Locus 1893

Sequence ID 2R_DroMel_CAF1
Location 7,131,971 – 7,132,233
Length 262
Max. P 0.973938
window3135 window3136 window3137 window3138 window3139

overview

Window 5

Location 7,131,971 – 7,132,079
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.16
Mean single sequence MFE -45.92
Consensus MFE -36.92
Energy contribution -37.48
Covariance contribution 0.56
Combinations/Pair 1.11
Mean z-score -2.24
Structure conservation index 0.80
SVM decision value 1.72
SVM RNA-class probability 0.973938
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7131971 108 + 20766785
CUCUUCGAUUUUCGCUGCCUGCAGUGCUGCCGCU------------GCACGAGUGUGAGUGCAUGUUAGUCGCUGGCAGAGCUAUGUUAACUAACAGUGGCGAGAGCGUGGCGGCGAAAC
.........(((((((((((((....((((((((------------((((........)))))(((((((.((((((...)))).))..)))))))))))).)).))).)))))))))). ( -44.70)
>DroSec_CAF1 159448 108 + 1
CCCUUCGAUUUUCGCUGCCUGCCGCGCUGCCGCU------------GCACGAGUGUGAGUGCAUGUUAGUCGCUGGCAGAGCUAUGUUAACUAACAGAGGCGAGAGCGUGGCGGCGAAAC
.........((((((((((...(((.(((((..(------------((((........)))))(((((((.((((((...)))).))..)))))))..))).)).))).)))))))))). ( -44.30)
>DroSim_CAF1 157750 108 + 1
CUCUUCGAUUUUCGCUGCCUGCCGUGCUGCCGCU------------GCACGAGUGUGAGUGCAUGUUAGUCGCUGGCAGAGCUAUGUUAACUAACAGUGGCGAGAGCGUGGCGGCGAAAC
.........((((((((((...(((.((((((((------------((((........)))))(((((((.((((((...)))).))..)))))))))))).)).))).)))))))))). ( -45.60)
>DroEre_CAF1 165055 120 + 1
CUCUUCGAUUUUCGCUGCCUGCAGUUCUGCCGCUGCCGCUGCCACUGCACGAGUGUGAGUGCAUGUUAGGCGCUGGCAGAGCCAUGUUAACUAACAGAGAUGAGAGCGGAGCGGCGAAAC
.........(((((((((((((.(((((((((.((((...((...(((((........))))).))..)))).)))))))))(((.((........)).)))...)))).))))))))). ( -51.50)
>DroYak_CAF1 169102 108 + 1
CUCUUCGAUUUUCGCUGCCUGCAGUUCUGCCGCU------------GCACGAGUGUGAGUGCAUGUUAGUCGCUGGCAGAGCUAUGUUAACUAACAGCGAUGAGAGUGAGGCGGCGAAAC
.........(((((((((((((((((((((((((------------((((........)))))........)).))))))))).((((....)))))).((....)).))))))))))). ( -43.50)
>consensus
CUCUUCGAUUUUCGCUGCCUGCAGUGCUGCCGCU____________GCACGAGUGUGAGUGCAUGUUAGUCGCUGGCAGAGCUAUGUUAACUAACAGAGGCGAGAGCGUGGCGGCGAAAC
.........(((((((((((((....(((((((.............((((........)))).(((((((.((((((...)))).))..)))))))))))).)).))).)))))))))). (-36.92 = -37.48 +   0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,131,971 – 7,132,079
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.16
Mean single sequence MFE -37.58
Consensus MFE -28.48
Energy contribution -28.72
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.60
Structure conservation index 0.76
SVM decision value 0.12
SVM RNA-class probability 0.594457
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7131971 108 - 20766785
GUUUCGCCGCCACGCUCUCGCCACUGUUAGUUAACAUAGCUCUGCCAGCGACUAACAUGCACUCACACUCGUGC------------AGCGGCAGCACUGCAGGCAGCGAAAAUCGAAGAG
.((((((.(((.(((.........((((((((......(((.....)))))))))))(((((........))))------------))))(((....))).))).))))))......... ( -34.90)
>DroSec_CAF1 159448 108 - 1
GUUUCGCCGCCACGCUCUCGCCUCUGUUAGUUAACAUAGCUCUGCCAGCGACUAACAUGCACUCACACUCGUGC------------AGCGGCAGCGCGGCAGGCAGCGAAAAUCGAAGGG
.((((((.(((.(((.((.(((..((((((((......(((.....)))))))))))(((((........))))------------)..))))).)))...))).))))))......... ( -38.60)
>DroSim_CAF1 157750 108 - 1
GUUUCGCCGCCACGCUCUCGCCACUGUUAGUUAACAUAGCUCUGCCAGCGACUAACAUGCACUCACACUCGUGC------------AGCGGCAGCACGGCAGGCAGCGAAAAUCGAAGAG
.((((((.(((.((..((.(((..((((((((......(((.....)))))))))))(((((........))))------------)..)))))..))...))).))))))......... ( -34.70)
>DroEre_CAF1 165055 120 - 1
GUUUCGCCGCUCCGCUCUCAUCUCUGUUAGUUAACAUGGCUCUGCCAGCGCCUAACAUGCACUCACACUCGUGCAGUGGCAGCGGCAGCGGCAGAACUGCAGGCAGCGAAAAUCGAAGAG
.(((((((((((((((.((((...((((((......((((...))))....))))))(((((........))))))))).))))).))))))....(((....))).))))......... ( -44.00)
>DroYak_CAF1 169102 108 - 1
GUUUCGCCGCCUCACUCUCAUCGCUGUUAGUUAACAUAGCUCUGCCAGCGACUAACAUGCACUCACACUCGUGC------------AGCGGCAGAACUGCAGGCAGCGAAAAUCGAAGAG
.((((((.((((((........(((((........)))))((((((.(((.....).(((((........))))------------)))))))))..)).)))).))))))......... ( -35.70)
>consensus
GUUUCGCCGCCACGCUCUCGCCACUGUUAGUUAACAUAGCUCUGCCAGCGACUAACAUGCACUCACACUCGUGC____________AGCGGCAGCACUGCAGGCAGCGAAAAUCGAAGAG
.((((((.(((.((((........((((((((......(((.....))))))))))).((((........))))............))))((......)).))).))))))......... (-28.48 = -28.72 +   0.24)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,132,079 – 7,132,193
Length 114
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 91.02
Mean single sequence MFE -23.67
Consensus MFE -17.79
Energy contribution -18.03
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.99
Structure conservation index 0.75
SVM decision value 0.59
SVM RNA-class probability 0.790717
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7132079 114 + 20766785
AAGUGGACAUGAAACCAAAUCUUGCUGUGUAGUUGUGGGCACAAACAAACAAACACGCACACUUGCACACGGUUCUAUCUAUUAAUCAUUUAAUAGUCAUCCAAAUUAUUAGGA
...((((..(((...........(((((((.((.(((.((................)).)))..))))))))).....(((((((....))))))))))))))........... ( -21.59)
>DroSec_CAF1 159556 114 + 1
AAGUGGAAAUGAAACCAAAUCUUACCGUGUAGUUGUGGGCACAAACAAACAAACACGCACACAUGCACACGGCUCUGUCUAUUAAUCAUUUAAUAGUCAUCCAAAUUAUUAGGA
...((((.................((((((.((((((.((................)).)))).))))))))...((.(((((((....))))))).))))))........... ( -24.99)
>DroSim_CAF1 157858 114 + 1
AAGUGGAAAUGAAACCAAAUCUUACCGUGUAGUUGUGGGCACAAACAAACAAACACGCACACAUGCACACGGCUCUGUCUAUUAAUCAUUUAAUAGUCAUCCAAAUUAUUAGGA
...((((.................((((((.((((((.((................)).)))).))))))))...((.(((((((....))))))).))))))........... ( -24.99)
>DroEre_CAF1 165175 108 + 1
AACUGGAA-UGAAACCAAAUCUUGC-AUGUAGUUGUGGGCACAAAC----AAACACGCACACAUGCACACGCUUCUGUCUAUUAAUCAUUUAAUAGUCAUCCAAAUUAUUAGGA
...((((.-.............(((-((((.((((((.........----...)))).)))))))))........((.(((((((....))))))).))))))........... ( -22.90)
>DroYak_CAF1 169210 110 + 1
AUGUGGAAUUGAAACAAAAUCUUGCCGUGUAUUUGUGUGCACAAAC----AAACACACACACUUGCGCACGCUUCUGUCUAUUAAUCAUUUAAUAGUCAUCCAAAUUAUUAGGA
...((((................((.(((((..((((((.......----.....))))))..)))))..))...((.(((((((....))))))).))))))........... ( -23.90)
>consensus
AAGUGGAAAUGAAACCAAAUCUUGCCGUGUAGUUGUGGGCACAAACAAACAAACACGCACACAUGCACACGGUUCUGUCUAUUAAUCAUUUAAUAGUCAUCCAAAUUAUUAGGA
...((((...................(((((..((((.(................).))))..))))).......((.(((((((....))))))).))))))........... (-17.79 = -18.03 +   0.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,132,119 – 7,132,233
Length 114
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 92.17
Mean single sequence MFE -16.84
Consensus MFE -12.18
Energy contribution -12.58
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.89
Structure conservation index 0.72
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7132119 114 + 20766785
ACAAACAAACAAACACGCACACUUGCACACGGUUCUAUCUAUUAAUCAUUUAAUAGUCAUCCAAAUUAUUAGGAAUUCUGCGCUUGUUUAGACAAAACCUUUAACCACAUUUUG
......((((((...((((...................(((((((....)))))))...(((.........)))....)))).))))))......................... ( -12.70)
>DroSec_CAF1 159596 114 + 1
ACAAACAAACAAACACGCACACAUGCACACGGCUCUGUCUAUUAAUCAUUUAAUAGUCAUCCAAAUUAUUAGGAAUUUUGAGCUUGUUUACUCAAAACCUUUAACCACAUUUUG
......((((((....(((....))).....((((((.(((((((....))))))).))(((.........))).....))))))))))......................... ( -18.50)
>DroSim_CAF1 157898 114 + 1
ACAAACAAACAAACACGCACACAUGCACACGGCUCUGUCUAUUAAUCAUUUAAUAGUCAUCCAAAUUAUUAGGAAUUUUGCGCUUGUUUACUCAAAACCUUUAACCACAUUUUG
......((((((...((((.....((.....))..((.(((((((....))))))).))(((.........)))....)))).))))))......................... ( -15.10)
>DroEre_CAF1 165213 110 + 1
ACAAAC----AAACACGCACACAUGCACACGCUUCUGUCUAUUAAUCAUUUAAUAGUCAUCCAAAUUAUUAGGAAUUCUGCGCUUGUUUGCGCAAAACCUUUAACCACAUUUUG
......----.....((((.(((.((.((......((.(((((((....))))))).))(((.........)))....)).)).))).))))...................... ( -19.20)
>DroYak_CAF1 169250 109 + 1
ACAAAC----AAACACACACACUUGCGCACGCUUCUGUCUAUUAAUCAUUUAAUAGUCAUCCAAAUUAUUAGGAAUUCUGCGCUUGUUUGCUCAAAACCUUUAACCACAUU-CG
.(((((----((............(((((......((.(((((((....))))))).))(((.........)))....)))))))))))).....................-.. ( -18.70)
>consensus
ACAAACAAACAAACACGCACACAUGCACACGGUUCUGUCUAUUAAUCAUUUAAUAGUCAUCCAAAUUAUUAGGAAUUCUGCGCUUGUUUACUCAAAACCUUUAACCACAUUUUG
..........(((((.((.((..............((.(((((((....))))))).))(((.........)))....)).)).)))))......................... (-12.18 = -12.58 +   0.40)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,132,119 – 7,132,233
Length 114
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 92.17
Mean single sequence MFE -27.34
Consensus MFE -22.04
Energy contribution -22.52
Covariance contribution 0.48
Combinations/Pair 1.23
Mean z-score -1.84
Structure conservation index 0.81
SVM decision value 1.02
SVM RNA-class probability 0.902164
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7132119 114 - 20766785
CAAAAUGUGGUUAAAGGUUUUGUCUAAACAAGCGCAGAAUUCCUAAUAAUUUGGAUGACUAUUAAAUGAUUAAUAGAUAGAACCGUGUGCAAGUGUGCGUGUUUGUUUGUUUGU
((((((.(......).))))))..(((((((((((.....(((.........)))...(((((((....)))))))..........(..(....)..))))))))))))..... ( -23.70)
>DroSec_CAF1 159596 114 - 1
CAAAAUGUGGUUAAAGGUUUUGAGUAAACAAGCUCAAAAUUCCUAAUAAUUUGGAUGACUAUUAAAUGAUUAAUAGACAGAGCCGUGUGCAUGUGUGCGUGUUUGUUUGUUUGU
((....(((((((...(((((((((......)))))))))(((.........))))))))))....))...((((((((((..((..((....))..))..))))))))))... ( -27.00)
>DroSim_CAF1 157898 114 - 1
CAAAAUGUGGUUAAAGGUUUUGAGUAAACAAGCGCAAAAUUCCUAAUAAUUUGGAUGACUAUUAAAUGAUUAAUAGACAGAGCCGUGUGCAUGUGUGCGUGUUUGUUUGUUUGU
((((((.(......).))))))..(((((((((((.................((.((.(((((((....))))))).))...))..(..(....)..))))))))))))..... ( -26.60)
>DroEre_CAF1 165213 110 - 1
CAAAAUGUGGUUAAAGGUUUUGCGCAAACAAGCGCAGAAUUCCUAAUAAUUUGGAUGACUAUUAAAUGAUUAAUAGACAGAAGCGUGUGCAUGUGUGCGUGUUU----GUUUGU
((....(((((((...(((((((((......)))))))))(((.........))))))))))....))....(((((((((.(((..((....))..))).)))----)))))) ( -31.00)
>DroYak_CAF1 169250 109 - 1
CG-AAUGUGGUUAAAGGUUUUGAGCAAACAAGCGCAGAAUUCCUAAUAAUUUGGAUGACUAUUAAAUGAUUAAUAGACAGAAGCGUGCGCAAGUGUGUGUGUUU----GUUUGU
..-....................((((((((((((.....(((.........)))((.(((((((....))))))).))...(((..(....)..)))))))))----)))))) ( -28.40)
>consensus
CAAAAUGUGGUUAAAGGUUUUGAGUAAACAAGCGCAGAAUUCCUAAUAAUUUGGAUGACUAUUAAAUGAUUAAUAGACAGAACCGUGUGCAUGUGUGCGUGUUUGUUUGUUUGU
((....(((((((...(((((((((......)))))))))(((.........))))))))))....))....(((((((((...(..((((....))))..)...))))))))) (-22.04 = -22.52 +   0.48)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:47 2006