Locus 4559

Sequence ID	3R_DroMel_CAF1
Location	12,064,888 – 12,065,087
Length	199
Max. P	0.972466

overview

Window 9

Location	12,064,888 – 12,065,008
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.66
Mean single sequence MFE	-43.20
Consensus MFE	-38.60
Energy contribution	-38.56
Covariance contribution	-0.04
Combinations/Pair	1.08
Mean z-score	-1.65
Structure conservation index	0.89
SVM decision value	1.69
SVM RNA-class probability	0.972466
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12064888 120 + 27905053
CAAGACUAUGCAAAGCGGACACCUGUUUUUGCAACACGAUCGCUAUUGUUGUAGCGGGUCUGCCGAUGUUGCUGCCGUGGAUGUUGCAGCAGUAGCAGUAUAAUGGUGGUGGUGCUGCUU
...........(((((((....))))))).(((.(((.(((((((((((.....(((.....))).(((((((((.(..(...)..).)))))))))..))))))))))).))).))).. ( -41.60)
>DroSec_CAF1 1466 120 + 1
CAAGACUAUGCAAAGCGGACACCUGUUUUUGCAACACGAUCGCUAUUGUUGUAGCGGGGCUGCCGAUGUUGCUGCCGUGGAUGUUGCAGCAGUAGCAGUAUAAUGGUGGUGGUGCUGCUG
...(((..((((((((((....))).))))))).(((..(((((((....)))))))(((.((.......)).))))))...))).((((((((.((.(((....))).)).)))))))) ( -43.40)
>DroSim_CAF1 1935 120 + 1
CAAGACUAUGCAAAGCGGACACCUGUUUUUGCAACACGAUCGCUAUUGUUGUAGCGGGGCUGCCGAUGUUGCUGCCGUGGAUGUUGCAGCAGUAGCAGUAUAAUGGUGGUGGUGCUGCUG
...(((..((((((((((....))).))))))).(((..(((((((....)))))))(((.((.......)).))))))...))).((((((((.((.(((....))).)).)))))))) ( -43.40)
>DroEre_CAF1 3450 119 + 1
AAAGACUAUACGAAGCGGACACCUGUUUUUGCAACACGAUCGCUAUUGUUGUAGCGGGGCUGU-GGUGUUGCUGCCGUGGAAGUUUCAGCAGUAGCAGUACAAUGAUGGUGGUGCUGCUG
..(((((.((((.((((.((((((((....)))(((...(((((((....)))))))...)))-)))))))))..))))..)))))...((((((((.(((.......))).)))))))) ( -43.20)
>DroYak_CAF1 3500 119 + 1
CAAGACUUUGCGAAGCGGACACCUGUUUUUGCAACACGAUCGCUAUUGUUGUUGAGCGGCUGC-GGUGUUGCUGCCGUGGAUGGUGCAGCAGUAGCAGUACAAUGGUGGUGGUGCUGCUG
...........(((((((....))))))).(((.(((.(((((((((((((.....))(((((-..((((((.((((....))))))))))...)))))))))))))))).))).))).. ( -44.40)
>consensus
CAAGACUAUGCAAAGCGGACACCUGUUUUUGCAACACGAUCGCUAUUGUUGUAGCGGGGCUGCCGAUGUUGCUGCCGUGGAUGUUGCAGCAGUAGCAGUAUAAUGGUGGUGGUGCUGCUG
...........(((((((....))))))).(((.(((.(((((((((((.((((.....))))...(((((((((.((.......)).)))))))))..))))))))))).))).))).. (-38.60 = -38.56 +  -0.04)

alignment

secondary structure

dotplot

Window 0

Location	12,064,888 – 12,065,008
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.66
Mean single sequence MFE	-30.66
Consensus MFE	-25.32
Energy contribution	-26.52
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-1.47
Structure conservation index	0.83
SVM decision value	0.38
SVM RNA-class probability	0.713923
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12064888 120 - 27905053
AAGCAGCACCACCACCAUUAUACUGCUACUGCUGCAACAUCCACGGCAGCAACAUCGGCAGACCCGCUACAACAAUAGCGAUCGUGUUGCAAAAACAGGUGUCCGCUUUGCAUAGUCUUG
..(((((((.............(((((..((((((..........)))))).....)))))...(((((......)))))...))))))).....((((.....((...)).....)))) ( -32.00)
>DroSec_CAF1 1466 120 - 1
CAGCAGCACCACCACCAUUAUACUGCUACUGCUGCAACAUCCACGGCAGCAACAUCGGCAGCCCCGCUACAACAAUAGCGAUCGUGUUGCAAAAACAGGUGUCCGCUUUGCAUAGUCUUG
.(((.(((((..............((....))((((((((....(((.((.......)).))).(((((......)))))...))))))))......)))))..)))............. ( -32.10)
>DroSim_CAF1 1935 120 - 1
CAGCAGCACCACCACCAUUAUACUGCUACUGCUGCAACAUCCACGGCAGCAACAUCGGCAGCCCCGCUACAACAAUAGCGAUCGUGUUGCAAAAACAGGUGUCCGCUUUGCAUAGUCUUG
.(((.(((((..............((....))((((((((....(((.((.......)).))).(((((......)))))...))))))))......)))))..)))............. ( -32.10)
>DroEre_CAF1 3450 119 - 1
CAGCAGCACCACCAUCAUUGUACUGCUACUGCUGAAACUUCCACGGCAGCAACACC-ACAGCCCCGCUACAACAAUAGCGAUCGUGUUGCAAAAACAGGUGUCCGCUUCGUAUAGUCUUU
((((((...((.((....))...))...))))))..(((...((((.(((.(((((-.......(((((......)))))....((((.....)))))))))..)))))))..))).... ( -28.90)
>DroYak_CAF1 3500 119 - 1
CAGCAGCACCACCACCAUUGUACUGCUACUGCUGCACCAUCCACGGCAGCAACACC-GCAGCCGCUCAACAACAAUAGCGAUCGUGUUGCAAAAACAGGUGUCCGCUUCGCAAAGUCUUG
.(((.(((((.........(((....)))(((.((((.(((...(((.((......-)).)))(((..........)))))).)))).)))......)))))..)))............. ( -28.20)
>consensus
CAGCAGCACCACCACCAUUAUACUGCUACUGCUGCAACAUCCACGGCAGCAACAUCGGCAGCCCCGCUACAACAAUAGCGAUCGUGUUGCAAAAACAGGUGUCCGCUUUGCAUAGUCUUG
..(((((((.............(((((..((((((..........)))))).....)))))...(((((......)))))...)))))))......((((....))))............ (-25.32 = -26.52 +   1.20)

alignment

secondary structure

dotplot

Window 1

Location	12,064,928 – 12,065,047
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.16
Mean single sequence MFE	-45.91
Consensus MFE	-36.18
Energy contribution	-36.78
Covariance contribution	0.60
Combinations/Pair	1.07
Mean z-score	-2.15
Structure conservation index	0.79
SVM decision value	1.34
SVM RNA-class probability	0.943464
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12064928 119 + 27905053
CGCUAUUGUUGUAGCGGGUCUGCCGAUGUUGCUGCCGUGGAUGUUGCAGCAGUAGCAGUAUAAUGGUGGUGGUGCUGCUUCUGAAAAGUCCUCCUACCCAACCACC-UCUGCUUUCAUCU
.((((((((((((((..(((..(.(.........).)..)))))))))))))))))((((....((((((((((......((....))......))))..))))))-..))))....... ( -39.60)
>DroSec_CAF1 1506 120 + 1
CGCUAUUGUUGUAGCGGGGCUGCCGAUGUUGCUGCCGUGGAUGUUGCAGCAGUAGCAGUAUAAUGGUGGUGGUGCUGCUGCUGAAAAGUCCUCCUCCCCAACCCCCUUCUGCUUUCAUCU
.(((((....)))))(((((.((.......)).)))(.((((....(((((((((((.(((.......))).)))))))))))....)))).)....))..................... ( -42.10)
>DroSim_CAF1 1975 120 + 1
CGCUAUUGUUGUAGCGGGGCUGCCGAUGUUGCUGCCGUGGAUGUUGCAGCAGUAGCAGUAUAAUGGUGGUGGUGCUGCUGCUGAAAAGUCCUCCUCCCCAACCCCCUUCUGCUUUCAUCU
.(((((....)))))(((((.((.......)).)))(.((((....(((((((((((.(((.......))).)))))))))))....)))).)....))..................... ( -42.10)
>DroEre_CAF1 3490 119 + 1
CGCUAUUGUUGUAGCGGGGCUGU-GGUGUUGCUGCCGUGGAAGUUUCAGCAGUAGCAGUACAAUGAUGGUGGUGCUGCUGCUGAAAAGUCCUCUUCCCCAACACCCCGCUCCUUUCAUCU
.(((((....)))))(((((.(.-(((((((..(..(.(((..((((((((((((((.(((.......))).))))))))))))))..))).)..)..)))))))).)))))........ ( -58.60)
>DroYak_CAF1 3540 119 + 1
CGCUAUUGUUGUUGAGCGGCUGC-GGUGUUGCUGCCGUGGAUGGUGCAGCAGUAGCAGUACAAUGGUGGUGGUGCUGCUGCUGAAAAGUCCUCCUCCCCGACACCCCUCUCCACUCAUCU
............((((.((..(.-(((((((.......((((....(((((((((((.(((.......))).)))))))))))....)))).......))))))).)...)).))))... ( -47.14)
>consensus
CGCUAUUGUUGUAGCGGGGCUGCCGAUGUUGCUGCCGUGGAUGUUGCAGCAGUAGCAGUAUAAUGGUGGUGGUGCUGCUGCUGAAAAGUCCUCCUCCCCAACCCCCCUCUGCUUUCAUCU
((((((....)))))).(((.((.......)).)))(.((((....(((((((((((.(((.......))).)))))))))))....)))).)........................... (-36.18 = -36.78 +   0.60)

alignment

secondary structure

dotplot

Window 2

Location	12,064,968 – 12,065,087
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.67
Mean single sequence MFE	-34.69
Consensus MFE	-27.82
Energy contribution	-28.62
Covariance contribution	0.80
Combinations/Pair	1.07
Mean z-score	-2.04
Structure conservation index	0.80
SVM decision value	1.31
SVM RNA-class probability	0.941025
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12064968 119 + 27905053
AUGUUGCAGCAGUAGCAGUAUAAUGGUGGUGGUGCUGCUUCUGAAAAGUCCUCCUACCCAACCACC-UCUGCUUUCAUCUGCUGCUUCUGCAAGUCGGACCAUUUAUUCAGCAUUCAAAA
((((((((((((.(((((......((((((((((......((....))......))))..))))))-.))))).....))))))).((((.....))))..........)))))...... ( -35.30)
>DroSec_CAF1 1546 120 + 1
AUGUUGCAGCAGUAGCAGUAUAAUGGUGGUGGUGCUGCUGCUGAAAAGUCCUCCUCCCCAACCCCCUUCUGCUUUCAUCUGCUGCUUCUGCAACUCGGGCCAUUUAUUCAGCAUUCAAAA
(((((((((((((((((.(((.......))).)))))))))))....((((...................((........))(((....)))....))))........))))))...... ( -34.10)
>DroSim_CAF1 2015 120 + 1
AUGUUGCAGCAGUAGCAGUAUAAUGGUGGUGGUGCUGCUGCUGAAAAGUCCUCCUCCCCAACCCCCUUCUGCUUUCAUCUGCUGCUUCUGCAACUCGGGCCAUUUAUUCAGCAUUCAAAA
(((((((((((((((((.(((.......))).)))))))))))....((((...................((........))(((....)))....))))........))))))...... ( -34.10)
>DroEre_CAF1 3529 120 + 1
AAGUUUCAGCAGUAGCAGUACAAUGAUGGUGGUGCUGCUGCUGAAAAGUCCUCUUCCCCAACACCCCGCUCCUUUCAUCUGCUGCUUCUGCCACUCGGGCCAUUUAUUCAGCAUUCAAAA
...((((((((((((((.(((.......))).)))))))))))))).................................(((((.....(((.....)))........)))))....... ( -34.82)
>DroYak_CAF1 3579 120 + 1
AUGGUGCAGCAGUAGCAGUACAAUGGUGGUGGUGCUGCUGCUGAAAAGUCCUCCUCCCCGACACCCCUCUCCACUCAUCUGCUGCUUCUGCCACUCGGGCCAUUUAUUCAGCAUUCAAAA
(((((((((((((((((.(((.......))).)))))))))))....(((.........))).........))).))).(((((.....(((.....)))........)))))....... ( -35.12)
>consensus
AUGUUGCAGCAGUAGCAGUAUAAUGGUGGUGGUGCUGCUGCUGAAAAGUCCUCCUCCCCAACCCCCCUCUGCUUUCAUCUGCUGCUUCUGCAACUCGGGCCAUUUAUUCAGCAUUCAAAA
(((((((((((((((((.(((.......))).)))))))))))....((((...................((........)).((....)).....))))........))))))...... (-27.82 = -28.62 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:25 2006