Locus 5792

Sequence ID	X_DroMel_CAF1
Location	15,026,950 – 15,027,081
Length	131
Max. P	0.969416

overview

Window 9

Location	15,026,950 – 15,027,057
Length	107
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	79.97
Mean single sequence MFE	-36.38
Consensus MFE	-23.08
Energy contribution	-24.45
Covariance contribution	1.37
Combinations/Pair	1.09
Mean z-score	-1.88
Structure conservation index	0.63
SVM decision value	0.42
SVM RNA-class probability	0.731049
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15026950 107 + 22224390
GUGGCGGGGCGGGGCGGUAUGGUGAGGUGCGGUGCUAAUUUCAUCGCCGGACACGUUUCCCCCCGGCCAAAAUGGCCAAAAAUCAAAUUGAGGA-------GAACCGGAAACGG
.....((((.(..(((((.((((((..((..((....))..)))))))).)).)))..).))))((((.....)))).................-------...(((....))) ( -40.40)
>DroSec_CAF1 44466 87 + 1
GGGGCGGGGC--------------------GGUGCUAAUUUCAUCGCCGGCCACGUUUCCCCCCGGCCAAAAUGGCCAAAAAUCAAAUUGAGGA-------GAACCGGAAACGG
((((.(((((--------------------((((.......)))))))(....)....))))))((((.....)))).................-------...(((....))) ( -34.60)
>DroSim_CAF1 47956 87 + 1
GGGGCGGGGC--------------------GGUGCUAAUUUCAUCGCCGGCCACGUUUCCCCCCGGCCAAAAUGGCCAAAAAUCAAAUUGAGGA-------GAACCGGAAACGG
((((.(((((--------------------((((.......)))))))(....)....))))))((((.....)))).................-------...(((....))) ( -34.60)
>DroEre_CAF1 45368 99 + 1
GGGGCGG----------UUUGG-----AGCGGAGCUAAUUUCAUCGCCGGCCACGUUUUCCUCCGGCCAAAAUGGCCAAAAAUCAAAUUGGUGGGGGGUGGGAACCGGAAACGG
..(((((----------(....-----(((...)))......))))))..((((.....(((((((((.....))))....(((.....))))))))))))...(((....))) ( -35.90)
>consensus
GGGGCGGGGC____________________GGUGCUAAUUUCAUCGCCGGCCACGUUUCCCCCCGGCCAAAAUGGCCAAAAAUCAAAUUGAGGA_______GAACCGGAAACGG
((((.(((....................((((((.......))))))((....))..)))))))((((.....))))...........................(((....))) (-23.08 = -24.45 +   1.37)

alignment

secondary structure

dotplot

Window 0

Location	15,026,990 – 15,027,081
Length	91
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	78.29
Mean single sequence MFE	-33.78
Consensus MFE	-21.46
Energy contribution	-21.78
Covariance contribution	0.32
Combinations/Pair	1.14
Mean z-score	-2.27
Structure conservation index	0.64
SVM decision value	1.64
SVM RNA-class probability	0.969416
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15026990 91 + 22224390
UCAUCGCCGGACACGUUUCCCCCCGGCCAAAAUGGCCAAAAAUCAAAUUGAGGA------------GAACCGGAAACGGAAGCAUUGAAGAAGUGAGGG-------CAG---------G
.....(((...(((.(((((....((((.....)))).....((.....)))))------------)).(((....))).............)))..))-------)..---------. ( -27.00)
>DroSec_CAF1 44486 91 + 1
UCAUCGCCGGCCACGUUUCCCCCCGGCCAAAAUGGCCAAAAAUCAAAUUGAGGA------------GAACCGGAAACGGAAGCAUUGAAGAGGUGGGGG-------CAG---------G
.....(((..((((.(((((....((((.....)))).....((.....)))))------------)).(((....))).............)))).))-------)..---------. ( -30.20)
>DroSim_CAF1 47976 91 + 1
UCAUCGCCGGCCACGUUUCCCCCCGGCCAAAAUGGCCAAAAAUCAAAUUGAGGA------------GAACCGGAAACGGAAGCAUUGAAGAGGUGGGGG-------CAG---------G
.....(((..((((.(((((....((((.....)))).....((.....)))))------------)).(((....))).............)))).))-------)..---------. ( -30.20)
>DroEre_CAF1 45393 105 + 1
UCAUCGCCGGCCACGUUUUCCUCCGGCCAAAAUGGCCAAAAAUCAAAUUGGUGGGGG-----GUGGGAACCGGAAACGGAAGCCGUAAAGGAGUGGUGGAGUGGUGGAG---------G
((((((((.(((((....((((((((((.....))))....(((.....))))))))-----)..((..(((....)))...))........))))).).)))))))..---------. ( -44.80)
>DroYak_CAF1 45783 119 + 1
UCAUCGCCGGCCACGUUUCCCUCUGGCCAAAAUGGCCAAAAAUCAAAUUAAGGGGAACCGGAACCGGAACCGGAAACGGAAGCAGUGAAGGAGUGUGGGUGUGAGGGAAGAAGAACAAG
(((.((((.((.((.(((((((.(((((.....)))))............)))))))(((....)))..(((....))).............)))).)))))))............... ( -36.72)
>consensus
UCAUCGCCGGCCACGUUUCCCCCCGGCCAAAAUGGCCAAAAAUCAAAUUGAGGA____________GAACCGGAAACGGAAGCAUUGAAGAAGUGGGGG_______CAG_________G
.......((....))....(((((((((.....))))................................(((....)))...............))))).................... (-21.46 = -21.78 +   0.32)

alignment

secondary structure

dotplot

Window 1

Location	15,026,990 – 15,027,081
Length	91
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	78.29
Mean single sequence MFE	-29.06
Consensus MFE	-21.96
Energy contribution	-21.76
Covariance contribution	-0.20
Combinations/Pair	1.11
Mean z-score	-1.49
Structure conservation index	0.76
SVM decision value	0.47
SVM RNA-class probability	0.748518
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15026990 91 - 22224390
C---------CUG-------CCCUCACUUCUUCAAUGCUUCCGUUUCCGGUUC------------UCCUCAAUUUGAUUUUUGGCCAUUUUGGCCGGGGGGAAACGUGUCCGGCGAUGA
.---------.((-------((..(((.............(((....)))(((------------(((((((........))((((.....))))))))))))..)))...)))).... ( -26.40)
>DroSec_CAF1 44486 91 - 1
C---------CUG-------CCCCCACCUCUUCAAUGCUUCCGUUUCCGGUUC------------UCCUCAAUUUGAUUUUUGGCCAUUUUGGCCGGGGGGAAACGUGGCCGGCGAUGA
.---------.((-------((.((((.............(((....)))(((------------(((((((........))((((.....))))))))))))..))))..)))).... ( -28.40)
>DroSim_CAF1 47976 91 - 1
C---------CUG-------CCCCCACCUCUUCAAUGCUUCCGUUUCCGGUUC------------UCCUCAAUUUGAUUUUUGGCCAUUUUGGCCGGGGGGAAACGUGGCCGGCGAUGA
.---------.((-------((.((((.............(((....)))(((------------(((((((........))((((.....))))))))))))..))))..)))).... ( -28.40)
>DroEre_CAF1 45393 105 - 1
C---------CUCCACCACUCCACCACUCCUUUACGGCUUCCGUUUCCGGUUCCCAC-----CCCCCACCAAUUUGAUUUUUGGCCAUUUUGGCCGGAGGAAAACGUGGCCGGCGAUGA
.---------........................(((((..((((((((((....))-----)................(((((((.....))))))))).))))).)))))....... ( -27.10)
>DroYak_CAF1 45783 119 - 1
CUUGUUCUUCUUCCCUCACACCCACACUCCUUCACUGCUUCCGUUUCCGGUUCCGGUUCCGGUUCCCCUUAAUUUGAUUUUUGGCCAUUUUGGCCAGAGGGAAACGUGGCCGGCGAUGA
...............................(((.(((((((((((((((..(((....)))..))............((((((((.....))))))))))))))).))..)))).))) ( -35.00)
>consensus
C_________CUG_______CCCCCACUUCUUCAAUGCUUCCGUUUCCGGUUC____________UCCUCAAUUUGAUUUUUGGCCAUUUUGGCCGGGGGGAAACGUGGCCGGCGAUGA
.........................................((((.((((((..........................((((((((.....))))))))(....)..)))))).)))). (-21.96 = -21.76 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:31 2006