Locus 4024

Sequence ID	3R_DroMel_CAF1
Location	10,995,937 – 10,996,064
Length	127
Max. P	0.884814

overview

Window 2

Location	10,995,937 – 10,996,040
Length	103
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	89.00
Mean single sequence MFE	-40.98
Consensus MFE	-30.38
Energy contribution	-29.66
Covariance contribution	-0.72
Combinations/Pair	1.17
Mean z-score	-2.26
Structure conservation index	0.74
SVM decision value	0.93
SVM RNA-class probability	0.884814
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10995937 103 - 27905053
UCUGGGAAAACCCAGAGGGAGCGGGAAACAUUAUUGG-------GGAAAAAUUCGCUGGCCUAGCGGGAGCCUGUCAAGUUCCUGGCCUAUGAAACACGCUUCAUUGUGU
((((((....)))))).(((((((....)........-------.......((((..((((....((((((.......))))))))))..))))...))))))....... ( -36.40)
>DroSec_CAF1 56679 110 - 1
GCUGGGAAAACCCAGAGGGAGCGGGAAAAAUCAUUGGGGGAGGGGGAAAUAUUCACUGGCCUGGCGGGAGCCUGUCAAGUUCCUGGCCUAUGAAACACGCUUCAUUGUGU
.(((((....)))))..((((((.......((((.(((..(((((((.....))..((((..(((....))).))))..)))))..)))))))....))))))....... ( -35.50)
>DroSim_CAF1 65672 110 - 1
GCUGGGAAAACCCAGAGGGAGUGGAAAAAAUCAUUGGGGGAGGGGGAAAUAUUCGCUGGCCUGGCGGGAGCCUGUCAAGUUCCUGGCCUAUGAAACACGCUUCAUUGUGU
.(((((....)))))..((((((.......((((.(((((..((.((.....)).))..)))..(((((((.......))))))).)).))))....))))))....... ( -34.80)
>DroEre_CAF1 58948 109 - 1
GCUGGGAAAACCCGGAGGGAGCGGGAAAAU-UCAUGGGGGCUGGGGAAAUAUUCCCUGGCCUGGCGGGAGCCUGUCAAGCUCCUGGCCUAUGAAACACGCUUCAUUGUGU
.(((((....)))))..((((((......(-((((((((((..((((.....))))..)))...(((((((.......))))))).))))))))...))))))....... ( -52.70)
>DroYak_CAF1 66415 110 - 1
GCUGGGAAAACCCAGAGGAAGCGGGAAAAUUUCAUGGGGACUGGGGAAAUAUUCCCUGGCCUGGUGGGAGCCUGUCAAGCUCCUGGCCUAUGGAACACGCUUCAUUGUGU
.(((((....)))))..((((((......((((((((((.(..((((.....))))..))).(.(((((((.......))))))).)))))))))..))))))....... ( -45.50)
>consensus
GCUGGGAAAACCCAGAGGGAGCGGGAAAAAUUAUUGGGGGAGGGGGAAAUAUUCCCUGGCCUGGCGGGAGCCUGUCAAGUUCCUGGCCUAUGAAACACGCUUCAUUGUGU
.(((((....)))))..((((((.....................(((....)))...((((....((((((.......)))))))))).........))))))....... (-30.38 = -29.66 +  -0.72)

alignment

secondary structure

dotplot

Window 3

Location	10,995,969 – 10,996,064
Length	95
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	86.27
Mean single sequence MFE	-25.44
Consensus MFE	-18.04
Energy contribution	-18.48
Covariance contribution	0.44
Combinations/Pair	1.06
Mean z-score	-1.73
Structure conservation index	0.71
SVM decision value	0.11
SVM RNA-class probability	0.589468
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10995969 95 + 27905053
UUGACAGGCUCCCGCUAGGCCAGCGAAUUUUUCC-------CCAAUAAUGUUUCCCGCUCCCUCUGGGUUUUCCCAGACCUCUGCAAACUUGGCCAAAAGCC
......((((.......((((((((.........-------..............)))....((((((....))))))............)))))...)))) ( -22.30)
>DroSec_CAF1 56711 102 + 1
UUGACAGGCUCCCGCCAGGCCAGUGAAUAUUUCCCCCUCCCCCAAUGAUUUUUCCCGCUCCCUCUGGGUUUUCCCAGCCCUGUGCAAACUUGGCCAAAAGCC
......(((....))).(((((((......................((....))..((.(...(((((....)))))....).))..)).)))))....... ( -23.20)
>DroSim_CAF1 65704 102 + 1
UUGACAGGCUCCCGCCAGGCCAGCGAAUAUUUCCCCCUCCCCCAAUGAUUUUUUCCACUCCCUCUGGGUUUUCCCAGCCCUGUGCAAACUUGGCCAAAAGCC
......(((....))).((((((.(((.(..((.............))..).)))(((.....(((((....)))))....))).....))))))....... ( -22.72)
>DroEre_CAF1 58980 101 + 1
UUGACAGGCUCCCGCCAGGCCAGGGAAUAUUUCCCCAGCCCCCAUGA-AUUUUCCCGCUCCCUCCGGGUUUUCCCAGCGCUUCGCUAACUUGGCCAAAAGCC
......((((...(((((((..((((.....))))..))).....((-(....((((.......))))..)))..((((...))))....))))....)))) ( -28.50)
>DroYak_CAF1 66447 102 + 1
UUGACAGGCUCCCACCAGGCCAGGGAAUAUUUCCCCAGUCCCCAUGAAAUUUUCCCGCUUCCUCUGGGUUUUCCCAGCUCUCCGCAAACUUGGCCAACAGCC
......((((.......((((((((((.(((((............))))).)))))((.....(((((....)))))......)).....)))))...)))) ( -30.50)
>consensus
UUGACAGGCUCCCGCCAGGCCAGCGAAUAUUUCCCCAGCCCCCAAUAAUUUUUCCCGCUCCCUCUGGGUUUUCCCAGCCCUCUGCAAACUUGGCCAAAAGCC
......(((....))).((((((.((.....)).......................((.....(((((....)))))......))....))))))....... (-18.04 = -18.48 +   0.44)

alignment

secondary structure

dotplot

Window 4

Location	10,995,969 – 10,996,064
Length	95
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	86.27
Mean single sequence MFE	-34.78
Consensus MFE	-24.66
Energy contribution	-24.42
Covariance contribution	-0.24
Combinations/Pair	1.17
Mean z-score	-1.74
Structure conservation index	0.71
SVM decision value	0.13
SVM RNA-class probability	0.599468
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10995969 95 - 27905053
GGCUUUUGGCCAAGUUUGCAGAGGUCUGGGAAAACCCAGAGGGAGCGGGAAACAUUAUUGG-------GGAAAAAUUCGCUGGCCUAGCGGGAGCCUGUCAA
(((((((((((..((((.(.....((((((....))))))).)))).(....)......((-------.((.....)).))))))....)))))))...... ( -29.20)
>DroSec_CAF1 56711 102 - 1
GGCUUUUGGCCAAGUUUGCACAGGGCUGGGAAAACCCAGAGGGAGCGGGAAAAAUCAUUGGGGGAGGGGGAAAUAUUCACUGGCCUGGCGGGAGCCUGUCAA
((((((((.((...(((((.(....(((((....)))))...).)))))............(((..(((((....))).))..)))))))))))))...... ( -30.40)
>DroSim_CAF1 65704 102 - 1
GGCUUUUGGCCAAGUUUGCACAGGGCUGGGAAAACCCAGAGGGAGUGGAAAAAAUCAUUGGGGGAGGGGGAAAUAUUCGCUGGCCUGGCGGGAGCCUGUCAA
((((((((.((((.(((.(((....(((((....))))).....))).)))......))))(((..((.((.....)).))..)))..))))))))...... ( -32.90)
>DroEre_CAF1 58980 101 - 1
GGCUUUUGGCCAAGUUAGCGAAGCGCUGGGAAAACCCGGAGGGAGCGGGAAAAU-UCAUGGGGGCUGGGGAAAUAUUCCCUGGCCUGGCGGGAGCCUGUCAA
((((((((.(((..((((((...)))))).....((((.......)))).....-...)))((((..((((.....))))..))))..))))))))...... ( -41.10)
>DroYak_CAF1 66447 102 - 1
GGCUGUUGGCCAAGUUUGCGGAGAGCUGGGAAAACCCAGAGGAAGCGGGAAAAUUUCAUGGGGACUGGGGAAAUAUUCCCUGGCCUGGUGGGAGCCUGUCAA
((((.((.((.......)).)).))))(((....))).......(((((....(..(((.(((.(..((((.....))))..)))).)))..).)))))... ( -40.30)
>consensus
GGCUUUUGGCCAAGUUUGCACAGGGCUGGGAAAACCCAGAGGGAGCGGGAAAAAUUAUUGGGGGAGGGGGAAAUAUUCCCUGGCCUGGCGGGAGCCUGUCAA
(((....(((((..(((((......(((((....))))).....)))))...................(((....)))..))))).(((....))).))).. (-24.66 = -24.42 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:04 2006