Locus 752

Sequence ID 3R_DroMel_CAF1
Location 2,641,954 – 2,642,185
Length 231
Max. P 0.992924
window1193 window1194 window1195 window1196 window1197 window1198 window1199

overview

Window 3

Location 2,641,954 – 2,642,074
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -53.07
Consensus MFE -49.63
Energy contribution -50.30
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.25
Structure conservation index 0.94
SVM decision value 0.97
SVM RNA-class probability 0.891584
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2641954 120 + 27905053
AUCAGGUCGCAGCCUCUUGCAGGAUAAUGGCCGCAUUGCUGCUGCGACGCCAGCAGAAGCAGCGGCGGGCGAUGGCCGCAUUUUCUUGUUUGGUCUGUGAGCGGAACGCUCUACGUUCCG
....(.((((((((....((((((.(((((((((..((((.((((.......)))).))))))))).(((....))).)))).))))))..)).)))))).)((((((.....)))))). ( -57.60)
>DroSim_CAF1 30371 120 + 1
AUCAGGUCGCAGCCUCCUGCAGGAUAAUGGCCGCAUUGCUGCUGCGACGCCAGCAGAAGCAGCGGCGGGCGAUGGCCGCAUUUUCUUGUUUGGUCUGUGAGCAGAACGCUCUACGUUCCG
....(.((((((((....((((((.(((((((((..((((.((((.......)))).))))))))).(((....))).)))).))))))..)).)))))).).(((((.....))))).. ( -53.30)
>DroEre_CAF1 32829 120 + 1
AUCAGGUCGCAGCCUCCUGCAGGAUAAUGGCCGCACUGCUGCUGCGACGCCAGCUGAAGCAGCGGCGGGCGAUGGCCGCAUUUUCUUUUUUGGUCUGUGAGCAGAACGCUCUACGUUCCG
....(.(((((((((((....)))....((((((.((((((((((..((.....))..))))))))))))...))))..............)).)))))).).(((((.....))))).. ( -48.30)
>consensus
AUCAGGUCGCAGCCUCCUGCAGGAUAAUGGCCGCAUUGCUGCUGCGACGCCAGCAGAAGCAGCGGCGGGCGAUGGCCGCAUUUUCUUGUUUGGUCUGUGAGCAGAACGCUCUACGUUCCG
....(.((((((((....((((((.(((((((((..((((.((((.......)))).))))))))).(((....))).)))).))))))..)).)))))).).(((((.....))))).. (-49.63 = -50.30 +   0.67)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,641,954 – 2,642,074
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -46.80
Consensus MFE -46.52
Energy contribution -46.63
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.81
Structure conservation index 0.99
SVM decision value 0.78
SVM RNA-class probability 0.849949
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2641954 120 - 27905053
CGGAACGUAGAGCGUUCCGCUCACAGACCAAACAAGAAAAUGCGGCCAUCGCCCGCCGCUGCUUCUGCUGGCGUCGCAGCAGCAAUGCGGCCAUUAUCCUGCAAGAGGCUGCGACCUGAU
(((((((.....)))))))....(((.(((....((((...(((((........)))))...))))..))).((((((((..(..(((((........))))).)..))))))))))).. ( -48.10)
>DroSim_CAF1 30371 120 - 1
CGGAACGUAGAGCGUUCUGCUCACAGACCAAACAAGAAAAUGCGGCCAUCGCCCGCCGCUGCUUCUGCUGGCGUCGCAGCAGCAAUGCGGCCAUUAUCCUGCAGGAGGCUGCGACCUGAU
(((((((.....)))))))....(((.(((....((((...(((((........)))))...))))..))).((((((((.....(((((........)))))....))))))))))).. ( -47.00)
>DroEre_CAF1 32829 120 - 1
CGGAACGUAGAGCGUUCUGCUCACAGACCAAAAAAGAAAAUGCGGCCAUCGCCCGCCGCUGCUUCAGCUGGCGUCGCAGCAGCAGUGCGGCCAUUAUCCUGCAGGAGGCUGCGACCUGAU
(((((((.....)))))))....(((...............(.(((....))))(((((((...)))).)))((((((((..(..(((((........))))).)..))))))))))).. ( -45.30)
>consensus
CGGAACGUAGAGCGUUCUGCUCACAGACCAAACAAGAAAAUGCGGCCAUCGCCCGCCGCUGCUUCUGCUGGCGUCGCAGCAGCAAUGCGGCCAUUAUCCUGCAGGAGGCUGCGACCUGAU
(((((((.....)))))))....(((.(((....((((...(((((........)))))...))))..))).((((((((..(..(((((........))))).)..))))))))))).. (-46.52 = -46.63 +   0.11)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,641,994 – 2,642,114
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.78
Mean single sequence MFE -46.77
Consensus MFE -45.17
Energy contribution -45.50
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.47
Structure conservation index 0.97
SVM decision value 0.00
SVM RNA-class probability 0.535546
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2641994 120 + 27905053
GCUGCGACGCCAGCAGAAGCAGCGGCGGGCGAUGGCCGCAUUUUCUUGUUUGGUCUGUGAGCGGAACGCUCUACGUUCCGCCGCGCUCGGCGUCAAAUUUCAAACUGAAACUGAAGUGAG
.....((((((((((((((..(((((.(....).)))))..)))))..........(((.((((((((.....)))))))))))))).))))))..((((((.........))))))... ( -48.90)
>DroSim_CAF1 30411 120 + 1
GCUGCGACGCCAGCAGAAGCAGCGGCGGGCGAUGGCCGCAUUUUCUUGUUUGGUCUGUGAGCAGAACGCUCUACGUUCCGCCGCGCUCGGCGUCAAAUUUCAAACUAAAACUGAAGUGAG
.....((((((.((....)).((((((((((..(((((((......)))..))))...((((.....))))..)).))))))))....))))))..((((((.........))))))... ( -46.50)
>DroEre_CAF1 32869 120 + 1
GCUGCGACGCCAGCUGAAGCAGCGGCGGGCGAUGGCCGCAUUUUCUUUUUUGGUCUGUGAGCAGAACGCUCUACGUUCCGCCGCGCUCGGCGUCAAAUUUCAAACUGAAACUGAAGUGAG
.....((((((.((....)).((((((((((..(((((.(........).)))))...((((.....))))..)).))))))))....))))))..((((((.........))))))... ( -44.90)
>consensus
GCUGCGACGCCAGCAGAAGCAGCGGCGGGCGAUGGCCGCAUUUUCUUGUUUGGUCUGUGAGCAGAACGCUCUACGUUCCGCCGCGCUCGGCGUCAAAUUUCAAACUGAAACUGAAGUGAG
.....((((((.((....)).((((((((((..(((((.((......)).)))))...((((.....))))..)).))))))))....))))))..((((((.........))))))... (-45.17 = -45.50 +   0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,641,994 – 2,642,114
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.78
Mean single sequence MFE -44.03
Consensus MFE -43.11
Energy contribution -42.67
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.69
Structure conservation index 0.98
SVM decision value 0.45
SVM RNA-class probability 0.742401
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2641994 120 - 27905053
CUCACUUCAGUUUCAGUUUGAAAUUUGACGCCGAGCGCGGCGGAACGUAGAGCGUUCCGCUCACAGACCAAACAAGAAAAUGCGGCCAUCGCCCGCCGCUGCUUCUGCUGGCGUCGCAGC
........((((((.....)))))).((((((.(((..(((((((((.....))))))))).............((((...(((((........)))))...)))))))))))))..... ( -45.90)
>DroSim_CAF1 30411 120 - 1
CUCACUUCAGUUUUAGUUUGAAAUUUGACGCCGAGCGCGGCGGAACGUAGAGCGUUCUGCUCACAGACCAAACAAGAAAAUGCGGCCAUCGCCCGCCGCUGCUUCUGCUGGCGUCGCAGC
.....(((((.......)))))....((((((.(((..(((((((((.....))))))))).............((((...(((((........)))))...)))))))))))))..... ( -43.00)
>DroEre_CAF1 32869 120 - 1
CUCACUUCAGUUUCAGUUUGAAAUUUGACGCCGAGCGCGGCGGAACGUAGAGCGUUCUGCUCACAGACCAAAAAAGAAAAUGCGGCCAUCGCCCGCCGCUGCUUCAGCUGGCGUCGCAGC
........((((((.....)))))).((((((.(((..(((((((((.....)))))))))..............(((...(((((........)))))...))).)))))))))..... ( -43.20)
>consensus
CUCACUUCAGUUUCAGUUUGAAAUUUGACGCCGAGCGCGGCGGAACGUAGAGCGUUCUGCUCACAGACCAAACAAGAAAAUGCGGCCAUCGCCCGCCGCUGCUUCUGCUGGCGUCGCAGC
........((((((.....)))))).((((((.(((..(((((((((.....)))))))))..............(((...(((((........)))))...))).)))))))))..... (-43.11 = -42.67 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,642,034 – 2,642,154
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -44.00
Consensus MFE -41.70
Energy contribution -42.03
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.52
Structure conservation index 0.95
SVM decision value 1.35
SVM RNA-class probability 0.944983
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2642034 120 + 27905053
UUUUCUUGUUUGGUCUGUGAGCGGAACGCUCUACGUUCCGCCGCGCUCGGCGUCAAAUUUCAAACUGAAACUGAAGUGAGCUCAGCUCACCAUUUCAGCGCAGUCGACGUCCGCCGAGCG
................(((.((((((((.....)))))))))))((((((((....((.((..((((...(((((((((((...))))))...)))))..)))).)).)).)))))))). ( -49.50)
>DroSim_CAF1 30451 120 + 1
UUUUCUUGUUUGGUCUGUGAGCAGAACGCUCUACGUUCCGCCGCGCUCGGCGUCAAAUUUCAAACUAAAACUGAAGUGAGCUCAGCUCACCAUUUCAGCGCAGUCGACGUCCGCCGAGCG
................(((.((.(((((.....))))).)))))((((((((....((.((..(((....(((((((((((...))))))...)))))...))).)).)).)))))))). ( -39.10)
>DroEre_CAF1 32909 120 + 1
UUUUCUUUUUUGGUCUGUGAGCAGAACGCUCUACGUUCCGCCGCGCUCGGCGUCAAAUUUCAAACUGAAACUGAAGUGAGCUCAGCUCACCAUUUCAGCGCAGUCGACGUCCGCCGAGCG
................(((.((.(((((.....))))).)))))((((((((....((.((..((((...(((((((((((...))))))...)))))..)))).)).)).)))))))). ( -43.40)
>consensus
UUUUCUUGUUUGGUCUGUGAGCAGAACGCUCUACGUUCCGCCGCGCUCGGCGUCAAAUUUCAAACUGAAACUGAAGUGAGCUCAGCUCACCAUUUCAGCGCAGUCGACGUCCGCCGAGCG
................(((.((.(((((.....))))).)))))((((((((....((.((..((((...(((((((((((...))))))...)))))..)))).)).)).)))))))). (-41.70 = -42.03 +   0.33)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,642,034 – 2,642,154
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -51.33
Consensus MFE -51.77
Energy contribution -51.33
Covariance contribution -0.44
Combinations/Pair 1.05
Mean z-score -3.99
Structure conservation index 1.01
SVM decision value 2.36
SVM RNA-class probability 0.992924
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2642034 120 - 27905053
CGCUCGGCGGACGUCGACUGCGCUGAAAUGGUGAGCUGAGCUCACUUCAGUUUCAGUUUGAAAUUUGACGCCGAGCGCGGCGGAACGUAGAGCGUUCCGCUCACAGACCAAACAAGAAAA
(((((((((....(((((((.(((((...(((((((...))))))))))))..))).)))).......))))))))).(((((((((.....)))))))))................... ( -53.40)
>DroSim_CAF1 30451 120 - 1
CGCUCGGCGGACGUCGACUGCGCUGAAAUGGUGAGCUGAGCUCACUUCAGUUUUAGUUUGAAAUUUGACGCCGAGCGCGGCGGAACGUAGAGCGUUCUGCUCACAGACCAAACAAGAAAA
(((((((((....(((((((.(((((...(((((((...))))))))))))..))).)))).......))))))))).(((((((((.....)))))))))................... ( -49.40)
>DroEre_CAF1 32909 120 - 1
CGCUCGGCGGACGUCGACUGCGCUGAAAUGGUGAGCUGAGCUCACUUCAGUUUCAGUUUGAAAUUUGACGCCGAGCGCGGCGGAACGUAGAGCGUUCUGCUCACAGACCAAAAAAGAAAA
(((((((((....(((((((.(((((...(((((((...))))))))))))..))).)))).......))))))))).(((((((((.....)))))))))................... ( -51.20)
>consensus
CGCUCGGCGGACGUCGACUGCGCUGAAAUGGUGAGCUGAGCUCACUUCAGUUUCAGUUUGAAAUUUGACGCCGAGCGCGGCGGAACGUAGAGCGUUCUGCUCACAGACCAAACAAGAAAA
(((((((((....(((((((.(((((...(((((((...))))))))))))..))).)))).......))))))))).(((((((((.....)))))))))................... (-51.77 = -51.33 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,642,074 – 2,642,185
Length 111
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.30
Mean single sequence MFE -43.07
Consensus MFE -40.82
Energy contribution -40.60
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.09
Structure conservation index 0.95
SVM decision value 1.00
SVM RNA-class probability 0.898320
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2642074 111 - 27905053
CAUUAUGGCUGUU---------GGCAAAAACACCGCUUACCGCUCGGCGGACGUCGACUGCGCUGAAAUGGUGAGCUGAGCUCACUUCAGUUUCAGUUUGAAAUUUGACGCCGAGCGCGG
......((.((((---------......)))))).....((((((((((....(((((((.(((((...(((((((...))))))))))))..))).)))).......))))))))).). ( -43.30)
>DroSim_CAF1 30491 111 - 1
CAUUAUGGCUGUU---------GGCAAAAACACCGCUUACCGCUCGGCGGACGUCGACUGCGCUGAAAUGGUGAGCUGAGCUCACUUCAGUUUUAGUUUGAAAUUUGACGCCGAGCGCGG
......((.((((---------......)))))).....((((((((((....(((((((.(((((...(((((((...))))))))))))..))).)))).......))))))))).). ( -41.50)
>DroEre_CAF1 32949 120 - 1
CAUUAUGGCUGUUAUCAACGUGGGCAAAAACACCGCUUACCGCUCGGCGGACGUCGACUGCGCUGAAAUGGUGAGCUGAGCUCACUUCAGUUUCAGUUUGAAAUUUGACGCCGAGCGCGG
.......((..........((((((.........)))))).((((((((....(((((((.(((((...(((((((...))))))))))))..))).)))).......)))))))))).. ( -44.40)
>consensus
CAUUAUGGCUGUU_________GGCAAAAACACCGCUUACCGCUCGGCGGACGUCGACUGCGCUGAAAUGGUGAGCUGAGCUCACUUCAGUUUCAGUUUGAAAUUUGACGCCGAGCGCGG
.......(((............))).......((((.....((((((((....(((((((.(((((...(((((((...))))))))))))..))).)))).......)))))))))))) (-40.82 = -40.60 +  -0.22)

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 09:51:13 2006