Locus 6802

Sequence ID X_DroMel_CAF1
Location 16,930,802 – 16,931,002
Length 200
Max. P 0.854918
window11139 window11140 window11141 window11142 window11143

overview

Window 9

Location 16,930,802 – 16,930,922
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.28
Mean single sequence MFE -42.52
Consensus MFE -31.82
Energy contribution -31.47
Covariance contribution -0.36
Combinations/Pair 1.25
Mean z-score -1.33
Structure conservation index 0.75
SVM decision value 0.01
SVM RNA-class probability 0.537109
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16930802 120 + 22224390
CAUAACGUUGUACUAUGCCCUCAAGGACGGACUGCCGGAGGUUGAGGAACGCGCCCUCUGGACGAAUGGCUCCCAGCUGGCUCUCUUCUUCGGCACCGCCAUCUUUGCCUUCGAAGGCAU
..............(((((.((((((..(((.((.(((..(((((((((.(.(((..((((...........))))..))).)..))))))))).))).)))))...)))).)).))))) ( -39.70)
>DroPse_CAF1 13700 120 + 1
CAUCACCCUCUACUAUGCUCUGAAGGAUGGACUGCCGGAGGUUAAGGAGCGCGCCUAUUGGACAAGCGGCUCCCAGUUGGCUCUCUUCUUUGGCACCGCCAUCUUUGCCUUUGAGGGCAU
.....(((((......((....((((((((..((((((((((((((((((((.((....))....)).)))))...))))).)))).....))))...))))))))))....)))))... ( -42.50)
>DroGri_CAF1 962 120 + 1
GAUAACAUUAUAUUAUGCACUGAAGGAUGGCUUGCCGGAGGUGAAGGAACGCGCCCUUUGGACGAAUGGUAGCCAGUUGGCGCUCUUCUUUGGCACCGCCAUCUUUGCCUUCGAAGGCAU
......................(((((((((.((((((((((......))(((((..((((.(........)))))..)))))....))))))))..)))))))))((((....)))).. ( -44.70)
>DroWil_CAF1 520 120 + 1
CAUCACCUUGUACUAUGCCCUCAAAGAUGGACUGCCAGAGAUCGGGGAACGCGCCUACUGGACAAAUGGAUCGCAGUUGGCACUCUUCUUUGGCACCGCCAUAUUUGCCUUCGAGGGCAU
..............((((((((.(((((((..(((((((((..((((.....(((.((((((........)).)))).))).)))))))))))))...))))......))).)))))))) ( -42.60)
>DroMoj_CAF1 591 120 + 1
CAUCACCCUCUACUACGCCCUCAAGGACGGCCUGCCGGAGGUGACGGAACGCGCCUACUGGACGAACGGCUCCCAGCUGGCGCUCUUCUUCGGCACCGCCAUCUUUGCCUUCGAGGGCAU
................((((((((((..(((.((((((((((......))(((((..((((...........))))..)))))....))))))))..))).......)))).)))))).. ( -49.60)
>DroAna_CAF1 581 120 + 1
CAUAACCCUGUACUAUGCUUUGAAGGAUGGCCUGCCGGAUGUACCGGAUCGUGCUCUCUGGACCAAUGGCUCCCAGCUGGCCCUCUUCUUUGGCACGGCGAUCUUUGCUUAUGAGGGCAU
.....(((((((....((....((((((.(((..((((.....))))...(((((....((.(((.(((...)))..))).))........)))))))).)))))))).))).))))... ( -36.00)
>consensus
CAUAACCCUGUACUAUGCCCUCAAGGAUGGACUGCCGGAGGUGAAGGAACGCGCCCACUGGACGAAUGGCUCCCAGCUGGCGCUCUUCUUUGGCACCGCCAUCUUUGCCUUCGAGGGCAU
......................((((((((..(((((((((....(((..(.(((..((((...........))))..))).)))))))))))))...))))))))((((....)))).. (-31.82 = -31.47 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,930,842 – 16,930,962
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.22
Mean single sequence MFE -44.92
Consensus MFE -32.91
Energy contribution -33.05
Covariance contribution 0.14
Combinations/Pair 1.23
Mean z-score -1.61
Structure conservation index 0.73
SVM decision value 0.25
SVM RNA-class probability 0.651683
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16930842 120 + 22224390
GUUGAGGAACGCGCCCUCUGGACGAAUGGCUCCCAGCUGGCUCUCUUCUUCGGCACCGCCAUCUUUGCCUUCGAAGGCAUUGCCUUAGUGAUGCCGUUGAAGAACGCCAUGCGAAAGCCA
(((((((.......))))..)))...(((((....((((((..(((((..(((((.(((...(..(((((....)))))..).....))).)))))..)))))..)))).))...))))) ( -45.70)
>DroPse_CAF1 13740 120 + 1
GUUAAGGAGCGCGCCUAUUGGACAAGCGGCUCCCAGUUGGCUCUCUUCUUUGGCACCGCCAUCUUUGCCUUUGAGGGCAUUGCACUGGUGAUGCCACUAAAGAAUGCGAUGCGAAAGCCA
.....(((((((.((....))....)).)))))......((..((((...(((((.(((((.(..(((((....)))))..)...))))).)))))...))))..))...((....)).. ( -44.20)
>DroGri_CAF1 1002 120 + 1
GUGAAGGAACGCGCCCUUUGGACGAAUGGUAGCCAGUUGGCGCUCUUCUUUGGCACCGCCAUCUUUGCCUUCGAAGGCAUUGCACUGGUGAUGCCCCUGAAGAAUGCCAUGCGCAAGUCG
(((..((...(((((..((((.(........)))))..)))))(((((...((((.(((((.(..(((((....)))))..)...))))).))))...)))))...))...)))...... ( -45.60)
>DroWil_CAF1 560 120 + 1
AUCGGGGAACGCGCCUACUGGACAAAUGGAUCGCAGUUGGCACUCUUCUUUGGCACCGCCAUAUUUGCCUUCGAGGGCAUUGCUCUGGUGAUGCCAUUGAAGAAUGCCAUGAGAAAACCC
...(((....(((((............))..)))...(((((.(((((..(((((.(((((....(((((....)))))......))))).)))))..))))).)))))........))) ( -45.70)
>DroMoj_CAF1 631 120 + 1
GUGACGGAACGCGCCUACUGGACGAACGGCUCCCAGCUGGCGCUCUUCUUCGGCACCGCCAUCUUUGCCUUCGAGGGCAUUGCCCUGGUGAUGCCCCUGAAGAAUGCCAUGCGCAAGCCG
..((.(((..(((((..((((...........))))..)))))..))).))((((..((.......))(((((.((((((..(....)..)))))).)))))..))))..((....)).. ( -49.70)
>DroAna_CAF1 621 120 + 1
GUACCGGAUCGUGCUCUCUGGACCAAUGGCUCCCAGCUGGCCCUCUUCUUUGGCACGGCGAUCUUUGCUUAUGAGGGCAUUGCCCUUGUGAUGCCCCUGAAGAACUCCAUGGCCAAGACC
((((......))))(((.(((.(((.(((......(((((((.........))).))))..((((((((((..(((((...)))))..))).))....)))))...)))))))))))).. ( -38.60)
>consensus
GUGAAGGAACGCGCCCACUGGACGAAUGGCUCCCAGCUGGCGCUCUUCUUUGGCACCGCCAUCUUUGCCUUCGAGGGCAUUGCCCUGGUGAUGCCCCUGAAGAAUGCCAUGCGAAAGCCA
.....((..((((((..((((...........))))..)))..(((((...((((.(((((....(((((....)))))......))))).))))...))))).......)))....)). (-32.91 = -33.05 +   0.14)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,930,842 – 16,930,962
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.22
Mean single sequence MFE -49.27
Consensus MFE -33.00
Energy contribution -34.92
Covariance contribution 1.92
Combinations/Pair 1.09
Mean z-score -2.69
Structure conservation index 0.67
SVM decision value 0.80
SVM RNA-class probability 0.854918
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16930842 120 - 22224390
UGGCUUUCGCAUGGCGUUCUUCAACGGCAUCACUAAGGCAAUGCCUUCGAAGGCAAAGAUGGCGGUGCCGAAGAAGAGAGCCAGCUGGGAGCCAUUCGUCCAGAGGGCGCGUUCCUCAAC
(((((..(((.((((.((((((..(((((((.(((...(..(((((....)))))..).))).)))))))..)))))).)))))).)..)))))........(((((.....)))))... ( -55.10)
>DroPse_CAF1 13740 120 - 1
UGGCUUUCGCAUCGCAUUCUUUAGUGGCAUCACCAGUGCAAUGCCCUCAAAGGCAAAGAUGGCGGUGCCAAAGAAGAGAGCCAACUGGGAGCCGCUUGUCCAAUAGGCGCGCUCCUUAAC
((((((((((...)).(((((...(((((((.(((...(..((((......))))..).))).))))))))))))))))))))...(((((((((((((...))))))).)))))).... ( -53.30)
>DroGri_CAF1 1002 120 - 1
CGACUUGCGCAUGGCAUUCUUCAGGGGCAUCACCAGUGCAAUGCCUUCGAAGGCAAAGAUGGCGGUGCCAAAGAAGAGCGCCAACUGGCUACCAUUCGUCCAAAGGGCGCGUUCCUUCAC
.((...((((.((((.((((((...((((((.(((...(..(((((....)))))..).))).))))))...)))))).))))..............((((...))))))))....)).. ( -46.00)
>DroWil_CAF1 560 120 - 1
GGGUUUUCUCAUGGCAUUCUUCAAUGGCAUCACCAGAGCAAUGCCCUCGAAGGCAAAUAUGGCGGUGCCAAAGAAGAGUGCCAACUGCGAUCCAUUUGUCCAGUAGGCGCGUUCCCCGAU
(((........(((((((((((..(((((((.(((......((((......))))....))).)))))))..)))))))))))((((.(((......)))))))..........)))... ( -48.90)
>DroMoj_CAF1 631 120 - 1
CGGCUUGCGCAUGGCAUUCUUCAGGGGCAUCACCAGGGCAAUGCCCUCGAAGGCAAAGAUGGCGGUGCCGAAGAAGAGCGCCAGCUGGGAGCCGUUCGUCCAGUAGGCGCGUUCCGUCAC
(((..(((((.((((.((((((...((((((.(((...(..((((......))))..).))).))))))...)))))).))))(((((..(.....)..)))))..)))))..))).... ( -53.30)
>DroAna_CAF1 621 120 - 1
GGUCUUGGCCAUGGAGUUCUUCAGGGGCAUCACAAGGGCAAUGCCCUCAUAAGCAAAGAUCGCCGUGCCAAAGAAGAGGGCCAGCUGGGAGCCAUUGGUCCAGAGAGCACGAUCCGGUAC
(((....))).((((..(((((...(((((....(((((...))))).....((.......)).)))))...)))))(((((((.(((...))))))))))...........)))).... ( -39.00)
>consensus
CGGCUUGCGCAUGGCAUUCUUCAGGGGCAUCACCAGGGCAAUGCCCUCGAAGGCAAAGAUGGCGGUGCCAAAGAAGAGAGCCAACUGGGAGCCAUUCGUCCAGAAGGCGCGUUCCUUAAC
.(((((.(...((((.((((((...((((((.(((......((((......))))....))).))))))...)))))).))))...).)))))...((((.....))))........... (-33.00 = -34.92 +   1.92)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,930,882 – 16,931,002
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.89
Mean single sequence MFE -45.50
Consensus MFE -29.68
Energy contribution -31.13
Covariance contribution 1.45
Combinations/Pair 1.22
Mean z-score -2.01
Structure conservation index 0.65
SVM decision value 0.13
SVM RNA-class probability 0.598050
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16930882 120 + 22224390
CUCUCUUCUUCGGCACCGCCAUCUUUGCCUUCGAAGGCAUUGCCUUAGUGAUGCCGUUGAAGAACGCCAUGCGAAAGCCACACCAGUUCGAGCGACCCUUGGGUGUGCUCAAUGUGGGCA
...(((((..(((((.(((...(..(((((....)))))..).....))).)))))..)))))..(((..((....))..(((..(((.((((((((....))).)))))))))))))). ( -46.40)
>DroPse_CAF1 13780 120 + 1
CUCUCUUCUUUGGCACCGCCAUCUUUGCCUUUGAGGGCAUUGCACUGGUGAUGCCACUAAAGAAUGCGAUGCGAAAGCCAAGCCAAUUCGAGAGCCGACUGGGGGUCCUCAAUGUGGGCA
.((((.....(((((.(((((.(..(((((....)))))..)...))))).))))).....((((((...((....))...))..))))))))(((.((((((....))))..)).))). ( -45.90)
>DroGri_CAF1 1042 120 + 1
CGCUCUUCUUUGGCACCGCCAUCUUUGCCUUCGAAGGCAUUGCACUGGUGAUGCCCCUGAAGAAUGCCAUGCGCAAGUCGCAACAAUUUGAGAGUACACUGGGCGUUCUCAAUGUGGGCA
...(((((...((((.(((((.(..(((((....)))))..)...))))).))))...))))).((((.((((.....)))).((..(((((((..(.....)..)))))))..)))))) ( -43.60)
>DroWil_CAF1 600 120 + 1
CACUCUUCUUUGGCACCGCCAUAUUUGCCUUCGAGGGCAUUGCUCUGGUGAUGCCAUUGAAGAAUGCCAUGAGAAAACCCCACCAGUUCGAGAGCACAUUGGGUGUGCUCAAUGUGGGCA
...(((((..(((((.(((((....(((((....)))))......))))).)))))..))))).((((.((((...((((((...((.(....).))..)))).)).)))).....)))) ( -46.40)
>DroMoj_CAF1 671 120 + 1
CGCUCUUCUUCGGCACCGCCAUCUUUGCCUUCGAGGGCAUUGCCCUGGUGAUGCCCCUGAAGAAUGCCAUGCGCAAGCCGCGCCAGUUUGAGAGCACGCUGGGCGUCCUCAAUGUGGGCA
.((((......((((..((.......))(((((.((((((..(....)..)))))).)))))..))))..((....))(((.(((((.((....)).))))))))..........)))). ( -48.70)
>DroAna_CAF1 661 120 + 1
CCCUCUUCUUUGGCACGGCGAUCUUUGCUUAUGAGGGCAUUGCCCUUGUGAUGCCCCUGAAGAACUCCAUGGCCAAGACCGAGCAGUUCGAGAUGACGUUCGGGGUCCUCAACGUGGGCA
........((((((..((.(.((((((((((..(((((...)))))..))).))....))))).).))...)))))).((((((.(((......))))))))).((((.......)))). ( -42.00)
>consensus
CGCUCUUCUUUGGCACCGCCAUCUUUGCCUUCGAGGGCAUUGCCCUGGUGAUGCCCCUGAAGAAUGCCAUGCGAAAGCCACACCAGUUCGAGAGCACACUGGGCGUCCUCAAUGUGGGCA
...(((((...((((.(((((....(((((....)))))......))))).))))...)))))..(((..((....))................((((.((((....)))).))))))). (-29.68 = -31.13 +   1.45)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,930,882 – 16,931,002
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.89
Mean single sequence MFE -43.83
Consensus MFE -29.10
Energy contribution -29.02
Covariance contribution -0.08
Combinations/Pair 1.28
Mean z-score -1.67
Structure conservation index 0.66
SVM decision value -0.05
SVM RNA-class probability 0.509022
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16930882 120 - 22224390
UGCCCACAUUGAGCACACCCAAGGGUCGCUCGAACUGGUGUGGCUUUCGCAUGGCGUUCUUCAACGGCAUCACUAAGGCAAUGCCUUCGAAGGCAAAGAUGGCGGUGCCGAAGAAGAGAG
.((((((.((((((..(((....))).))))))....))).)))...(((...)))((((((..(((((((.(((...(..(((((....)))))..).))).)))))))..)))))).. ( -47.30)
>DroPse_CAF1 13780 120 - 1
UGCCCACAUUGAGGACCCCCAGUCGGCUCUCGAAUUGGCUUGGCUUUCGCAUCGCAUUCUUUAGUGGCAUCACCAGUGCAAUGCCCUCAAAGGCAAAGAUGGCGGUGCCAAAGAAGAGAG
((((((..(((((..((.......))..)))))..)))....((....))...)))((((((..(((((((.(((...(..((((......))))..).))).)))))))..)))))).. ( -40.20)
>DroGri_CAF1 1042 120 - 1
UGCCCACAUUGAGAACGCCCAGUGUACUCUCAAAUUGUUGCGACUUGCGCAUGGCAUUCUUCAGGGGCAUCACCAGUGCAAUGCCUUCGAAGGCAAAGAUGGCGGUGCCAAAGAAGAGCG
((((....((((((((((...))))..)))))).....((((.....)))).))))((((((...((((((.(((...(..(((((....)))))..).))).))))))...)))))).. ( -43.80)
>DroWil_CAF1 600 120 - 1
UGCCCACAUUGAGCACACCCAAUGUGCUCUCGAACUGGUGGGGUUUUCUCAUGGCAUUCUUCAAUGGCAUCACCAGAGCAAUGCCCUCGAAGGCAAAUAUGGCGGUGCCAAAGAAGAGUG
..(((((...(((((((.....)))))))........)))))............((((((((..(((((((.(((......((((......))))....))).)))))))..)))))))) ( -48.20)
>DroMoj_CAF1 671 120 - 1
UGCCCACAUUGAGGACGCCCAGCGUGCUCUCAAACUGGCGCGGCUUGCGCAUGGCAUUCUUCAGGGGCAUCACCAGGGCAAUGCCCUCGAAGGCAAAGAUGGCGGUGCCGAAGAAGAGCG
((((......(((.((((...)))).)))........((((.....))))..))))((((((...((((((.(((...(..((((......))))..).))).))))))...)))))).. ( -45.90)
>DroAna_CAF1 661 120 - 1
UGCCCACGUUGAGGACCCCGAACGUCAUCUCGAACUGCUCGGUCUUGGCCAUGGAGUUCUUCAGGGGCAUCACAAGGGCAAUGCCCUCAUAAGCAAAGAUCGCCGUGCCAAAGAAGAGGG
(((((..((.((.(.((((((........))(((((.(..(((....)))..).)))))....))))).))))..)))))...(((((....(((..(....)..))).......))))) ( -37.60)
>consensus
UGCCCACAUUGAGGACACCCAAUGUGCUCUCGAACUGGUGCGGCUUGCGCAUGGCAUUCUUCAGGGGCAUCACCAGGGCAAUGCCCUCGAAGGCAAAGAUGGCGGUGCCAAAGAAGAGAG
((((....((((((.............))))))......(((.....)))..))))((((((...((((((.(((......((((......))))....))).))))))...)))))).. (-29.10 = -29.02 +  -0.08)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:21 2006