Locus 2721

Sequence ID 2L_DroMel_CAF1
Location 7,645,243 – 7,645,483
Length 240
Max. P 0.977181
window4330 window4331 window4332 window4333 window4334

overview

Window 0

Location 7,645,243 – 7,645,363
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.50
Mean single sequence MFE -57.38
Consensus MFE -43.05
Energy contribution -44.42
Covariance contribution 1.38
Combinations/Pair 1.12
Mean z-score -2.43
Structure conservation index 0.75
SVM decision value 1.21
SVM RNA-class probability 0.930493
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7645243 120 + 22407834
GGAAGUUGUUUGGGGAACUCUCGCGACAGGGCGAUGAAAUCGCCGAGUCCUGGGAGACCAUACUCCUAGGAAUGGUGGCUAGUUCCAGGCAGGUUUCAUUACCACCUGUGGUGGUGGCUA
((((.(((((...((((((...((.((..((((((...))))))...(((((((((......)))))))))...)).)).)))))).))))).)))).((((((((...))))))))... ( -52.60)
>DroPse_CAF1 185234 120 + 1
GGAAGUUGCUCGGCGAACUCUCGCGGCAGGGCGAGGAGAUGGCCGAGUCCUGGGAGACCAUGCUCCUGGGAACGGUGGCCAGCUCCAGGCAGGUCUCGUUGCCGCCCGUCGUCGUGGCUA
...(((..(...((((....))))(((.((((..((((.((((((..(((..((((......))))..)))....)))))).)))).(((((......))))))))))))...)..))). ( -62.40)
>DroAna_CAF1 156851 120 + 1
GGAAGUUGUUGGGGGAACUCUCGCGACAUGGCGACGAUAUGGCCGAGUCCUGCGAUACCAUACUCCUGGGUAUGGUGGCCAACUCCAGGCAGGUCUCGUUGCCACCCGUUGUGGUGGCUA
...((((((((.(((....))).))))((.((((((...((((((((.(((((...((((((((....))))))))((......))..))))).))))..))))..)))))).)))))). ( -51.40)
>DroPer_CAF1 182056 120 + 1
GGAAGUUGCUCGGCGAGCUCUCGCGGCAGGGCGAGGAGAUGGCCGAGUCCUGGGAGACCAUGCUCCUGGGAACGGUGGCCAGCUCCAGGCAGGUCUCGUUGCCGCCCGUCGUCGUGGCUA
...(((..(...((((....))))(((.((((..((((.((((((..(((..((((......))))..)))....)))))).)))).(((((......))))))))))))...)..))). ( -63.10)
>consensus
GGAAGUUGCUCGGCGAACUCUCGCGACAGGGCGAGGAGAUGGCCGAGUCCUGGGAGACCAUACUCCUGGGAACGGUGGCCAGCUCCAGGCAGGUCUCGUUGCCACCCGUCGUCGUGGCUA
(..(.(((((.((((..(((((((......)))).))).((((((.((((((((((......)))))))).))..)))))).)))).))))).)..)...((((((......)))))).. (-43.05 = -44.42 +   1.38)

alignment

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secondary structure

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Window 1

Location 7,645,243 – 7,645,363
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.50
Mean single sequence MFE -44.52
Consensus MFE -32.91
Energy contribution -34.60
Covariance contribution 1.69
Combinations/Pair 1.09
Mean z-score -1.37
Structure conservation index 0.74
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7645243 120 - 22407834
UAGCCACCACCACAGGUGGUAAUGAAACCUGCCUGGAACUAGCCACCAUUCCUAGGAGUAUGGUCUCCCAGGACUCGGCGAUUUCAUCGCCCUGUCGCGAGAGUUCCCCAAACAACUUCC
..((((((......))))))..............((((((.((.((...((((.((((......)))).))))...((((((...))))))..)).))...))))))............. ( -39.50)
>DroPse_CAF1 185234 120 - 1
UAGCCACGACGACGGGCGGCAACGAGACCUGCCUGGAGCUGGCCACCGUUCCCAGGAGCAUGGUCUCCCAGGACUCGGCCAUCUCCUCGCCCUGCCGCGAGAGUUCGCCGAGCAACUUCC
..(((.((....)))))(....)((((((((((((((((.(....).)))))..)).))).))))))...(((((((((...(((.((((......)))))))...)))))).....))) ( -48.30)
>DroAna_CAF1 156851 120 - 1
UAGCCACCACAACGGGUGGCAACGAGACCUGCCUGGAGUUGGCCACCAUACCCAGGAGUAUGGUAUCGCAGGACUCGGCCAUAUCGUCGCCAUGUCGCGAGAGUUCCCCCAACAACUUCC
..((((((......))))))..((((.(((((..((......))(((((((......)))))))...))))).)))).........((((......))))(((((........))))).. ( -41.80)
>DroPer_CAF1 182056 120 - 1
UAGCCACGACGACGGGCGGCAACGAGACCUGCCUGGAGCUGGCCACCGUUCCCAGGAGCAUGGUCUCCCAGGACUCGGCCAUCUCCUCGCCCUGCCGCGAGAGCUCGCCGAGCAACUUCC
..((..((.(((.((((((((........)))).((((.(((((...((((....))))..(((((....))))).))))).))))..))))....((....))))).)).))....... ( -48.50)
>consensus
UAGCCACCACGACGGGCGGCAACGAGACCUGCCUGGAGCUGGCCACCAUUCCCAGGAGCAUGGUCUCCCAGGACUCGGCCAUCUCCUCGCCCUGCCGCGAGAGUUCCCCGAACAACUUCC
..(((((........)))))...(((.((((...((((...((((..((((....)))).)))))))))))).)))(((...(((.((((......)))))))...)))........... (-32.91 = -34.60 +   1.69)

alignment

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secondary structure

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Window 2

Location 7,645,283 – 7,645,403
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.89
Mean single sequence MFE -57.12
Consensus MFE -46.21
Energy contribution -46.15
Covariance contribution -0.06
Combinations/Pair 1.20
Mean z-score -2.76
Structure conservation index 0.81
SVM decision value 1.79
SVM RNA-class probability 0.977181
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7645283 120 + 22407834
CGCCGAGUCCUGGGAGACCAUACUCCUAGGAAUGGUGGCUAGUUCCAGGCAGGUUUCAUUACCACCUGUGGUGGUGGCUAUGAUGACAUCCUCGACGCCCUCGUCAAUGGGCGAUGAAAU
.((((..(((((((((......)))))))))....))))....((.(((...(((((((..(((((......)))))..)))).)))..))).))(((((........)))))....... ( -50.30)
>DroPse_CAF1 185274 120 + 1
GGCCGAGUCCUGGGAGACCAUGCUCCUGGGAACGGUGGCCAGCUCCAGGCAGGUCUCGUUGCCGCCCGUCGUCGUGGCUAUGAUGAUGUCCUCGACGCCCUCGUCGAUGGGCGACGAGAU
(((((..(((..((((......))))..)))....))))).((.....))..((((((((((((..(((((((((....)))))))))..)((((((....))))))..))))))))))) ( -61.50)
>DroAna_CAF1 156891 120 + 1
GGCCGAGUCCUGCGAUACCAUACUCCUGGGUAUGGUGGCCAACUCCAGGCAGGUCUCGUUGCCACCCGUUGUGGUGGCUAUGAUGAUGUCCUCGACACCUUCGUCGAUGGGCGAGGAGAU
((((..(((....)))((((((((....))))))))))))..((((......(((((((.((((((......)))))).)))).)))(((((((((......))))).))))..)))).. ( -55.20)
>DroPer_CAF1 182096 120 + 1
GGCCGAGUCCUGGGAGACCAUGCUCCUGGGAACGGUGGCCAGCUCCAGGCAGGUCUCGUUGCCGCCCGUCGUCGUGGCUAUGAUGAUGUCCUCGACGCCCUCGUCGAUGGGCGACGAGAU
(((((..(((..((((......))))..)))....))))).((.....))..((((((((((((..(((((((((....)))))))))..)((((((....))))))..))))))))))) ( -61.50)
>consensus
GGCCGAGUCCUGGGAGACCAUACUCCUGGGAACGGUGGCCAGCUCCAGGCAGGUCUCGUUGCCACCCGUCGUCGUGGCUAUGAUGAUGUCCUCGACGCCCUCGUCGAUGGGCGACGAGAU
(((((.((((((((((......)))))))).))..)))))..(((.(((.(.(((((((.((((((......)))))).)))).))).))))...(((((........)))))..))).. (-46.21 = -46.15 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,645,283 – 7,645,403
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.89
Mean single sequence MFE -49.33
Consensus MFE -39.33
Energy contribution -40.45
Covariance contribution 1.12
Combinations/Pair 1.18
Mean z-score -2.04
Structure conservation index 0.80
SVM decision value 0.91
SVM RNA-class probability 0.879798
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7645283 120 - 22407834
AUUUCAUCGCCCAUUGACGAGGGCGUCGAGGAUGUCAUCAUAGCCACCACCACAGGUGGUAAUGAAACCUGCCUGGAACUAGCCACCAUUCCUAGGAGUAUGGUCUCCCAGGACUCGGCG
........((((........))))((((((.......((((.((((((......)))))).))))......(((((.....((((..((((....)))).))))...))))).)))))). ( -46.50)
>DroPse_CAF1 185274 120 - 1
AUCUCGUCGCCCAUCGACGAGGGCGUCGAGGACAUCAUCAUAGCCACGACGACGGGCGGCAACGAGACCUGCCUGGAGCUGGCCACCGUUCCCAGGAGCAUGGUCUCCCAGGACUCGGCC
.(((((.(((((........))))).)))))...........(((.((....)))))(((..((((.((((...((((...((((..((((....)))).)))))))))))).))))))) ( -50.90)
>DroAna_CAF1 156891 120 - 1
AUCUCCUCGCCCAUCGACGAAGGUGUCGAGGACAUCAUCAUAGCCACCACAACGGGUGGCAACGAGACCUGCCUGGAGUUGGCCACCAUACCCAGGAGUAUGGUAUCGCAGGACUCGGCC
...((((((..((((......)))).))))))..........((((((......))))))..((((.(((((..((......))(((((((......)))))))...))))).))))... ( -49.00)
>DroPer_CAF1 182096 120 - 1
AUCUCGUCGCCCAUCGACGAGGGCGUCGAGGACAUCAUCAUAGCCACGACGACGGGCGGCAACGAGACCUGCCUGGAGCUGGCCACCGUUCCCAGGAGCAUGGUCUCCCAGGACUCGGCC
.(((((.(((((........))))).)))))...........(((.((....)))))(((..((((.((((...((((...((((..((((....)))).)))))))))))).))))))) ( -50.90)
>consensus
AUCUCGUCGCCCAUCGACGAGGGCGUCGAGGACAUCAUCAUAGCCACCACGACGGGCGGCAACGAGACCUGCCUGGAGCUGGCCACCAUUCCCAGGAGCAUGGUCUCCCAGGACUCGGCC
.((((((((.....))))))))..((((((..(.........(((((........)))))...((((((..((((((((........))))).))).....))))))...)..)))))). (-39.33 = -40.45 +   1.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,645,363 – 7,645,483
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.15
Mean single sequence MFE -42.03
Consensus MFE -33.44
Energy contribution -32.75
Covariance contribution -0.69
Combinations/Pair 1.31
Mean z-score -1.55
Structure conservation index 0.80
SVM decision value 0.23
SVM RNA-class probability 0.646333
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7645363 120 - 22407834
AGGACUCAGCCUUUGGCUCUCUGACUGACAACGACCUGUCCAUUGGAUCGUCCAGCAUUAGGUUGAGCAGCUUUCAGUCCAUUUCAUCGCCCAUUGACGAGGGCGUCGAGGAUGUCAUCA
.(((((.((((...))))......(((....(((((((....((((.....))))...)))))))..))).....))))).((((..(((((........)))))..))))......... ( -36.20)
>DroPse_CAF1 185354 117 - 1
AGGACUCGGCCUUCGGCUCGCUCACCGACAACGACCUGUCCAUCG---CGUCGAGCAUCCGGCUGAGCAGCUUCCAGUCCAUCUCGUCGCCCAUCGACGAGGGCGUCGAGGACAUCAUCA
.(((((.((.....((((.(((((((((((......))))....(---(.....))....)).))))))))).))))))).(((((.(((((........))))).)))))......... ( -46.70)
>DroAna_CAF1 156971 120 - 1
AGGACUCGGCCUUCGGUUCUCUGACCGACAAUGACCUCUCCAUUGGUUCGUCCAGCAUCCGGCUGAGCAGUUUCCAGUCCAUCUCCUCGCCCAUCGACGAAGGUGUCGAGGACAUCAUCA
.(((((.((...((((((....))))))(((((.......)))))....(..((((.....))))..).....)))))))...((((((..((((......)))).))))))........ ( -38.50)
>DroPer_CAF1 182176 117 - 1
AGGACUCGGCCUUCGGCUCGCUCACCGACAACGACCUGUCCAUCG---CGUCGAGCAUCCGGCUGAGCAGCUUCCAGUCCAUCUCGUCGCCCAUCGACGAGGGCGUCGAGGACAUCAUCA
.(((((.((.....((((.(((((((((((......))))....(---(.....))....)).))))))))).))))))).(((((.(((((........))))).)))))......... ( -46.70)
>consensus
AGGACUCGGCCUUCGGCUCGCUCACCGACAACGACCUGUCCAUCG___CGUCCAGCAUCCGGCUGAGCAGCUUCCAGUCCAUCUCGUCGCCCAUCGACGAGGGCGUCGAGGACAUCAUCA
.(((((.(((.(((((((.((((..(((...(((........)))..)))..))))....)))))))..)))...))))).(((((.(((((........))))).)))))......... (-33.44 = -32.75 +  -0.69)

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 10:34:41 2006