Locus 6060

Sequence ID 2L_DroMel_CAF1
Location 17,048,936 – 17,049,172
Length 236
Max. P 0.999830
window9625 window9626 window9627 window9628 window9629 window9630

overview

Window 5

Location 17,048,936 – 17,049,052
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.40
Mean single sequence MFE -34.90
Consensus MFE -31.58
Energy contribution -31.26
Covariance contribution -0.32
Combinations/Pair 1.06
Mean z-score -2.40
Structure conservation index 0.90
SVM decision value 3.70
SVM RNA-class probability 0.999539
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17048936 116 - 22407834
GCAUUAACAAAGGGGGCAGGGACCCCAAGUCCGCUU--UCCG--UUCCGUUGGAAAUGUAUCUGCAUUUUUAACGGCAUAUUUUAAUGCCUGAUUUUUAACGUCAACUCGACGCACUUAU
(((((((.((((.((((.((....))..)))).)))--)..(--(.(((((((((((((....))))))))))))).))...)))))))...........((((.....))))....... ( -35.70)
>DroSec_CAF1 12996 116 - 1
GCAUUAACAAAGGGGGCAGGGACACCAAGUCCGCUU--UCCG--UUCUGUUGGAAAUGGAUCUGCAUUUUUAACGGCAUAUUUUAAUGCCUGAUUUUUAACGUCAACUCGACGCACUUAU
(((((((....(..(((..((((.....))))))).--.).(--(.((((((((((((......)))))))))))).))...)))))))...........((((.....))))....... ( -32.10)
>DroSim_CAF1 7089 116 - 1
GCAUUAACAAAGGGGGCAGGGACACCAAGUCCGCUU--UCCG--UUCCGUUGGAAAUGGAUCUGCAUUUUUAACGGCAUAUUUUAAUGCCUGAUUUUUAACGUCAACUCGACGCACUUAU
(((((((....(..(((..((((.....))))))).--.).(--(.((((((((((((......)))))))))))).))...)))))))...........((((.....))))....... ( -34.30)
>DroEre_CAF1 12751 111 - 1
GCAUUAACAAGGGGGGCAGGGACCCCAAGUCCGC---------UUUCCGUUGGAAAUGGAUCUGCAUUUUUAACGGCAUAUUUUAAUGCCUGAUUUUUAACGUCAACUCGACGCACUUAU
((........((..(((..((((.....))))))---------)..))((((((((((......))))))))))(((((......)))))...........(((.....)))))...... ( -34.30)
>DroYak_CAF1 10752 120 - 1
GCAUUAACAAAGGGGGCAGGGACCCCAAGUCCGCUGGAUCCAUUUUCCGUUGGAAAUGGAUCUGCAUUUUUAACGGCAUAUUUUAAUGCCUGAUUUUUAACGUCAACUCGACGCACUUAU
((.........((((.......))))(((((.((.((((((((((((....)))))))))))))).........(((((......))))).))))).....(((.....)))))...... ( -38.10)
>consensus
GCAUUAACAAAGGGGGCAGGGACCCCAAGUCCGCUU__UCCG__UUCCGUUGGAAAUGGAUCUGCAUUUUUAACGGCAUAUUUUAAUGCCUGAUUUUUAACGUCAACUCGACGCACUUAU
((.((((.(((..(((((.((((.....))))..............((((((((((((......))))))))))))..........)))))..))))))).(((.....)))))...... (-31.58 = -31.26 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,048,976 – 17,049,092
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.86
Mean single sequence MFE -37.10
Consensus MFE -30.00
Energy contribution -30.28
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -1.39
Structure conservation index 0.81
SVM decision value 0.08
SVM RNA-class probability 0.574878
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17048976 116 - 22407834
CAAGUGGCACCGCAUCACUAGCAGCUGUGGCUUAUGAAGUGCAUUAACAAAGGGGGCAGGGACCCCAAGUCCGCUU--UCCG--UUCCGUUGGAAAUGUAUCUGCAUUUUUAACGGCAUA
.((((((.((.((((((..(((.......)))..)))..))).........((((.......))))..))))))))--...(--(.(((((((((((((....))))))))))))).)). ( -37.90)
>DroSec_CAF1 13036 116 - 1
CAAGUGGCACCGCAUCACUGCCAGCUGUGGCUUAUGAAAUGCAUUAACAAAGGGGGCAGGGACACCAAGUCCGCUU--UCCG--UUCUGUUGGAAAUGGAUCUGCAUUUUUAACGGCAUA
....(((((.........)))))(((((.......((((((((......(((.((((.((....))..)))).)))--((((--(((.....).))))))..))))))))..)))))... ( -33.20)
>DroSim_CAF1 7129 116 - 1
CAAGUGGCACCGCAUCACUGCCAGCUGUGGCUUAUGAAAUGCAUUAACAAAGGGGGCAGGGACACCAAGUCCGCUU--UCCG--UUCCGUUGGAAAUGGAUCUGCAUUUUUAACGGCAUA
...(((....))).(((..((((....))))...))).((((.........(..(((..((((.....))))))).--.)..--...(((((((((((......))))))))))))))). ( -35.40)
>DroEre_CAF1 12791 111 - 1
CAAGUGGCACCGCAUCACUGCCAGCUGUGGCUUAUGAAAUGCAUUAACAAGGGGGGCAGGGACCCCAAGUCCGC---------UUUCCGUUGGAAAUGGAUCUGCAUUUUUAACGGCAUA
.((((((.((.((((((..((((....))))...)))..)))........((((........))))..))))))---------)).((((((((((((......)))))))))))).... ( -38.30)
>DroYak_CAF1 10792 116 - 1
CAAGUGGCACCGCAUCACUGGCAGCUGUGGCUUA----AUGCAUUAACAAAGGGGGCAGGGACCCCAAGUCCGCUGGAUCCAUUUUCCGUUGGAAAUGGAUCUGCAUUUUUAACGGCAUA
...(((....)))..........(((((.....(----((((........((.((((.((....))..)))).))((((((((((((....)))))))))))))))))....)))))... ( -40.70)
>consensus
CAAGUGGCACCGCAUCACUGCCAGCUGUGGCUUAUGAAAUGCAUUAACAAAGGGGGCAGGGACCCCAAGUCCGCUU__UCCG__UUCCGUUGGAAAUGGAUCUGCAUUUUUAACGGCAUA
..(((((.((.((((.......(((....)))......)))).........((((.......))))..)))))))...........((((((((((((......)))))))))))).... (-30.00 = -30.28 +   0.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,049,014 – 17,049,132
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.69
Mean single sequence MFE -37.16
Consensus MFE -29.26
Energy contribution -30.90
Covariance contribution 1.64
Combinations/Pair 1.03
Mean z-score -1.49
Structure conservation index 0.79
SVM decision value -0.04
SVM RNA-class probability 0.513789
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17049014 118 + 22407834
GA--AAGCGGACUUGGGGUCCCUGCCCCCUUUGUUAAUGCACUUCAUAAGCCACAGCUGCUAGUGAUGCGGUGCCACUUGCAUAUGGCAAGUGAAUUUAAUGCCGUACAAAGCAAACUUU
..--..((((....(((((....)))))....(((((.(((((((((.(((.......))).))))...)))))(((((((.....)))))))...))))).)))).............. ( -34.60)
>DroSec_CAF1 13074 118 + 1
GA--AAGCGGACUUGGUGUCCCUGCCCCCUUUGUUAAUGCAUUUCAUAAGCCACAGCUGGCAGUGAUGCGGUGCCACUUGCAUGUGGCAAGUGAAUUUAAUGCCGUACAAAGCAAACUUU
..--.((.((((.....)))))).....((((((....(((((((((..(((((((((((((.((...)).)))))...)).))))))..))))....)))))...))))))........ ( -37.50)
>DroSim_CAF1 7167 118 + 1
GA--AAGCGGACUUGGUGUCCCUGCCCCCUUUGUUAAUGCAUUUCAUAAGCCACAGCUGGCAGUGAUGCGGUGCCACUUGCAUGUGGCAAGUGAAUUUAAUGCCGUACAAAGCAAACUUU
..--.((.((((.....)))))).....((((((....(((((((((..(((((((((((((.((...)).)))))...)).))))))..))))....)))))...))))))........ ( -37.50)
>DroEre_CAF1 12828 114 + 1
------GCGGACUUGGGGUCCCUGCCCCCCUUGUUAAUGCAUUUCAUAAGCCACAGCUGGCAGUGAUGCGGUGCCACUUGCAUGUGGCAAGUGAAUUUAAUGCCGUACAAAGCGAACUUU
------((((....(((((....)))))))((((....(((((((((..(((((((((((((.((...)).)))))...)).))))))..))))....)))))...)))).))....... ( -38.20)
>DroYak_CAF1 10832 116 + 1
GAUCCAGCGGACUUGGGGUCCCUGCCCCCUUUGUUAAUGCAU----UAAGCCACAGCUGCCAGUGAUGCGGUGCCACUUGCAUGUGGCAAGUGAAUUUAAUGCCGUACAAAGCAAACUUU
....(((.((((.....)))))))....((((((....((((----((((.(((.(((((.(....))))))(((((......)))))..)))..))))))))...))))))........ ( -38.00)
>consensus
GA__AAGCGGACUUGGGGUCCCUGCCCCCUUUGUUAAUGCAUUUCAUAAGCCACAGCUGGCAGUGAUGCGGUGCCACUUGCAUGUGGCAAGUGAAUUUAAUGCCGUACAAAGCAAACUUU
......((((((.....))))..))...((((((....(((((((((..(((((((((((((.((...)).)))))...)).))))))..)))))....))))...))))))........ (-29.26 = -30.90 +   1.64)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,049,014 – 17,049,132
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.69
Mean single sequence MFE -38.56
Consensus MFE -35.48
Energy contribution -35.20
Covariance contribution -0.28
Combinations/Pair 1.09
Mean z-score -2.07
Structure conservation index 0.92
SVM decision value 3.22
SVM RNA-class probability 0.998781
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17049014 118 - 22407834
AAAGUUUGCUUUGUACGGCAUUAAAUUCACUUGCCAUAUGCAAGUGGCACCGCAUCACUAGCAGCUGUGGCUUAUGAAGUGCAUUAACAAAGGGGGCAGGGACCCCAAGUCCGCUU--UC
...((((.((((((...((((....((((...(((((((((.(((((.......))))).)))..))))))...))))))))....)))))).))))..((((.....))))....--.. ( -36.90)
>DroSec_CAF1 13074 118 - 1
AAAGUUUGCUUUGUACGGCAUUAAAUUCACUUGCCACAUGCAAGUGGCACCGCAUCACUGCCAGCUGUGGCUUAUGAAAUGCAUUAACAAAGGGGGCAGGGACACCAAGUCCGCUU--UC
...((((.((((((...(((((....(((...((((((.((...(((((.........)))))))))))))...))))))))....)))))).))))..((((.....))))....--.. ( -39.00)
>DroSim_CAF1 7167 118 - 1
AAAGUUUGCUUUGUACGGCAUUAAAUUCACUUGCCACAUGCAAGUGGCACCGCAUCACUGCCAGCUGUGGCUUAUGAAAUGCAUUAACAAAGGGGGCAGGGACACCAAGUCCGCUU--UC
...((((.((((((...(((((....(((...((((((.((...(((((.........)))))))))))))...))))))))....)))))).))))..((((.....))))....--.. ( -39.00)
>DroEre_CAF1 12828 114 - 1
AAAGUUCGCUUUGUACGGCAUUAAAUUCACUUGCCACAUGCAAGUGGCACCGCAUCACUGCCAGCUGUGGCUUAUGAAAUGCAUUAACAAGGGGGGCAGGGACCCCAAGUCCGC------
...((((.((((((...(((((....(((...((((((.((...(((((.........)))))))))))))...))))))))....)))))).))))..((((.....))))..------ ( -39.90)
>DroYak_CAF1 10832 116 - 1
AAAGUUUGCUUUGUACGGCAUUAAAUUCACUUGCCACAUGCAAGUGGCACCGCAUCACUGGCAGCUGUGGCUUA----AUGCAUUAACAAAGGGGGCAGGGACCCCAAGUCCGCUGGAUC
...((((.((((((...(((((((........(((((((((.(((((.......))))).)))..)))))))))----))))....)))))).))))((((((.....)))).))..... ( -38.00)
>consensus
AAAGUUUGCUUUGUACGGCAUUAAAUUCACUUGCCACAUGCAAGUGGCACCGCAUCACUGCCAGCUGUGGCUUAUGAAAUGCAUUAACAAAGGGGGCAGGGACCCCAAGUCCGCUU__UC
...((((.((((((...(((((....((((((((.....))))))))..(((((.(.......).))))).......)))))....)))))).))))..((((.....))))........ (-35.48 = -35.20 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,049,052 – 17,049,172
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.83
Mean single sequence MFE -37.78
Consensus MFE -36.98
Energy contribution -37.02
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -2.25
Structure conservation index 0.98
SVM decision value 4.19
SVM RNA-class probability 0.999830
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17049052 120 + 22407834
ACUUCAUAAGCCACAGCUGCUAGUGAUGCGGUGCCACUUGCAUAUGGCAAGUGAAUUUAAUGCCGUACAAAGCAAACUUUGUAUCGAUUUCGGGCACCCACACUAUAUGGUCCAUGCACC
...((((((((....)))..(((((.((.((((((((((((.....))))))...........(((((((((....))))))).))......)))))))))))))))))).......... ( -37.20)
>DroSec_CAF1 13112 120 + 1
AUUUCAUAAGCCACAGCUGGCAGUGAUGCGGUGCCACUUGCAUGUGGCAAGUGAAUUUAAUGCCGUACAAAGCAAACUUUGUAUCGAUUUCGGGCACCCACACUCUACGGUCCAUGCACC
.........((....((((..((((.((.((((((((((((.....))))))...........(((((((((....))))))).))......))))))))))))...))))....))... ( -38.40)
>DroSim_CAF1 7205 120 + 1
AUUUCAUAAGCCACAGCUGGCAGUGAUGCGGUGCCACUUGCAUGUGGCAAGUGAAUUUAAUGCCGUACAAAGCAAACUUUGUAUCGAUUUCGGGCACCCACACUCUACGGUCCAUGCACC
.........((....((((..((((.((.((((((((((((.....))))))...........(((((((((....))))))).))......))))))))))))...))))....))... ( -38.40)
>DroEre_CAF1 12862 120 + 1
AUUUCAUAAGCCACAGCUGGCAGUGAUGCGGUGCCACUUGCAUGUGGCAAGUGAAUUUAAUGCCGUACAAAGCGAACUUUGUAUCGAUUUCGGGCACCCACACCCUACGGUCCAUGCACC
...((((..((((....)))).))))...((((((((((((.....)))))))........(((((((((((....)))))).........(((........))).)))))....))))) ( -37.60)
>DroYak_CAF1 10872 116 + 1
AU----UAAGCCACAGCUGCCAGUGAUGCGGUGCCACUUGCAUGUGGCAAGUGAAUUUAAUGCCGUACAAAGCAAACUUUGUAUCGAUUUCGGGCACCCACACUCUACGGUCCAUGCACC
..----...((....((((..((((.((.((((((((((((.....))))))...........(((((((((....))))))).))......))))))))))))...))))....))... ( -37.30)
>consensus
AUUUCAUAAGCCACAGCUGGCAGUGAUGCGGUGCCACUUGCAUGUGGCAAGUGAAUUUAAUGCCGUACAAAGCAAACUUUGUAUCGAUUUCGGGCACCCACACUCUACGGUCCAUGCACC
.........((....((((..((((.((.((((((((((((.....))))))...........(((((((((....))))))).))......))))))))))))...))))....))... (-36.98 = -37.02 +   0.04)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,049,052 – 17,049,172
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -41.26
Consensus MFE -37.98
Energy contribution -38.26
Covariance contribution 0.28
Combinations/Pair 1.05
Mean z-score -2.15
Structure conservation index 0.92
SVM decision value 3.23
SVM RNA-class probability 0.998790
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17049052 120 - 22407834
GGUGCAUGGACCAUAUAGUGUGGGUGCCCGAAAUCGAUACAAAGUUUGCUUUGUACGGCAUUAAAUUCACUUGCCAUAUGCAAGUGGCACCGCAUCACUAGCAGCUGUGGCUUAUGAAGU
....((((..((((((((((((((((((.....(((.(((((((....))))))))))..........((((((.....)))))))))))).)).))))).....)))))..)))).... ( -41.20)
>DroSec_CAF1 13112 120 - 1
GGUGCAUGGACCGUAGAGUGUGGGUGCCCGAAAUCGAUACAAAGUUUGCUUUGUACGGCAUUAAAUUCACUUGCCACAUGCAAGUGGCACCGCAUCACUGCCAGCUGUGGCUUAUGAAAU
(((((..........((((...((((((((....)).(((((((....))))))).))))))..))))((((((.....)))))).)))))...(((..((((....))))...)))... ( -41.10)
>DroSim_CAF1 7205 120 - 1
GGUGCAUGGACCGUAGAGUGUGGGUGCCCGAAAUCGAUACAAAGUUUGCUUUGUACGGCAUUAAAUUCACUUGCCACAUGCAAGUGGCACCGCAUCACUGCCAGCUGUGGCUUAUGAAAU
(((((..........((((...((((((((....)).(((((((....))))))).))))))..))))((((((.....)))))).)))))...(((..((((....))))...)))... ( -41.10)
>DroEre_CAF1 12862 120 - 1
GGUGCAUGGACCGUAGGGUGUGGGUGCCCGAAAUCGAUACAAAGUUCGCUUUGUACGGCAUUAAAUUCACUUGCCACAUGCAAGUGGCACCGCAUCACUGCCAGCUGUGGCUUAUGAAAU
(((.(((((...((((((((((((((((((....)).(((((((....))))))).))))).....((((((((.....))))))))..))))))).))))...))))))))........ ( -43.90)
>DroYak_CAF1 10872 116 - 1
GGUGCAUGGACCGUAGAGUGUGGGUGCCCGAAAUCGAUACAAAGUUUGCUUUGUACGGCAUUAAAUUCACUUGCCACAUGCAAGUGGCACCGCAUCACUGGCAGCUGUGGCUUA----AU
(((......)))...(((((..((((((((....)).(((((((....))))))).)))))).....)))))(((((((((.(((((.......))))).)))..))))))...----.. ( -39.00)
>consensus
GGUGCAUGGACCGUAGAGUGUGGGUGCCCGAAAUCGAUACAAAGUUUGCUUUGUACGGCAUUAAAUUCACUUGCCACAUGCAAGUGGCACCGCAUCACUGCCAGCUGUGGCUUAUGAAAU
....((((..((((((((((((((((((.....(((.(((((((....))))))))))..........((((((.....)))))))))))).)).)))).....))))))..)))).... (-37.98 = -38.26 +   0.28)

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 12:00:08 2006