Locus 2311

Sequence ID	2R_DroMel_CAF1
Location	8,497,401 – 8,497,547
Length	146
Max. P	0.999659

overview

Window 4

Location	8,497,401 – 8,497,507
Length	106
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.07
Mean single sequence MFE	-30.28
Consensus MFE	-16.08
Energy contribution	-19.00
Covariance contribution	2.92
Combinations/Pair	1.13
Mean z-score	-2.07
Structure conservation index	0.53
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8497401 106 - 20766785
CAAU---UUAUCCGUUAGAUCUGCAUUGUUACGUUACGUAGAGCAGUCUAACGGUUAAUUCGCCAAGACGGAAACG-----------AAGUUGCUGCUUUUAUUGUUGUUGGCUGCCACU
....---(((.((((((((.((((....(((((...))))).)))))))))))).)))...(((((((((....)(-----------((((....)))))....))).)))))....... ( -32.30)
>DroSec_CAF1 9716 106 - 1
CAAA---UUAUCCGUUAGAUCUGCAUUGUUACGUUACGUAGAGCAGUCUAACGGUUAAUUCGCCAAGACGGAAACG-----------AAGUUGCUGCUUUUAUUGUUGUUGGUUGCCACU
..((---(((.((((((((.((((....(((((...))))).)))))))))))).))))).(((((((((....)(-----------((((....)))))....))).)))))....... ( -31.40)
>DroSim_CAF1 9629 106 - 1
CAAA---UUAUCCGUUAGAUCUGCAUUGUUACGUUACGUAGAGCAGUCUAACGGUUAAUUCGCCAAGACGGAAACG-----------AAGUUGCUGCUUUUAUUGUUGUUGGCUGCCACU
..((---(((.((((((((.((((....(((((...))))).)))))))))))).))))).(((((((((....)(-----------((((....)))))....))).)))))....... ( -33.90)
>DroEre_CAF1 7288 90 - 1
CAAA---UUAUCCGUUAGAU----------------CGUAGAGCAGUCUAACGGUUAAUUCGCCAAGACGGAAACG-----------AAGUUGCUGCUUUUAUUGUUGUUGGCUGCCACU
..((---(((.(((((((((----------------.(.....).))))))))).))))).(((((((((....)(-----------((((....)))))....))).)))))....... ( -26.90)
>DroYak_CAF1 10050 106 - 1
CAAA---UUAUCCGUUAGAUCUGCAUUGUUACGUUACGUAGAGCAGUCUAACGGUUAAUUCGCCAAGACGGAAACG-----------AAGUUGCUGCUUUUAUUGUUGUUGGCUGCCACU
..((---(((.((((((((.((((....(((((...))))).)))))))))))).))))).(((((((((....)(-----------((((....)))))....))).)))))....... ( -33.90)
>DroAna_CAF1 7244 113 - 1
CAAAGCGUUAUCCGUUAGAUCAGCAUUGUUA-GUUUCGUGGGUUAAGCAAAAAAUAAAA---AAAAAACGGAAACGGGAACGGUGUGGAGUUGUUG---UUCUUGGAGCUUGUUGCCACU
(((.((...(((.....)))..)).)))...-.....((((..(((((...........---......((....))((((((..(......)..))---))))....)))))...)))). ( -23.30)
>consensus
CAAA___UUAUCCGUUAGAUCUGCAUUGUUACGUUACGUAGAGCAGUCUAACGGUUAAUUCGCCAAGACGGAAACG___________AAGUUGCUGCUUUUAUUGUUGUUGGCUGCCACU
.......(((.((((((((.((((....((((.....)))).)))))))))))).)))..........((....))............(((.((.(((..((....))..))).)).))) (-16.08 = -19.00 +   2.92)

alignment

secondary structure

dotplot

Window 5

Location	8,497,434 – 8,497,547
Length	113
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	92.21
Mean single sequence MFE	-34.32
Consensus MFE	-29.43
Energy contribution	-30.87
Covariance contribution	1.44
Combinations/Pair	1.03
Mean z-score	-3.05
Structure conservation index	0.86
SVM decision value	3.85
SVM RNA-class probability	0.999659
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8497434 113 + 20766785
CGUUUCCGUCUUGGCGAAUUAACCGUUAGACUGCUCUACGUAACGUAACAAUGCAGAUCUAACGGAUAAAUUGCGAACGAAGGAACCGUACCAUGACGAUACUUUCCAUGCAA
((.((((.((((.((((.(((.((((((((((((..((((...)))).....)))).)))))))).))).)))).)).)).)))).))...((((..((.....))))))... ( -33.70)
>DroSec_CAF1 9749 113 + 1
CGUUUCCGUCUUGGCGAAUUAACCGUUAGACUGCUCUACGUAACGUAACAAUGCAGAUCUAACGGAUAAUUUGCGAGCGAAGGAACCGUACCAUGACGAUACUUUCCAUGCAA
((.((((.((((.((((((((.((((((((((((..((((...)))).....)))).)))))))).)))))))).)).)).)))).))...((((..((.....))))))... ( -37.10)
>DroSim_CAF1 9662 113 + 1
CGUUUCCGUCUUGGCGAAUUAACCGUUAGACUGCUCUACGUAACGUAACAAUGCAGAUCUAACGGAUAAUUUGCGAGCGAAGGAACCGUACCAUGACGAUACUUUCCAUGCAA
((.((((.((((.((((((((.((((((((((((..((((...)))).....)))).)))))))).)))))))).)).)).)))).))...((((..((.....))))))... ( -37.10)
>DroEre_CAF1 7321 97 + 1
CGUUUCCGUCUUGGCGAAUUAACCGUUAGACUGCUCUACG----------------AUCUAACGGAUAAUUUGCGAGCGCAGGAACCGUACCAUGACGAUUCUUUCCAUGCAA
((.((((((.((.((((((((.((((((((.((.....))----------------.)))))))).)))))))).)).)).)))).))...((((..((.....))))))... ( -29.60)
>DroYak_CAF1 10083 113 + 1
CGUUUCCGUCUUGGCGAAUUAACCGUUAGACUGCUCUACGUAACGUAACAAUGCAGAUCUAACGGAUAAUUUGCGAGCAAAGGAACCGUACCAUGACGAUACUUUCAAUGCAA
((.((((...((.((((((((.((((((((((((..((((...)))).....)))).)))))))).)))))))).))....)))).))......................... ( -34.10)
>consensus
CGUUUCCGUCUUGGCGAAUUAACCGUUAGACUGCUCUACGUAACGUAACAAUGCAGAUCUAACGGAUAAUUUGCGAGCGAAGGAACCGUACCAUGACGAUACUUUCCAUGCAA
((.((((.((((.((((((((.((((((((((((..................)))).)))))))).)))))))).)).)).)))).))...((((..((.....))))))... (-29.43 = -30.87 +   1.44)

alignment

secondary structure

dotplot

Window 6

Location	8,497,434 – 8,497,547
Length	113
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	92.21
Mean single sequence MFE	-35.52
Consensus MFE	-29.74
Energy contribution	-31.78
Covariance contribution	2.04
Combinations/Pair	1.03
Mean z-score	-2.51
Structure conservation index	0.84
SVM decision value	2.76
SVM RNA-class probability	0.996884
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8497434 113 - 20766785
UUGCAUGGAAAGUAUCGUCAUGGUACGGUUCCUUCGUUCGCAAUUUAUCCGUUAGAUCUGCAUUGUUACGUUACGUAGAGCAGUCUAACGGUUAAUUCGCCAAGACGGAAACG
......((((.(((((.....)))))..))))((((((.((((((...((((((((.((((....(((((...))))).))))))))))))..)))).))...)))))).... ( -35.70)
>DroSec_CAF1 9749 113 - 1
UUGCAUGGAAAGUAUCGUCAUGGUACGGUUCCUUCGCUCGCAAAUUAUCCGUUAGAUCUGCAUUGUUACGUUACGUAGAGCAGUCUAACGGUUAAUUCGCCAAGACGGAAACG
..((..((((.(((((.....)))))..))))...))..((.(((((.((((((((.((((....(((((...))))).)))))))))))).))))).)).....((....)) ( -38.10)
>DroSim_CAF1 9662 113 - 1
UUGCAUGGAAAGUAUCGUCAUGGUACGGUUCCUUCGCUCGCAAAUUAUCCGUUAGAUCUGCAUUGUUACGUUACGUAGAGCAGUCUAACGGUUAAUUCGCCAAGACGGAAACG
..((..((((.(((((.....)))))..))))...))..((.(((((.((((((((.((((....(((((...))))).)))))))))))).))))).)).....((....)) ( -38.10)
>DroEre_CAF1 7321 97 - 1
UUGCAUGGAAAGAAUCGUCAUGGUACGGUUCCUGCGCUCGCAAAUUAUCCGUUAGAU----------------CGUAGAGCAGUCUAACGGUUAAUUCGCCAAGACGGAAACG
..(((.(((....(((((......)))))))))))....((.(((((.(((((((((----------------.(.....).))))))))).))))).)).....((....)) ( -29.50)
>DroYak_CAF1 10083 113 - 1
UUGCAUUGAAAGUAUCGUCAUGGUACGGUUCCUUUGCUCGCAAAUUAUCCGUUAGAUCUGCAUUGUUACGUUACGUAGAGCAGUCUAACGGUUAAUUCGCCAAGACGGAAACG
..(((..(((.(((((.....)))))..)))...)))..((.(((((.((((((((.((((....(((((...))))).)))))))))))).))))).)).....((....)) ( -36.20)
>consensus
UUGCAUGGAAAGUAUCGUCAUGGUACGGUUCCUUCGCUCGCAAAUUAUCCGUUAGAUCUGCAUUGUUACGUUACGUAGAGCAGUCUAACGGUUAAUUCGCCAAGACGGAAACG
..((..((((.(((((.....)))))..))))...))..((.(((((.((((((((.((((....((((.....)))).)))))))))))).))))).)).....((....)) (-29.74 = -31.78 +   2.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:31 2006