Locus 4676

Sequence ID	3L_DroMel_CAF1
Location	13,217,802 – 13,217,943
Length	141
Max. P	0.999535

overview

Window 3

Location	13,217,802 – 13,217,904
Length	102
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	94.31
Mean single sequence MFE	-22.58
Consensus MFE	-21.24
Energy contribution	-21.16
Covariance contribution	-0.08
Combinations/Pair	1.08
Mean z-score	-2.15
Structure conservation index	0.94
SVM decision value	3.70
SVM RNA-class probability	0.999535
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13217802 102 + 23771897
GAUAAAUAUAUGAGGAAAAGCCGAGGAAAAACUCAGAAUGGCAUUUAUAUUCUCUUAGAGCUGAGUUUGCUUGUUUGUGCAAACGUAGCAGGAAAUUCAAUA
..............(((...(((((......)))((((((.......))))))......((((.((((((........)))))).)))).))...))).... ( -22.70)
>DroSec_CAF1 11169 96 + 1
GAUAAAU--AUGAGGAAAAGCCGAGAAAAAACUCAGAAUGGCAUUUAUGUUCUCCUAGAGCUGAGUUUGCUU----GUGCAAACGAAGCAGGAAAUUCAAUA
....(((--(((((.....((((((......))).....))).)))))))).((((...(((..((((((..----..))))))..)))))))......... ( -22.40)
>DroSim_CAF1 16267 96 + 1
GAUAAAU--AUGAGGAAAAGCCGAGGAAAAACUCAGAAUGGCAUUUAUAUUCUCUUAGAGCUGAGUUUGCUU----GUGCAAACGAAGCAGGAAAUUCAAUA
.......--.....(((...(((((......)))((((((.......))))))......(((..((((((..----..))))))..))).))...))).... ( -22.80)
>DroEre_CAF1 1080 96 + 1
GAUAAAU--AUGAAGAAAAGCCGAGGAAAAGCUCAGAAUGGCAUUUAUAUUCUCUUAGAGCUGAGUUUGCUU----GUGCAAACGUAGCAGGAAACUCAAUA
....(((--(((((.....((((((......))).....))).))))))))........((((.((((((..----..)))))).))))((....))..... ( -22.10)
>DroYak_CAF1 11079 96 + 1
GAUAAAU--AUGAAGAAAAGCCGAGGAAAAACUCAGAAUGGCAUUUAUAUUCUCUUAGAGCUGAGUUUGCUU----GUGCAAACGUAGCAGGAAAUUCAAUA
.......--.....(((...(((((......)))((((((.......))))))......((((.((((((..----..)))))).)))).))...))).... ( -22.90)
>consensus
GAUAAAU__AUGAGGAAAAGCCGAGGAAAAACUCAGAAUGGCAUUUAUAUUCUCUUAGAGCUGAGUUUGCUU____GUGCAAACGUAGCAGGAAAUUCAAUA
..........((((......(((((......)))((((((.......))))))......(((..((((((........))))))..))).))...))))... (-21.24 = -21.16 +  -0.08)

alignment

secondary structure

dotplot

Window 4

Location	13,217,802 – 13,217,904
Length	102
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	94.31
Mean single sequence MFE	-17.16
Consensus MFE	-15.46
Energy contribution	-15.46
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.59
Structure conservation index	0.90
SVM decision value	1.58
SVM RNA-class probability	0.965220
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13217802 102 - 23771897
UAUUGAAUUUCCUGCUACGUUUGCACAAACAAGCAAACUCAGCUCUAAGAGAAUAUAAAUGCCAUUCUGAGUUUUUCCUCGGCUUUUCCUCAUAUAUUUAUC
.............(((..((((((........))))))..))).......(((((((.........(((((......)))))..........)))))))... ( -16.71)
>DroSec_CAF1 11169 96 - 1
UAUUGAAUUUCCUGCUUCGUUUGCAC----AAGCAAACUCAGCUCUAGGAGAACAUAAAUGCCAUUCUGAGUUUUUUCUCGGCUUUUCCUCAU--AUUUAUC
...(((.(((((((((..((((((..----..))))))..)))...))))))..............(((((......))))).......))).--....... ( -20.60)
>DroSim_CAF1 16267 96 - 1
UAUUGAAUUUCCUGCUUCGUUUGCAC----AAGCAAACUCAGCUCUAAGAGAAUAUAAAUGCCAUUCUGAGUUUUUCCUCGGCUUUUCCUCAU--AUUUAUC
.............(((..((((((..----..))))))..))).....(((.....(((.(((.....(((......)))))))))..)))..--....... ( -15.60)
>DroEre_CAF1 1080 96 - 1
UAUUGAGUUUCCUGCUACGUUUGCAC----AAGCAAACUCAGCUCUAAGAGAAUAUAAAUGCCAUUCUGAGCUUUUCCUCGGCUUUUCUUCAU--AUUUAUC
...((((......(((..((((((..----..))))))..(((((....(((((.........)))))))))).......))).....)))).--....... ( -16.80)
>DroYak_CAF1 11079 96 - 1
UAUUGAAUUUCCUGCUACGUUUGCAC----AAGCAAACUCAGCUCUAAGAGAAUAUAAAUGCCAUUCUGAGUUUUUCCUCGGCUUUUCUUCAU--AUUUAUC
...((((((((..(((..((((((..----..))))))..))).....))))..............(((((......)))))......)))).--....... ( -16.10)
>consensus
UAUUGAAUUUCCUGCUACGUUUGCAC____AAGCAAACUCAGCUCUAAGAGAAUAUAAAUGCCAUUCUGAGUUUUUCCUCGGCUUUUCCUCAU__AUUUAUC
...(((.((((..(((..((((((........))))))..))).....))))..............(((((......))))).......))).......... (-15.46 = -15.46 +  -0.00)

alignment

secondary structure

dotplot

Window 5

Location	13,217,833 – 13,217,943
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	95.91
Mean single sequence MFE	-28.48
Consensus MFE	-25.02
Energy contribution	-24.62
Covariance contribution	-0.40
Combinations/Pair	1.07
Mean z-score	-2.18
Structure conservation index	0.88
SVM decision value	2.58
SVM RNA-class probability	0.995451
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13217833 110 + 23771897
CUCAGAAUGGCAUUUAUAUUCUCUUAGAGCUGAGUUUGCUUGUUUGUGCAAACGUAGCAGGAAAUUCAAUAGGAAGAGCGCUGGAAAUUGCCAAAUUAUGAGGAAAUUUA
((((...((((((((.....(((((.....(((((((.(((((((((....))).))))))))))))).....)))))......))).))))).....))))........ ( -28.00)
>DroSec_CAF1 11198 106 + 1
CUCAGAAUGGCAUUUAUGUUCUCCUAGAGCUGAGUUUGCUU----GUGCAAACGAAGCAGGAAAUUCAAUAGGAAGAGCGCUGGAAAUUGCCAAAUUAUGAGGAAAUUUA
((((...(((((((((((((((((((..(((..((((((..----..))))))..)))..(.....)..)))).)))))).))))...))))).....))))........ ( -33.20)
>DroSim_CAF1 16296 106 + 1
CUCAGAAUGGCAUUUAUAUUCUCUUAGAGCUGAGUUUGCUU----GUGCAAACGAAGCAGGAAAUUCAAUAGGAAGAGCGCUGGAAAUUGCCAAAUUAUGAGGAAAUUUA
((((...((((((((.....(((((...(((..((((((..----..))))))..)))..(.....)......)))))......))).))))).....))))........ ( -26.60)
>DroEre_CAF1 1109 106 + 1
CUCAGAAUGGCAUUUAUAUUCUCUUAGAGCUGAGUUUGCUU----GUGCAAACGUAGCAGGAAACUCAAUAGGAAGGGCGCUGGAAAUUGCCAAAUUAUGAGGAAAUUUA
((((...((((((((.....(((((...((((.((((((..----..)))))).))))((....)).......)))))......))).))))).....))))........ ( -29.20)
>DroYak_CAF1 11108 106 + 1
CUCAGAAUGGCAUUUAUAUUCUCUUAGAGCUGAGUUUGCUU----GUGCAAACGUAGCAGGAAAUUCAAUAGGAAGGGCGCUGGAAAUUGCCAAAUUAUGAGAAAAUUUA
((((...((((((((.....(((((...((((.((((((..----..)))))).))))..(.....)......)))))......))).))))).....))))........ ( -25.40)
>consensus
CUCAGAAUGGCAUUUAUAUUCUCUUAGAGCUGAGUUUGCUU____GUGCAAACGUAGCAGGAAAUUCAAUAGGAAGAGCGCUGGAAAUUGCCAAAUUAUGAGGAAAUUUA
((((...((((((((...((((((((..(((..((((((........))))))..)))..(.....)..)))).))))......))).))))).....))))........ (-25.02 = -24.62 +  -0.40)

alignment

secondary structure

dotplot

Window 6

Location	13,217,833 – 13,217,943
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	95.91
Mean single sequence MFE	-20.90
Consensus MFE	-19.24
Energy contribution	-19.08
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.78
Structure conservation index	0.92
SVM decision value	2.23
SVM RNA-class probability	0.990678
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13217833 110 - 23771897
UAAAUUUCCUCAUAAUUUGGCAAUUUCCAGCGCUCUUCCUAUUGAAUUUCCUGCUACGUUUGCACAAACAAGCAAACUCAGCUCUAAGAGAAUAUAAAUGCCAUUCUGAG
........((((.....(((((.((.......(((((.(....)........(((..((((((........))))))..)))...))))).....)).)))))...)))) ( -20.90)
>DroSec_CAF1 11198 106 - 1
UAAAUUUCCUCAUAAUUUGGCAAUUUCCAGCGCUCUUCCUAUUGAAUUUCCUGCUUCGUUUGCAC----AAGCAAACUCAGCUCUAGGAGAACAUAAAUGCCAUUCUGAG
........((((.....(((((...........((........)).(((((((((..((((((..----..))))))..)))...)))))).......)))))...)))) ( -24.40)
>DroSim_CAF1 16296 106 - 1
UAAAUUUCCUCAUAAUUUGGCAAUUUCCAGCGCUCUUCCUAUUGAAUUUCCUGCUUCGUUUGCAC----AAGCAAACUCAGCUCUAAGAGAAUAUAAAUGCCAUUCUGAG
........((((.....(((((.((.......(((((.(....)........(((..((((((..----..))))))..)))...))))).....)).)))))...)))) ( -20.90)
>DroEre_CAF1 1109 106 - 1
UAAAUUUCCUCAUAAUUUGGCAAUUUCCAGCGCCCUUCCUAUUGAGUUUCCUGCUACGUUUGCAC----AAGCAAACUCAGCUCUAAGAGAAUAUAAAUGCCAUUCUGAG
........((((.....(((((............(((......)))((((..(((..((((((..----..))))))..))).....)))).......)))))...)))) ( -19.30)
>DroYak_CAF1 11108 106 - 1
UAAAUUUUCUCAUAAUUUGGCAAUUUCCAGCGCCCUUCCUAUUGAAUUUCCUGCUACGUUUGCAC----AAGCAAACUCAGCUCUAAGAGAAUAUAAAUGCCAUUCUGAG
........((((.....(((((.............(((.....)))((((..(((..((((((..----..))))))..))).....)))).......)))))...)))) ( -19.00)
>consensus
UAAAUUUCCUCAUAAUUUGGCAAUUUCCAGCGCUCUUCCUAUUGAAUUUCCUGCUACGUUUGCAC____AAGCAAACUCAGCUCUAAGAGAAUAUAAAUGCCAUUCUGAG
........((((.....(((((.............(((.....)))((((..(((..((((((........))))))..))).....)))).......)))))...)))) (-19.24 = -19.08 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:29 2006