((....)))))))))..........................((((((..(.....)..)))))).((((((....))))))...... (-16.56 = -18.76 +   2.20)

alignment

secondary structure

dotplot

Window 6

Location	23,396,583 – 23,396,676
Length	93
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	83.14
Mean single sequence MFE	-32.86
Consensus MFE	-21.72
Energy contribution	-23.24
Covariance contribution	1.52
Combinations/Pair	1.13
Mean z-score	-3.17
Structure conservation index	0.66
SVM decision value	2.16
SVM RNA-class probability	0.989288
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23396583 93 - 27905053
AUGAUUUCGAUAGUAAUAUCGAUUGGGCAGUCG--UAGCUUGCCCAUCUUCAAUUUGCAAGAGGCGGCUUAUCGUGGGAAAUUAAUUUCCCACCG
......((((((....))))))..((..(((((--(..(((((.............)))))..))))))..))((((((((....)))))))).. ( -32.32)
>DroSec_CAF1 11198 93 - 1
AUAAUUUCGAUAGGAAUAUCGAUUGGGCAAUCG--UAGCUUGCCCAUCUUCAAUUUGCAAGAGGCGGCUUUGGGUGGGAAAUUAAUUUCCCAGCG
......((((((....)))))).(((((((...--....)))))))....(((.((((.....))))..)))(.(((((((....))))))).). ( -28.20)
>DroSim_CAF1 11219 93 - 1
AUAAUUUUGAUAGAAAUAUCGAUUGGGCAGUCG--UAGCUUGCCCAUCUUCACUUUGCAAGAGGUGGCUUUGGGUGGGAAAUUAAUUUCCCAGCG
......((((((....)))))).((((((((..--..)).))))))...(((((((....))))))).....(.(((((((....))))))).). ( -30.70)
>DroEre_CAF1 14291 92 - 1
AUAAGUUCGAUAGGAAUAUCGAUUGUGCAGUCG--UAGCCUUGCCACCUCCCAUUGGGGAG-GGUGGUUUUGGGUGGGAAAUUAAUUUCCCCCCA
...........(((.....(((((....)))))--...))).((((((((((....)))).-))))))..((((.((((((....)))))))))) ( -35.80)
>DroYak_CAF1 12127 94 - 1
AUAAGUUCGAUAGCAAUAUCGAUUGGGCAGUCAUCUAGCUAUGCCACUUCCAUUUUGGGCG-GGUGGCGUUGGGUGGGAAAUUAAUUUCCCACCA
......((((((....))))))...(((((....)).)))(((((((((((......)).)-))))))))..(((((((((....))))))))). ( -37.30)
>consensus
AUAAUUUCGAUAGGAAUAUCGAUUGGGCAGUCG__UAGCUUGCCCAUCUUCAAUUUGCAAGAGGUGGCUUUGGGUGGGAAAUUAAUUUCCCACCG
......((((((....)))))).(((((((.(.....).)))))))..........................(((((((((....))))))))). (-21.72 = -23.24 +   1.52)

alignment

secondary structure

dotplot

Window 7

Location	23,396,605 – 23,396,716
Length	111
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	77.71
Mean single sequence MFE	-23.84
Consensus MFE	-13.66
Energy contribution	-15.14
Covariance contribution	1.48
Combinations/Pair	1.14
Mean z-score	-1.79
Structure conservation index	0.57
SVM decision value	0.26
SVM RNA-class probability	0.657278
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23396605 111 + 27905053
GAUAAGCCGCCUCUUGCAAAUUGAAGAUGGGCAAGCUA--CGACUGCCCAAUCGAUAUUACUAUCGAAAUCAUCGAUGCUUCUUUAUCGAUAAACUAAAAACACUUGAUUCCU
(((((((.((.....))..(((((.((((((((.....--....)))))..((((((....)))))).))).))))))))....))))......................... ( -22.00)
>DroSec_CAF1 11220 102 + 1
CCAAAGCCGCCUCUUGCAAAUUGAAGAUGGGCAAGCUA--CGAUUGCCCAAUCGAUAUUCCUAUCGAAAUUAUCGACACUUCUUUAUCGAUAAG---------CUUGAUUCCU
...........((..((..........(((((((....--...))))))).((((((....))))))..(((((((..........))))))))---------)..))..... ( -23.80)
>DroSim_CAF1 11241 102 + 1
CCAAAGCCACCUCUUGCAAAGUGAAGAUGGGCAAGCUA--CGACUGCCCAAUCGAUAUUUCUAUCAAAAUUAUCGACGCUUCAUUAUCGAUAAG---------CUUGAUUCCU
...((((......(((...(((((((.((((((.....--....)))))).((((((.............))))))..)))))))..)))...)---------)))....... ( -21.32)
>DroEre_CAF1 14313 110 + 1
CCAAAACCACC-CUCCCCAAUGGGAGGUGGCAAGGCUA--CGACUGCACAAUCGAUAUUCCUAUCGAACUUAUCGGUGCUUCUUUAUCGAUGAACCUAACAUAAUUCAUUCCU
......(((((-.((((....)))))))))..(((...--...........((((((....))))))..(((((((((......))))))))).)))................ ( -28.70)
>DroYak_CAF1 12149 112 + 1
CCAACGCCACC-CGCCCAAAAUGGAAGUGGCAUAGCUAGAUGACUGCCCAAUCGAUAUUGCUAUCGAACUUAUCGGUGCUUCUUUAUCGAUAAACAUAAAAUACUUGAUUCUU
.....(((((.-..((......))..)))))........(((.........((((((....))))))..(((((((((......))))))))).)))................ ( -23.40)
>consensus
CCAAAGCCACCUCUUGCAAAUUGAAGAUGGGCAAGCUA__CGACUGCCCAAUCGAUAUUCCUAUCGAAAUUAUCGAUGCUUCUUUAUCGAUAAAC__AA_A_ACUUGAUUCCU
...........................((((((..(.....)..)))))).((((((....))))))..(((((((((......))))))))).................... (-13.66 = -15.14 +   1.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:19:11 2006