Locus 659

Sequence ID	3R_DroMel_CAF1
Location	2,425,402 – 2,425,555
Length	153
Max. P	0.977987

overview

Window 1

Location	2,425,402 – 2,425,516
Length	114
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	74.01
Mean single sequence MFE	-29.48
Consensus MFE	-14.15
Energy contribution	-16.27
Covariance contribution	2.12
Combinations/Pair	1.22
Mean z-score	-2.38
Structure conservation index	0.48
SVM decision value	1.80
SVM RNA-class probability	0.977987
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2425402 114 + 27905053
AAC---GCU---UUGCGUGUUGCUCUUCUGAUGUCGUUUAACCAUUAUGUGGCAUGAAUUUGCCAUUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGUCAACUCGUUGGCUUUUUAGCGAC
...---(((---..(((.(((((((..........((((((.......((((((......))))))......))))))(((((.....)))))))).)))).))).)))........... ( -34.52)
>DroSec_CAF1 138373 114 + 1
AAC---GCU---UUGCGUGUUGCUCUUCUGAUGCCGUUUAACCAUUAUGUGGCAUGAAUUUGCCAUUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGUCAACUCGUUGGCUUUUUAGCGAA
...---(((---..(((.(((((((..........((((((.......((((((......))))))......))))))(((((.....)))))))).)))).))).)))........... ( -34.52)
>DroSim_CAF1 132348 114 + 1
AAC---GCU---UUGCGUGUUGCUCUUCUGAUGCCGUUUAACCAUUAUGUGGCAUGAAUUUGCCAUUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGUCAACUCGUUGGCUUUUUAGCGAA
...---(((---..(((.(((((((..........((((((.......((((((......))))))......))))))(((((.....)))))))).)))).))).)))........... ( -34.52)
>DroEre_CAF1 133437 114 + 1
AAU---GUU---UUGCGUUUUGCUCUUCUGAUGUCGUUUAACCAUUAUGUGGCAUGAGUUUGCCAUUUUCAUUUAAAUGGUUCUCUUGGCAGCGAGUCAACUCGUUGGCUUUUUUGCGAU
...---...---(((((....((.......((((((..((.....))..))))))(((...(((((((......))))))).)))....(((((((....))))))))).....))))). ( -29.10)
>DroYak_CAF1 127567 87 + 1
AAA---GUU---UUGCG-----------UGAUGUCGUUUAGCCAUUAUGUGGCAUGAAUUUGCCACUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGCCAACUCU----------------
..(---(((---..(((-----------(((((.(.....).))))))((((((......))))))...........((((((.....)))))).)).))))..---------------- ( -25.20)
>DroAna_CAF1 134005 98 + 1
UAUUCAGCUUUAUUGCGUAUGACUUUUCUGAUGUCGGUUAACCACUUUUUG-AGUAAAAGUGUCAUUUCCAUUUUAC---UCCAUUUGGUAAUGACAGAAAU------------------
((((((((......))....(((.........)))((....))......))-))))....(((((((.(((......---......))).))))))).....------------------ ( -19.00)
>consensus
AAC___GCU___UUGCGUGUUGCUCUUCUGAUGUCGUUUAACCAUUAUGUGGCAUGAAUUUGCCAUUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGUCAACUCGUUGGCUUUUUAGCGA_
......((......))..................(((((((.......((((((......))))))......)))))))........(.(((((((....))))))).)........... (-14.15 = -16.27 +   2.12)

alignment

secondary structure

dotplot

Window 2

Location	2,425,402 – 2,425,516
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	74.01
Mean single sequence MFE	-24.64
Consensus MFE	-9.77
Energy contribution	-11.22
Covariance contribution	1.45
Combinations/Pair	1.07
Mean z-score	-2.15
Structure conservation index	0.40
SVM decision value	0.67
SVM RNA-class probability	0.818785
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2425402 114 - 27905053
GUCGCUAAAAAGCCAACGAGUUGACUCGCUGCCAAGAGCAGCAUUUAAAUGAAAAUGGCAAAUUCAUGCCACAUAAUGGUUAAACGACAUCAGAAGAGCAACACGCAA---AGC---GUU
((((......(((((..(((....)))(((((.....))))).............(((((......))))).....)))))...))))..............((((..---.))---)). ( -27.70)
>DroSec_CAF1 138373 114 - 1
UUCGCUAAAAAGCCAACGAGUUGACUCGCUGCCAAGAGCAGCAUUUAAAUGAAAAUGGCAAAUUCAUGCCACAUAAUGGUUAAACGGCAUCAGAAGAGCAACACGCAA---AGC---GUU
..((((.....(((...(((....)))(((((.....))))).(((((.......(((((......)))))........))))).))).........((.....))..---)))---).. ( -28.86)
>DroSim_CAF1 132348 114 - 1
UUCGCUAAAAAGCCAACGAGUUGACUCGCUGCCAAGAGCAGCAUUUAAAUGAAAAUGGCAAAUUCAUGCCACAUAAUGGUUAAACGGCAUCAGAAGAGCAACACGCAA---AGC---GUU
..((((.....(((...(((....)))(((((.....))))).(((((.......(((((......)))))........))))).))).........((.....))..---)))---).. ( -28.86)
>DroEre_CAF1 133437 114 - 1
AUCGCAAAAAAGCCAACGAGUUGACUCGCUGCCAAGAGAACCAUUUAAAUGAAAAUGGCAAACUCAUGCCACAUAAUGGUUAAACGACAUCAGAAGAGCAAAACGCAA---AAC---AUU
.((((......))....((((((.(((........)))(((((((...(((....(((((......)))))))))))))))...)))).)).))...((.....))..---...---... ( -21.20)
>DroYak_CAF1 127567 87 - 1
----------------AGAGUUGGCUCGCUGCCAAGAGCAGCAUUUAAAUGAAAGUGGCAAAUUCAUGCCACAUAAUGGCUAAACGACAUCA-----------CGCAA---AAC---UUU
----------------....((((((.(((((.....)))))............((((((......)))))).....)))))).........-----------.....---...---... ( -23.50)
>DroAna_CAF1 134005 98 - 1
------------------AUUUCUGUCAUUACCAAAUGGA---GUAAAAUGGAAAUGACACUUUUACU-CAAAAAGUGGUUAACCGACAUCAGAAAAGUCAUACGCAAUAAAGCUGAAUA
------------------.((((((((...((((....((---((((((((.......)).)))))))-)......)))).....)))...)))))........((......))...... ( -17.70)
>consensus
_UCGCUAAAAAGCCAACGAGUUGACUCGCUGCCAAGAGCAGCAUUUAAAUGAAAAUGGCAAAUUCAUGCCACAUAAUGGUUAAACGACAUCAGAAGAGCAACACGCAA___AGC___GUU
...................((((....(((((.....))))).............(((((......))))).............))))................................ ( -9.77 = -11.22 +   1.45)

alignment

secondary structure

dotplot

Window 3

Location	2,425,436 – 2,425,555
Length	119
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	93.42
Mean single sequence MFE	-34.75
Consensus MFE	-29.15
Energy contribution	-30.28
Covariance contribution	1.13
Combinations/Pair	1.07
Mean z-score	-2.73
Structure conservation index	0.84
SVM decision value	1.44
SVM RNA-class probability	0.954318
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2425436 119 + 27905053
ACCAUUAUGUGGCAUGAAUUUGCCAUUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGUCAACUCGUUGGCUUUUUAGCGACUGUUCUGCAUUCAUAAGCAGCAAUCGUAUAUAUCCUGCG
........((((((......))))))...........(((((((..((((((((((....)))))))(((....))).............)))..)))))))..((((.......)))) ( -34.30)
>DroSec_CAF1 138407 119 + 1
ACCAUUAUGUGGCAUGAAUUUGCCAUUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGUCAACUCGUUGGCUUUUUAGCGAAUGUUCUGCAUUCAUAAGCAGCAAUCGUAUAUAUCCUGCG
........((((((......))))))...........(((((((.....(((((((....)))))))(((....)))(((((.....)))))...)))))))..((((.......)))) ( -36.30)
>DroSim_CAF1 132382 119 + 1
ACCAUUAUGUGGCAUGAAUUUGCCAUUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGUCAACUCGUUGGCUUUUUAGCGAAUGUUCUGCAUUCAUAAGCAGCAAUCGUAUAUAUCCUGCG
........((((((......))))))...........(((((((.....(((((((....)))))))(((....)))(((((.....)))))...)))))))..((((.......)))) ( -36.30)
>DroEre_CAF1 133471 118 + 1
ACCAUUAUGUGGCAUGAGUUUGCCAUUUUCAUUUAAAUGGUUCUCUUGGCAGCGAGUCAACUCGUUGGCUUUUUUGCGAUUGCUCUGCCUUUGUUACCAGCAA-CGUAUAAUUCCUGGG
.(((......(((..(((...(((((((......))))))).)))....(((((((....))))))))))....((((.(((((..((....))....)))))-)))).......))). ( -32.10)
>consensus
ACCAUUAUGUGGCAUGAAUUUGCCAUUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGUCAACUCGUUGGCUUUUUAGCGAAUGUUCUGCAUUCAUAAGCAGCAAUCGUAUAUAUCCUGCG
........((((((......))))))...........(((((((...(.(((((((....))))))).)........((((((...))))))...)))))))................. (-29.15 = -30.28 +   1.13)

alignment

secondary structure

dotplot

Window 4

Location	2,425,436 – 2,425,555
Length	119
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	93.42
Mean single sequence MFE	-31.38
Consensus MFE	-24.19
Energy contribution	-25.62
Covariance contribution	1.44
Combinations/Pair	1.04
Mean z-score	-2.35
Structure conservation index	0.77
SVM decision value	0.44
SVM RNA-class probability	0.738976
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2425436 119 - 27905053
CGCAGGAUAUAUACGAUUGCUGCUUAUGAAUGCAGAACAGUCGCUAAAAAGCCAACGAGUUGACUCGCUGCCAAGAGCAGCAUUUAAAUGAAAAUGGCAAAUUCAUGCCACAUAAUGGU
.(((((((.....((((((((((........))))..)))))).......((((..(((....)))(((((.....))))).............))))..)))).)))........... ( -33.60)
>DroSec_CAF1 138407 119 - 1
CGCAGGAUAUAUACGAUUGCUGCUUAUGAAUGCAGAACAUUCGCUAAAAAGCCAACGAGUUGACUCGCUGCCAAGAGCAGCAUUUAAAUGAAAAUGGCAAAUUCAUGCCACAUAAUGGU
.(((((((.....(((.((((((........))))..)).))).......((((..(((....)))(((((.....))))).............))))..)))).)))........... ( -30.40)
>DroSim_CAF1 132382 119 - 1
CGCAGGAUAUAUACGAUUGCUGCUUAUGAAUGCAGAACAUUCGCUAAAAAGCCAACGAGUUGACUCGCUGCCAAGAGCAGCAUUUAAAUGAAAAUGGCAAAUUCAUGCCACAUAAUGGU
.(((((((.....(((.((((((........))))..)).))).......((((..(((....)))(((((.....))))).............))))..)))).)))........... ( -30.40)
>DroEre_CAF1 133471 118 - 1
CCCAGGAAUUAUACG-UUGCUGGUAACAAAGGCAGAGCAAUCGCAAAAAAGCCAACGAGUUGACUCGCUGCCAAGAGAACCAUUUAAAUGAAAAUGGCAAACUCAUGCCACAUAAUGGU
.((((.(((.....)-)).)))).......(((((.((....))...........((((....)))))))))......((((((...(((....(((((......)))))))))))))) ( -31.10)
>consensus
CGCAGGAUAUAUACGAUUGCUGCUUAUGAAUGCAGAACAUUCGCUAAAAAGCCAACGAGUUGACUCGCUGCCAAGAGCAGCAUUUAAAUGAAAAUGGCAAAUUCAUGCCACAUAAUGGU
.............((((((((((........))))..)))))).......((((..(((....)))(((((.....))))).............(((((......))))).....)))) (-24.19 = -25.62 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:35 2006