Locus 5919

Sequence ID 2R_DroMel_CAF1
Location 18,667,832 – 18,668,007
Length 175
Max. P 0.844225
window9498 window9499 window9500 window9501

overview

Window 8

Location 18,667,832 – 18,667,940
Length 108
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 82.28
Mean single sequence MFE -36.37
Consensus MFE -23.21
Energy contribution -23.52
Covariance contribution 0.31
Combinations/Pair 1.24
Mean z-score -2.81
Structure conservation index 0.64
SVM decision value 0.76
SVM RNA-class probability 0.844225
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18667832 108 + 20766785
AUGGCGUCAAUGCCUACCAGAAGGCAAUAGACAUUUACUUGAGCCAGGGACAUCAGAUACCGAUUGAGUGGCUCAAUAACUUGGCCAGCAGUCAGCUGAUGGCCAAAA
.(((((((..(((((......)))))...))).....((((...))))..((((((.....(((((..((((.(((....))))))).)))))..))))))))))... ( -36.50)
>DroSec_CAF1 31458 108 + 1
AAGUCGUCAAUGCCUACCAGAAGGCAAUAGACAUUUACUUGAGCCGGGGACAUCAGAUACCGAUUGAGUGGCUCAAUAACCUGGCCAACAGUCAGCUGAUGGCCAAAA
.....(((..(((((......)))))...)))......((((((((....).((((.......))))..))))))).....((((((.(((....))).))))))... ( -36.80)
>DroSim_CAF1 31742 108 + 1
AAGUCGUCAAUGCCUACCAGAAGGCAAUGGACAUUUACUUGAGCCGGGGACAUCAGAUACCGAUUGAGUGGCUCAAUAACCUGGCCAACAGUCAGCUGAUGGCCAAAA
.....(((..(((((......)))))...)))......((((((((....).((((.......))))..))))))).....((((((.(((....))).))))))... ( -37.90)
>DroEre_CAF1 31020 108 + 1
AGGCCGUCAAUGCCUACCAGAAGGCAAUUUCCAUUUACUCUGGCGAGGGACAUCACAUACCGAUUGAGUGGCUCAAUAACCUGGCCAACAGCCAACUGAUGGCCAAAA
.((((((((.(((((......)))))..............((((.((((....)........((((((...))))))..))).)))).........)))))))).... ( -36.10)
>DroYak_CAF1 31811 108 + 1
AGACCGUCAAUGCCUACCAGAAGGCAAUAUCCAUUUGCUCGGUUCAGGGACAUCACAUACCGAUUGAGUGGCUCAACAACCUGGCCAACAGCCAACUGAUGGCCAAAA
..........(((((......)))))....((((((..(((((.....(....)....)))))..))))))..........((((((.(((....))).))))))... ( -32.10)
>DroAna_CAF1 30910 108 + 1
AGGCCAUCGAUUCCUACCAAAAGGCCAUGGCCAUUUGCGAGAAAUCGGGUCGAGAGGUGCCCGUCGAGUGGGUCAACAAUCUGGCAGCCACCCAGCAGCUGGCCAAGA
.((((.................)))).((((((.((((((....))(((((.(((..((((((.....)))).))....))).).....)))).)))).))))))... ( -38.83)
>consensus
AGGCCGUCAAUGCCUACCAGAAGGCAAUAGACAUUUACUUGAGCCAGGGACAUCAGAUACCGAUUGAGUGGCUCAAUAACCUGGCCAACAGCCAGCUGAUGGCCAAAA
.((((((((((((((......)))).....................((...........)).))))).)))))........((((((.(((....))).))))))... (-23.21 = -23.52 +   0.31)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,667,832 – 18,667,940
Length 108
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 82.28
Mean single sequence MFE -39.37
Consensus MFE -23.33
Energy contribution -25.28
Covariance contribution 1.95
Combinations/Pair 1.20
Mean z-score -2.68
Structure conservation index 0.59
SVM decision value 0.52
SVM RNA-class probability 0.768460
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18667832 108 - 20766785
UUUUGGCCAUCAGCUGACUGCUGGCCAAGUUAUUGAGCCACUCAAUCGGUAUCUGAUGUCCCUGGCUCAAGUAAAUGUCUAUUGCCUUCUGGUAGGCAUUGACGCCAU
.((((((((.(((....))).))))))))...((((((((....(((((...))))).....))))))))......(((...(((((......)))))..)))..... ( -40.60)
>DroSec_CAF1 31458 108 - 1
UUUUGGCCAUCAGCUGACUGUUGGCCAGGUUAUUGAGCCACUCAAUCGGUAUCUGAUGUCCCCGGCUCAAGUAAAUGUCUAUUGCCUUCUGGUAGGCAUUGACGACUU
...((((((.(((....))).))))))((((.(((((((.....(((((...)))))......)))))))......(((...(((((......)))))..))))))). ( -39.20)
>DroSim_CAF1 31742 108 - 1
UUUUGGCCAUCAGCUGACUGUUGGCCAGGUUAUUGAGCCACUCAAUCGGUAUCUGAUGUCCCCGGCUCAAGUAAAUGUCCAUUGCCUUCUGGUAGGCAUUGACGACUU
...((((((.(((....))).))))))((((.(((((((.....(((((...)))))......)))))))......(((...(((((......)))))..))))))). ( -38.50)
>DroEre_CAF1 31020 108 - 1
UUUUGGCCAUCAGUUGGCUGUUGGCCAGGUUAUUGAGCCACUCAAUCGGUAUGUGAUGUCCCUCGCCAGAGUAAAUGGAAAUUGCCUUCUGGUAGGCAUUGACGGCCU
.((((((((.(((....))).))))))))..((((((...)))))).(((...(((((((....(((((((..(((....)))...))))))).)))))))...))). ( -38.10)
>DroYak_CAF1 31811 108 - 1
UUUUGGCCAUCAGUUGGCUGUUGGCCAGGUUGUUGAGCCACUCAAUCGGUAUGUGAUGUCCCUGAACCGAGCAAAUGGAUAUUGCCUUCUGGUAGGCAUUGACGGUCU
...((((((.(((....))).))))))(..(((..((((.....(((((...(..((((((.((.......))...))))))..)...))))).))).)..)))..). ( -37.10)
>DroAna_CAF1 30910 108 - 1
UCUUGGCCAGCUGCUGGGUGGCUGCCAGAUUGUUGACCCACUCGACGGGCACCUCUCGACCCGAUUUCUCGCAAAUGGCCAUGGCCUUUUGGUAGGAAUCGAUGGCCU
....(((((.....((((.((.((((....((((((.....)))))))))))).))))...(((((((((.((((.(((....))).))))).)))))))).))))). ( -42.70)
>consensus
UUUUGGCCAUCAGCUGACUGUUGGCCAGGUUAUUGAGCCACUCAAUCGGUAUCUGAUGUCCCUGGCUCAAGUAAAUGGCUAUUGCCUUCUGGUAGGCAUUGACGGCCU
..(((((((.(((....))).)))))))(((((((((((.....((((.....))))......)))))))............(((((......))))).))))..... (-23.33 = -25.28 +   1.95)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,667,872 – 18,667,980
Length 108
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 82.65
Mean single sequence MFE -40.58
Consensus MFE -30.66
Energy contribution -31.83
Covariance contribution 1.17
Combinations/Pair 1.24
Mean z-score -1.45
Structure conservation index 0.76
SVM decision value 0.07
SVM RNA-class probability 0.569436
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18667872 108 - 20766785
GAAAGGGCAUCGUCAAGGGUAUUGAGUGCCUUCUCUGGCAUUUUGGCCAUCAGCUGACUGCUGGCCAAGUUAUUGAGCCACUCAAUCGGUAUCUGAUGUCCCUGGCUC
(..((((((((.....((((((((((((((......)))))((((((((.(((....))).))))))))...(((((...)))))))))))))))))).))))..).. ( -42.00)
>DroSec_CAF1 31498 108 - 1
GAAAGCGCUUCGUCAAGGGUAUCGAGUGCCCUCUCUGGCAUUUUGGCCAUCAGCUGACUGUUGGCCAGGUUAUUGAGCCACUCAAUCGGUAUCUGAUGUCCCCGGCUC
......(((.(((((..(((((((((((((......)))))..((((((.(((....))).))))))((((....))))......))))))))))))).....))).. ( -36.70)
>DroSim_CAF1 31782 108 - 1
GAAAGCGCUUCGUCAAGGGUAUCGAGUGCCCUCUCUGGCAUUUUGGCCAUCAGCUGACUGUUGGCCAGGUUAUUGAGCCACUCAAUCGGUAUCUGAUGUCCCCGGCUC
......(((.(((((..(((((((((((((......)))))..((((((.(((....))).))))))((((....))))......))))))))))))).....))).. ( -36.70)
>DroEre_CAF1 31060 108 - 1
GAAAGGGCAUCGUCAAGGGUAUCGAGUGCCUGCUCUGGCAUUUUGGCCAUCAGUUGGCUGUUGGCCAGGUUAUUGAGCCACUCAAUCGGUAUGUGAUGUCCCUCGCCA
(..((((...(((((...((((((((((((......)))))..((((((.(((....))).))))))((((....))))......))))))).))))).))))..).. ( -42.00)
>DroYak_CAF1 31851 108 - 1
GAAAGGGCAUCGUCGAGGGUUUCGAGUGCCUGCGCUGGCAUUUUGGCCAUCAGUUGGCUGUUGGCCAGGUUGUUGAGCCACUCAAUCGGUAUGUGAUGUCCCUGAACC
...(((((((((((((((((...(((((((......)))))))((((((.(((....))).))))))((((....))))))))..))))....))))).))))..... ( -41.40)
>DroAna_CAF1 30950 108 - 1
GCCAGGGCCUCGUCGAUGGUGGCGAGGGCCUGCUGCGGCAUCUUGGCCAGCUGCUGGGUGGCUGCCAGAUUGUUGACCCACUCGACGGGCACCUCUCGACCCGAUUUC
((.(((.((((((((....)))))))).)))))..(((((..(((((.(((..(...)..))))))))..)))))..........(((((.......).))))..... ( -44.70)
>consensus
GAAAGGGCAUCGUCAAGGGUAUCGAGUGCCUGCUCUGGCAUUUUGGCCAUCAGCUGACUGUUGGCCAGGUUAUUGAGCCACUCAAUCGGUAUCUGAUGUCCCUGGCUC
....(((...(((((..(((((((((((((......))))))(((((((.(((....))).)))))))...((((((...)))))))))))))))))).)))...... (-30.66 = -31.83 +   1.17)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,667,903 – 18,668,007
Length 104
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 80.26
Mean single sequence MFE -36.52
Consensus MFE -22.78
Energy contribution -22.95
Covariance contribution 0.17
Combinations/Pair 1.36
Mean z-score -1.52
Structure conservation index 0.62
SVM decision value 0.05
SVM RNA-class probability 0.560671
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18667903 104 - 20766785
UUAUCGCUAUUCAUUACU-CUACAUUUGGAAAGGGCAUCGUCAAGGGUAUUGAGUGCCUUCUCUGGCAUUUUGGCCAUCAGCUGACUGCUGGCCAAGUUAUUGAG
................((-(.....(..((.(((((((..((((.....))))))))))).))..)...((((((((.(((....))).)))))))).....))) ( -30.60)
>DroSec_CAF1 31529 104 - 1
UGUUCGCUAUUCAAUACU-CUACAUUUGGAAAGCGCUUCGUCAAGGGUAUCGAGUGCCCUCUCUGGCAUUUUGGCCAUCAGCUGACUGUUGGCCAGGUUAUUGAG
....((((.(((((....-......))))).))))....(((((((((((...)))))))...))))..((((((((.(((....))).))))))))........ ( -32.70)
>DroSim_CAF1 31813 104 - 1
UGUUCGCUAUUCAAUACU-CUACAUUUGGAAAGCGCUUCGUCAAGGGUAUCGAGUGCCCUCUCUGGCAUUUUGGCCAUCAGCUGACUGUUGGCCAGGUUAUUGAG
....((((.(((((....-......))))).))))....(((((((((((...)))))))...))))..((((((((.(((....))).))))))))........ ( -32.70)
>DroEre_CAF1 31091 104 - 1
UGCUCCCCAUUCAGUGUU-CUACAUUUGGAAAGGGCAUCGUCAAGGGUAUCGAGUGCCUGCUCUGGCAUUUUGGCCAUCAGUUGGCUGUUGGCCAGGUUAUUGAG
(((((.(((...((((..-...)))))))...)))))...((((....((((((((((......)))))))((((((.(((....))).)))))))))..)))). ( -34.70)
>DroYak_CAF1 31882 104 - 1
UGAUCGCCAUUCGAUGUU-CUGCACUUGGAAAGGGCAUCGUCGAGGGUUUCGAGUGCCUGCGCUGGCAUUUUGGCCAUCAGUUGGCUGUUGGCCAGGUUGUUGAG
.(((((((.(((((((..-.(((.(((....)))))).))))))))))...(((((((......)))))))((((((.(((....))).))))))))))...... ( -41.50)
>DroAna_CAF1 30981 104 - 1
UGCUCGUCC-CCAGCCCUGUCGCUCCUGGCCAGGGCCUCGUCGAUGGUGGCGAGGGCCUGCUGCGGCAUCUUGGCCAGCUGCUGGGUGGCUGCCAGAUUGUUGAC
.((..((((-(((((..........((((((((((((((((((....))))))))(((......))).))))))))))..)))))).))).))............ ( -46.90)
>consensus
UGAUCGCCAUUCAAUACU_CUACAUUUGGAAAGGGCAUCGUCAAGGGUAUCGAGUGCCUGCUCUGGCAUUUUGGCCAUCAGCUGACUGUUGGCCAGGUUAUUGAG
..........((((((.......................((((.(((((.....)))))....))))...(((((((.(((....))).)))))))..)))))). (-22.78 = -22.95 +   0.17)

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 11:58:07 2006