Locus 6133

Sequence ID	2L_DroMel_CAF1
Location	17,131,198 – 17,131,394
Length	196
Max. P	0.980526

overview

Window 6

Location	17,131,198 – 17,131,314
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.44
Mean single sequence MFE	-28.62
Consensus MFE	-27.34
Energy contribution	-27.02
Covariance contribution	-0.32
Combinations/Pair	1.08
Mean z-score	-1.30
Structure conservation index	0.96
SVM decision value	0.90
SVM RNA-class probability	0.878044
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17131198 116 + 22407834
AAGAGCCAUCCUGGCAUCGGGAAAUCCAAAGGCGCCACC-CAC---CGCCCACUCCUACACAUAAACUACAUUAGCAAUCGGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCG
..((((((((.((((...((((........((((.....-...---))))...)))).................((..((((.....))))..)).)))).).....)))))))...... ( -29.10)
>DroSec_CAF1 99676 116 + 1
AAGAGCCAUCCUGGCAUCGGGAAAUCCAAAGGCGCCACC-CAC---CACCCACUCCUACACAUAAACUACAUUAGCAAUCGGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCG
..(((((((((((....)))))........((((((...-...---....................(((...)))...((((.....)))).))).))).........))))))...... ( -27.60)
>DroSim_CAF1 111603 116 + 1
AAGAGCCAUCCUGGCAUCGGGAAAUCCAAAGGCGCCACC-CAC---CACCCACUCCUACACAUAAACUACAUUAGCAAUCGGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCG
..(((((((((((....)))))........((((((...-...---....................(((...)))...((((.....)))).))).))).........))))))...... ( -27.60)
>DroEre_CAF1 97385 117 + 1
UAGAGCCAUCCUGGCAUCGGGAAAUCCAAAGACGCCACCGCAC---CAUCCACUCCUACACAUAAACUACAUUAGCAAUCGGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCG
...........((((.((.((....))...)).)))).(((..---............................((..((((.....))))..))((((((......))))))....))) ( -29.00)
>DroYak_CAF1 97782 120 + 1
UAGAGCCAUCCUGGCAUCGGGAAAUCCAAAGGCGCUACCGCACCACCAUCCACUCCUACACAUAAACUACAUUAGCAAUCGGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCG
....(((.(((((....)))))........(((((....))...........((((......(((......)))......))))..)))...)))((((((......))))))....... ( -29.80)
>consensus
AAGAGCCAUCCUGGCAUCGGGAAAUCCAAAGGCGCCACC_CAC___CACCCACUCCUACACAUAAACUACAUUAGCAAUCGGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCG
..(((((((..((((.((.((....))...)).))))..............................(((((..((..((((.....))))..))....)))))...)))))))...... (-27.34 = -27.02 +  -0.32)

alignment

secondary structure

dotplot

Window 7

Location	17,131,237 – 17,131,354
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.14
Mean single sequence MFE	-19.98
Consensus MFE	-19.50
Energy contribution	-19.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.53
Structure conservation index	0.98
SVM decision value	1.45
SVM RNA-class probability	0.955034
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17131237 117 + 22407834
CAC---CGCCCACUCCUACACAUAAACUACAUUAGCAAUCGGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCGCAAAUCUUUCAACUAAACAUUAAUCCUAAUGGUUUUCAAU
...---(((.........................((..((((.....))))..))((((((......))))))....))).................(((((....)))))......... ( -21.10)
>DroSec_CAF1 99715 117 + 1
CAC---CACCCACUCCUACACAUAAACUACAUUAGCAAUCGGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCGCAAAUCUUUCAACUAAACAUUAAUCCUAAUGGUUUUCAAU
...---......((((......(((......)))......)))).....((((((((((((......))))))........................(((((....)))))))))))... ( -19.50)
>DroSim_CAF1 111642 117 + 1
CAC---CACCCACUCCUACACAUAAACUACAUUAGCAAUCGGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCGCAAAUCUUUCAACUAAACAUUAAUCCUAAUGGUUUUCAAU
...---......((((......(((......)))......)))).....((((((((((((......))))))........................(((((....)))))))))))... ( -19.50)
>DroEre_CAF1 97425 117 + 1
CAC---CAUCCACUCCUACACAUAAACUACAUUAGCAAUCGGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCGCAAAUCUUUCAACUAAACAUUAAUCCUAAUGGUUUUCAAU
.((---(((.........................((..((((.....))))..))((((((......))))))...................................)))))....... ( -19.90)
>DroYak_CAF1 97822 120 + 1
CACCACCAUCCACUCCUACACAUAAACUACAUUAGCAAUCGGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCGCAAAUCUUUCAACUAAACAUUAAUCCUAAUGGUUUUCAAU
....(((((.........................((..((((.....))))..))((((((......))))))...................................)))))....... ( -19.90)
>consensus
CAC___CACCCACUCCUACACAUAAACUACAUUAGCAAUCGGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCGCAAAUCUUUCAACUAAACAUUAAUCCUAAUGGUUUUCAAU
............((((......(((......)))......)))).....((((((((((((......))))))........................(((((....)))))))))))... (-19.50 = -19.50 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	17,131,237 – 17,131,354
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.14
Mean single sequence MFE	-34.48
Consensus MFE	-30.32
Energy contribution	-30.32
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.08
Structure conservation index	0.88
SVM decision value	1.80
SVM RNA-class probability	0.977718
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17131237 117 - 22407834
AUUGAAAACCAUUAGGAUUAAUGUUUAGUUGAAAGAUUUGCGCGUUAAGCCAUUUUUACAUGGCUGCCUUCGGCUGCUCCGAUUGCUAAUGUAGUUUAUGUGUAGGAGUGGGCG---GUG
.......(((.......(((((((..((((....))))...))))))).(((((((((((((((.(((...))).)))..((((((....))))))...))))))))))))..)---)). ( -33.00)
>DroSec_CAF1 99715 117 - 1
AUUGAAAACCAUUAGGAUUAAUGUUUAGUUGAAAGAUUUGCGCGUUAAGCCAUUUUUACAUGGCUGCCUUCGGCUGCUCCGAUUGCUAAUGUAGUUUAUGUGUAGGAGUGGGUG---GUG
.......(((((.....(((((((..((((....))))...))))))).(((((((((((((((.(((...))).)))..((((((....))))))...)))))))))))))))---)). ( -34.50)
>DroSim_CAF1 111642 117 - 1
AUUGAAAACCAUUAGGAUUAAUGUUUAGUUGAAAGAUUUGCGCGUUAAGCCAUUUUUACAUGGCUGCCUUCGGCUGCUCCGAUUGCUAAUGUAGUUUAUGUGUAGGAGUGGGUG---GUG
.......(((((.....(((((((..((((....))))...))))))).(((((((((((((((.(((...))).)))..((((((....))))))...)))))))))))))))---)). ( -34.50)
>DroEre_CAF1 97425 117 - 1
AUUGAAAACCAUUAGGAUUAAUGUUUAGUUGAAAGAUUUGCGCGUUAAGCCAUUUUUACAUGGCUGCCUUCGGCUGCUCCGAUUGCUAAUGUAGUUUAUGUGUAGGAGUGGAUG---GUG
.......(((((.....(((((((..((((....))))...))))))).(((((((((((((((.(((...))).)))..((((((....))))))...)))))))))))))))---)). ( -34.00)
>DroYak_CAF1 97822 120 - 1
AUUGAAAACCAUUAGGAUUAAUGUUUAGUUGAAAGAUUUGCGCGUUAAGCCAUUUUUACAUGGCUGCCUUCGGCUGCUCCGAUUGCUAAUGUAGUUUAUGUGUAGGAGUGGAUGGUGGUG
.......(((((((...(((((((..((((....))))...))))))).(((((((((((((((.(((...))).)))..((((((....))))))...)))))))))))).))))))). ( -36.40)
>consensus
AUUGAAAACCAUUAGGAUUAAUGUUUAGUUGAAAGAUUUGCGCGUUAAGCCAUUUUUACAUGGCUGCCUUCGGCUGCUCCGAUUGCUAAUGUAGUUUAUGUGUAGGAGUGGGUG___GUG
........((....)).(((((((..((((....))))...))))))).(((((((((((((((.(((...))).)))..((((((....))))))...))))))))))))......... (-30.32 = -30.32 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	17,131,274 – 17,131,394
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	100.00
Mean single sequence MFE	-33.53
Consensus MFE	-33.53
Energy contribution	-33.53
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.86
Structure conservation index	1.00
SVM decision value	1.86
SVM RNA-class probability	0.980526
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17131274 120 + 22407834
GGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCGCAAAUCUUUCAACUAAACAUUAAUCCUAAUGGUUUUCAAUUUUGUUGCGCCUUCUGUGGCAAGUCAAGUUCGCGUCUCCU
(((((.(((((((((((((((......))))))......((((..............(((((....))))).............))))))))))...)))..((.......))).)))). ( -33.53)
>DroSec_CAF1 99752 120 + 1
GGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCGCAAAUCUUUCAACUAAACAUUAAUCCUAAUGGUUUUCAAUUUUGUUGCGCCUUCUGUGGCAAGUCAAGUUCGCGUCUCCU
(((((.(((((((((((((((......))))))......((((..............(((((....))))).............))))))))))...)))..((.......))).)))). ( -33.53)
>DroSim_CAF1 111679 120 + 1
GGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCGCAAAUCUUUCAACUAAACAUUAAUCCUAAUGGUUUUCAAUUUUGUUGCGCCUUCUGUGGCAAGUCAAGUUCGCGUCUCCU
(((((.(((((((((((((((......))))))......((((..............(((((....))))).............))))))))))...)))..((.......))).)))). ( -33.53)
>DroEre_CAF1 97462 120 + 1
GGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCGCAAAUCUUUCAACUAAACAUUAAUCCUAAUGGUUUUCAAUUUUGUUGCGCCUUCUGUGGCAAGUCAAGUUCGCGUCUCCU
(((((.(((((((((((((((......))))))......((((..............(((((....))))).............))))))))))...)))..((.......))).)))). ( -33.53)
>DroYak_CAF1 97862 120 + 1
GGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCGCAAAUCUUUCAACUAAACAUUAAUCCUAAUGGUUUUCAAUUUUGUUGCGCCUUCUGUGGCAAGUCAAGUUCGCGUCUCCU
(((((.(((((((((((((((......))))))......((((..............(((((....))))).............))))))))))...)))..((.......))).)))). ( -33.53)
>consensus
GGAGCAGCCGAAGGCAGCCAUGUAAAAAUGGCUUAACGCGCAAAUCUUUCAACUAAACAUUAAUCCUAAUGGUUUUCAAUUUUGUUGCGCCUUCUGUGGCAAGUCAAGUUCGCGUCUCCU
(((((.(((((((((((((((......))))))......((((..............(((((....))))).............))))))))))...)))..((.......))).)))). (-33.53 = -33.53 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:06 2006