Locus 7717

Sequence ID	X_DroMel_CAF1
Location	19,222,487 – 19,222,632
Length	145
Max. P	0.986423

overview

Window 6

Location	19,222,487 – 19,222,605
Length	118
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	96.78
Mean single sequence MFE	-32.67
Consensus MFE	-29.30
Energy contribution	-29.70
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.89
Structure conservation index	0.90
SVM decision value	2.04
SVM RNA-class probability	0.986423
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19222487 118 + 22224390
UGUGUUUUCGCACCGGGCUUUUUCCGCCUGCACUUUUUCCACACUUUUCUGACAAUUUUCACGCGGAAAGUCAUUUCGAGUCGAUGUCAGCAAAAGUGAAUUCCGCUGAAAAACUGCG
.((.(((((((..(((((.......)))))...........(((((((((((((....((((.(((((.....))))).)).)))))))).)))))))......)).)))))...)). ( -31.50)
>DroSec_CAF1 9473 118 + 1
UGUGUUUUCGCACCGGGCUUUUUCCGCCUGCACUUUUUCCACACUUUUCUGACAAUUUUCACGCGGAAAGUCAUUUCGAGUCGAUGUCAGCACAAGUGAAUUCCGCUGAAAAACUGCG
........((((.(((((.......))))).........................((((((.((((((..((((((.(.((.(....).)).))))))).))))))))))))..)))) ( -28.50)
>DroSim_CAF1 9532 118 + 1
UGUGUUUUCGCACCGGGCUUUUUCCGCCUGCACUUUUUCCACACUUUUCUGACAAUUUUCACGCGGAAAGUCAUUUCGAGUCGAUGUCAGCAAAAGUGAAUUCCGCUGAAAAACUGCG
.((.(((((((..(((((.......)))))...........(((((((((((((....((((.(((((.....))))).)).)))))))).)))))))......)).)))))...)). ( -31.50)
>DroEre_CAF1 8234 118 + 1
UGUGUUUUCGCAUCGCGCUUUUUCCGCCUGCACUUUUUCCGCACUUUUCUGACAAUUUUCACGCGGAAAGUCAUUUCGAGUUGAUGUCAGCAAAAGUGAAUUCUGCUGAAAAACUGCG
((((....)))).((((.((((((.((..............(((((((((((((....((((.(((((.....))))).).))))))))).)))))))......)).)))))).)))) ( -29.25)
>DroYak_CAF1 8672 118 + 1
UGUGUUUUCGCAUCGGGCUUUUUCCGCCUGCAGUUUUUCCACACUUUUCUGACAAUUUUCACGCGGAAAGUCAUUUCGCGUUGAUGUCAGCAAAAGUGAAUUCUGCUGAAAAACUGCG
((((....))))..((((.......))))(((((((((((((((((((((((((....((((((((((.....))))))).))))))))).))))))).....))..)))))))))). ( -42.60)
>consensus
UGUGUUUUCGCACCGGGCUUUUUCCGCCUGCACUUUUUCCACACUUUUCUGACAAUUUUCACGCGGAAAGUCAUUUCGAGUCGAUGUCAGCAAAAGUGAAUUCCGCUGAAAAACUGCG
.((.(((((((..(((((.......)))))...........(((((((((((((....((((.(((((.....))))).)).)))))))).)))))))......)).)))))...)). (-29.30 = -29.70 +   0.40)

alignment

secondary structure

dotplot

Window 7

Location	19,222,487 – 19,222,605
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	96.78
Mean single sequence MFE	-32.46
Consensus MFE	-27.14
Energy contribution	-27.30
Covariance contribution	0.16
Combinations/Pair	1.03
Mean z-score	-1.55
Structure conservation index	0.84
SVM decision value	0.26
SVM RNA-class probability	0.656800
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19222487 118 - 22224390
CGCAGUUUUUCAGCGGAAUUCACUUUUGCUGACAUCGACUCGAAAUGACUUUCCGCGUGAAAAUUGUCAGAAAAGUGUGGAAAAAGUGCAGGCGGAAAAAGCCCGGUGCGAAAACACA
.(((((((((..((((((.(((.(((((.((....))...))))))))..))))))..))))))))).......((((.......(..(.(((.......)))..)..)....)))). ( -31.30)
>DroSec_CAF1 9473 118 - 1
CGCAGUUUUUCAGCGGAAUUCACUUGUGCUGACAUCGACUCGAAAUGACUUUCCGCGUGAAAAUUGUCAGAAAAGUGUGGAAAAAGUGCAGGCGGAAAAAGCCCGGUGCGAAAACACA
.(((((((((..((((((.(((.(((.(.((....)).).)))..)))..))))))..))))))))).......((((.......(..(.(((.......)))..)..)....)))). ( -31.00)
>DroSim_CAF1 9532 118 - 1
CGCAGUUUUUCAGCGGAAUUCACUUUUGCUGACAUCGACUCGAAAUGACUUUCCGCGUGAAAAUUGUCAGAAAAGUGUGGAAAAAGUGCAGGCGGAAAAAGCCCGGUGCGAAAACACA
.(((((((((..((((((.(((.(((((.((....))...))))))))..))))))..))))))))).......((((.......(..(.(((.......)))..)..)....)))). ( -31.30)
>DroEre_CAF1 8234 118 - 1
CGCAGUUUUUCAGCAGAAUUCACUUUUGCUGACAUCAACUCGAAAUGACUUUCCGCGUGAAAAUUGUCAGAAAAGUGCGGAAAAAGUGCAGGCGGAAAAAGCGCGAUGCGAAAACACA
((((.....(((((((((.....))))))))).......(((.......(((((((.(((......))).....(..(.......)..)..))))))).....)))))))........ ( -29.90)
>DroYak_CAF1 8672 118 - 1
CGCAGUUUUUCAGCAGAAUUCACUUUUGCUGACAUCAACGCGAAAUGACUUUCCGCGUGAAAAUUGUCAGAAAAGUGUGGAAAAACUGCAGGCGGAAAAAGCCCGAUGCGAAAACACA
.((((((((((.........(((((((.((((((...(((((.((.....)).)))))......)))))))))))))..)))))))))).(((.......)))............... ( -38.80)
>consensus
CGCAGUUUUUCAGCGGAAUUCACUUUUGCUGACAUCGACUCGAAAUGACUUUCCGCGUGAAAAUUGUCAGAAAAGUGUGGAAAAAGUGCAGGCGGAAAAAGCCCGGUGCGAAAACACA
.(((.((((((.........(((((((.(((((((((....((((....))))....)))....)))))))))))))..)))))).))).(((.......)))............... (-27.14 = -27.30 +   0.16)

alignment

secondary structure

dotplot

Window 8

Location	19,222,525 – 19,222,632
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.72
Mean single sequence MFE	-32.78
Consensus MFE	-25.64
Energy contribution	-25.92
Covariance contribution	0.28
Combinations/Pair	1.03
Mean z-score	-1.81
Structure conservation index	0.78
SVM decision value	0.69
SVM RNA-class probability	0.824183
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19222525 107 + 22224390
CCACACUUUUCUGACAAUUUUCACGCGGAAAGUCAUUUCGAGUCGAUGUCAGCAAAAGUGAAUUCCGCUGAAAAACUGCGACUCUGAAUGUCGACGCUGGGAACCGA-------------
.................((..((.(((....(.(((((.((((((...(((((.............))))).......)))))).))))).)..)))))..))....------------- ( -28.32)
>DroSec_CAF1 9511 107 + 1
CCACACUUUUCUGACAAUUUUCACGCGGAAAGUCAUUUCGAGUCGAUGUCAGCACAAGUGAAUUCCGCUGAAAAACUGCGACUCUGAAUGUCGACGCUGGGAAGCGA-------------
...(.(((..((((......))).(((....(.(((((.((((((...(((((.............))))).......)))))).))))).)..))).)..))).).------------- ( -29.22)
>DroSim_CAF1 9570 107 + 1
CCACACUUUUCUGACAAUUUUCACGCGGAAAGUCAUUUCGAGUCGAUGUCAGCAAAAGUGAAUUCCGCUGAAAAACUGCGACUCUGAAUGUCGACGCUGGGAAGCGA-------------
...(((((((((((((....((((.(((((.....))))).)).)))))))).))))))).....((((.........((((.......)))).........)))).------------- ( -30.17)
>DroEre_CAF1 8272 106 + 1
CCGCACUUUUCUGACAAUUUUCACGCGGAAAGUCAUUUCGAGUUGAUGUCAGCAAAAGUGAAUUCUGCUGAAAAACUGCGACUCUGAAUGUCGACGGUGG-ACUCGA-------------
..(.((((((((((......)))...))))))))...(((((((....((((((.((.....)).))))))...((((((((.......)))).)))).)-))))))------------- ( -29.80)
>DroYak_CAF1 8710 119 + 1
CCACACUUUUCUGACAAUUUUCACGCGGAAAGUCAUUUCGCGUUGAUGUCAGCAAAAGUGAAUUCUGCUGAAAAACUGCGACUCUGAAUGUCGACGGUGG-AAUCGGUGGAAUCGGUUCC
((.(((((((((((((....((((((((((.....))))))).))))))))).))))))).((((..((((...((((((((.......)))).))))..-..))))..)))).)).... ( -46.40)
>consensus
CCACACUUUUCUGACAAUUUUCACGCGGAAAGUCAUUUCGAGUCGAUGUCAGCAAAAGUGAAUUCCGCUGAAAAACUGCGACUCUGAAUGUCGACGCUGGGAAGCGA_____________
...(((((((((((((....((((.(((((.....))))).)).)))))))).)))))))..................((((.......)))).((((....)))).............. (-25.64 = -25.92 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:45:48 2006