Locus 2229

Sequence ID	2L_DroMel_CAF1
Location	6,056,453 – 6,056,551
Length	98
Max. P	0.993149

overview

Window 2

Location	6,056,453 – 6,056,551
Length	98
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	84.57
Mean single sequence MFE	-31.96
Consensus MFE	-25.78
Energy contribution	-25.70
Covariance contribution	-0.08
Combinations/Pair	1.11
Mean z-score	-2.75
Structure conservation index	0.81
SVM decision value	2.38
SVM RNA-class probability	0.993149
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6056453 98 + 22407834
AUUCCAAAUCUCCGUUGAUUGGGGAAAUCCCCGAAAAACAUUCGAACCAUUCGUCCCUGGCGA---------GCACAGAAACAGCGUCUCUGAUUCUGGCAGGAAUU
(((((...((.(((((..((((((....))))))..)))...(((.....))).....)).))---------((.(((((.(((.....))).))))))).))))). ( -31.00)
>DroSec_CAF1 18262 98 + 1
AUUCCAAAUGUACGUUGAUUGGGGAAAUCCCCGAAAAACAUUCGAACCAUUCGCCCCUGGCGA---------GCACAGAAACAGCAUCUCUGAUUCUAGCAGGAAUU
(((((........(((..((((((....))))))..)))...........(((((...)))))---------((..((((.(((.....))).)))).)).))))). ( -28.70)
>DroSim_CAF1 19324 98 + 1
AUUCCAAAUGUCCGUUGAUUGGGGAAGUCCCCGAAAAACAUUCGAACCAUUCGCCCCUGGCGA---------GCACAGAAACAGCGUCUCUGAUUCUGGCAGGAAUU
(((((........(((..((((((....))))))..)))...........(((((...)))))---------((.(((((.(((.....))).))))))).))))). ( -33.30)
>DroEre_CAF1 19481 101 + 1
AUUCCAU-----C-CUGGUUGCGGAAAUCCCCGAAAAGUAGUCGAACCAUUCGCCCCUGGCGAAGUAGCCAGAAACAGAAACAGCGUCUCUGAUUCUGGCAGGAAUU
(((((..-----.-.(((((..((....)).(((.......))))))))((((((...))))))...(((((((.((((.((...)).)))).))))))).))))). ( -34.10)
>DroYak_CAF1 19454 93 + 1
AUUGCAU-----CCCUGAUUGGGGAAAUCCCCGAAAAGGUUUCGAACCAUUCGCCCCUGGCGA---------GAACAGAAACAGCGUCUCUGAUUCUGGCCGGAAUA
.(((.(.-----.(((..((((((....))))))..)))..))))...........(((((.(---------(((((((.((...)).)))).)))).))))).... ( -32.70)
>consensus
AUUCCAAAU_U_CGUUGAUUGGGGAAAUCCCCGAAAAACAUUCGAACCAUUCGCCCCUGGCGA_________GCACAGAAACAGCGUCUCUGAUUCUGGCAGGAAUU
(((((........(((..((((((....))))))..)))...........(((((...)))))............(((((.(((.....))).)))))...))))). (-25.78 = -25.70 +  -0.08)

alignment

secondary structure

dotplot

Window 3

Location	6,056,453 – 6,056,551
Length	98
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	84.57
Mean single sequence MFE	-32.98
Consensus MFE	-23.56
Energy contribution	-23.32
Covariance contribution	-0.24
Combinations/Pair	1.14
Mean z-score	-2.03
Structure conservation index	0.71
SVM decision value	0.64
SVM RNA-class probability	0.809276
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6056453 98 - 22407834
AAUUCCUGCCAGAAUCAGAGACGCUGUUUCUGUGC---------UCGCCAGGGACGAAUGGUUCGAAUGUUUUUCGGGGAUUUCCCCAAUCAACGGAGAUUUGGAAU
.(((((.(((((((.(((.....))).))))).))---------((.((..((((.....))))(((.....)))((((....)))).......)).))...))))) ( -29.50)
>DroSec_CAF1 18262 98 - 1
AAUUCCUGCUAGAAUCAGAGAUGCUGUUUCUGUGC---------UCGCCAGGGGCGAAUGGUUCGAAUGUUUUUCGGGGAUUUCCCCAAUCAACGUACAUUUGGAAU
.(((((....((((.(((.....))).))))((((---------(((((...))))).(((((.(((.....)))((((....)))))))))..))))....))))) ( -30.30)
>DroSim_CAF1 19324 98 - 1
AAUUCCUGCCAGAAUCAGAGACGCUGUUUCUGUGC---------UCGCCAGGGGCGAAUGGUUCGAAUGUUUUUCGGGGACUUCCCCAAUCAACGGACAUUUGGAAU
.(((((.(((((((.(((.....))).))))).))---------(((((...)))))...(((((((.....)))((((....)))).......))))....))))) ( -33.70)
>DroEre_CAF1 19481 101 - 1
AAUUCCUGCCAGAAUCAGAGACGCUGUUUCUGUUUCUGGCUACUUCGCCAGGGGCGAAUGGUUCGACUACUUUUCGGGGAUUUCCGCAACCAG-G-----AUGGAAU
.(((((.(((((((.(((((((...))))))).)))))))...((((((...))))))(((((.((.......))(.((....)).)))))).-.-----..))))) ( -36.60)
>DroYak_CAF1 19454 93 - 1
UAUUCCGGCCAGAAUCAGAGACGCUGUUUCUGUUC---------UCGCCAGGGGCGAAUGGUUCGAAACCUUUUCGGGGAUUUCCCCAAUCAGGG-----AUGCAAU
(((((((((.((((.(((((((...))))))))))---------).)))((((.(((.....)))...))))...((((....)))).....)))-----))).... ( -34.80)
>consensus
AAUUCCUGCCAGAAUCAGAGACGCUGUUUCUGUGC_________UCGCCAGGGGCGAAUGGUUCGAAUGUUUUUCGGGGAUUUCCCCAAUCAACG_A_AUUUGGAAU
.(((((.((((....(((((((...)))))))............(((((...))))).))))......(((..(.((((....)))).)..)))........))))) (-23.56 = -23.32 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:40 2006