Locus 1483

Sequence ID	3R_DroMel_CAF1
Location	4,288,100 – 4,288,220
Length	120
Max. P	0.991430

overview

Window 2

Location	4,288,100 – 4,288,207
Length	107
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	95.64
Mean single sequence MFE	-26.70
Consensus MFE	-24.62
Energy contribution	-24.50
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-2.62
Structure conservation index	0.92
SVM decision value	1.78
SVM RNA-class probability	0.977125
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4288100 107 + 27905053
AGAUGAGCUCUGCGGAAAAGAACUCGAAAGCGGAAAAACAAACAGCAGAUAUGCGAAAAGCAUUCGGAAAAGGGCCAUGAAAUUCAUGACCUUUAGCGCUUUAAAAU
...((((.(((.......))).))))((((((...............((.((((.....))))))...(((((..((((.....)))).)))))..))))))..... ( -26.10)
>DroSec_CAF1 89538 107 + 1
UGAUGAGCUCUGCGGAAAAGAACUCGAAAGCGGAAAAACAAACAGCAGAUAUGGGAAAAGCAUUCGGAAAAAGGCCAUGAAAUUCAUGACCUUUAGCGCUUUAAAAC
...((((.(((.......))).))))((((((...............((.(((.......)))))....(((((.((((.....)))).)))))..))))))..... ( -21.80)
>DroSim_CAF1 88994 107 + 1
AGAUGAGCUCUGCGGAAAAGAACUCGAAAGCGGAAAAACAAACAGCAGAUAUGCGAAAAGCAUUCGGGAAAAGGCCAUGGAAUUCAUGACCUUUAGCGCUUUAAAAC
...((((.(((.......))).))))((((((...............((.((((.....))))))....(((((.((((.....)))).)))))..))))))..... ( -25.40)
>DroEre_CAF1 92572 106 + 1
AGAUGAGCUCUGCG-AAAAGAACUCGAAAGCGGAAAAACAAACAGCAGAUAUGCGAAAAGCGUUCGGAAAAAGGCCAUGAAAUUCAUGGCCUUUAGCGCUUUAAAAU
...((((.(((...-...))).))))((((((...............((.((((.....))))))....((((((((((.....))))))))))..))))))..... ( -33.50)
>consensus
AGAUGAGCUCUGCGGAAAAGAACUCGAAAGCGGAAAAACAAACAGCAGAUAUGCGAAAAGCAUUCGGAAAAAGGCCAUGAAAUUCAUGACCUUUAGCGCUUUAAAAC
...((((.(((.......))).))))((((((...............((.((((.....))))))....(((((.((((.....)))).)))))..))))))..... (-24.62 = -24.50 +  -0.12)

alignment

secondary structure

dotplot

Window 3

Location	4,288,100 – 4,288,207
Length	107
Sequences	4
Columns	107
Reading direction	reverse
Mean pairwise identity	95.64
Mean single sequence MFE	-30.03
Consensus MFE	-29.17
Energy contribution	-29.04
Covariance contribution	-0.13
Combinations/Pair	1.07
Mean z-score	-3.86
Structure conservation index	0.97
SVM decision value	2.27
SVM RNA-class probability	0.991430
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4288100 107 - 27905053
AUUUUAAAGCGCUAAAGGUCAUGAAUUUCAUGGCCCUUUUCCGAAUGCUUUUCGCAUAUCUGCUGUUUGUUUUUCCGCUUUCGAGUUCUUUUCCGCAGAGCUCAUCU
.....((((((..((((((((((.....))))))).......((((((.....)))).))..........)))..)))))).(((((((.......))))))).... ( -28.00)
>DroSec_CAF1 89538 107 - 1
GUUUUAAAGCGCUAAAGGUCAUGAAUUUCAUGGCCUUUUUCCGAAUGCUUUUCCCAUAUCUGCUGUUUGUUUUUCCGCUUUCGAGUUCUUUUCCGCAGAGCUCAUCA
.....((((((..((((((((((.....))))))))))...(((((((.............)).)))))......)))))).(((((((.......))))))).... ( -28.82)
>DroSim_CAF1 88994 107 - 1
GUUUUAAAGCGCUAAAGGUCAUGAAUUCCAUGGCCUUUUCCCGAAUGCUUUUCGCAUAUCUGCUGUUUGUUUUUCCGCUUUCGAGUUCUUUUCCGCAGAGCUCAUCU
.....((((((..((((((((((.....))))))))))....((((((.....)))).))...............)))))).(((((((.......))))))).... ( -29.50)
>DroEre_CAF1 92572 106 - 1
AUUUUAAAGCGCUAAAGGCCAUGAAUUUCAUGGCCUUUUUCCGAACGCUUUUCGCAUAUCUGCUGUUUGUUUUUCCGCUUUCGAGUUCUUUU-CGCAGAGCUCAUCU
.....((((((..((((((((((.....))))))))))...(((((((.............)).)))))......)))))).(((((((...-...))))))).... ( -33.82)
>consensus
AUUUUAAAGCGCUAAAGGUCAUGAAUUUCAUGGCCUUUUUCCGAAUGCUUUUCGCAUAUCUGCUGUUUGUUUUUCCGCUUUCGAGUUCUUUUCCGCAGAGCUCAUCU
.....((((((..((((((((((.....))))))))))...(((((((.............)).)))))......)))))).(((((((.......))))))).... (-29.17 = -29.04 +  -0.13)

alignment

secondary structure

dotplot

Window 4

Location	4,288,128 – 4,288,220
Length	92
Sequences	4
Columns	102
Reading direction	forward
Mean pairwise identity	88.40
Mean single sequence MFE	-24.48
Consensus MFE	-17.11
Energy contribution	-18.05
Covariance contribution	0.94
Combinations/Pair	1.11
Mean z-score	-2.61
Structure conservation index	0.70
SVM decision value	0.84
SVM RNA-class probability	0.864503
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4288128 92 + 27905053
AGCGGAAAAACAAACAGCAGAUAUGCGAAAAGCAUUCGGAAAAGGGCCAUGAAAUUCAUGACCUUUAGCGCUUUAAAAUUUAAGC----------CCUGUAA
.((((...........((.((.((((.....))))))...(((((..((((.....)))).))))).))((((........))))----------.)))).. ( -22.10)
>DroSec_CAF1 89566 102 + 1
AGCGGAAAAACAAACAGCAGAUAUGGGAAAAGCAUUCGGAAAAAGGCCAUGAAAUUCAUGACCUUUAGCGCUUUAAAACUUAAAGUCUAUGCGAGUCUGUAA
.((.............))...((((((....((((...(..(((((.((((.....)))).)))))..)((((((.....))))))..))))...)))))). ( -19.82)
>DroSim_CAF1 89022 102 + 1
AGCGGAAAAACAAACAGCAGAUAUGCGAAAAGCAUUCGGGAAAAGGCCAUGGAAUUCAUGACCUUUAGCGCUUUAAAACUUAAAGUCUAUGCGAGUCUGUAA
................((((((((((.....))))(((.(.(((((.((((.....)))).)))))((.((((((.....)))))))).).))))))))).. ( -23.00)
>DroEre_CAF1 92599 102 + 1
AGCGGAAAAACAAACAGCAGAUAUGCGAAAAGCGUUCGGAAAAAGGCCAUGAAAUUCAUGGCCUUUAGCGCUUUAAAAUUUAAACAUUAUGCGAAUCUGUUA
...............(((((((.((((.((((((((.....((((((((((.....))))))))))))))))))..(((......))).)))).))))))). ( -33.00)
>consensus
AGCGGAAAAACAAACAGCAGAUAUGCGAAAAGCAUUCGGAAAAAGGCCAUGAAAUUCAUGACCUUUAGCGCUUUAAAACUUAAACUCUAUGCGAGUCUGUAA
.(((((..........((.((.((((.....))))))....(((((.((((.....)))).))))).))((((((.....)))))).........))))).. (-17.11 = -18.05 +   0.94)

alignment

secondary structure

dotplot

Window 5

Location	4,288,128 – 4,288,220
Length	92
Sequences	4
Columns	102
Reading direction	reverse
Mean pairwise identity	88.40
Mean single sequence MFE	-24.08
Consensus MFE	-19.49
Energy contribution	-19.55
Covariance contribution	0.06
Combinations/Pair	1.16
Mean z-score	-2.51
Structure conservation index	0.81
SVM decision value	1.59
SVM RNA-class probability	0.966061
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4288128 92 - 27905053
UUACAGG----------GCUUAAAUUUUAAAGCGCUAAAGGUCAUGAAUUUCAUGGCCCUUUUCCGAAUGCUUUUCGCAUAUCUGCUGUUUGUUUUUCCGCU
.....((----------(...((((.....((((..((((((((((.....))))).)))))..)((((((.....)))).)).)))....)))).)))... ( -20.20)
>DroSec_CAF1 89566 102 - 1
UUACAGACUCGCAUAGACUUUAAGUUUUAAAGCGCUAAAGGUCAUGAAUUUCAUGGCCUUUUUCCGAAUGCUUUUCCCAUAUCUGCUGUUUGUUUUUCCGCU
..((((((..(((.((((.....)))).((((((..((((((((((.....)))))))))).......)))))).........))).))))))......... ( -23.50)
>DroSim_CAF1 89022 102 - 1
UUACAGACUCGCAUAGACUUUAAGUUUUAAAGCGCUAAAGGUCAUGAAUUCCAUGGCCUUUUCCCGAAUGCUUUUCGCAUAUCUGCUGUUUGUUUUUCCGCU
..((((((..((((...(((((.....)))))((..((((((((((.....))))))))))...)).)))).....(((....))).))))))......... ( -25.10)
>DroEre_CAF1 92599 102 - 1
UAACAGAUUCGCAUAAUGUUUAAAUUUUAAAGCGCUAAAGGCCAUGAAUUUCAUGGCCUUUUUCCGAACGCUUUUCGCAUAUCUGCUGUUUGUUUUUCCGCU
.(((((((..(((..((((.........((((((..((((((((((.....)))))))))).......))))))..))))...))).)))))))........ ( -27.50)
>consensus
UUACAGACUCGCAUAGACUUUAAAUUUUAAAGCGCUAAAGGUCAUGAAUUUCAUGGCCUUUUUCCGAAUGCUUUUCGCAUAUCUGCUGUUUGUUUUUCCGCU
..((((((....................((((((..((((((((((.....)))))))))).......))))))..(((....))).))))))......... (-19.49 = -19.55 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:42 2006