Locus 5959

Sequence ID	3R_DroMel_CAF1
Location	15,730,762 – 15,730,958
Length	196
Max. P	0.983776

overview

Window 0

Location	15,730,762 – 15,730,882
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	82.50
Mean single sequence MFE	-30.40
Consensus MFE	-21.26
Energy contribution	-22.58
Covariance contribution	1.31
Combinations/Pair	1.24
Mean z-score	-2.67
Structure conservation index	0.70
SVM decision value	1.95
SVM RNA-class probability	0.983776
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15730762 120 + 27905053
GCCUAAGCUCUGAGAAAUCUCAACAGGCAUUUAUCAAACAGUGUUACCAAAUACGAACUUUCGAAAAAGGCGCUCUCCAGCCUUUUGUCAUUUCCCAGCGCUCCCGCUGCGGUCACACCC
((((......((((....))))..))))............((((.(((..............(((((((((........))))))).))......(((((....))))).))).)))).. ( -32.00)
>DroSec_CAF1 26692 120 + 1
GCUCAAGCUCUGAGAAAUCUCUCUAGGCAUUUAUCAAACAGUGUGACCAAAUACGAAUUUUUGAAAAAGGUGCUCUCCAGCCUUUUGUCAUUUCCCAGCGCUCUCGCUGCGGUCACACCC
......(((..((((....))))..)))............((((((((......(((....((((((((((........))))))).))).))).(((((....))))).)))))))).. ( -37.50)
>DroEre_CAF1 27162 120 + 1
GCUGAAACUCUCAGAAAUCCGUCCAGACAGUUAUCAAACAGUGUGACCAAACGCACGCUUUUGAAAAACGCUUUCUCCAGCCUUUCGUCAUUUCUUAGCGCUCCCGCUGCGGUCCCACCA
.((((.....))))....((((...(((.(((.(((((.((((((........)))))))))))..)))(((......))).....))).......((((....))))))))........ ( -26.00)
>DroYak_CAF1 29904 120 + 1
GCUUAAAACCGUAGAAAUCUCUAUAAGCAGUCAUCAAACAGUGUGACCAAAUACACACUUUUGAAAAAUGCGUUCUCCAGCCUUUUGUCAUUUCUUAGCGCUCCCCCUACGGUCACAUCC
.......(((((((............(((....(((((.((((((........)))))))))))....))).......(((((...(......)..)).)))....)))))))....... ( -26.10)
>consensus
GCUUAAACUCUGAGAAAUCUCUACAGGCAGUUAUCAAACAGUGUGACCAAAUACAAACUUUUGAAAAAGGCGCUCUCCAGCCUUUUGUCAUUUCCCAGCGCUCCCGCUGCGGUCACACCC
((((.......(((....)))...))))............((((((((..............(((((((((........))))))).))......(((((....))))).)))))))).. (-21.26 = -22.58 +   1.31)

alignment

secondary structure

dotplot

Window 1

Location	15,730,802 – 15,730,921
Length	119
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	89.22
Mean single sequence MFE	-28.51
Consensus MFE	-24.83
Energy contribution	-25.82
Covariance contribution	1.00
Combinations/Pair	1.16
Mean z-score	-1.94
Structure conservation index	0.87
SVM decision value	1.13
SVM RNA-class probability	0.920020
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15730802 119 + 27905053
GUGUUACCAAAUACGAACUUUCGAAAAAGGCGCUCUCCAGCCUUUUGUCAUUUCCCAGCGCUCCCGCUGCGGUCACACCCGCCUCACUUUUCCGUAAAACAUCGUUGAAGAAUGACUAA
(((((....)))))..........(((((((........)))))))(((((((..((((((....)).((((......)))).....................))))..)))))))... ( -29.30)
>DroSec_CAF1 26732 119 + 1
GUGUGACCAAAUACGAAUUUUUGAAAAAGGUGCUCUCCAGCCUUUUGUCAUUUCCCAGCGCUCUCGCUGCGGUCACACCCGCCUCACUUUUCCGUAAAACAUUGUUGAAGAAUGACUAA
((((((((......(((....((((((((((........))))))).))).))).(((((....))))).)))))))).....(((.(((((..(((....)))..))))).))).... ( -32.80)
>DroEre_CAF1 27202 119 + 1
GUGUGACCAAACGCACGCUUUUGAAAAACGCUUUCUCCAGCCUUUCGUCAUUUCUUAGCGCUCCCGCUGCGGUCCCACCAGUCUCACUUUUCCGUAAAACAUCGUUGAAGAAUGACUAA
(((((......)))))(((...((((.....))))...))).....((((((..(((((((....))(((((...................))))).......)))))..))))))... ( -27.11)
>DroYak_CAF1 29944 119 + 1
GUGUGACCAAAUACACACUUUUGAAAAAUGCGUUCUCCAGCCUUUUGUCAUUUCUUAGCGCUCCCCCUACGGUCACAUCCGUCUCACUUUUCCGUAAAACAUCGUUGAAGAAUGACUAA
(((((........)))))......((((.((........)).))))((((((..((((((.......(((((...................)))))......))))))..))))))... ( -24.83)
>consensus
GUGUGACCAAAUACAAACUUUUGAAAAAGGCGCUCUCCAGCCUUUUGUCAUUUCCCAGCGCUCCCGCUGCGGUCACACCCGCCUCACUUUUCCGUAAAACAUCGUUGAAGAAUGACUAA
((((((((..............(((((((((........))))))).))......(((((....))))).))))))))..(((...((((..((........))..))))...)))... (-24.83 = -25.82 +   1.00)

alignment

secondary structure

dotplot

Window 2

Location	15,730,842 – 15,730,958
Length	116
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	93.68
Mean single sequence MFE	-32.60
Consensus MFE	-29.33
Energy contribution	-30.07
Covariance contribution	0.75
Combinations/Pair	1.09
Mean z-score	-2.37
Structure conservation index	0.90
SVM decision value	1.70
SVM RNA-class probability	0.972728
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15730842 116 - 27905053
UUAGCUGGGCAUUGAGUAAAUACUUAAAACAGGCAAAUUAGUCAUUCUUCAACGAUGUUUUACGGAAAAGUGAGGCGGGUGUGACCGCAGCGGGAGCGCUGGGAAAUGACAAAAGG
...(((.(...((((((....))))))..).)))......((((((..(((....((((((((......))))))))....)))((.(((((....))))))).))))))...... ( -33.90)
>DroSec_CAF1 26772 116 - 1
UUAGCUGGGCAUUGAGUAAAUACUUAAAACAGGCAAAUUAGUCAUUCUUCAACAAUGUUUUACGGAAAAGUGAGGCGGGUGUGACCGCAGCGAGAGCGCUGGGAAAUGACAAAAGG
...(((.(...((((((....))))))..).)))......((((((..(((.((.((((((((......))))))))..)))))((.(((((....))))))).))))))...... ( -32.40)
>DroEre_CAF1 27242 116 - 1
UUAGCUAGGCAUUGAGUAAAUACUUAAAACUGGCAAAUUAGUCAUUCUUCAACGAUGUUUUACGGAAAAGUGAGACUGGUGGGACCGCAGCGGGAGCGCUAAGAAAUGACGAAAGG
...(((((...((((((....))))))..)))))......(((((((((.......(((((((......)))))))..(((....)))((((....))))))).))))))...... ( -33.20)
>DroYak_CAF1 29984 116 - 1
UUAGCUAGGCAUUGAGUAAAUACUUAAAACUGGCAAAUUAGUCAUUCUUCAACGAUGUUUUACGGAAAAGUGAGACGGAUGUGACCGUAGGGGGAGCGCUAAGAAAUGACAAAAGG
...(((((...((((((....))))))..)))))......(((((((((.......(((((((......)))))))((.(((..((.....))..)))))))).))))))...... ( -30.90)
>consensus
UUAGCUAGGCAUUGAGUAAAUACUUAAAACAGGCAAAUUAGUCAUUCUUCAACGAUGUUUUACGGAAAAGUGAGACGGGUGUGACCGCAGCGGGAGCGCUAAGAAAUGACAAAAGG
...(((((...((((((....))))))..)))))......(((((((((((....((((((((......))))))))....)))...(((((....))))))).))))))...... (-29.33 = -30.07 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:59 2006