Locus 5304

Sequence ID	3R_DroMel_CAF1
Location	13,854,594 – 13,854,742
Length	148
Max. P	0.761144

overview

Window 3

Location	13,854,594 – 13,854,684
Length	90
Sequences	4
Columns	95
Reading direction	forward
Mean pairwise identity	86.59
Mean single sequence MFE	-27.68
Consensus MFE	-20.19
Energy contribution	-21.00
Covariance contribution	0.81
Combinations/Pair	1.04
Mean z-score	-1.45
Structure conservation index	0.73
SVM decision value	0.03
SVM RNA-class probability	0.547957
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13854594 90 + 27905053
AGAGCUCUAAGUGCAUGGAAUUUAUCAUUGACGAUGGUCGACGAUCGUCGUCAGUGGCGGUAA-----AGGAAGUCGGCGGUGGAGGCGUUUGCC
...((((((......))))......((((((((((((((...))))))))))))))))(((((-----(.(...(((....)))...).)))))) ( -29.10)
>DroSec_CAF1 125777 84 + 1
AGAGCUCUAAGUGCAUGGAAUUUAUCAUUGACGAUGG------AUCGUCGUCAGUGGCGGUGU-----GUGGAGUCGAAGGUGGAGGCGUUUGCC
.((.(((((...((((.(......((((((((((((.------..))))))))))))).))))-----.)))))))...((..((....))..)) ( -26.90)
>DroSim_CAF1 131801 84 + 1
AGAGCUCUAAGUGCAUGGAAUUUAUCAUUGACGAUGG------AUCGUCGUCAGUGGCGGUGU-----GUGGAGUCGAAGGUGGAGGCGUUUGCC
.((.(((((...((((.(......((((((((((((.------..))))))))))))).))))-----.)))))))...((..((....))..)) ( -26.90)
>DroYak_CAF1 136784 89 + 1
AGAGCUCUAAGUGCAUGGAAUUUAUCAUUGCCGUUGG------AUCGUCGUCAGUGGCGAUGGCGGUGGUGGAGUUAGAGGUGGAGGCGUUUGCC
..((((((((((.......))))).(((..(((((..------(((((((....))))))))))))..))))))))...((..((....))..)) ( -27.80)
>consensus
AGAGCUCUAAGUGCAUGGAAUUUAUCAUUGACGAUGG______AUCGUCGUCAGUGGCGGUGU_____GUGGAGUCGAAGGUGGAGGCGUUUGCC
...((((((............(..(((((((((((((.......)))))))))))))..).........))))))....((..((....))..)) (-20.19 = -21.00 +   0.81)

alignment

secondary structure

dotplot

Window 4

Location	13,854,609 – 13,854,724
Length	115
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.17
Mean single sequence MFE	-31.80
Consensus MFE	-15.59
Energy contribution	-16.70
Covariance contribution	1.11
Combinations/Pair	1.07
Mean z-score	-2.05
Structure conservation index	0.49
SVM decision value	0.48
SVM RNA-class probability	0.752179
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13854609 115 + 27905053
UGGAAUUUAUCAUUGACGAUGGUCGACGAUCGUCGUCAGUGGCGGUAA-----AGGAAGUCGGCGGUGGAGGCGUUUGCCAAAAAUGGCACAAAUAACGACAUAAUUUGGCCAAAGAUCU
.........(((((((((((((((...))))))))))))))).(((((-----(.(...(((....)))...).)))))).....((((.(((((.........)))))))))....... ( -36.50)
>DroPse_CAF1 184543 88 + 1
UGGAAUUUAUCAUCAUCCAC------------UCAUCGGUGG-------------------GGCAGAGGAGGCGUUUGCCAAAAAUGGCACAAAUAACGACAUAAUUUG-CUGAAGAUUU
........(((.((..((((------------(....)))))-------------------((((((....((((((((((....))))).....)))).)....))))-)))).))).. ( -22.30)
>DroSec_CAF1 125792 109 + 1
UGGAAUUUAUCAUUGACGAUGG------AUCGUCGUCAGUGGCGGUGU-----GUGGAGUCGAAGGUGGAGGCGUUUGCCAAAAAUGGCACAAAUAACGACAUAAUUUGGCCACAGAUCU
.........((((((((((((.------..)))))))))))).(((.(-----((((...((((.(((..(..((((((((....)))))..)))..)..)))..)))).))))).))). ( -37.00)
>DroSim_CAF1 131816 109 + 1
UGGAAUUUAUCAUUGACGAUGG------AUCGUCGUCAGUGGCGGUGU-----GUGGAGUCGAAGGUGGAGGCGUUUGCCAAAAAUGGCACAAAUAACGACAUAAUUUGGCCACAGAUCU
.........((((((((((((.------..)))))))))))).(((.(-----((((...((((.(((..(..((((((((....)))))..)))..)..)))..)))).))))).))). ( -37.00)
>DroYak_CAF1 136799 114 + 1
UGGAAUUUAUCAUUGCCGUUGG------AUCGUCGUCAGUGGCGAUGGCGGUGGUGGAGUUAGAGGUGGAGGCGUUUGCCAAAAAUGGCACAAAUAACGACAUAAUUUGGCCACAGAUCU
.........((((..(((((..------(((((((....))))))))))))..))))....(((..((..(((...(((((....)))))(((((.........)))))))).))..))) ( -35.70)
>DroPer_CAF1 178832 88 + 1
UGGAAUUUAUCAUCAUCCAC------------UCAUCGGUGG-------------------GGCAGAGGAGGCGUUUGCCAAAAAUGGCACAAAUAACGACAUAAUUUG-CUGAAGAUUU
........(((.((..((((------------(....)))))-------------------((((((....((((((((((....))))).....)))).)....))))-)))).))).. ( -22.30)
>consensus
UGGAAUUUAUCAUUGACGAUGG______AUCGUCGUCAGUGGCGGUG______GUGGAGUCGGAGGUGGAGGCGUUUGCCAAAAAUGGCACAAAUAACGACAUAAUUUGGCCAAAGAUCU
.........((((((.((((((.......)))))).))))))......................(((.(((.(((((((((....))))).....))))......))).)))........ (-15.59 = -16.70 +   1.11)

alignment

secondary structure

dotplot

Window 5

Location	13,854,649 – 13,854,742
Length	93
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	78.00
Mean single sequence MFE	-24.60
Consensus MFE	-14.60
Energy contribution	-14.22
Covariance contribution	-0.39
Combinations/Pair	1.21
Mean z-score	-1.74
Structure conservation index	0.59
SVM decision value	0.50
SVM RNA-class probability	0.761144
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13854649 93 + 27905053
GGCGGUAA-----AGGAAGUCGGCGGUGGAGGCGUUUGCCAAAAAUGGCACAAAUAACGACAUAAUUUGGCCAAAGAUCUGGCCAACAUCGCAGAUCA
.(((((..-----.....((((((.......))...(((((....))))).......)))).....(((((((......))))))).)))))...... ( -29.40)
>DroPse_CAF1 184571 78 + 1
GG-------------------GGCAGAGGAGGCGUUUGCCAAAAAUGGCACAAAUAACGACAUAAUUUG-CUGAAGAUUUGGCCAACAUCAGAGAUCG
..-------------------((((((.(...).)))))).....((((.(((((..((.((.....))-.))...)))))))))............. ( -17.60)
>DroSim_CAF1 131850 93 + 1
GGCGGUGU-----GUGGAGUCGAAGGUGGAGGCGUUUGCCAAAAAUGGCACAAAUAACGACAUAAUUUGGCCACAGAUCUGGCCAACAUCGCAGAUCA
.(((((((-----.....((((((.((....)).))(((((....))))).......))))......((((((......)))))))))))))...... ( -30.90)
>DroYak_CAF1 136833 98 + 1
GGCGAUGGCGGUGGUGGAGUUAGAGGUGGAGGCGUUUGCCAAAAAUGGCACAAAUAACGACAUAAUUUGGCCACAGAUCUGGCCAACAUCGCAGAUCA
...(((.(((((((((..((((....((..(.(((((.....))))).).))..))))..)))...(((((((......)))))))))))))..))). ( -33.80)
>DroAna_CAF1 129393 74 + 1
------------------------GGAGGGGGCGUUUGCCAAAAAUGGCACAAAUAACGACAUAAUUUGGCCACAGAUCUGGCCAGCAUCGGAUAUCA
------------------------....(..((...(((((....))))).................((((((......))))))))..)........ ( -18.30)
>DroPer_CAF1 178860 78 + 1
GG-------------------GGCAGAGGAGGCGUUUGCCAAAAAUGGCACAAAUAACGACAUAAUUUG-CUGAAGAUUUGGCCAACAUCAGAGAUCG
..-------------------((((((.(...).)))))).....((((.(((((..((.((.....))-.))...)))))))))............. ( -17.60)
>consensus
GG___________________GGCGGAGGAGGCGUUUGCCAAAAAUGGCACAAAUAACGACAUAAUUUGGCCAAAGAUCUGGCCAACAUCGCAGAUCA
............................(((.(((((((((....))))).....)))).).....(((((((......)))))))..))........ (-14.60 = -14.22 +  -0.39)

alignment

secondary structure

dotplot

Window 6

Location	13,854,649 – 13,854,742
Length	93
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	78.00
Mean single sequence MFE	-20.60
Consensus MFE	-13.54
Energy contribution	-14.48
Covariance contribution	0.95
Combinations/Pair	1.06
Mean z-score	-1.40
Structure conservation index	0.66
SVM decision value	0.37
SVM RNA-class probability	0.710353
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13854649 93 - 27905053
UGAUCUGCGAUGUUGGCCAGAUCUUUGGCCAAAUUAUGUCGUUAUUUGUGCCAUUUUUGGCAAACGCCUCCACCGCCGACUUCCU-----UUACCGCC
......(((...((((((((....)))))))).....((((.......(((((....)))))...((.......)))))).....-----....))). ( -25.20)
>DroPse_CAF1 184571 78 - 1
CGAUCUCUGAUGUUGGCCAAAUCUUCAG-CAAAUUAUGUCGUUAUUUGUGCCAUUUUUGGCAAACGCCUCCUCUGCC-------------------CC
...........(((.((((((......(-(((((.........))))))......)))))).)))............-------------------.. ( -13.90)
>DroSim_CAF1 131850 93 - 1
UGAUCUGCGAUGUUGGCCAGAUCUGUGGCCAAAUUAUGUCGUUAUUUGUGCCAUUUUUGGCAAACGCCUCCACCUUCGACUCCAC-----ACACCGCC
......(((.(((((((((......))))))......((((.......(((((....)))))..............)))).....-----))).))). ( -24.00)
>DroYak_CAF1 136833 98 - 1
UGAUCUGCGAUGUUGGCCAGAUCUGUGGCCAAAUUAUGUCGUUAUUUGUGCCAUUUUUGGCAAACGCCUCCACCUCUAACUCCACCACCGCCAUCGCC
......(((((((((((((......))))))).....(.((((.....(((((....))))))))).).......................)))))). ( -26.60)
>DroAna_CAF1 129393 74 - 1
UGAUAUCCGAUGCUGGCCAGAUCUGUGGCCAAAUUAUGUCGUUAUUUGUGCCAUUUUUGGCAAACGCCCCCUCC------------------------
.(((((..(((..((((((......)))))).))))))))........(((((....)))))............------------------------ ( -20.00)
>DroPer_CAF1 178860 78 - 1
CGAUCUCUGAUGUUGGCCAAAUCUUCAG-CAAAUUAUGUCGUUAUUUGUGCCAUUUUUGGCAAACGCCUCCUCUGCC-------------------CC
...........(((.((((((......(-(((((.........))))))......)))))).)))............-------------------.. ( -13.90)
>consensus
UGAUCUCCGAUGUUGGCCAGAUCUGUGGCCAAAUUAUGUCGUUAUUUGUGCCAUUUUUGGCAAACGCCUCCACCGCC___________________CC
.......((((((((((((......))))))....)))))).......(((((....))))).................................... (-13.54 = -14.48 +   0.95)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:35 2006