Locus 7044

Sequence ID	3R_DroMel_CAF1
Location	18,594,749 – 18,594,959
Length	210
Max. P	0.863145

overview

Window 7

Location	18,594,749 – 18,594,847
Length	98
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	78.77
Mean single sequence MFE	-17.80
Consensus MFE	-10.14
Energy contribution	-11.18
Covariance contribution	1.04
Combinations/Pair	1.28
Mean z-score	-1.97
Structure conservation index	0.57
SVM decision value	0.56
SVM RNA-class probability	0.783265
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18594749 98 - 27905053
CAAUCCA---------CAGAAACUUUUACCCCAACCAACUUUGAAGCCAUCUUCCACUUUAACCACAACCGAAG---UCAGCUUGGAAAGGGAAGAUCAAAUUCAGGAUG
..((((.---------.(((....)))..............((((...(((((((.((((........((.(((---....))))))))))))))))....)))))))). ( -16.20)
>DroSec_CAF1 24318 98 - 1
CAAUCCA---------CAGAAACUUCUACCCCAACCAACUUUGAAGCCAUCUUCCACUUCAACCACAACCGAAG---UCCGCUUGGAAACGGAAGAUCAAAUUCAGGAUG
..((((.---------.(((....)))..............((((...((((((((((((..........))))---)......(....))))))))....)))))))). ( -20.80)
>DroSim_CAF1 20758 98 - 1
CAAUCCU---------CAGAAACUUCUACCCCAACCGACUUUGAAGCCAUCUUCCACUUCAACCACAACCGAAG---UUCGCCUGGAAACGGAAGAUCAAAUUCAGGAAG
...((((---------.(((....))).........((.(((((.....(((((((((((..........))))---)......(....)))))))))))).)))))).. ( -19.90)
>DroEre_CAF1 19733 107 - 1
CAAUUCAAUACCAAUUGAAAAACUUGUACCACUACCAACUCUAAGGCCAACUUCCACUUCAACAACUACCGAAG---CUCUCUUGGAAACGGAAGACCAAACCCAGGAUG
...((((((....))))))...((((........((........))....(((((.((((..........))))---.......(....))))))........))))... ( -16.20)
>DroYak_CAF1 20040 110 - 1
CAAUACAAUUCCAAUUAAAAAACUCGUAGCACUACCAACUCUGAAGCCAACUUCCACAUCAACAACAACCGGAAACAACCUCUUGGAAACGGAGGACCAAACUCAGGAUG
........((((.............(((....))).......((((....))))................))))....(((((.(....)))))).((.......))... ( -15.90)
>consensus
CAAUCCA_________CAGAAACUUCUACCCCAACCAACUUUGAAGCCAUCUUCCACUUCAACCACAACCGAAG___UCCGCUUGGAAACGGAAGAUCAAAUUCAGGAUG
.......................................((((((...(((((((.((((..........))))..........(....))))))))....))))))... (-10.14 = -11.18 +   1.04)

alignment

secondary structure

dotplot

Window 8

Location	18,594,825 – 18,594,919
Length	94
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	80.46
Mean single sequence MFE	-24.46
Consensus MFE	-10.50
Energy contribution	-12.82
Covariance contribution	2.32
Combinations/Pair	1.10
Mean z-score	-2.38
Structure conservation index	0.43
SVM decision value	0.65
SVM RNA-class probability	0.812785
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18594825 94 + 27905053
GGGUAAAAGUUUCUG---------UGGAUUGGGUACACUUUCAUCAACCCUUUCUUUAAUUAAUUCCAGUGCCCUUGUGGCCAAUGGAAUUAAACCCAUAAUA
((((...........---------.(((..((((............))))..)))....(((((((((..(((.....)))...)))))))))))))...... ( -26.70)
>DroSec_CAF1 24394 94 + 1
GGGUAGAAGUUUCUG---------UGGAUUGGGUACACUUUCAUCAACCCUUUCUUUAAUUAAUUCCAGUGCCCUUGUGGCCAAUGGAAUUAAUCCCAUAAUA
(((((((....))))---------.(((..((((............))))..)))...((((((((((..(((.....)))...)))))))))))))...... ( -25.20)
>DroSim_CAF1 20834 94 + 1
GGGUAGAAGUUUCUG---------AGGAUUGGGUACACUUUCAUCAACCCUUUCUUUAAUUAAUUCCAGUGCCCUUGUGGCCAAUGGAAUUAAUCCCAUAAUA
(((..........((---------((((..((((............))))..))))))((((((((((..(((.....)))...)))))))))))))...... ( -28.60)
>DroEre_CAF1 19809 103 + 1
UGGUACAAGUUUUUCAAUUGGUAUUGAAUUGGGUACAAUUUCAUCAACCUUUUCUUUAAUUAUUCGCAGUGCCUUUGCAGCCAAUGGAAUUAUUUCUCUAAUA
(((...((((..(((.((((((...(((..((((............)))).)))...........((((.....)))).)))))).)))..))))..)))... ( -18.00)
>DroYak_CAF1 20119 103 + 1
UGCUACGAGUUUUUUAAUUGGAAUUGUAUUGGGUACAAUAUCAUCCAACCUUUCUUUAAGUAUUCCCACUGCCUUUGGGGCGAAAGGAAUUAAUUCCCUAAUA
......(((((..((..(((((...((((((....))))))..)))))((((((....(((......)))(((.....)))))))))))..)))))....... ( -23.80)
>consensus
GGGUACAAGUUUCUG_________UGGAUUGGGUACACUUUCAUCAACCCUUUCUUUAAUUAAUUCCAGUGCCCUUGUGGCCAAUGGAAUUAAUCCCAUAAUA
(((......................(((..((((............))))..))).....((((((((..(((.....)))...))))))))..)))...... (-10.50 = -12.82 +   2.32)

alignment

secondary structure

dotplot

Window 9

Location	18,594,825 – 18,594,919
Length	94
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	80.46
Mean single sequence MFE	-23.08
Consensus MFE	-13.64
Energy contribution	-15.20
Covariance contribution	1.56
Combinations/Pair	1.15
Mean z-score	-2.16
Structure conservation index	0.59
SVM decision value	0.82
SVM RNA-class probability	0.858244
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18594825 94 - 27905053
UAUUAUGGGUUUAAUUCCAUUGGCCACAAGGGCACUGGAAUUAAUUAAAGAAAGGGUUGAUGAAAGUGUACCCAAUCCA---------CAGAAACUUUUACCC
.....((((((((((((((.((.((....)).)).))))))))..........((((..((....))..))))))))))---------............... ( -26.00)
>DroSec_CAF1 24394 94 - 1
UAUUAUGGGAUUAAUUCCAUUGGCCACAAGGGCACUGGAAUUAAUUAAAGAAAGGGUUGAUGAAAGUGUACCCAAUCCA---------CAGAAACUUCUACCC
.....((((((((((((((.((.((....)).)).))))))))))).......((((..((....))..))))...)))---------............... ( -27.10)
>DroSim_CAF1 20834 94 - 1
UAUUAUGGGAUUAAUUCCAUUGGCCACAAGGGCACUGGAAUUAAUUAAAGAAAGGGUUGAUGAAAGUGUACCCAAUCCU---------CAGAAACUUCUACCC
......(((((((((((((.((.((....)).)).))))))))))...((((.((((..((....))..))))..((..---------..))...)))).))) ( -26.40)
>DroEre_CAF1 19809 103 - 1
UAUUAGAGAAAUAAUUCCAUUGGCUGCAAAGGCACUGCGAAUAAUUAAAGAAAAGGUUGAUGAAAUUGUACCCAAUUCAAUACCAAUUGAAAAACUUGUACCA
.....(((..((((((.(((..(((((....)).((............))....)))..))).))))))......((((((....))))))...)))...... ( -14.40)
>DroYak_CAF1 20119 103 - 1
UAUUAGGGAAUUAAUUCCUUUCGCCCCAAAGGCAGUGGGAAUACUUAAAGAAAGGUUGGAUGAUAUUGUACCCAAUACAAUUCCAAUUAAAAAACUCGUAGCA
.....(((.....((((((...(((.....)))...))))))...........(((((((((.(((((....)))))))..)))))))......)))...... ( -21.50)
>consensus
UAUUAUGGGAUUAAUUCCAUUGGCCACAAGGGCACUGGAAUUAAUUAAAGAAAGGGUUGAUGAAAGUGUACCCAAUCCA_________CAGAAACUUCUACCC
........(((((((((((...(((.....)))..))))))))))).......((((..((....))..)))).............................. (-13.64 = -15.20 +   1.56)

alignment

secondary structure

dotplot

Window 0

Location	18,594,847 – 18,594,959
Length	112
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	87.95
Mean single sequence MFE	-24.41
Consensus MFE	-18.42
Energy contribution	-18.02
Covariance contribution	-0.40
Combinations/Pair	1.21
Mean z-score	-2.06
Structure conservation index	0.75
SVM decision value	0.84
SVM RNA-class probability	0.863145
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18594847 112 + 27905053
GGUACACUUUCAUCAACCCUUUCUUUAAUUAAUUCCAGUGCCCUUGUGGCCAAUGGAAUUAAACCCAUAAUACCGCUGUGAGGUACAUUCCUUUGACCAUAGUCACUGCCAA
((((.(((....((((............(((((((((..(((.....)))...)))))))))(((((((.......)))).)))........))))....)))...)))).. ( -24.80)
>DroSec_CAF1 24416 112 + 1
GGUACACUUUCAUCAACCCUUUCUUUAAUUAAUUCCAGUGCCCUUGUGGCCAAUGGAAUUAAUCCCAUAAUACCGCUGUGAGGUACAUUCCUUUGGCCAUCGUCACUGCCAA
(((............))).................(((((.(...((((((((.(((((....((((((.......)))).))...))))).)))))))).).))))).... ( -27.80)
>DroSim_CAF1 20856 112 + 1
GGUACACUUUCAUCAACCCUUUCUUUAAUUAAUUCCAGUGCCCUUGUGGCCAAUGGAAUUAAUCCCAUAAUACCGCUGUGAGGUACAUUCCUUUGGCCAUCGUCACUGCCAA
(((............))).................(((((.(...((((((((.(((((....((((((.......)))).))...))))).)))))))).).))))).... ( -27.80)
>DroEre_CAF1 19840 112 + 1
GGUACAAUUUCAUCAACCUUUUCUUUAAUUAUUCGCAGUGCCUUUGCAGCCAAUGGAAUUAUUUCUCUAAUACCGCUGUGAGGUACACUCCUUUGAUCAUCUUCACUGCUAG
(((............)))................((((((((.(..((((....((.((((......)))).))))))..)))))).......(((......))).)))... ( -21.20)
>DroYak_CAF1 20150 112 + 1
GGUACAAUAUCAUCCAACCUUUCUUUAAGUAUUCCCACUGCCUUUGGGGCGAAAGGAAUUAAUUCCCUAAUACCGCUUUGAGGUACAUUACUUUGACCAUCUUCACUGCCAA
((((.............((((((....(((......)))(((.....)))))))))..............))))((..((((((.((......)))))....)))..))... ( -20.43)
>consensus
GGUACACUUUCAUCAACCCUUUCUUUAAUUAAUUCCAGUGCCCUUGUGGCCAAUGGAAUUAAUCCCAUAAUACCGCUGUGAGGUACAUUCCUUUGACCAUCGUCACUGCCAA
((((.................................(((((.(..((((....((.((((......)))).))))))..)))))).......((((....)))).)))).. (-18.42 = -18.02 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:36:12 2006