Locus 6058

Sequence ID 3L_DroMel_CAF1
Location 16,132,156 – 16,132,433
Length 277
Max. P 0.956822
window9708 window9709 window9710 window9711 window9712 window9713 window9714 window9715

overview

Window 8

Location 16,132,156 – 16,132,273
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 89.36
Mean single sequence MFE -26.90
Consensus MFE -22.12
Energy contribution -22.23
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.02
Structure conservation index 0.82
SVM decision value 0.21
SVM RNA-class probability 0.635921
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16132156 117 - 23771897
UCCGAUGAAUCGAACGGCCAGGUGGCACAAAGCAGCCGCCAAAAAGUCAACAGAAAGCAAAUUGCCACCGCGAAUAGCCAACCUGAGACCCACAAAUCGUCUUUCCCCCA--CAU-CAAA
...((((....(((.(((..((((((........)))))).....(((..(((...((...((((....))))...))....))).))).........))).))).....--)))-)... ( -25.80)
>DroSim_CAF1 7383 117 - 1
UCCGAUGAAUCAAACGGCCAGGUGGCUCAAAGCAGCCGCCAAAAAGUCAACAGAAAGCAAUUUGCCACCGCGAAUCGCCAACCUGAGACCCACAAAUCGUCUUCCCCCCUUACAC-CC--
...(((((............(((((((......))))))).....(((..(((...((.((((((....)))))).))....))).))).......)))))..............-..-- ( -28.00)
>DroYak_CAF1 191 117 - 1
UCCAAUGAGUCGAACGGCCAGGUGGCUCAAAGCAGCCGCCAAAAAGUCAACAGAAAGCAAAUUGCCACCGCAAAUCGCCAACCUGAGACCCAGAAUUCGUCUUCCCCC-A--CACACAAA
......(((.((((.(((..(((((((......))))))).....................((((....))))...)))...(((.....)))..)))).))).....-.--........ ( -26.90)
>consensus
UCCGAUGAAUCGAACGGCCAGGUGGCUCAAAGCAGCCGCCAAAAAGUCAACAGAAAGCAAAUUGCCACCGCGAAUCGCCAACCUGAGACCCACAAAUCGUCUUCCCCCCA__CAC_CAAA
...(((((............((((((........)))))).....(((..(((...((...((((....))))...))....))).))).......)))))................... (-22.12 = -22.23 +   0.11)

alignment

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secondary structure

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Window 9

Location 16,132,193 – 16,132,313
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -40.37
Consensus MFE -35.14
Energy contribution -35.03
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -1.81
Structure conservation index 0.87
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16132193 120 + 23771897
UGGCUAUUCGCGGUGGCAAUUUGCUUUCUGUUGACUUUUUGGCGGCUGCUUUGUGCCACCUGGCCGUUCGAUUCAUCGGAUUGAUCGAUUCGAUCGCAUUGGAUCACAUAGAAUCGAUGG
.(((((.....(((((((....((...((((..(....)..))))..))....))))))))))))..(((((((...(((((....)))))((((......)))).....)))))))... ( -43.60)
>DroSim_CAF1 7420 120 + 1
UGGCGAUUCGCGGUGGCAAAUUGCUUUCUGUUGACUUUUUGGCGGCUGCUUUGAGCCACCUGGCCGUUUGAUUCAUCGGAUUGAUCGAUUCGAUCGCAUUGGAUCACAUAGAAUCGAUGG
...((((((((((((((..(..((...((((..(....)..))))..))..)..))))))..))....(((((((..(((((((.....)))))).)..)))))))....)))))).... ( -41.00)
>DroYak_CAF1 228 120 + 1
UGGCGAUUUGCGGUGGCAAUUUGCUUUCUGUUGACUUUUUGGCGGCUGCUUUGAGCCACCUGGCCGUUCGACUCAUUGGAUUGAUCGAUUGGAUCGCAUUGGAUCACAUAGAAUCGAUUG
..(((((....((((((.....((...((((..(....)..))))..)).....))))))...(((.((((.(((......))))))).))))))))(((((.((.....)).))))).. ( -36.50)
>consensus
UGGCGAUUCGCGGUGGCAAUUUGCUUUCUGUUGACUUUUUGGCGGCUGCUUUGAGCCACCUGGCCGUUCGAUUCAUCGGAUUGAUCGAUUCGAUCGCAUUGGAUCACAUAGAAUCGAUGG
.(((.(.....((((((.....((...((((..(....)..))))..)).....))))))).)))..((((((((((.((((((((.....))))).))).)))......)))))))... (-35.14 = -35.03 +  -0.11)

alignment

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secondary structure

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Window 0

Location 16,132,193 – 16,132,313
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -32.17
Consensus MFE -29.61
Energy contribution -29.50
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -2.14
Structure conservation index 0.92
SVM decision value 0.80
SVM RNA-class probability 0.853866
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16132193 120 - 23771897
CCAUCGAUUCUAUGUGAUCCAAUGCGAUCGAAUCGAUCAAUCCGAUGAAUCGAACGGCCAGGUGGCACAAAGCAGCCGCCAAAAAGUCAACAGAAAGCAAAUUGCCACCGCGAAUAGCCA
...(((((((....(((((......))))).((((.......)))))))))))..(((..((((((........)))))).....................((((....))))...))). ( -32.90)
>DroSim_CAF1 7420 120 - 1
CCAUCGAUUCUAUGUGAUCCAAUGCGAUCGAAUCGAUCAAUCCGAUGAAUCAAACGGCCAGGUGGCUCAAAGCAGCCGCCAAAAAGUCAACAGAAAGCAAUUUGCCACCGCGAAUCGCCA
.....(((((....(((((......))))).((((.......)))))))))....(((..(((((((......)))))))...................((((((....)))))).))). ( -31.80)
>DroYak_CAF1 228 120 - 1
CAAUCGAUUCUAUGUGAUCCAAUGCGAUCCAAUCGAUCAAUCCAAUGAGUCGAACGGCCAGGUGGCUCAAAGCAGCCGCCAAAAAGUCAACAGAAAGCAAAUUGCCACCGCAAAUCGCCA
...(((((((..((.(((......((((...))))....)))))..)))))))..(((..(((((((......))))))).....................((((....))))...))). ( -31.80)
>consensus
CCAUCGAUUCUAUGUGAUCCAAUGCGAUCGAAUCGAUCAAUCCGAUGAAUCGAACGGCCAGGUGGCUCAAAGCAGCCGCCAAAAAGUCAACAGAAAGCAAAUUGCCACCGCGAAUCGCCA
...(((((((...((........))((((.....))))........)))))))..(((..((((((........)))))).....................((((....))))...))). (-29.61 = -29.50 +  -0.11)

alignment

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secondary structure

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Window 1

Location 16,132,233 – 16,132,353
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.67
Mean single sequence MFE -46.00
Consensus MFE -43.65
Energy contribution -44.10
Covariance contribution 0.45
Combinations/Pair 1.02
Mean z-score -2.16
Structure conservation index 0.95
SVM decision value 0.99
SVM RNA-class probability 0.896691
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16132233 120 + 23771897
GGCGGCUGCUUUGUGCCACCUGGCCGUUCGAUUCAUCGGAUUGAUCGAUUCGAUCGCAUUGGAUCACAUAGAAUCGAUGGGAUCGAUGCGAUCAAGUGAUCGUGCCAAGGCUGUGAGCUG
(((.((.((((((.(((....))).((.((((.(((....(((((((..((((((.((((((.((.....)).)))))).))))))..)))))))))))))).)))))))).))..))). ( -47.40)
>DroSim_CAF1 7460 120 + 1
GGCGGCUGCUUUGAGCCACCUGGCCGUUUGAUUCAUCGGAUUGAUCGAUUCGAUCGCAUUGGAUCACAUAGAAUCGAUGGGAUCGAUGCGAUCAAGUGAUCGUGCCAAGGCUGUGAGCUG
(((.((.((((((.(((....))).((.((((.(((....(((((((..((((((.((((((.((.....)).)))))).))))))..)))))))))))))).)))))))).))..))). ( -46.50)
>DroYak_CAF1 268 120 + 1
GGCGGCUGCUUUGAGCCACCUGGCCGUUCGACUCAUUGGAUUGAUCGAUUGGAUCGCAUUGGAUCACAUAGAAUCGAUUGGAUCGAUGCGAUCAAGUGAUCGUGCCAAGGCUGUGAGCUG
(((.((.((((((.(((....))).((.(((.(((((.((((((((((((.(((((...((.....))......))))).))))))).))))).)))))))).)))))))).))..))). ( -44.10)
>consensus
GGCGGCUGCUUUGAGCCACCUGGCCGUUCGAUUCAUCGGAUUGAUCGAUUCGAUCGCAUUGGAUCACAUAGAAUCGAUGGGAUCGAUGCGAUCAAGUGAUCGUGCCAAGGCUGUGAGCUG
(((.((.((((((.(((....))).((.(((.((((....(((((((..((((((.((((((.((.....)).)))))).))))))..)))))))))))))).)))))))).))..))). (-43.65 = -44.10 +   0.45)

alignment

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secondary structure

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Window 2

Location 16,132,233 – 16,132,353
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -39.47
Consensus MFE -36.65
Energy contribution -37.43
Covariance contribution 0.78
Combinations/Pair 1.03
Mean z-score -2.72
Structure conservation index 0.93
SVM decision value 1.47
SVM RNA-class probability 0.956822
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16132233 120 - 23771897
CAGCUCACAGCCUUGGCACGAUCACUUGAUCGCAUCGAUCCCAUCGAUUCUAUGUGAUCCAAUGCGAUCGAAUCGAUCAAUCCGAUGAAUCGAACGGCCAGGUGGCACAAAGCAGCCGCC
..((.....))..((((.((.....((((((((((.((((.(((.......))).))))..)))))))))).(((((((......)).))))).))))))((((((........)))))) ( -40.90)
>DroSim_CAF1 7460 120 - 1
CAGCUCACAGCCUUGGCACGAUCACUUGAUCGCAUCGAUCCCAUCGAUUCUAUGUGAUCCAAUGCGAUCGAAUCGAUCAAUCCGAUGAAUCAAACGGCCAGGUGGCUCAAAGCAGCCGCC
..((.....))..((((.(((((....)))))(((((.....((((((((.....((((......)))))))))))).....))))).........))))(((((((......))))))) ( -39.40)
>DroYak_CAF1 268 120 - 1
CAGCUCACAGCCUUGGCACGAUCACUUGAUCGCAUCGAUCCAAUCGAUUCUAUGUGAUCCAAUGCGAUCCAAUCGAUCAAUCCAAUGAGUCGAACGGCCAGGUGGCUCAAAGCAGCCGCC
..((.....))..((((.((.......((((((((.((((((..........)).))))..))))))))...(((((((......))).)))).))))))(((((((......))))))) ( -38.10)
>consensus
CAGCUCACAGCCUUGGCACGAUCACUUGAUCGCAUCGAUCCCAUCGAUUCUAUGUGAUCCAAUGCGAUCGAAUCGAUCAAUCCGAUGAAUCGAACGGCCAGGUGGCUCAAAGCAGCCGCC
..((.....))..((((.((.....((((((((((.((((.(((.......))).))))..)))))))))).(((((((......)).))))).))))))((((((........)))))) (-36.65 = -37.43 +   0.78)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,132,273 – 16,132,393
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -35.07
Consensus MFE -32.50
Energy contribution -32.83
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.44
Structure conservation index 0.93
SVM decision value 1.04
SVM RNA-class probability 0.904446
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16132273 120 + 23771897
UUGAUCGAUUCGAUCGCAUUGGAUCACAUAGAAUCGAUGGGAUCGAUGCGAUCAAGUGAUCGUGCCAAGGCUGUGAGCUGUCUGUCUGCAUUUAUAAAUAAAUUGUGGCAAUUAAAUAAA
(((((((..((((((.((((((.((.....)).)))))).))))))..))))))).......((((.((((........))))....(((((((....)))).))))))).......... ( -36.00)
>DroSim_CAF1 7500 120 + 1
UUGAUCGAUUCGAUCGCAUUGGAUCACAUAGAAUCGAUGGGAUCGAUGCGAUCAAGUGAUCGUGCCAAGGCUGUGAGCUGUCUGUCUGCAUUUAUAAAUAAAUUGUGGCAAUUAAAUAAA
(((((((..((((((.((((((.((.....)).)))))).))))))..))))))).......((((.((((........))))....(((((((....)))).))))))).......... ( -36.00)
>DroYak_CAF1 308 120 + 1
UUGAUCGAUUGGAUCGCAUUGGAUCACAUAGAAUCGAUUGGAUCGAUGCGAUCAAGUGAUCGUGCCAAGGCUGUGAGCUGUCUGUCUGCAUUUAUAAAUAAAUUGUGGCAAUUAAAUAAA
..(((((....((((((((((.(((.((..........)))))))))))))))...))))).((((.((((........))))....(((((((....)))).))))))).......... ( -33.20)
>consensus
UUGAUCGAUUCGAUCGCAUUGGAUCACAUAGAAUCGAUGGGAUCGAUGCGAUCAAGUGAUCGUGCCAAGGCUGUGAGCUGUCUGUCUGCAUUUAUAAAUAAAUUGUGGCAAUUAAAUAAA
..(((((....((((((((((.(((.(((.......))).)))))))))))))...))))).((((.((((........))))....(((((((....)))).))))))).......... (-32.50 = -32.83 +   0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,132,273 – 16,132,393
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -27.47
Consensus MFE -26.33
Energy contribution -27.00
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.40
Structure conservation index 0.96
SVM decision value 1.27
SVM RNA-class probability 0.939071
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16132273 120 - 23771897
UUUAUUUAAUUGCCACAAUUUAUUUAUAAAUGCAGACAGACAGCUCACAGCCUUGGCACGAUCACUUGAUCGCAUCGAUCCCAUCGAUUCUAUGUGAUCCAAUGCGAUCGAAUCGAUCAA
..........(((((..(((((....)))))...........((.....))..))))).((((..((((((((((.((((.(((.......))).))))..))))))))))...)))).. ( -28.80)
>DroSim_CAF1 7500 120 - 1
UUUAUUUAAUUGCCACAAUUUAUUUAUAAAUGCAGACAGACAGCUCACAGCCUUGGCACGAUCACUUGAUCGCAUCGAUCCCAUCGAUUCUAUGUGAUCCAAUGCGAUCGAAUCGAUCAA
..........(((((..(((((....)))))...........((.....))..))))).((((..((((((((((.((((.(((.......))).))))..))))))))))...)))).. ( -28.80)
>DroYak_CAF1 308 120 - 1
UUUAUUUAAUUGCCACAAUUUAUUUAUAAAUGCAGACAGACAGCUCACAGCCUUGGCACGAUCACUUGAUCGCAUCGAUCCAAUCGAUUCUAUGUGAUCCAAUGCGAUCCAAUCGAUCAA
..........(((((..(((((....)))))...........((.....))..))))).((((..((((((((((.((((((..........)).))))..))))))).)))..)))).. ( -24.80)
>consensus
UUUAUUUAAUUGCCACAAUUUAUUUAUAAAUGCAGACAGACAGCUCACAGCCUUGGCACGAUCACUUGAUCGCAUCGAUCCCAUCGAUUCUAUGUGAUCCAAUGCGAUCGAAUCGAUCAA
..........(((((..(((((....)))))...........((.....))..))))).((((..((((((((((.((((.(((.......))).))))..))))))))))...)))).. (-26.33 = -27.00 +   0.67)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,132,313 – 16,132,433
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.78
Mean single sequence MFE -29.83
Consensus MFE -28.96
Energy contribution -29.41
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -1.59
Structure conservation index 0.97
SVM decision value 0.24
SVM RNA-class probability 0.646927
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16132313 120 + 23771897
GAUCGAUGCGAUCAAGUGAUCGUGCCAAGGCUGUGAGCUGUCUGUCUGCAUUUAUAAAUAAAUUGUGGCAAUUAAAUAAAUAAAAUGGAUGCAUAUGUAUGCUUUUUUAAUUGUCAGCCA
....(..((((((....))))))..)..((((((..((.....))..)))...............(((((((((((..........(.((((....)))).)...)))))))))))))). ( -28.42)
>DroSim_CAF1 7540 120 + 1
GAUCGAUGCGAUCAAGUGAUCGUGCCAAGGCUGUGAGCUGUCUGUCUGCAUUUAUAAAUAAAUUGUGGCAAUUAAAUAAAUAAAAUGGUUGCAUAUGUAUGCAUUUUUAAUUGUCAGCCA
....(..((((((....))))))..)..((((((..((.....))..)))...............(((((((((((.............(((((....)))))..)))))))))))))). ( -29.36)
>DroYak_CAF1 348 120 + 1
GAUCGAUGCGAUCAAGUGAUCGUGCCAAGGCUGUGAGCUGUCUGUCUGCAUUUAUAAAUAAAUUGUGGCAAUUAAAUAAAUAAAAUGGAUGCAUAUGUAUGCAUUUUUAAUUGUCGGCCU
....(..((((((....))))))..).(((((((..((.....))..)).................((((((((((.......((((.((((....)))).))))))))))))))))))) ( -31.71)
>consensus
GAUCGAUGCGAUCAAGUGAUCGUGCCAAGGCUGUGAGCUGUCUGUCUGCAUUUAUAAAUAAAUUGUGGCAAUUAAAUAAAUAAAAUGGAUGCAUAUGUAUGCAUUUUUAAUUGUCAGCCA
....(..((((((....))))))..)..((((((..((.....))..)).................((((((((((.......((((.((((....)))).)))))))))))))))))). (-28.96 = -29.41 +   0.45)

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 12:08:38 2006