Locus 29

Sequence ID 3R_DroMel_CAF1
Location 258,451 – 258,731
Length 280
Max. P 0.813606
window47 window48 window49 window50 window51

overview

Window 7

Location 258,451 – 258,571
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.50
Mean single sequence MFE -43.13
Consensus MFE -30.51
Energy contribution -30.27
Covariance contribution -0.25
Combinations/Pair 1.30
Mean z-score -2.30
Structure conservation index 0.71
SVM decision value 0.11
SVM RNA-class probability 0.588533
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 258451 120 + 27905053
CGUCAGCUGGAAGAGCUUCAGCAGCGCUGCAGCGUGGAACAACUGGUUGCCGGCCUUGCUAAAGACCAUGGCUAAUUUUUGGUAGUAGUUGGCCAUGGUUUUGGGCACGGGUGUCUUCUU
((.((((..(....(((.((((...)))).)))(.....)..)..)))).))((((((((.((((((((((((((((.........)))))))))))))))).)))).))))........ ( -48.10)
>DroVir_CAF1 1938 120 + 1
CGUCAACUGAAACAGUUUAAGCAAAGCGGCUGCAUGGAAUAGCUGGUUACCAGCCUUGCUAAAUACCAUAGCCAGCUUCUGAUAGUAAUUGGCCAUGGUUUUGGGCACCGGCGUCUUCUU
(((((((((...)))))..........((.(((........(((((...)))))....(((((.(((((.(((((((......)))...)))).)))))))))))))))))))....... ( -34.10)
>DroGri_CAF1 1875 120 + 1
CGUCAACUGGAACAGUUUGAGCAAAGCGGCCGCAUGGAAGAGCUGAUUGCCGGCCUUGCUGAAAACCAUGGCAAGUUUCUGAUAAUAAUUUGCCAUGGUUUUGGGCACCGGCGUCUUCUU
........((((((((((...(...((....))...)..))))))...(((((...((((.((((((((((((((((.........)))))))))))))))).)))))))))...)))). ( -47.90)
>DroWil_CAF1 2455 120 + 1
UGUUAGUUGGAACAACUUGAGCAAAGCAGCUGCAUGGAACAGUUGGUUGCCAGCCUUGCUGAAGACCAUUGCAAGUUUUUGGUAAUAGUUUGCCAUGGUCUUGGGCACGGGCGUCUUCUU
....(((((...)))))((.((((..((((((.......)))))).))))))((((((((.((((((((.((((..(.........)..)))).)))))))).)))).))))........ ( -42.30)
>DroMoj_CAF1 2513 120 + 1
AGUCAACUGGAACAGCUUGAGCAAAGCGGCUGCAUGGAAGAGCUGAUUGCCAGCCUUGCUGAAGACCAUAGCCAAUUUCUGAUAAUAAUUAGCCAUGGUUUUUGGCACCGGCGUCUUCUU
........((((..((((.....))))(((.((.((((((.((((.....)))))))((..((((((((.((.((((.........)))).)).))))))))..)).)))))))))))). ( -37.50)
>DroAna_CAF1 2509 120 + 1
AGUCAGCUGGAAGAGCUUCAGAAGAGCGGCAGCGUGGAACAACUGGUUGCCAGCCUUGCUGAAGACCAUCGCCAGUUUCUGAUAGUAAUUGGCCAUGGUUUUGGGCACCGGCGUCUUCUU
........((((((((((.....))))((((((..(......)..)))))).(((.((((.((((((((.(((((((.(.....).))))))).)))))))).))))..))).)))))). ( -48.90)
>consensus
CGUCAACUGGAACAGCUUGAGCAAAGCGGCUGCAUGGAACAGCUGGUUGCCAGCCUUGCUGAAGACCAUAGCCAGUUUCUGAUAAUAAUUGGCCAUGGUUUUGGGCACCGGCGUCUUCUU
.......(((..(((((....(...((....))...)...)))))....)))(((.((((.((((((((.(((((((.........))))))).)))))))).))))..)))........ (-30.51 = -30.27 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 258,451 – 258,571
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.50
Mean single sequence MFE -35.17
Consensus MFE -26.77
Energy contribution -26.56
Covariance contribution -0.21
Combinations/Pair 1.33
Mean z-score -1.68
Structure conservation index 0.76
SVM decision value -0.04
SVM RNA-class probability 0.514144
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 258451 120 - 27905053
AAGAAGACACCCGUGCCCAAAACCAUGGCCAACUACUACCAAAAAUUAGCCAUGGUCUUUAGCAAGGCCGGCAACCAGUUGUUCCACGCUGCAGCGCUGCUGAAGCUCUUCCAGCUGACG
..((((((..((.(((..((.((((((((...................)))))))).))..))).)).(((((....(((((........)))))..)))))..).)))))......... ( -32.21)
>DroVir_CAF1 1938 120 - 1
AAGAAGACGCCGGUGCCCAAAACCAUGGCCAAUUACUAUCAGAAGCUGGCUAUGGUAUUUAGCAAGGCUGGUAACCAGCUAUUCCAUGCAGCCGCUUUGCUUAAACUGUUUCAGUUGACG
(((.(((.((.(.(((.....((((((((((.((.(.....).)).)))))))))).........((((((...)))))).......))).).))))).))).(((((...))))).... ( -32.90)
>DroGri_CAF1 1875 120 - 1
AAGAAGACGCCGGUGCCCAAAACCAUGGCAAAUUAUUAUCAGAAACUUGCCAUGGUUUUCAGCAAGGCCGGCAAUCAGCUCUUCCAUGCGGCCGCUUUGCUCAAACUGUUCCAGUUGACG
..((((..(((..(((..(((((((((((((...............)))))))))))))..))).)))((((.....((........)).))))))))..((((.(((...))))))).. ( -38.66)
>DroWil_CAF1 2455 120 - 1
AAGAAGACGCCCGUGCCCAAGACCAUGGCAAACUAUUACCAAAAACUUGCAAUGGUCUUCAGCAAGGCUGGCAACCAACUGUUCCAUGCAGCUGCUUUGCUCAAGUUGUUCCAACUAACA
........(((..(((..((((((((.((((...............)))).))))))))..))).)))((((((.((.((((.....)))).))..)))).))(((((...))))).... ( -32.76)
>DroMoj_CAF1 2513 120 - 1
AAGAAGACGCCGGUGCCAAAAACCAUGGCUAAUUAUUAUCAGAAAUUGGCUAUGGUCUUCAGCAAGGCUGGCAAUCAGCUCUUCCAUGCAGCCGCUUUGCUCAAGCUGUUCCAGUUGACU
..((((((...(((.......)))((((((((((.........)))))))))).))))))((((((((.(((.....((........)).)))))))))))..(((((...))))).... ( -37.90)
>DroAna_CAF1 2509 120 - 1
AAGAAGACGCCGGUGCCCAAAACCAUGGCCAAUUACUAUCAGAAACUGGCGAUGGUCUUCAGCAAGGCUGGCAACCAGUUGUUCCACGCUGCCGCUCUUCUGAAGCUCUUCCAGCUGACU
.((((((.((.(((((..((.(((((.((((.((.(.....).)).)))).))))).))..))..((((((.(((.....)))))).))))))))))))))..((((.....)))).... ( -36.60)
>consensus
AAGAAGACGCCGGUGCCCAAAACCAUGGCCAAUUACUAUCAGAAACUGGCCAUGGUCUUCAGCAAGGCUGGCAACCAGCUGUUCCAUGCAGCCGCUUUGCUCAAGCUGUUCCAGCUGACG
..((((((((....)).......((((((((...............))))))))))))))((((((((.(((.....((........)).)))))))))))..((((.....)))).... (-26.77 = -26.56 +  -0.21)

alignment

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secondary structure

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dotplot

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Window 9

Location 258,491 – 258,611
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 85.17
Mean single sequence MFE -44.48
Consensus MFE -32.04
Energy contribution -30.80
Covariance contribution -1.24
Combinations/Pair 1.36
Mean z-score -2.90
Structure conservation index 0.72
SVM decision value 0.37
SVM RNA-class probability 0.708953
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 258491 120 + 27905053
AACUGGUUGCCGGCCUUGCUAAAGACCAUGGCUAAUUUUUGGUAGUAGUUGGCCAUGGUUUUGGGCACGGGUGUCUUCUUGGACAGAGCCAUCAGGCCAUGGAUAUCCUCGAUUGCCUUG
...(((((.(((((((.....((((((((((((((((.........)))))))))))))))))))).))).(((((....))))).)))))..((((.((.((.....)).)).)))).. ( -47.20)
>DroVir_CAF1 1978 120 + 1
AGCUGGUUACCAGCCUUGCUAAAUACCAUAGCCAGCUUCUGAUAGUAAUUGGCCAUGGUUUUGGGCACCGGCGUCUUCUUGGACAUGGCCAUCAGGCCGUGAAUGUCCUCAAUUGCCUUG
.(((((...)))))..((((....(((((.(((((((......)))...)))).)))))....))))..((((.......((((((((((....))))....)))))).....))))... ( -43.80)
>DroGri_CAF1 1915 120 + 1
AGCUGAUUGCCGGCCUUGCUGAAAACCAUGGCAAGUUUCUGAUAAUAAUUUGCCAUGGUUUUGGGCACCGGCGUCUUCUUGGACAUGGCCAUUAGGCCGUGAAUGUCCUCAAUGGCCUUG
........(((((...((((.((((((((((((((((.........)))))))))))))))).)))))))))((((....))))..((((((((((.((....)).))).)))))))... ( -56.70)
>DroWil_CAF1 2495 120 + 1
AGUUGGUUGCCAGCCUUGCUGAAGACCAUUGCAAGUUUUUGGUAAUAGUUUGCCAUGGUCUUGGGCACGGGCGUCUUCUUGGAGAGAGCCAUCAGACCGUGAAUAUCCUCGAUGGCCUUG
........((((((((((((.((((((((.((((..(.........)..)))).)))))))).)))).))))((((...(((......)))..))))...............)))).... ( -41.10)
>DroYak_CAF1 2542 120 + 1
AACUGGUUGCCAGCCUUGCUAAAGACCAUGGCUAAUUUUUGGUAAUAGUUGGCCAUUGUUUUGGGUACGGGUGUCUUUUUGGAUAAAGCCAUCAAGCCGUGGAUAUCCUCGAUUGCCCUG
..((((...))))...((((.(((((.((((((((((.........)))))))))).))))).))))((((.((..((..(((((...((((......)))).)))))..))..)))))) ( -36.30)
>DroMoj_CAF1 2553 120 + 1
AGCUGAUUGCCAGCCUUGCUGAAGACCAUAGCCAAUUUCUGAUAAUAAUUAGCCAUGGUUUUUGGCACCGGCGUCUUCUUGGACAUGGCCAUCAGACCGUGAAUGUCCUCGAUUGCCUUG
..(((((.(((((((.(((..((((((((.((.((((.........)))).)).))))))))..)))..)))((((....)))).)))).)))))...(..(.((....)).)..).... ( -41.80)
>consensus
AGCUGGUUGCCAGCCUUGCUAAAGACCAUGGCAAAUUUCUGAUAAUAAUUGGCCAUGGUUUUGGGCACCGGCGUCUUCUUGGACAUAGCCAUCAGGCCGUGAAUAUCCUCGAUUGCCUUG
.((((.....))))..((((.((((((((.(((((((.........))))))).)))))))).))))..(((((((...(((......)))..))))..(((......)))...)))... (-32.04 = -30.80 +  -1.24)

alignment

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secondary structure

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dotplot

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Window 0

Location 258,491 – 258,611
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 85.17
Mean single sequence MFE -38.01
Consensus MFE -29.08
Energy contribution -28.98
Covariance contribution -0.11
Combinations/Pair 1.31
Mean z-score -2.55
Structure conservation index 0.77
SVM decision value 0.48
SVM RNA-class probability 0.753088
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 258491 120 - 27905053
CAAGGCAAUCGAGGAUAUCCAUGGCCUGAUGGCUCUGUCCAAGAAGACACCCGUGCCCAAAACCAUGGCCAACUACUACCAAAAAUUAGCCAUGGUCUUUAGCAAGGCCGGCAACCAGUU
....((......((....)).((((((.((((...((((......)))).))))((..((.((((((((...................)))))))).))..)).))))))))........ ( -33.21)
>DroVir_CAF1 1978 120 - 1
CAAGGCAAUUGAGGACAUUCACGGCCUGAUGGCCAUGUCCAAGAAGACGCCGGUGCCCAAAACCAUGGCCAAUUACUAUCAGAAGCUGGCUAUGGUAUUUAGCAAGGCUGGUAACCAGCU
...(((......((((((....((((....))))))))))..(....))))..(((..((.((((((((((.((.(.....).)).)))))))))).))..))).((((((...)))))) ( -43.60)
>DroGri_CAF1 1915 120 - 1
CAAGGCCAUUGAGGACAUUCACGGCCUAAUGGCCAUGUCCAAGAAGACGCCGGUGCCCAAAACCAUGGCAAAUUAUUAUCAGAAACUUGCCAUGGUUUUCAGCAAGGCCGGCAAUCAGCU
...(((...(((((((((....((((....))))))))))........((((((((..(((((((((((((...............)))))))))))))..))...))))))..)))))) ( -48.86)
>DroWil_CAF1 2495 120 - 1
CAAGGCCAUCGAGGAUAUUCACGGUCUGAUGGCUCUCUCCAAGAAGACGCCCGUGCCCAAGACCAUGGCAAACUAUUACCAAAAACUUGCAAUGGUCUUCAGCAAGGCUGGCAACCAACU
....((((...............((((..(((......)))...))))(((..(((..((((((((.((((...............)))).))))))))..))).)))))))........ ( -34.76)
>DroYak_CAF1 2542 120 - 1
CAGGGCAAUCGAGGAUAUCCACGGCUUGAUGGCUUUAUCCAAAAAGACACCCGUACCCAAAACAAUGGCCAACUAUUACCAAAAAUUAGCCAUGGUCUUUAGCAAGGCUGGCAACCAGUU
....((......(((((.....((((....)))).)))))..((((((....((.......)).(((((...................))))).)))))).))..((((((...)))))) ( -24.21)
>DroMoj_CAF1 2553 120 - 1
CAAGGCAAUCGAGGACAUUCACGGUCUGAUGGCCAUGUCCAAGAAGACGCCGGUGCCAAAAACCAUGGCUAAUUAUUAUCAGAAAUUGGCUAUGGUCUUCAGCAAGGCUGGCAAUCAGCU
...(((..((..((((((....((((....))))))))))..))....((((((((..((.(((((((((((((.........))))))))))))).))..))...)))))).....))) ( -43.40)
>consensus
CAAGGCAAUCGAGGACAUUCACGGCCUGAUGGCCAUGUCCAAGAAGACGCCCGUGCCCAAAACCAUGGCCAACUAUUACCAAAAACUAGCCAUGGUCUUCAGCAAGGCUGGCAACCAGCU
....((......(((((.....((((....)))).)))))........(((..(((..((.((((((((((...............)))))))))).))..))).)))..))........ (-29.08 = -28.98 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 1

Location 258,611 – 258,731
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.61
Mean single sequence MFE -42.25
Consensus MFE -34.33
Energy contribution -33.67
Covariance contribution -0.66
Combinations/Pair 1.47
Mean z-score -1.92
Structure conservation index 0.81
SVM decision value 0.66
SVM RNA-class probability 0.813606
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 258611 120 - 27905053
GAGCAGCAACCAGACCACCGGUGUCUCGAUCAACAAGGUGGAAACGCAGCAGCUCUGCUUGGACACCAGGUUGUACCUUCUUGACUCGGCCAUCCAGAUGGAGCUGUGGCAAGAGGCCUA
.....((((((.(.....)(((((((...........(((....)))((((....)))).))))))).))))))..(((((((.(.((((..(((....))))))).).))))))).... ( -42.90)
>DroVir_CAF1 2098 120 - 1
GAGCAGCAAUCAAACAACUGGCGUUUCCAUUAACAAGGUCGAAACGCAGCAGCUAUGCCUGGACACUAGGCUUUACCUGCUGGACUCGGCCAUUCAGAUGGAGCUGUGGCAGGAAGCCUA
..(((((..(((......)))....((((((.....((((((..(.((((((.((.((((((...))))))..)).)))))))..)))))).....)))))))))))(((.....))).. ( -44.00)
>DroGri_CAF1 2035 120 - 1
GAGCAACAACCAAACGACUGGUGUCUCCAUUACGAAGCCCGAGACGCAGCAGUUGUGCUUGGACACCAGGCUGUACCUGCUCGACUCGGCCAUACAGAUGGAAUUGUGGCAGGAGGCCUA
........((((......))))((((((.((((((...(((((.((.(((((....((((((...)))))).....))))))).)))))((((....))))..))))))..))))))... ( -42.50)
>DroWil_CAF1 2615 120 - 1
GAGCAGCAACCAGACCACGGGCGUGUCUAUUAACAAGGUUGAGACCCAGCAGCUCUGCCUGGAUACUAGGCUCUAUCUGUUGGACUCAGCCAUUCAAAUGGAGCUAUGGCAGGAAGCCUA
.....((..((.(.(((..(((...((((((.....(((((((..(((((((....((((((...)))))).....))))))).))))))).....))))))))).)))).))..))... ( -41.60)
>DroMoj_CAF1 2673 120 - 1
GAGCAGCAAUCAAACAACAGGCGUGUCUAUCAACAAGGUCGAGACACAACAGUUGUGCUUGGAUACCAGGCUCUACCUGUUAGACUCGGCCAUACAAAUGGAGCUGUGGCAAGAAGCCUA
..(((((........((((((.(((((((((.....)))..)))))).......(.((((((...)))))).)..))))))........((((....)))).)))))(((.....))).. ( -37.10)
>DroAna_CAF1 2669 120 - 1
GAGCAGUAACCAGACCACCGGCGUCUCGAUCAACAAGGUGGAGACCCAGCAGCUGUGCCUGGACACCAGGCUAUACCUUCUGGACUCUGCCAUUCAGAUGGAACUCUGGCAGGAGGCUUA
((((.....(((((.....((.(((((.(((.....))).)))))))...((.(((((((((...)))))).))).))))))).(((((((((((.....)))...))))).))))))). ( -45.40)
>consensus
GAGCAGCAACCAAACCACCGGCGUCUCCAUCAACAAGGUCGAGACGCAGCAGCUGUGCCUGGACACCAGGCUCUACCUGCUGGACUCGGCCAUUCAGAUGGAGCUGUGGCAGGAAGCCUA
..(((((..((........))....((((((.....(((((((.((.(((((....((((((...)))))).....))))))).))))))).....)))))))))))(((.....))).. (-34.33 = -33.67 +  -0.66)

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 09:30:49 2006