Locus 6177

Sequence ID 3L_DroMel_CAF1
Location 16,361,813 – 16,361,982
Length 169
Max. P 0.751426
window9913 window9914 window9915 window9916

overview

Window 3

Location 16,361,813 – 16,361,916
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.13
Mean single sequence MFE -20.45
Consensus MFE -15.93
Energy contribution -16.13
Covariance contribution 0.20
Combinations/Pair 1.08
Mean z-score -1.59
Structure conservation index 0.78
SVM decision value 0.16
SVM RNA-class probability 0.612362
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16361813 103 - 23771897
CAUCAUUACCGAAGAUCGAACAUCAUGCAUUCAAUUAUCUCGAUCGGCUUAAUUAUCUUGUAUUUCGACAAGAUCAUUGCUAUCAGCUCGAAUUAGUGAUUC-----------------U
.(((((((.(((.((((((....................))))))(((..(((.(((((((......))))))).))))))......)))...)))))))..-----------------. ( -20.85)
>DroSec_CAF1 2074 103 - 1
CAUCAUUACCGAAGAUCGAACAUCAUGCAUUCAAUUAUCUCGAUCGGCUUAAUUAUCUUGUAUUUCGACAAGAUCAUUGCUAUCAGCUCGAAUUGGUGAUUC-----------------U
....((((((((.((((((....................))))))((((((((.(((((((......))))))).)))).....))))....))))))))..-----------------. ( -23.15)
>DroSim_CAF1 2078 103 - 1
CAUCAUUACCGAAGAUCGAACAUCAUGCAUUCAAUUAUCUCGAUCGGCUUAAUUAUCUUGUAUUUCGACAAGAUCAUUGCUAUCAGCUCGAAUUAGUGAUUC-----------------U
.(((((((.(((.((((((....................))))))(((..(((.(((((((......))))))).))))))......)))...)))))))..-----------------. ( -20.85)
>DroEre_CAF1 2004 119 - 1
CAUCAUUAUGGCAGAUCGAACAUCAUGCAUUCAAUUAUCUUGAUCGGCUUCAUUAUCUUGUAUUUCGACAAGAUCAUUGCUAUCAUCUCGAACUAGUGAUUCAUAAUACUUCC-CAUCAU
.(((((((..((((((.....))).)))...((((.((((((.((((...((......))....)))))))))).))))..............))))))).............-...... ( -19.20)
>DroYak_CAF1 1927 120 - 1
CAUCAUUAUGGAAGAUCGAACAUCAUGCACUCAAUUAUCUUGAUCGGCUUCAUUAUCUGGUAUUUCGACAAGAUCAUUGCUAUCAUCUCGAAUGAGUUAUUCAUAAUACAUCCACAUCAU
........((((...((((.....(((....((((.((((((.((((..(((.....)))....)))))))))).))))....))).))))(((((...)))))......))))...... ( -18.20)
>consensus
CAUCAUUACCGAAGAUCGAACAUCAUGCAUUCAAUUAUCUCGAUCGGCUUAAUUAUCUUGUAUUUCGACAAGAUCAUUGCUAUCAGCUCGAAUUAGUGAUUC_________________U
.(((((((.....((((((....................))))))(((...((.(((((((......))))))).)).)))............))))))).................... (-15.93 = -16.13 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,361,836 – 16,361,956
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.17
Mean single sequence MFE -30.81
Consensus MFE -23.77
Energy contribution -24.13
Covariance contribution 0.36
Combinations/Pair 1.03
Mean z-score -2.08
Structure conservation index 0.77
SVM decision value 0.48
SVM RNA-class probability 0.751426
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16361836 120 - 23771897
UCUGCGGAUUGAUCAUCAUCGAUGGACACGCGAUCGAUGUCAUCAUUACCGAAGAUCGAACAUCAUGCAUUCAAUUAUCUCGAUCGGCUUAAUUAUCUUGUAUUUCGACAAGAUCAUUGC
....(((..((((...(((((((.(.....).)))))))..))))...)))..((((((....................))))))....((((.(((((((......))))))).)))). ( -29.55)
>DroSec_CAF1 2097 120 - 1
UCUGCGGAUCGAUCAUCAUCGAUGGACACGCGAUCGAUGUCAUCAUUACCGAAGAUCGAACAUCAUGCAUUCAAUUAUCUCGAUCGGCUUAAUUAUCUUGUAUUUCGACAAGAUCAUUGC
...((.((((((....(((((((.(.....).)))))))...........((.(((.(((.........))).))).)))))))).)).((((.(((((((......))))))).)))). ( -29.20)
>DroSim_CAF1 2101 120 - 1
UCCGCGGAUCGAUCAUCAUCGAUGGACACGCGAUCGAUGUCAUCAUUACCGAAGAUCGAACAUCAUGCAUUCAAUUAUCUCGAUCGGCUUAAUUAUCUUGUAUUUCGACAAGAUCAUUGC
...((.((((((....(((((((.(.....).)))))))...........((.(((.(((.........))).))).)))))))).)).((((.(((((((......))))))).)))). ( -29.50)
>DroEre_CAF1 2043 120 - 1
UCUGCAGUUUGAUCAUCAUCGAUGGACACGCGAUCGAUGUCAUCAUUAUGGCAGAUCGAACAUCAUGCAUUCAAUUAUCUUGAUCGGCUUCAUUAUCUUGUAUUUCGACAAGAUCAUUGC
..((((((((((((...((((((.(.....).))))))(((((....))))).))))))))....))))..((((.((((((.((((...((......))....)))))))))).)))). ( -33.90)
>DroYak_CAF1 1967 120 - 1
UCUGCAGUUUGAUCAUCAUCGAUGGACACGCGAUCGAUGUCAUCAUUAUGGAAGAUCGAACAUCAUGCACUCAAUUAUCUUGAUCGGCUUCAUUAUCUGGUAUUUCGACAAGAUCAUUGC
..((((((((((((..(((((((.(.....).)))))))((((....))))..))))))))....))))..((((.((((((.((((..(((.....)))....)))))))))).)))). ( -31.90)
>consensus
UCUGCGGAUUGAUCAUCAUCGAUGGACACGCGAUCGAUGUCAUCAUUACCGAAGAUCGAACAUCAUGCAUUCAAUUAUCUCGAUCGGCUUAAUUAUCUUGUAUUUCGACAAGAUCAUUGC
...((.....(((...(((((((.(.....).)))))))..))).........((((((....................)))))).)).((((.(((((((......))))))).)))). (-23.77 = -24.13 +   0.36)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,361,876 – 16,361,982
Length 106
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 96.04
Mean single sequence MFE -27.14
Consensus MFE -23.20
Energy contribution -23.60
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -1.44
Structure conservation index 0.85
SVM decision value 0.37
SVM RNA-class probability 0.707850
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16361876 106 + 23771897
AGAUAAUUGAAUGCAUGAUGUUCGAUCUUCGGUAAUGAUGACAUCGAUCGCGUGUCCAUCGAUGAUGAUCAAUCCGCAGACAGUAUCGACAUGUUAAUUAUUAGCU
.((((((((...(((((.((..(..(((.(((...((((.((((((((.(.....).))))))).).))))..))).)))..)...)).))))))))))))).... ( -26.80)
>DroSec_CAF1 2137 106 + 1
AGAUAAUUGAAUGCAUGAUGUUCGAUCUUCGGUAAUGAUGACAUCGAUCGCGUGUCCAUCGAUGAUGAUCGAUCCGCAGACAGUAUCGACAUGUUAAUUAUUAGCU
.((..(((((((.......)))))))..))(.((((((((((((((((.((.((((.((((((....)))))).....)))))))))))..)))).))))))).). ( -27.40)
>DroSim_CAF1 2141 106 + 1
AGAUAAUUGAAUGCAUGAUGUUCGAUCUUCGGUAAUGAUGACAUCGAUCGCGUGUCCAUCGAUGAUGAUCGAUCCGCGGACAGUAUCGACAUGUUAAUUAUUAGCU
.((..(((((((.......)))))))..))(.((((((((((((((((.((.(((((((((((....))))))....))))))))))))..)))).))))))).). ( -31.30)
>DroEre_CAF1 2083 106 + 1
AGAUAAUUGAAUGCAUGAUGUUCGAUCUGCCAUAAUGAUGACAUCGAUCGCGUGUCCAUCGAUGAUGAUCAAACUGCAGACAGUAUCGACAUGUUAAUUAUUAGCU
.((((((((...(((((.((..(..(((((.....((((.((((((((.(.....).))))))).).))))....)))))..)...)).))))))))))))).... ( -26.40)
>DroYak_CAF1 2007 106 + 1
AGAUAAUUGAGUGCAUGAUGUUCGAUCUUCCAUAAUGAUGACAUCGAUCGCGUGUCCAUCGAUGAUGAUCAAACUGCAGACAGUAUCGACAUGUUAAUUAUUAGCU
.((((((((...(((((....(((((.........((((.((((((((.(.....).))))))).).)))).((((....)))))))))))))))))))))).... ( -23.80)
>consensus
AGAUAAUUGAAUGCAUGAUGUUCGAUCUUCGGUAAUGAUGACAUCGAUCGCGUGUCCAUCGAUGAUGAUCAAUCCGCAGACAGUAUCGACAUGUUAAUUAUUAGCU
.((((((((...(((((.((..(..(((.(((...((((.((((((((.(.....).))))))).).))))..))).)))..)...)).))))))))))))).... (-23.20 = -23.60 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,361,876 – 16,361,982
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 96.04
Mean single sequence MFE -23.98
Consensus MFE -19.82
Energy contribution -19.54
Covariance contribution -0.28
Combinations/Pair 1.08
Mean z-score -1.50
Structure conservation index 0.83
SVM decision value 0.13
SVM RNA-class probability 0.599585
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16361876 106 - 23771897
AGCUAAUAAUUAACAUGUCGAUACUGUCUGCGGAUUGAUCAUCAUCGAUGGACACGCGAUCGAUGUCAUCAUUACCGAAGAUCGAACAUCAUGCAUUCAAUUAUCU
.............(((((((((.((.....(((..((((...(((((((.(.....).)))))))..))))...))).)))))))....))))............. ( -23.50)
>DroSec_CAF1 2137 106 - 1
AGCUAAUAAUUAACAUGUCGAUACUGUCUGCGGAUCGAUCAUCAUCGAUGGACACGCGAUCGAUGUCAUCAUUACCGAAGAUCGAACAUCAUGCAUUCAAUUAUCU
...................((((.((..((((((((((((..(((((((.(.....).)))))))...((......)).))))))...)).))))..))..)))). ( -23.30)
>DroSim_CAF1 2141 106 - 1
AGCUAAUAAUUAACAUGUCGAUACUGUCCGCGGAUCGAUCAUCAUCGAUGGACACGCGAUCGAUGUCAUCAUUACCGAAGAUCGAACAUCAUGCAUUCAAUUAUCU
.....((((((...((((.(((.(((....))).((((((..(((((((.(.....).)))))))...((......)).))))))..)))..))))..)))))).. ( -21.90)
>DroEre_CAF1 2083 106 - 1
AGCUAAUAAUUAACAUGUCGAUACUGUCUGCAGUUUGAUCAUCAUCGAUGGACACGCGAUCGAUGUCAUCAUUAUGGCAGAUCGAACAUCAUGCAUUCAAUUAUCU
...................((((.((..((((((((((((...((((((.(.....).))))))(((((....))))).))))))))....))))..))..)))). ( -26.30)
>DroYak_CAF1 2007 106 - 1
AGCUAAUAAUUAACAUGUCGAUACUGUCUGCAGUUUGAUCAUCAUCGAUGGACACGCGAUCGAUGUCAUCAUUAUGGAAGAUCGAACAUCAUGCACUCAAUUAUCU
...................((((.((..((((((((((((..(((((((.(.....).)))))))((((....))))..))))))))....))))..))..)))). ( -24.90)
>consensus
AGCUAAUAAUUAACAUGUCGAUACUGUCUGCGGAUUGAUCAUCAUCGAUGGACACGCGAUCGAUGUCAUCAUUACCGAAGAUCGAACAUCAUGCAUUCAAUUAUCU
.............((((..(...(((....))).((((((..(((((((.(.....).)))))))...((......)).)))))).)..))))............. (-19.82 = -19.54 +  -0.28)

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 12:11:58 2006