Locus 8088

Sequence ID	3L_DroMel_CAF1
Location	21,277,439 – 21,277,631
Length	192
Max. P	0.897798

overview

Window 6

Location	21,277,439 – 21,277,559
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	97.08
Mean single sequence MFE	-29.85
Consensus MFE	-27.75
Energy contribution	-28.25
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.14
Structure conservation index	0.93
SVM decision value	0.98
SVM RNA-class probability	0.893893
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21277439 120 - 23771897
GGGCACACUUGCCACAAAAACAGCAAUCAGCGCUCGAUGCAGAAUUAAACAAAGAGUAAUUUUGUAUUUAGAGCCUGGCACGGGCUAAGAACAAUCAAAAUGUGGAUUCAGCCCAAGGAG
((((.......(((((.....(((..((((.((((((((((((((((.........))))))))))))..)))))))).....)))..((....))....))))).....))))...... ( -34.30)
>DroSec_CAF1 35721 120 - 1
GGGCACACUUGCCACAAAAACAACAAUCAGCGCUCGAUGAAGAAUUAAACAAAGAGUAAUUUUGUAUUUAGAGCCUCGCACGGGAUAAAAGCAAUCAAAAUGUGGAUUCAGCCCAAGGAG
((((.......(((((...............((((..((..........))..))))....((((.((((...(((.....))).)))).))))......))))).....))))...... ( -23.90)
>DroSim_CAF1 37985 120 - 1
GGGCACACUUGCCACAAAAACAACAAUCAGCGCUCGAUGCAGAAUUAAACAAAGAGUAAUUUUGUAUUUAGAGCCUCGCACGGGCUAAAAACAAUCAAAAUGUGGAUUCAGCCCAAGGAG
((((.......(((((................((.((((((((((((.........)))))))))))).))(((((.....)))))..............))))).....))))...... ( -30.50)
>DroEre_CAF1 36879 120 - 1
GGGCACACUUGCCACAAAAACAACAAUCAGAGCUCGAUGCAGAAUUAAACAAAGAGUAAUUUUGUAUUUAGAGCCUCGCACGGGCUAAAAACAAUCAAAAUGUGGAUUCAGCCCAAGGAG
((((.......(((((.............((((((((((((((((((.........))))))))))))..))).)))((....))...............))))).....))))...... ( -30.70)
>consensus
GGGCACACUUGCCACAAAAACAACAAUCAGCGCUCGAUGCAGAAUUAAACAAAGAGUAAUUUUGUAUUUAGAGCCUCGCACGGGCUAAAAACAAUCAAAAUGUGGAUUCAGCCCAAGGAG
((((.......(((((................((.((((((((((((.........)))))))))))).))(((((.....)))))..............))))).....))))...... (-27.75 = -28.25 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	21,277,519 – 21,277,631
Length	112
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.89
Mean single sequence MFE	-39.80
Consensus MFE	-33.56
Energy contribution	-33.62
Covariance contribution	0.06
Combinations/Pair	1.16
Mean z-score	-1.94
Structure conservation index	0.84
SVM decision value	1.00
SVM RNA-class probability	0.897798
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21277519 112 + 23771897
GCAUCGAGCGCUGAUUGCUGUUUUUGUGGCAAGUGUGCCCGUUGGCUGGAAAGCACAAAACGCACAAAGAACUAAGCAAUCUAUUGUGAAUGGGUGCACU------CU--GCGUCCGAUU
..((((..(((.((((((..(....)..))))(((..((((((.(((....)))........((((((((.........))).)))))))))))..))))------).--)))..)))). ( -42.00)
>DroSec_CAF1 35801 114 + 1
UCAUCGAGCGCUGAUUGUUGUUUUUGUGGCAAGUGUGCCCGUUGACUGGAAAGCACAAAACGCACCAAGAACGAAGCGAACUAUUGUGAAUGGGUGCACU------CUUAGCGCGCGAUU
..((((.(((((((((((..(....)..))))(((..((((((..((....))(((((..(((..(......)..))).....)))))))))))..))).------.))))))).)))). ( -41.10)
>DroSim_CAF1 38065 114 + 1
GCAUCGAGCGCUGAUUGUUGUUUUUGUGGCAAGUGUGCCCGUUGACUGGAAAGCACAAAACGCACCAAGAACGAAGCGAACUAUUGUGAAUGGGUGCACU------CUUAGCGCGCGAUU
..((((.(((((((((((..(....)..))))(((..((((((..((....))(((((..(((..(......)..))).....)))))))))))..))).------.))))))).)))). ( -41.10)
>DroEre_CAF1 36959 120 + 1
GCAUCGAGCUCUGAUUGUUGUUUUUGUGGCAAGUGUGCCCGUUAGCUGGAAAGCGGAAAACGCACCGAGUACGAAGCGAUCUAUUGUGAAUGGGUGUAAACGACUGCGCAGCGCGCGAUU
..((((.((.(((...(((((((..(.((((....)))))....(((....))).....((((.(((..(((((((....)).)))))..))))))))))))))....))).)).)))). ( -35.00)
>consensus
GCAUCGAGCGCUGAUUGUUGUUUUUGUGGCAAGUGUGCCCGUUGACUGGAAAGCACAAAACGCACCAAGAACGAAGCGAACUAUUGUGAAUGGGUGCACU______CUUAGCGCGCGAUU
..((((.((((((.((((..(....)..))))(((..((((((.(((((...((.....................))...)))..)).))))))..))).........)))))).)))). (-33.56 = -33.62 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:05:55 2006