Locus 1231

Sequence ID 2R_DroMel_CAF1
Location 4,843,301 – 4,843,425
Length 124
Max. P 0.991533
window2138 window2139 window2140 window2141

overview

Window 8

Location 4,843,301 – 4,843,400
Length 99
Sequences 3
Columns 108
Reading direction forward
Mean pairwise identity 89.21
Mean single sequence MFE -30.13
Consensus MFE -28.23
Energy contribution -27.57
Covariance contribution -0.66
Combinations/Pair 1.12
Mean z-score -2.00
Structure conservation index 0.94
SVM decision value 1.13
SVM RNA-class probability 0.920059
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4843301 99 + 20766785
GGAGCUGGCUUAUUACUUGCAAUGAAUAAAUAAACAUGGGAUCGUGCGAACGCACAAAUGUACCACACACAGGA---------UGUGCCUGUGUUCAUGUUUAUGCGA
...((..((.........)).........((((((((((....((((....))))...........(((((((.---------....))))))))))))))))))).. ( -27.90)
>DroSim_CAF1 3915 99 + 1
GGAGCUGGCUUAUUACUUGCAAUGAAUAAAUAAACAUGGGAUCGUGCGAACGCACAAAUGUACUACACACAGGA---------UGUGCCUGUGCCCAUGUUUAUGCGA
...((..((.........)).........(((((((((((...((((....))))............((((((.---------....))))))))))))))))))).. ( -32.60)
>DroYak_CAF1 4226 108 + 1
GAAGCUGGCUUAUUACUUGCAAUGAAUAAAUAAACAUGGGAUCGUGCGAACGCACAAAUGUACUACACACAGGGUUCUGCGAGUGUGUCUGUGUCCAUGUUUAUGCCC
......((((((((......)))))....(((((((((((...((((....)))).....(((.((((((..(......)..))))))..))))))))))))))))). ( -29.90)
>consensus
GGAGCUGGCUUAUUACUUGCAAUGAAUAAAUAAACAUGGGAUCGUGCGAACGCACAAAUGUACUACACACAGGA_________UGUGCCUGUGUCCAUGUUUAUGCGA
...((..((.........)).........(((((((((((...((((....))))............((((((..............))))))))))))))))))).. (-28.23 = -27.57 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,843,301 – 4,843,400
Length 99
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 89.21
Mean single sequence MFE -29.60
Consensus MFE -25.31
Energy contribution -25.42
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.66
Structure conservation index 0.86
SVM decision value 1.15
SVM RNA-class probability 0.923147
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4843301 99 - 20766785
UCGCAUAAACAUGAACACAGGCACA---------UCCUGUGUGUGGUACAUUUGUGCGUUCGCACGAUCCCAUGUUUAUUUAUUCAUUGCAAGUAAUAAGCCAGCUCC
..(((((((((((.(((((((....---------.)))))))..((.....((((((....)))))).)))))))))))......((((....))))......))... ( -27.00)
>DroSim_CAF1 3915 99 - 1
UCGCAUAAACAUGGGCACAGGCACA---------UCCUGUGUGUAGUACAUUUGUGCGUUCGCACGAUCCCAUGUUUAUUUAUUCAUUGCAAGUAAUAAGCCAGCUCC
..(((((((((((((((((((....---------.))))))).........((((((....))))))..))))))))))......((((....))))......))... ( -30.40)
>DroYak_CAF1 4226 108 - 1
GGGCAUAAACAUGGACACAGACACACUCGCAGAACCCUGUGUGUAGUACAUUUGUGCGUUCGCACGAUCCCAUGUUUAUUUAUUCAUUGCAAGUAAUAAGCCAGCUUC
.(((((((((((((........((((.(((((....))))).)).))....((((((....))))))..))))))))))......((((....))))..)))...... ( -31.40)
>consensus
UCGCAUAAACAUGGACACAGGCACA_________UCCUGUGUGUAGUACAUUUGUGCGUUCGCACGAUCCCAUGUUUAUUUAUUCAUUGCAAGUAAUAAGCCAGCUCC
..((((((((((((((((((................)))))).........((((((....))))))..))))))))))......((((....))))......))... (-25.31 = -25.42 +   0.11)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,843,329 – 4,843,425
Length 96
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 79.77
Mean single sequence MFE -32.97
Consensus MFE -28.20
Energy contribution -27.87
Covariance contribution -0.33
Combinations/Pair 1.10
Mean z-score -2.32
Structure conservation index 0.86
SVM decision value 2.27
SVM RNA-class probability 0.991533
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4843329 96 + 20766785
AAUAAACAUGGGAUCGUGCGAACGCACAAAUGUACCACACACAGGA---------UGUGCCUGUGUUCAUGUUUAUGCGAUGCCCAUUUCAUGAAAUGAAUUCCU---------------
.((((((((((....((((....))))...........(((((((.---------....)))))))))))))))))........(((((....))))).......--------------- ( -27.30)
>DroSim_CAF1 3943 111 + 1
AAUAAACAUGGGAUCGUGCGAACGCACAAAUGUACUACACACAGGA---------UGUGCCUGUGCCCAUGUUUAUGCGAUGCGCAUUUCACGAAAUGAAUUCCUUGUGUGCAAACACGC
.(((((((((((...((((....))))............((((((.---------....)))))))))))))))))(((.(((((((.....(((.....)))...)))))))....))) ( -39.40)
>DroYak_CAF1 4254 120 + 1
AAUAAACAUGGGAUCGUGCGAACGCACAAAUGUACUACACACAGGGUUCUGCGAGUGUGUCUGUGUCCAUGUUUAUGCCCUGCCCAUUUCACGAAAUGAAUUCCCGGUGUGCAAACACAG
.(((((((((((...((((....)))).....(((.((((((..(......)..))))))..))))))))))))))........(((((....)))))........((((....)))).. ( -32.20)
>consensus
AAUAAACAUGGGAUCGUGCGAACGCACAAAUGUACUACACACAGGA_________UGUGCCUGUGUCCAUGUUUAUGCGAUGCCCAUUUCACGAAAUGAAUUCCU_GUGUGCAAACAC__
.(((((((((((...((((....))))............((((((..............)))))))))))))))))........(((((....)))))........((((....)))).. (-28.20 = -27.87 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,843,329 – 4,843,425
Length 96
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 79.77
Mean single sequence MFE -34.17
Consensus MFE -25.71
Energy contribution -26.16
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -2.28
Structure conservation index 0.75
SVM decision value 1.75
SVM RNA-class probability 0.975593
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4843329 96 - 20766785
---------------AGGAAUUCAUUUCAUGAAAUGGGCAUCGCAUAAACAUGAACACAGGCACA---------UCCUGUGUGUGGUACAUUUGUGCGUUCGCACGAUCCCAUGUUUAUU
---------------.((..(((((((....)))))))..))..(((((((((.(((((((....---------.)))))))..((.....((((((....)))))).))))))))))). ( -28.90)
>DroSim_CAF1 3943 111 - 1
GCGUGUUUGCACACAAGGAAUUCAUUUCGUGAAAUGCGCAUCGCAUAAACAUGGGCACAGGCACA---------UCCUGUGUGUAGUACAUUUGUGCGUUCGCACGAUCCCAUGUUUAUU
((((((((.(((.....(....).....))))))))))).....(((((((((((((((((....---------.))))))).........((((((....))))))..)))))))))). ( -39.70)
>DroYak_CAF1 4254 120 - 1
CUGUGUUUGCACACCGGGAAUUCAUUUCGUGAAAUGGGCAGGGCAUAAACAUGGACACAGACACACUCGCAGAACCCUGUGUGUAGUACAUUUGUGCGUUCGCACGAUCCCAUGUUUAUU
.((((....))))((..(...((((((....)))))).).))..((((((((((........((((.(((((....))))).)).))....((((((....))))))..)))))))))). ( -33.90)
>consensus
__GUGUUUGCACAC_AGGAAUUCAUUUCGUGAAAUGGGCAUCGCAUAAACAUGGACACAGGCACA_________UCCUGUGUGUAGUACAUUUGUGCGUUCGCACGAUCCCAUGUUUAUU
....................(((((((....)))))))......((((((((((((((((................)))))).........((((((....))))))..)))))))))). (-25.71 = -26.16 +   0.45)

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 09:59:38 2006