Locus 8198

Sequence ID	3R_DroMel_CAF1
Location	22,024,504 – 22,024,658
Length	154
Max. P	0.924380

overview

Window 1

Location	22,024,504 – 22,024,618
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	96.49
Mean single sequence MFE	-29.88
Consensus MFE	-26.42
Energy contribution	-26.66
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.28
Structure conservation index	0.88
SVM decision value	0.15
SVM RNA-class probability	0.609161
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22024504 114 + 27905053
UCAUCAGACAUGAAUAAUGCCGGCUAAUGUGUCGCCAGGGAAUGGCUAAUGAAAGUGCUCGGAUAGAUCACGUUCCGAGCGAAACAAAUUGCCAACUACCAGUUAUUAAACUCA
......((....(((((((.((((......)))).).((...((((.(((.....((((((((..........))))))))......)))))))....)).))))))....)). ( -29.20)
>DroSec_CAF1 22946 114 + 1
UCAUCAGACAUGAAUAAUGCCGGCUAAUGUGUCGCCAGGGAAUGGCUAAUGAAAGUGCUCGGAUAGAUCACGUUCCGAGCGAAACAAAUUGCCAACUACCAGUUAUUAAACUCA
......((....(((((((.((((......)))).).((...((((.(((.....((((((((..........))))))))......)))))))....)).))))))....)). ( -29.20)
>DroSim_CAF1 15009 114 + 1
UCAUCAGACAUGAAUAAUGCCGGCUAAUGUGUCGCCAGGGAAUGGCUAAUGAAAGUGCUCGGAUAGAUCACGUUCCGAGCGAAGCAAAUUGCCAACUACCAGUUAUUAAACUCA
......((....(((((((.((((......)))).).((...((((...((....((((((((..........))))))))...))....))))....)).))))))....)). ( -29.40)
>DroEre_CAF1 16775 114 + 1
UCAUCGGACAUGAAUAAUGCCGGCUAAUGUGUCGCCAGGGAAUGGCUAAUGAAAGUGCUCGGAUAGAUCACGUUCCGAGCGCCACAAAUUGCCAGCUACCAGUUAUUAAACUCU
.....((.(((.....)))))(((...((((..((((.....))))........(((((((((..........)))))))))))))....)))..................... ( -33.90)
>DroYak_CAF1 24241 114 + 1
UCAUCGGACAUGAAUAAUGCUGGCUAAUGUGUCGCCAGGGAAUGGCUAAUGAAAGUGCUCGGAUAGAUCACGUUCCAAGCGCAACAAAUUGCCAACUAGCAGUUAUUAAACUCA
......((....((((((((((((.(((.(((.((((.....))))........(((((.(((..........))).))))).))).))))))....)))).)))))....)). ( -27.70)
>consensus
UCAUCAGACAUGAAUAAUGCCGGCUAAUGUGUCGCCAGGGAAUGGCUAAUGAAAGUGCUCGGAUAGAUCACGUUCCGAGCGAAACAAAUUGCCAACUACCAGUUAUUAAACUCA
......((....(((((((.((((......)))).).((...((((.(((.....((((((((..........))))))))......)))))))....)).))))))....)). (-26.42 = -26.66 +   0.24)

alignment

secondary structure

dotplot

Window 2

Location	22,024,504 – 22,024,618
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	96.49
Mean single sequence MFE	-31.44
Consensus MFE	-30.50
Energy contribution	-30.42
Covariance contribution	-0.08
Combinations/Pair	1.09
Mean z-score	-1.35
Structure conservation index	0.97
SVM decision value	1.16
SVM RNA-class probability	0.924380
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22024504 114 - 27905053
UGAGUUUAAUAACUGGUAGUUGGCAAUUUGUUUCGCUCGGAACGUGAUCUAUCCGAGCACUUUCAUUAGCCAUUCCCUGGCGACACAUUAGCCGGCAUUAUUCAUGUCUGAUGA
..((((....))))....((((((....(((.(((((((((..........)))))))..........((((.....)))))).)))...)))))).....((((.....)))) ( -31.30)
>DroSec_CAF1 22946 114 - 1
UGAGUUUAAUAACUGGUAGUUGGCAAUUUGUUUCGCUCGGAACGUGAUCUAUCCGAGCACUUUCAUUAGCCAUUCCCUGGCGACACAUUAGCCGGCAUUAUUCAUGUCUGAUGA
..((((....))))....((((((....(((.(((((((((..........)))))))..........((((.....)))))).)))...)))))).....((((.....)))) ( -31.30)
>DroSim_CAF1 15009 114 - 1
UGAGUUUAAUAACUGGUAGUUGGCAAUUUGCUUCGCUCGGAACGUGAUCUAUCCGAGCACUUUCAUUAGCCAUUCCCUGGCGACACAUUAGCCGGCAUUAUUCAUGUCUGAUGA
..((((....))))....((((((....((..(((((((((..........)))))))..........((((.....))))))..))...)))))).....((((.....)))) ( -29.20)
>DroEre_CAF1 16775 114 - 1
AGAGUUUAAUAACUGGUAGCUGGCAAUUUGUGGCGCUCGGAACGUGAUCUAUCCGAGCACUUUCAUUAGCCAUUCCCUGGCGACACAUUAGCCGGCAUUAUUCAUGUCCGAUGA
..((((....))))....((((((....((((..(((((((..........)))))))..........((((.....))))..))))...)))))).....((((.....)))) ( -35.00)
>DroYak_CAF1 24241 114 - 1
UGAGUUUAAUAACUGCUAGUUGGCAAUUUGUUGCGCUUGGAACGUGAUCUAUCCGAGCACUUUCAUUAGCCAUUCCCUGGCGACACAUUAGCCAGCAUUAUUCAUGUCCGAUGA
..((((....))))....(((((((((.((((..(((((((..........)))))))..........((((.....)))))))).))).)))))).....((((.....)))) ( -30.40)
>consensus
UGAGUUUAAUAACUGGUAGUUGGCAAUUUGUUUCGCUCGGAACGUGAUCUAUCCGAGCACUUUCAUUAGCCAUUCCCUGGCGACACAUUAGCCGGCAUUAUUCAUGUCUGAUGA
..((((....))))....(((((((((.((((..(((((((..........)))))))..........((((.....)))))))).))).)))))).....((((.....)))) (-30.50 = -30.42 +  -0.08)

alignment

secondary structure

dotplot

Window 3

Location	22,024,539 – 22,024,658
Length	119
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	96.30
Mean single sequence MFE	-24.40
Consensus MFE	-20.52
Energy contribution	-20.60
Covariance contribution	0.08
Combinations/Pair	1.04
Mean z-score	-1.40
Structure conservation index	0.84
SVM decision value	0.03
SVM RNA-class probability	0.550398
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22024539 119 + 27905053
CAGGGAAUGGCUAAUGAAAGUGCUCGGAUAGAUCACGUUCCGAGCGAAACAAAUUGCCAACUACCAGUUAUUAAACUCAGUCAUUAAUUAUAUUUUACUACCAACAUUUUCGUUAAUAU
..((...((((.(((.....((((((((..........))))))))......)))))))(((...((((....)))).)))...................))................. ( -22.00)
>DroSec_CAF1 22981 119 + 1
CAGGGAAUGGCUAAUGAAAGUGCUCGGAUAGAUCACGUUCCGAGCGAAACAAAUUGCCAACUACCAGUUAUUAAACUCAGUCAUUAAUUAUAUUUUACUACCAACAUUUUCGUUAAUAU
..((...((((.(((.....((((((((..........))))))))......)))))))(((...((((....)))).)))...................))................. ( -22.00)
>DroSim_CAF1 15044 119 + 1
CAGGGAAUGGCUAAUGAAAGUGCUCGGAUAGAUCACGUUCCGAGCGAAGCAAAUUGCCAACUACCAGUUAUUAAACUCAGUCAUUAAUUAUAUUUUACUACCAACAUUUUCGUUAAUAU
..(..(((((((.((....))(((((((..........)))))))..))).(((((...(((...((((....)))).)))...)))))...............))))..)........ ( -22.50)
>DroEre_CAF1 16810 119 + 1
CAGGGAAUGGCUAAUGAAAGUGCUCGGAUAGAUCACGUUCCGAGCGCCACAAAUUGCCAGCUACCAGUUAUUAAACUCUGCCAUUAAUUAUAUUUUAUUACCAACAUUUUCGUUAAUAU
..(..((((..(((((((((((((((((..........)))))))))....(((((...((....((((....))))..))...)))))...))))))))....))))..)........ ( -28.00)
>DroYak_CAF1 24276 119 + 1
CAGGGAAUGGCUAAUGAAAGUGCUCGGAUAGAUCACGUUCCAAGCGCAACAAAUUGCCAACUAGCAGUUAUUAAACUCAGUCAUUAAUUAUAUUUCAUUACCAACAUUUUCGUUAAUAU
..(..((((..(((((((((((((.(((..........))).)))))....((((((......)))))).......................))))))))....))))..)........ ( -27.50)
>consensus
CAGGGAAUGGCUAAUGAAAGUGCUCGGAUAGAUCACGUUCCGAGCGAAACAAAUUGCCAACUACCAGUUAUUAAACUCAGUCAUUAAUUAUAUUUUACUACCAACAUUUUCGUUAAUAU
..((...((((.(((.....((((((((..........))))))))......)))))))(((...((((....)))).)))...................))................. (-20.52 = -20.60 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:05:04 2006