Locus 1246

Sequence ID	3R_DroMel_CAF1
Location	3,746,463 – 3,746,606
Length	143
Max. P	0.754217

overview

Window 8

Location	3,746,463 – 3,746,581
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	88.47
Mean single sequence MFE	-32.18
Consensus MFE	-21.82
Energy contribution	-21.74
Covariance contribution	-0.08
Combinations/Pair	1.18
Mean z-score	-1.95
Structure conservation index	0.68
SVM decision value	-0.03
SVM RNA-class probability	0.517169
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3746463 118 - 27905053
UCAGAGUCUUCUGACUCCUGGGAAUUUUGCGAGUUGUCGGACUCAUCGGACUUUUCGGAUUCCGCAGUCUCACUCGACUGGGACUCUUCCUCCUCUGAUUGCGUUUCAUCUAUAACCA
((((((((....)))).))))(((...((((((((....)))))((((((......(((.(((.(((((......)))))))).)))......)))))).))).)))........... ( -34.60)
>DroSec_CAF1 97 118 - 1
UUAGAGUCUUCAGACUCCUGGGAAUUCUGCGAGUUCUCGGACUCACCGGACUUAUCGGAUUCCGCAGACUCACUCGACUGGGACUCCUCCUCCUCUGAUUCCGUUUCAUCUAUAACCA
...(((((....)))))..((((((((...))))))))(((.(((..(((......(((.(((.(((.(......).)))))).)))...)))..))).)))................ ( -31.90)
>DroSim_CAF1 99 118 - 1
UUAGAGUCUUCAGACUCCUGGGAAUUCUGCGAGUUCUCGGACUCACCGGACUUAUCGGAUUCCGCAGACUCACUCGACUGGGACUCCUCCUCCUCUGAUUCUGUUUCAUCUAUAACCA
.((((.....((((.((..((((..((((((((((....))))).((((.....)))).....)))))((((......))))........))))..)).)))).....))))...... ( -32.60)
>DroEre_CAF1 111 115 - 1
UCAGAGUUGUCAGAAUCCUGGGAAUUCUGUGAGUUUUCGGAUUCACCGGACUCUUCGGAUUGCGCUGACUCACUCGUCUGGAACUCC---UCGUCUGAUUUCGUUUCAUCUAUAACCA
...((((.((((((((((..(((.(((.(((((((....))))))).))).)))..)))))...)))))..))))...((((((...---((....))....)))))).......... ( -31.50)
>DroYak_CAF1 60 118 - 1
UCAGAGACUUCAGACUCCUGGGAAUUUUGUGAGUUCUCGGAUUCACCGGACUCUUCAGAUUCCGCUGACUCACUUGACUGGGCCUCCUCCUCCUCCGAUUCCGUUUCAUCUAUAACCA
...(((((..(((....)))((((((..(((((((..((((.((....((....)).)).))))..)))))))..((..(((......)))..)).)))))))))))........... ( -30.30)
>consensus
UCAGAGUCUUCAGACUCCUGGGAAUUCUGCGAGUUCUCGGACUCACCGGACUUUUCGGAUUCCGCAGACUCACUCGACUGGGACUCCUCCUCCUCUGAUUCCGUUUCAUCUAUAACCA
...(((((.((((.....((((...((((((((((....)))))...(((.((....)).)))))))))))).....)))))))))................................ (-21.82 = -21.74 +  -0.08)

alignment

secondary structure

dotplot

Window 9

Location	3,746,503 – 3,746,606
Length	103
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	88.45
Mean single sequence MFE	-37.04
Consensus MFE	-29.72
Energy contribution	-29.92
Covariance contribution	0.20
Combinations/Pair	1.17
Mean z-score	-1.64
Structure conservation index	0.80
SVM decision value	0.48
SVM RNA-class probability	0.754217
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3746503 103 - 27905053
AGCGGACGGACGAACGCUGUCGUCCUCAGAGUCUUCUGACUCCUGGGAAUUUUGCGAGUUGUCGGACUCAUCGGACUUUUCGGAUUCCGCAGUCUCACUCGAC
.(((((.((((((......))))))...(((((....)))))(((..((.((((.(((((....)))))..)))).))..)))..))))).(((......))) ( -36.30)
>DroSec_CAF1 137 103 - 1
AGCGGACGGACGAAAGCUGUCGUCCUUAGAGUCUUCAGACUCCUGGGAAUUCUGCGAGUUCUCGGACUCACCGGACUUAUCGGAUUCCGCAGACUCACUCGAC
.((((((((.(....)))))).((((..(((((....)))))..))))....)))(((((..((((....((((.....))))..))))..)))))....... ( -38.20)
>DroSim_CAF1 139 103 - 1
AGCGGACGGACGAAAGCUGUCGUCCUUAGAGUCUUCAGACUCCUGGGAAUUCUGCGAGUUCUCGGACUCACCGGACUUAUCGGAUUCCGCAGACUCACUCGAC
.((((((((.(....)))))).((((..(((((....)))))..))))....)))(((((..((((....((((.....))))..))))..)))))....... ( -38.20)
>DroEre_CAF1 148 103 - 1
GGCGGGCGGACGAACGCUGUCGUCCUCAGAGUUGUCAGAAUCCUGGGAAUUCUGUGAGUUUUCGGAUUCACCGGACUCUUCGGAUUGCGCUGACUCACUCGUC
((((((.((((((......))))))...((((((.(..(((((..(((.(((.(((((((....))))))).))).)))..)))))..).)))))).)))))) ( -39.80)
>DroYak_CAF1 100 103 - 1
GACGGGCGGACGAACGCUGUCGUCAUCAGAGACUUCAGACUCCUGGGAAUUUUGUGAGUUCUCGGAUUCACCGGACUCUUCAGAUUCCGCUGACUCACUUGAC
(((((.((......)))))))((((...(((...........((((((((((...))))))))))..(((.((((.((....)).)))).))))))...)))) ( -32.70)
>consensus
AGCGGACGGACGAACGCUGUCGUCCUCAGAGUCUUCAGACUCCUGGGAAUUCUGCGAGUUCUCGGACUCACCGGACUUUUCGGAUUCCGCAGACUCACUCGAC
.(((((.((((((......))))))...((((((...((.(((.((((((((...))))))))))).))...)))))).......)))))............. (-29.72 = -29.92 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:30 2006