Locus 3399

Sequence ID 3R_DroMel_CAF1
Location 9,202,764 – 9,202,982
Length 218
Max. P 0.987395
window5453 window5454 window5455 window5456 window5457 window5458 window5459

overview

Window 3

Location 9,202,764 – 9,202,865
Length 101
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 80.53
Mean single sequence MFE -29.57
Consensus MFE -22.15
Energy contribution -22.52
Covariance contribution 0.38
Combinations/Pair 1.21
Mean z-score -1.89
Structure conservation index 0.75
SVM decision value 0.87
SVM RNA-class probability 0.870491
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9202764 101 + 27905053
GCGUAAGGAUCCCCAGGAAAACCAUGAACAUUGUGGACACCACGGCCAUCAUUGGCAUCAUGGGCAUCAUGGAUUUCAUGGACACCAUGGUCACCAUGGAC
((....((....)).......((((((....(((((...)))))((((....)))).)))))))).((((((...((((((...))))))...)))))).. ( -35.00)
>DroSec_CAF1 38383 101 + 1
GCGUAAGGAUCCCCAGGAAAACCAUGAGCAUCAUGGACACCAUGGACACCAUUGGCAUCAUGGACAUCAUGGAUUUCAUGGUUACCAUGGCCACCAUAGCC
((.((.((....(((((....(((((.....)))))...)).))).......((((..(((((..((((((.....))))))..))))))))))).)))). ( -29.70)
>DroSim_CAF1 37203 101 + 1
GCGUAAGGAUCCCCAGGAAAACCAUGAGCAUCAUGGACACCACGGACACCAUUGGCAUCAUGGACAUCAUGGAUUUCAUGGUUACCAUGGCCACCACGGAC
.(((..((.(((...((....(((((.....)))))...))..)))..))..((((..(((((..((((((.....))))))..)))))))))..)))... ( -29.30)
>DroYak_CAF1 37296 92 + 1
CCGUAAGGAACACCAUGAAGACCACGGACACCAUGGACAUCACGAACACCCUUGGCAUCAUGGACACCAUGGACAUCAUGGACACC---------CCUGGC
((....))....((((((.(.(((.((...((((((...(((.(......).)))..))))))...)).))).).)))))).....---------...... ( -24.30)
>consensus
GCGUAAGGAUCCCCAGGAAAACCAUGAACAUCAUGGACACCACGGACACCAUUGGCAUCAUGGACAUCAUGGAUUUCAUGGACACCAUGGCCACCACGGAC
............(((.((((.((((((...((((((...(((..........)))..))))))...)))))).)))).)))...((((((...)))))).. (-22.15 = -22.52 +   0.38)

alignment

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secondary structure

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Window 4

Location 9,202,764 – 9,202,865
Length 101
Sequences 4
Columns 101
Reading direction reverse
Mean pairwise identity 80.53
Mean single sequence MFE -34.05
Consensus MFE -25.29
Energy contribution -26.10
Covariance contribution 0.81
Combinations/Pair 1.19
Mean z-score -1.48
Structure conservation index 0.74
SVM decision value -0.02
SVM RNA-class probability 0.521671
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9202764 101 - 27905053
GUCCAUGGUGACCAUGGUGUCCAUGAAAUCCAUGAUGCCCAUGAUGCCAAUGAUGGCCGUGGUGUCCACAAUGUUCAUGGUUUUCCUGGGGAUCCUUACGC
..((((((...))))))(.((((.((((.((((((.(((((((..((((....))))))))).)).........)))))).)))).)))).)......... ( -32.30)
>DroSec_CAF1 38383 101 - 1
GGCUAUGGUGGCCAUGGUAACCAUGAAAUCCAUGAUGUCCAUGAUGCCAAUGGUGUCCAUGGUGUCCAUGAUGCUCAUGGUUUUCCUGGGGAUCCUUACGC
((((.....))))..(((..(((.((((.((((((.((.((((((((((.(((...))))))))).))))..)))))))).)))).)))..)))....... ( -36.20)
>DroSim_CAF1 37203 101 - 1
GUCCGUGGUGGCCAUGGUAACCAUGAAAUCCAUGAUGUCCAUGAUGCCAAUGGUGUCCGUGGUGUCCAUGAUGCUCAUGGUUUUCCUGGGGAUCCUUACGC
..((((((...))))))...(((.((((.((((((.((.((((((((((.(((...))))))))).))))..)))))))).)))).)))............ ( -34.10)
>DroYak_CAF1 37296 92 - 1
GCCAGG---------GGUGUCCAUGAUGUCCAUGGUGUCCAUGAUGCCAAGGGUGUUCGUGAUGUCCAUGGUGUCCGUGGUCUUCAUGGUGUUCCUUACGG
...(((---------..((.((((((.(.((((((........((((((.(((..((...))..))).)))))))))))).).))))))))..)))..... ( -33.60)
>consensus
GUCCAUGGUGGCCAUGGUAACCAUGAAAUCCAUGAUGUCCAUGAUGCCAAUGGUGUCCGUGGUGUCCAUGAUGCUCAUGGUUUUCCUGGGGAUCCUUACGC
..((((((...))))))...(((.((((.((((((....((((((((((.((.....)))))))).))))....)))))).)))).)))............ (-25.29 = -26.10 +   0.81)

alignment

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secondary structure

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Window 5

Location 9,202,785 – 9,202,905
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.81
Mean single sequence MFE -35.73
Consensus MFE -28.69
Energy contribution -29.50
Covariance contribution 0.81
Combinations/Pair 1.23
Mean z-score -2.48
Structure conservation index 0.80
SVM decision value 2.08
SVM RNA-class probability 0.987395
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9202785 120 + 27905053
CCAUGAACAUUGUGGACACCACGGCCAUCAUUGGCAUCAUGGGCAUCAUGGAUUUCAUGGACACCAUGGUCACCAUGGACAUCAUGAACAUCAUGGUCAUCAUGGACACUAUUGGCACCA
((((((....(((((...)))))((((....)))).))))))((..(((((..(((((((...((((((...))))))...)))))))..)))))(((......))).......)).... ( -41.30)
>DroSec_CAF1 38404 120 + 1
CCAUGAGCAUCAUGGACACCAUGGACACCAUUGGCAUCAUGGACAUCAUGGAUUUCAUGGUUACCAUGGCCACCAUAGCCAUCAUGGACAUCAUGGUCACCAUGGACACUAUUGGCACCA
((((((...((((((...((((((...))).)))..))))))...))))))..((((((((.(((((((...((((.......))))...))))))).)))))))).............. ( -40.10)
>DroSim_CAF1 37224 120 + 1
CCAUGAGCAUCAUGGACACCACGGACACCAUUGGCAUCAUGGACAUCAUGGAUUUCAUGGUUACCAUGGCCACCACGGACAUCAUGAACAUCAUGGUCAUCAUGGACACUAUUGGCACCA
(((((.....))))).......((...(((.(((..((((((..(((((((..((((((((..((.(((...))).))..))))))))..)))))))..))))))...))).)))..)). ( -35.70)
>DroYak_CAF1 37317 111 + 1
CCACGGACACCAUGGACAUCACGAACACCCUUGGCAUCAUGGACACCAUGGACAUCAUGGACACC---------CCUGGCAUCAUGGACACCAUGGACAUCAUGGCUACUCUGCGCACCA
.(.((((..((((((......(((......)))...((((((...((((((...(((.((....)---------).)))..))))))...))))))...))))))....)))).)..... ( -25.80)
>consensus
CCAUGAACAUCAUGGACACCACGGACACCAUUGGCAUCAUGGACAUCAUGGAUUUCAUGGACACCAUGGCCACCACGGACAUCAUGAACAUCAUGGUCAUCAUGGACACUAUUGGCACCA
((((((...)))))).......((...(((.(((..((((((..(((((((..(((((((...((((((...))))))...)))))))..)))))))..))))))...))).)))..)). (-28.69 = -29.50 +   0.81)

alignment

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secondary structure

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Window 6

Location 9,202,785 – 9,202,905
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.81
Mean single sequence MFE -40.93
Consensus MFE -27.12
Energy contribution -28.88
Covariance contribution 1.75
Combinations/Pair 1.27
Mean z-score -1.64
Structure conservation index 0.66
SVM decision value 0.07
SVM RNA-class probability 0.566284
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9202785 120 - 27905053
UGGUGCCAAUAGUGUCCAUGAUGACCAUGAUGUUCAUGAUGUCCAUGGUGACCAUGGUGUCCAUGAAAUCCAUGAUGCCCAUGAUGCCAAUGAUGGCCGUGGUGUCCACAAUGUUCAUGG
.((..(((...((..(((((..(((((((.....))))..))))))))..))..)))..))((((((......((((((.(((..((((....))))))))))))).......)))))). ( -36.72)
>DroSec_CAF1 38404 120 - 1
UGGUGCCAAUAGUGUCCAUGGUGACCAUGAUGUCCAUGAUGGCUAUGGUGGCCAUGGUAACCAUGAAAUCCAUGAUGUCCAUGAUGCCAAUGGUGUCCAUGGUGUCCAUGAUGCUCAUGG
.....(((..((((((.((((..(((((((((..(((.((((.((((((.((....)).))))))....)))).)))..)))((((((...))))))))))))..))))))))))..))) ( -44.60)
>DroSim_CAF1 37224 120 - 1
UGGUGCCAAUAGUGUCCAUGAUGACCAUGAUGUUCAUGAUGUCCGUGGUGGCCAUGGUAACCAUGAAAUCCAUGAUGUCCAUGAUGCCAAUGGUGUCCGUGGUGUCCAUGAUGCUCAUGG
...............((((((.(((((((.....))))..)))(((((..(((((((..(((((...(((.(((.....))))))....)))))..)))))))..)))))....)))))) ( -39.00)
>DroYak_CAF1 37317 111 - 1
UGGUGCGCAGAGUAGCCAUGAUGUCCAUGGUGUCCAUGAUGCCAGG---------GGUGUCCAUGAUGUCCAUGGUGUCCAUGAUGCCAAGGGUGUUCGUGAUGUCCAUGGUGUCCGUGG
...(((.....)))((((((.....))))))..(((((((((((.(---------((..((.(((((..((.(((((((...))))))).))..).))))))..))).)))))).))))) ( -43.40)
>consensus
UGGUGCCAAUAGUGUCCAUGAUGACCAUGAUGUCCAUGAUGUCCAUGGUGGCCAUGGUAACCAUGAAAUCCAUGAUGUCCAUGAUGCCAAUGGUGUCCGUGGUGUCCAUGAUGCUCAUGG
((((((.....))).)))......((((((...(((((....((((((..(((((((((((.(((..(((...)))...))))))))).)))))..))))))....)))))...)))))) (-27.12 = -28.88 +   1.75)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,202,825 – 9,202,945
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.86
Mean single sequence MFE -32.80
Consensus MFE -27.10
Energy contribution -28.23
Covariance contribution 1.12
Combinations/Pair 1.12
Mean z-score -2.27
Structure conservation index 0.83
SVM decision value 1.51
SVM RNA-class probability 0.960229
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9202825 120 + 27905053
GGGCAUCAUGGAUUUCAUGGACACCAUGGUCACCAUGGACAUCAUGAACAUCAUGGUCAUCAUGGACACUAUUGGCACCAUUUCGGACAUCGCUGGAAUCACCCAGCAUACCAACACCAU
((....(((((..(((((((...((((((...))))))...)))))))..)))))(((...((((...(....)...))))....)))...(((((......)))))...))........ ( -35.50)
>DroSec_CAF1 38444 120 + 1
GGACAUCAUGGAUUUCAUGGUUACCAUGGCCACCAUAGCCAUCAUGGACAUCAUGGUCACCAUGGACACUAUUGGCACCAUUUCGGACAUCGCUGGAAUCACCCAGCAUACCAACACCAU
.......((((..((((((((.(((((((...((((.......))))...))))))).)))))))).....((((..((.....)).....(((((......)))))...))))..)))) ( -38.60)
>DroSim_CAF1 37264 120 + 1
GGACAUCAUGGAUUUCAUGGUUACCAUGGCCACCACGGACAUCAUGAACAUCAUGGUCAUCAUGGACACUAUUGGCACCAUUUCGGACAUCGCUGGAAUCACCCAGCAUACCAACACCAU
((....(((((..((((((((..((.(((...))).))..))))))))..)))))(((...((((...(....)...))))....)))...(((((......)))))...))........ ( -32.40)
>DroYak_CAF1 37357 111 + 1
GGACACCAUGGACAUCAUGGACACC---------CCUGGCAUCAUGGACACCAUGGACAUCAUGGCUACUCUGCGCACCAUUUCGGUCAUCGUUGGAAUCACCCCGCAUACCAACAUCCU
(((..(((((.....))))).....---------..((((...((((....((((.....))))((......))...))))....))))..(((((.((........)).))))).))). ( -24.70)
>consensus
GGACAUCAUGGAUUUCAUGGACACCAUGGCCACCACGGACAUCAUGAACAUCAUGGUCAUCAUGGACACUAUUGGCACCAUUUCGGACAUCGCUGGAAUCACCCAGCAUACCAACACCAU
((....(((((..(((((((...((((((...))))))...)))))))..)))))(((...((((...(....)...))))....)))...(((((......)))))...))........ (-27.10 = -28.23 +   1.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,202,865 – 9,202,982
Length 117
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 91.45
Mean single sequence MFE -29.71
Consensus MFE -22.70
Energy contribution -22.70
Covariance contribution -0.00
Combinations/Pair 1.16
Mean z-score -3.24
Structure conservation index 0.76
SVM decision value 1.10
SVM RNA-class probability 0.915696
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9202865 117 + 27905053
AUCAUGAACAUCAUGGUCAUCAUGGACACUAUUGGCACCAUUUCGGACAUCGCUGGAAUCACCCAGCAUACCAACACCAUCAUGGUGCCCCUCCAUUUUGCUCCCAUCAUCACCGCA
((((((.....))))))((..(((((.......((((((((...((.....(((((......))))).........))...))))))))..)))))..))................. ( -28.74)
>DroSec_CAF1 38484 117 + 1
AUCAUGGACAUCAUGGUCACCAUGGACACUAUUGGCACCAUUUCGGACAUCGCUGGAAUCACCCAGCAUACCAACACCAUCAUGGUGCUCCUCCAUUUUGCUCCCAUCAUCAUCGCA
.....(((((..((((.((((((((......((((..((.....)).....(((((......)))))...)))).....)))))))).....))))..)).)))............. ( -30.80)
>DroSim_CAF1 37304 117 + 1
AUCAUGAACAUCAUGGUCAUCAUGGACACUAUUGGCACCAUUUCGGACAUCGCUGGAAUCACCCAGCAUACCAACACCAUCAUGGUGCUCCUCCAUUUGGCUGCCAUCAUCAUCGCA
..((((.....))))(((......))).....((((((((..(.(((....(((((......))))).......((((.....))))....))))..))).)))))........... ( -33.10)
>DroYak_CAF1 37388 117 + 1
AUCAUGGACACCAUGGACAUCAUGGCUACUCUGCGCACCAUUUCGGUCAUCGUUGGAAUCACCCCGCAUACCAACAUCCUCAUGGUGCCCCUCCAUUUUGCUCCCAUCAUCACCGAA
.....(((((..(((((.......((......))(((((((...((.....(((((.((........)).)))))..))..)))))))...)))))..)).)))............. ( -26.20)
>consensus
AUCAUGAACAUCAUGGUCAUCAUGGACACUAUUGGCACCAUUUCGGACAUCGCUGGAAUCACCCAGCAUACCAACACCAUCAUGGUGCCCCUCCAUUUUGCUCCCAUCAUCACCGCA
.((((((...)))))).....(((((.......((((((((....(....)(((((......)))))..............))))))))..)))))..................... (-22.70 = -22.70 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,202,865 – 9,202,982
Length 117
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 91.45
Mean single sequence MFE -38.98
Consensus MFE -31.39
Energy contribution -32.20
Covariance contribution 0.81
Combinations/Pair 1.08
Mean z-score -2.11
Structure conservation index 0.81
SVM decision value 0.86
SVM RNA-class probability 0.868118
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9202865 117 - 27905053
UGCGGUGAUGAUGGGAGCAAAAUGGAGGGGCACCAUGAUGGUGUUGGUAUGCUGGGUGAUUCCAGCGAUGUCCGAAAUGGUGCCAAUAGUGUCCAUGAUGACCAUGAUGUUCAUGAU
...(((.((.((((..(((...((....((((((((.......(((((((((((((....)))))).))).)))).))))))))..)).))))))).)).)))(((.....)))... ( -41.00)
>DroSec_CAF1 38484 117 - 1
UGCGAUGAUGAUGGGAGCAAAAUGGAGGAGCACCAUGAUGGUGUUGGUAUGCUGGGUGAUUCCAGCGAUGUCCGAAAUGGUGCCAAUAGUGUCCAUGGUGACCAUGAUGUCCAUGAU
.......((.((((..(((..((((.....((((((((((.(((((((((((((((....)))))))....((.....)))))))))).))).))))))).))))..))))))).)) ( -41.40)
>DroSim_CAF1 37304 117 - 1
UGCGAUGAUGAUGGCAGCCAAAUGGAGGAGCACCAUGAUGGUGUUGGUAUGCUGGGUGAUUCCAGCGAUGUCCGAAAUGGUGCCAAUAGUGUCCAUGAUGACCAUGAUGUUCAUGAU
((.(((..((.(((((.(((..((((.(((((((.....))))))....(((((((....))))))).).))))...)))))))).))..))))).......((((.....)))).. ( -38.10)
>DroYak_CAF1 37388 117 - 1
UUCGGUGAUGAUGGGAGCAAAAUGGAGGGGCACCAUGAGGAUGUUGGUAUGCGGGGUGAUUCCAACGAUGACCGAAAUGGUGCGCAGAGUAGCCAUGAUGUCCAUGGUGUCCAUGAU
(((.((..((.......))..)).)))(((((((((..((((((((((.((..(((....)))..))...)))...(((((((.....))).))))))))))))))))))))..... ( -35.40)
>consensus
UGCGAUGAUGAUGGGAGCAAAAUGGAGGAGCACCAUGAUGGUGUUGGUAUGCUGGGUGAUUCCAGCGAUGUCCGAAAUGGUGCCAAUAGUGUCCAUGAUGACCAUGAUGUCCAUGAU
...((..((.((((...((..(((((.(.(((((((.......(((((((((((((....)))))).))).)))).)))))))......).)))))..)).)))).))..))..... (-31.39 = -32.20 +   0.81)

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 11:00:04 2006