Locus 1075

Sequence ID 2L_DroMel_CAF1
Location 2,966,997 – 2,967,187
Length 190
Max. P 0.999532
window1735 window1736 window1737 window1738 window1739 window1740

overview

Window 5

Location 2,966,997 – 2,967,089
Length 92
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 81.27
Mean single sequence MFE -38.58
Consensus MFE -25.98
Energy contribution -25.03
Covariance contribution -0.94
Combinations/Pair 1.17
Mean z-score -3.22
Structure conservation index 0.67
SVM decision value 1.35
SVM RNA-class probability 0.945374
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2966997 92 + 22407834
GUUUCUCGAUGCACCUUCGCGUUCUGAAGCCAAUAUGGUUGUGCAAAUGCCUGCAGACGCC--ACCGGAAACGGAAAC----------GUCUGCAGAGCGCCCU
(((((..(((((......)))))..)))))......((.(((((....))(((((((((..--.(((....)))...)----------)))))))).))).)). ( -36.90)
>DroPse_CAF1 127400 104 + 1
GUUUCUAGAGGCACAUUCGCGUUUUGGAGCCAAUAAGGUUGUGCAAUUGCCUGCAGGUUUCUAAUCGGAAGCGGAAGCGAACGUGGAAGCCUGCAGCGCCCUCU
......(((((((((..(.....(((....)))...)..)))))....(((((((((((((((..((...((....))...))))))))))))))).)).)))) ( -43.40)
>DroSim_CAF1 20092 92 + 1
GUUUCUCGAUGCACCUUCGCGUUCUGAAGCAAAUAUGGUUGUGCAAAUGCCUGCAGACGCU--ACCGGAAACGGAAAC----------GUCUGCAGAGCGCCCU
(((((..(((((......)))))..)))))......((.(((((....))(((((((((..--.(((....)))...)----------)))))))).))).)). ( -37.80)
>DroEre_CAF1 19487 88 + 1
--UUCUCGAGGCACCUUCGCGUUCUGAAGCCAAUAAGGUUGUGCAAAUGCCUGCAGACGCC--ACCGGAAACGGAA------------GUCUGCAGAGCGCCCU
--.......(((......(((((.((.((((.....))))...)))))))((((((((...--.(((....)))..------------))))))))...))).. ( -35.00)
>DroYak_CAF1 19628 88 + 1
--UUCUCGAGGCACCUUCGCGUUCUGAAGCCAAUAAGGUUGUGCAAAUGCCUGCAGACGCC--ACCGGAAACGGAA------------GUCUGCAGAGCGCCCU
--.......(((......(((((.((.((((.....))))...)))))))((((((((...--.(((....)))..------------))))))))...))).. ( -35.00)
>DroPer_CAF1 129005 104 + 1
GUUUCUAGAGGCACAUUCGCGUUUUGGAGCCAAUAAGGUUGUGCAAUUGCCUGCAGGUUUCUAAUCGGAAGCGGAAGCGAACGUGGAAGCCUGCAGCGCCCUCU
......(((((((((..(.....(((....)))...)..)))))....(((((((((((((((..((...((....))...))))))))))))))).)).)))) ( -43.40)
>consensus
GUUUCUCGAGGCACCUUCGCGUUCUGAAGCCAAUAAGGUUGUGCAAAUGCCUGCAGACGCC__ACCGGAAACGGAA_C__________GUCUGCAGAGCGCCCU
..........((((..(((.....)))((((.....))))))))....((((((((((......(((....)))..............)))))))).))..... (-25.98 = -25.03 +  -0.94)

alignment

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secondary structure

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Window 6

Location 2,966,997 – 2,967,089
Length 92
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 81.27
Mean single sequence MFE -32.27
Consensus MFE -20.13
Energy contribution -20.47
Covariance contribution 0.34
Combinations/Pair 1.08
Mean z-score -1.54
Structure conservation index 0.62
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2966997 92 - 22407834
AGGGCGCUCUGCAGAC----------GUUUCCGUUUCCGGU--GGCGUCUGCAGGCAUUUGCACAACCAUAUUGGCUUCAGAACGCGAAGGUGCAUCGAGAAAC
.....((.((((((((----------((..(((....))).--.))))))))))))...(((((..((.....))((((.......)))))))))......... ( -37.30)
>DroPse_CAF1 127400 104 - 1
AGAGGGCGCUGCAGGCUUCCACGUUCGCUUCCGCUUCCGAUUAGAAACCUGCAGGCAAUUGCACAACCUUAUUGGCUCCAAAACGCGAAUGUGCCUCUAGAAAC
(((((((.(((((((.(((..((...((....))...))....))).))))))))).............((((.((........)).))))..)))))...... ( -29.00)
>DroSim_CAF1 20092 92 - 1
AGGGCGCUCUGCAGAC----------GUUUCCGUUUCCGGU--AGCGUCUGCAGGCAUUUGCACAACCAUAUUUGCUUCAGAACGCGAAGGUGCAUCGAGAAAC
.....((.((((((((----------(((.(((....))).--)))))))))))))...(((((.......(((((........))))).)))))......... ( -35.90)
>DroEre_CAF1 19487 88 - 1
AGGGCGCUCUGCAGAC------------UUCCGUUUCCGGU--GGCGUCUGCAGGCAUUUGCACAACCUUAUUGGCUUCAGAACGCGAAGGUGCCUCGAGAA--
.((((((.((((((((------------..(((....))).--...)))))))))).........(((((....((........)).)))))))))......-- ( -31.20)
>DroYak_CAF1 19628 88 - 1
AGGGCGCUCUGCAGAC------------UUCCGUUUCCGGU--GGCGUCUGCAGGCAUUUGCACAACCUUAUUGGCUUCAGAACGCGAAGGUGCCUCGAGAA--
.((((((.((((((((------------..(((....))).--...)))))))))).........(((((....((........)).)))))))))......-- ( -31.20)
>DroPer_CAF1 129005 104 - 1
AGAGGGCGCUGCAGGCUUCCACGUUCGCUUCCGCUUCCGAUUAGAAACCUGCAGGCAAUUGCACAACCUUAUUGGCUCCAAAACGCGAAUGUGCCUCUAGAAAC
(((((((.(((((((.(((..((...((....))...))....))).))))))))).............((((.((........)).))))..)))))...... ( -29.00)
>consensus
AGGGCGCUCUGCAGAC__________G_UUCCGUUUCCGGU__GGCGUCUGCAGGCAUUUGCACAACCUUAUUGGCUUCAGAACGCGAAGGUGCCUCGAGAAAC
.(((.((.((((((((..............(((....)))......))))))))))....((((.......((.((........)).)).)))))))....... (-20.13 = -20.47 +   0.34)

alignment

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secondary structure

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Window 7

Location 2,967,071 – 2,967,161
Length 90
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 89.67
Mean single sequence MFE -39.62
Consensus MFE -31.42
Energy contribution -33.30
Covariance contribution 1.88
Combinations/Pair 1.12
Mean z-score -4.15
Structure conservation index 0.79
SVM decision value 3.29
SVM RNA-class probability 0.998937
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2967071 90 + 22407834
ACGUCUGCAGAGCGCCCUCUUUAGGCGGCUUGUAAACG--------AUGCAAACGUGCAACCCUGCAACCGCUGCAUCGUUUACACUCGGCUUGAAAU
.((((((.((((....)))).))))))(((((((((((--------(((((....((((....)))).....)))))))))))))...)))....... ( -36.20)
>DroSec_CAF1 28223 98 + 1
ACGUCCGCAGUGCGCCCUCUUUAGGCGGCUUGUAAGCGAUGCAGCUAUGCAAACAUGCAACCCUGCAACCGCUGCAUCGUUUACACUCGGCUUGAAAU
..(..(((...)))..)..(((((((.(..(((((((((((((((..((((............))))...)))))))))))))))..).))))))).. ( -38.10)
>DroSim_CAF1 20166 98 + 1
ACGUCUGCAGAGCGCCCUCUUUAGGCGGCUUGUAAGCGGUGCAGCGAUGCAAACGUGCAACCCUGCAACCGCUGCAUCGUUUACACUCGGCUUGAAAU
.((((((.((((....)))).))))))(((((((((((((((((((.((((............))))..))))))))))))))))...)))....... ( -42.60)
>DroEre_CAF1 19559 96 + 1
--GUCUGCAGAGCGCCCUCUUUAGGCGGCUUGUAAACGAUGCAGCGAUGCAACCGUGCCACCCUGCAACCGCUGCAUCGUUUACACUCAGCUUGAAAU
--(((((.((((....)))).)))))((((((((((((((((((((.((((............))))..))))))))))))))))...))))...... ( -41.50)
>DroYak_CAF1 19700 96 + 1
--GUCUGCAGAGCGCCCUCUUCAGGCGGCUUGUAAACGAUGCAGCGAUCCAAUCGGGCAACCCUGCAACCGCUGCACCGUUUACACUCAGCUUGAAAU
--(((((.((((....)))).)))))((((((((((((.(((((((..((....))(((....)))...))))))).))))))))...))))...... ( -39.70)
>consensus
ACGUCUGCAGAGCGCCCUCUUUAGGCGGCUUGUAAACGAUGCAGCGAUGCAAACGUGCAACCCUGCAACCGCUGCAUCGUUUACACUCGGCUUGAAAU
..(((((.((((....)))).)))))((((((((((((((((((((.((((............))))..))))))))))))))))...))))...... (-31.42 = -33.30 +   1.88)

alignment

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secondary structure

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Window 8

Location 2,967,071 – 2,967,161
Length 90
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 89.67
Mean single sequence MFE -41.06
Consensus MFE -34.28
Energy contribution -37.40
Covariance contribution 3.12
Combinations/Pair 1.03
Mean z-score -3.39
Structure conservation index 0.83
SVM decision value 3.69
SVM RNA-class probability 0.999532
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2967071 90 - 22407834
AUUUCAAGCCGAGUGUAAACGAUGCAGCGGUUGCAGGGUUGCACGUUUGCAU--------CGUUUACAAGCCGCCUAAAGAGGGCGCUCUGCAGACGU
.......((.(((((((((((((((((((..(((......))))).))))))--------))))))).....((((.....)))))))).))...... ( -36.50)
>DroSec_CAF1 28223 98 - 1
AUUUCAAGCCGAGUGUAAACGAUGCAGCGGUUGCAGGGUUGCAUGUUUGCAUAGCUGCAUCGCUUACAAGCCGCCUAAAGAGGGCGCACUGCGGACGU
.......(((((((((((.(((((((((...((((((........))))))..))))))))).))))..((.((((.....))))))))).))).).. ( -39.80)
>DroSim_CAF1 20166 98 - 1
AUUUCAAGCCGAGUGUAAACGAUGCAGCGGUUGCAGGGUUGCACGUUUGCAUCGCUGCACCGCUUACAAGCCGCCUAAAGAGGGCGCUCUGCAGACGU
.......((.((((((((.((.(((((((((.(((((........)))))))))))))).)).)))).....((((.....)))))))).))...... ( -37.80)
>DroEre_CAF1 19559 96 - 1
AUUUCAAGCUGAGUGUAAACGAUGCAGCGGUUGCAGGGUGGCACGGUUGCAUCGCUGCAUCGUUUACAAGCCGCCUAAAGAGGGCGCUCUGCAGAC--
.......((.(((((((((((((((((((((.((((..........))))))))))))))))))))).....((((.....)))))))).))....-- ( -45.20)
>DroYak_CAF1 19700 96 - 1
AUUUCAAGCUGAGUGUAAACGGUGCAGCGGUUGCAGGGUUGCCCGAUUGGAUCGCUGCAUCGUUUACAAGCCGCCUGAAGAGGGCGCUCUGCAGAC--
.......((.((((((((((((((((((((((...(((...))).....)))))))))))))))))).....((((.....)))))))).))....-- ( -46.00)
>consensus
AUUUCAAGCCGAGUGUAAACGAUGCAGCGGUUGCAGGGUUGCACGUUUGCAUCGCUGCAUCGUUUACAAGCCGCCUAAAGAGGGCGCUCUGCAGACGU
.......((.(((((((((((((((((((((.(((((........)))))))))))))))))))))).....((((.....)))))))).))...... (-34.28 = -37.40 +   3.12)

alignment

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secondary structure

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Window 9

Location 2,967,089 – 2,967,187
Length 98
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 92.36
Mean single sequence MFE -39.66
Consensus MFE -33.40
Energy contribution -35.12
Covariance contribution 1.72
Combinations/Pair 1.09
Mean z-score -5.07
Structure conservation index 0.84
SVM decision value 3.48
SVM RNA-class probability 0.999283
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2967089 98 + 22407834
CUUUAGGCGGCUUGUAAACG--------AUGCAAACGUGCAACCCUGCAACCGCUGCAUCGUUUACACUCGGCUUGAAAUGUCUGUUUCUCUCACACAGAUCACAC
.(((((((.(..((((((((--------(((((....((((....)))).....)))))))))))))..).)))))))..((((((.........))))))..... ( -35.60)
>DroSec_CAF1 28241 106 + 1
CUUUAGGCGGCUUGUAAGCGAUGCAGCUAUGCAAACAUGCAACCCUGCAACCGCUGCAUCGUUUACACUCGGCUUGAAAUGUCUGUUUCUCUCACACAGAUCACAC
.(((((((.(..(((((((((((((((..((((............))))...)))))))))))))))..).)))))))..((((((.........))))))..... ( -40.20)
>DroSim_CAF1 20184 106 + 1
CUUUAGGCGGCUUGUAAGCGGUGCAGCGAUGCAAACGUGCAACCCUGCAACCGCUGCAUCGUUUACACUCGGCUUGAAAUGUCUGUUUCUCUCACACAGAUCACAC
.(((((((.(..((((((((((((((((.((((............))))..))))))))))))))))..).)))))))..((((((.........))))))..... ( -42.00)
>DroEre_CAF1 19575 106 + 1
CUUUAGGCGGCUUGUAAACGAUGCAGCGAUGCAACCGUGCCACCCUGCAACCGCUGCAUCGUUUACACUCAGCUUGAAAUGUCUGUUUCUCUCACACAGAUCACAC
.(((((((....((((((((((((((((.((((............))))..))))))))))))))))....)))))))..((((((.........))))))..... ( -40.90)
>DroYak_CAF1 19716 106 + 1
CUUCAGGCGGCUUGUAAACGAUGCAGCGAUCCAAUCGGGCAACCCUGCAACCGCUGCACCGUUUACACUCAGCUUGAAAUGUCUGUUUCUCUCACACAGAUCACAC
.(((((((....((((((((.(((((((..((....))(((....)))...))))))).))))))))....)))))))..((((((.........))))))..... ( -39.60)
>consensus
CUUUAGGCGGCUUGUAAACGAUGCAGCGAUGCAAACGUGCAACCCUGCAACCGCUGCAUCGUUUACACUCGGCUUGAAAUGUCUGUUUCUCUCACACAGAUCACAC
.(((((((.(..((((((((((((((((.((((............))))..))))))))))))))))..).)))))))..((((((.........))))))..... (-33.40 = -35.12 +   1.72)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,967,089 – 2,967,187
Length 98
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 92.36
Mean single sequence MFE -38.72
Consensus MFE -32.32
Energy contribution -35.24
Covariance contribution 2.92
Combinations/Pair 1.03
Mean z-score -2.79
Structure conservation index 0.83
SVM decision value 3.10
SVM RNA-class probability 0.998440
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2967089 98 - 22407834
GUGUGAUCUGUGUGAGAGAAACAGACAUUUCAAGCCGAGUGUAAACGAUGCAGCGGUUGCAGGGUUGCACGUUUGCAU--------CGUUUACAAGCCGCCUAAAG
...(((..(((.((.......)).)))..))).((.(..((((((((((((((((..(((......))))).))))))--------))))))))..).))...... ( -33.50)
>DroSec_CAF1 28241 106 - 1
GUGUGAUCUGUGUGAGAGAAACAGACAUUUCAAGCCGAGUGUAAACGAUGCAGCGGUUGCAGGGUUGCAUGUUUGCAUAGCUGCAUCGCUUACAAGCCGCCUAAAG
...(((..(((.((.......)).)))..))).((.(..(((((.(((((((((...((((((........))))))..))))))))).)))))..).))...... ( -36.70)
>DroSim_CAF1 20184 106 - 1
GUGUGAUCUGUGUGAGAGAAACAGACAUUUCAAGCCGAGUGUAAACGAUGCAGCGGUUGCAGGGUUGCACGUUUGCAUCGCUGCACCGCUUACAAGCCGCCUAAAG
...(((..(((.((.......)).)))..))).((.(..(((((.((.(((((((((.(((((........)))))))))))))).)).)))))..).))...... ( -34.80)
>DroEre_CAF1 19575 106 - 1
GUGUGAUCUGUGUGAGAGAAACAGACAUUUCAAGCUGAGUGUAAACGAUGCAGCGGUUGCAGGGUGGCACGGUUGCAUCGCUGCAUCGUUUACAAGCCGCCUAAAG
...(((..(((.((.......)).)))..))).((.(..((((((((((((((((((.((((..........))))))))))))))))))))))..).))...... ( -42.20)
>DroYak_CAF1 19716 106 - 1
GUGUGAUCUGUGUGAGAGAAACAGACAUUUCAAGCUGAGUGUAAACGGUGCAGCGGUUGCAGGGUUGCCCGAUUGGAUCGCUGCAUCGUUUACAAGCCGCCUGAAG
..(((.(((((.........))))))))((((.((.(..(((((((((((((((((((...(((...))).....)))))))))))))))))))..).)).)))). ( -46.40)
>consensus
GUGUGAUCUGUGUGAGAGAAACAGACAUUUCAAGCCGAGUGUAAACGAUGCAGCGGUUGCAGGGUUGCACGUUUGCAUCGCUGCAUCGUUUACAAGCCGCCUAAAG
...(((..(((.((.......)).)))..))).((.(..((((((((((((((((((.(((((........)))))))))))))))))))))))..).))...... (-32.32 = -35.24 +   2.92)

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 09:52:52 2006