Locus 5226

Sequence ID 2R_DroMel_CAF1
Location 17,019,546 – 17,019,756
Length 210
Max. P 0.993023
window8348 window8349 window8350

overview

Window 8

Location 17,019,546 – 17,019,650
Length 104
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 76.02
Mean single sequence MFE -21.84
Consensus MFE -13.89
Energy contribution -13.38
Covariance contribution -0.51
Combinations/Pair 1.25
Mean z-score -2.41
Structure conservation index 0.64
SVM decision value 2.37
SVM RNA-class probability 0.993023
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17019546 104 + 20766785
GAAGGUUCUUACAAAUUUUAACCAACAUACAUAUGCGGUUGUAAUAAUUCAAUUAUAA-CCGACCGCAUAUCUAUGUAUUGUUAUUAAGUUCUGUUCGAUUGUAA
......((..((((((((((((..(((((.(((((((((((..(((((...)))))..-.))))))))))).)))))...))))..))))).)))..))...... ( -24.10)
>DroSec_CAF1 115753 92 + 1
GAAGGUUCUUAUAAAUUUUAACCGACAUACAUAUGCGGUUGUAAUAUUUC------------ACCGCAUAUCUGUGUAUUGUUAUU-AGUUCUGUUCGAUUGUAA
......((..(((((((.((((..(((((.(((((((((.(........)------------))))))))).)))))...))))..-)))).)))..))...... ( -19.80)
>DroSim_CAF1 122591 93 + 1
GAAGGUUCUUAUAAAUUUUAACCGACAUACAUAUGCGGUUGUAAUAUUUC------------ACCGCAUAUCUGUGUAUUUUUAUUAAGUUCUGUUCGAUUGUAA
(((((..((((((((.........(((((.(((((((((.(........)------------))))))))).)))))...)))).))))..)).)))........ ( -19.90)
>DroEre_CAF1 118142 80 + 1
GAAGGUUCUUAGAAAUUUUAACAUACAUACAUAUGCAG-------------------------CCGUAUAUAUAUGUAUUCCAAUUAAGUUCUGAUGGACUCUAA
..((((((((((((........(((((((.((((((..-------------------------..)))))).)))))))..........)))))).)))).)).. ( -18.97)
>DroYak_CAF1 124826 103 + 1
GAAGGUUCUUAGAAAUUUUAACACGCAUACAUGUGCGGUUGGGAUAU--GAGCUAUAUUCAGACCGUAUAUAUAUGUAUUCCAAUUAAGUUCCGUUCGAUUUUAA
(((((..(((((............(((((.((((((((((.((((((--(...))))))).)))))))))).))))).......)))))..)).)))........ ( -26.41)
>consensus
GAAGGUUCUUAGAAAUUUUAACCGACAUACAUAUGCGGUUGUAAUAUUUC____________ACCGCAUAUCUAUGUAUUCUUAUUAAGUUCUGUUCGAUUGUAA
...((..((((.............(((((.(((((((((.......................))))))))).)))))........))))..))............ (-13.89 = -13.38 +  -0.51)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,019,546 – 17,019,650
Length 104
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 76.02
Mean single sequence MFE -18.79
Consensus MFE -9.65
Energy contribution -10.74
Covariance contribution 1.09
Combinations/Pair 1.07
Mean z-score -2.19
Structure conservation index 0.51
SVM decision value 1.40
SVM RNA-class probability 0.950666
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17019546 104 - 20766785
UUACAAUCGAACAGAACUUAAUAACAAUACAUAGAUAUGCGGUCGG-UUAUAAUUGAAUUAUUACAACCGCAUAUGUAUGUUGGUUAAAAUUUGUAAGAACCUUC
((((((((.....))......((((...(((((.(((((((((..(-(.(((((...))))).)).))))))))).)))))..))))....))))))........ ( -27.00)
>DroSec_CAF1 115753 92 - 1
UUACAAUCGAACAGAACU-AAUAACAAUACACAGAUAUGCGGU------------GAAAUAUUACAACCGCAUAUGUAUGUCGGUUAAAAUUUAUAAGAACCUUC
..................-..((((...(((.(.(((((((((------------...........))))))))).).)))..)))).................. ( -17.80)
>DroSim_CAF1 122591 93 - 1
UUACAAUCGAACAGAACUUAAUAAAAAUACACAGAUAUGCGGU------------GAAAUAUUACAACCGCAUAUGUAUGUCGGUUAAAAUUUAUAAGAACCUUC
....((((((................(((((....((((((((------------...........))))))))))))).))))))................... ( -16.53)
>DroEre_CAF1 118142 80 - 1
UUAGAGUCCAUCAGAACUUAAUUGGAAUACAUAUAUAUACGG-------------------------CUGCAUAUGUAUGUAUGUUAAAAUUUCUAAGAACCUUC
((((((((((............))))((((((((((((....-------------------------....))))))))))))........))))))........ ( -16.20)
>DroYak_CAF1 124826 103 - 1
UUAAAAUCGAACGGAACUUAAUUGGAAUACAUAUAUAUACGGUCUGAAUAUAGCUC--AUAUCCCAACCGCACAUGUAUGCGUGUUAAAAUUUCUAAGAACCUUC
........(((.((..(((((((..(((((.(((((((.((((..(.((((.....--)))).)..))))...))))))).)))))..)))...))))..))))) ( -16.40)
>consensus
UUACAAUCGAACAGAACUUAAUAACAAUACAUAGAUAUGCGGU____________GAAAUAUUACAACCGCAUAUGUAUGUCGGUUAAAAUUUAUAAGAACCUUC
............................(((((.(((((((((.......................))))))))).)))))........................ ( -9.65 = -10.74 +   1.09)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,019,650 – 17,019,756
Length 106
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 77.83
Mean single sequence MFE -37.88
Consensus MFE -33.89
Energy contribution -34.70
Covariance contribution 0.81
Combinations/Pair 1.16
Mean z-score -1.43
Structure conservation index 0.89
SVM decision value 0.96
SVM RNA-class probability 0.890379
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17019650 106 + 20766785
UAAGCUUGUUUUUUCCACACACAGAUUUCCGAUUGCGCUUUGGUGCUGGAGGAGCAGCCGGCUAAGCUGGCCGAGGCCUUCCGGCUCUUCUUGCAGGGCGAGGGCU
....((((.(((((((((((.((((....((....)).))))))).))))))))..((((((...))))))))))((((((..(((((......))))))))))). ( -36.80)
>DroVir_CAF1 170252 99 + 1
UGAAAUUUU-------UGCCACAGAUCUCGGAUUGCGCCAUGGUGCUGGAGGAGCAACCGGCUAAGCUGGCUGAGGCCUUUCGGCUGUUCUUGCAGGGCGAGGGCU
.....((((-------((((..............((((....))))((.((((((..(((((...)))))....((((....)))))))))).)).)))))))).. ( -33.50)
>DroPse_CAF1 132890 100 + 1
AUUC------CUUCUGCCUUUCAGAUUUCCGAUUGCGCUCUGGUGCUCGAGGAGCAGCCGGCCAAGCUGGCCGAGGCCUUUCGGCUGUUCUUGCAGGGCGAGGGCU
...(------((((.(((((.(.......(((..((((....)))))))((((((((((((((.....))))(((....)))))))))))))).)))))))))).. ( -44.00)
>DroWil_CAF1 182358 90 + 1
----------------AUUCUUAGAUUUCCGAUUGCGCUUUGGUUCUGGAGGAGCAGCCAGCCAAAUUGGCUGAAGCCUUUCGGCUAUUCUUGCAGGGCGAGGGCU
----------------....................(((((.((((((.((((((((((((.....))))))).((((....)))).))))).)))))).))))). ( -34.70)
>DroMoj_CAF1 174669 99 + 1
AGAGUUUUU-------UUUUUUAGAUCUCUGAUUGCGCCAUGGUGUUGGAGGAGCAACCGGCUAAGCUGGCUGAAGCCUUCCGGCUGUUCUUGCAGGGCGAGGGCU
((((.(((.-------......))).))))......(((.(.((.(((.(((((((.((((....(((......)))...)))).))))))).))).)).).))). ( -34.30)
>DroPer_CAF1 132138 100 + 1
AUUC------CUUCUGCCUUUCAGAUUUCCGAUUGCGCUCUGGUGCUCGAGGAGCAGCCGGCCAAGCUGGCCGAGGCCUUUCGGCUGUUCUUGCAGGGCGAGGGCU
...(------((((.(((((.(.......(((..((((....)))))))((((((((((((((.....))))(((....)))))))))))))).)))))))))).. ( -44.00)
>consensus
AGAC____________ACUCUCAGAUUUCCGAUUGCGCUAUGGUGCUGGAGGAGCAGCCGGCCAAGCUGGCCGAGGCCUUUCGGCUGUUCUUGCAGGGCGAGGGCU
....................................(((((.((.(((.((((((((((((.......(((....)))..)))))))))))).))).)).))))). (-33.89 = -34.70 +   0.81)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:37 2006