Locus 6738

Sequence ID X_DroMel_CAF1
Location 16,757,205 – 16,757,417
Length 212
Max. P 0.981305
window11012 window11013 window11014 window11015 window11016 window11017

overview

Window 2

Location 16,757,205 – 16,757,325
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.06
Mean single sequence MFE -26.58
Consensus MFE -22.75
Energy contribution -23.00
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 0.86
SVM decision value 0.64
SVM RNA-class probability 0.809439
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16757205 120 + 22224390
UUAUUCAAAUGCCCACCAAUGCCAAUCGAAUGUAUGUAUGGUUUUUUUUUUUUGCUCCACCUAAGUCUUGGCAUUUUUUAUUUGGUUGCUUUGGCCCGAAAACUGGGUCAUCCAAAUAGC
.................((((((((..((...((.((..(((...........)))..)).))..))))))))))..((((((((......(((((((.....))))))).)))))))). ( -25.40)
>DroSec_CAF1 44201 113 + 1
UUAUUCAAAUGCCCACCAAUGCCAAUCGAA---GUGUAUGGUUUUUUUU----UCUCCACCUAAGUCUUGGCAUUUUUUAUUUGGUUGCUUUGGCCCGAAAACUGGGUCAUCCAAAUAGC
.................((((((((..((.---.((..(((........----...)))..))..))))))))))..((((((((......(((((((.....))))))).)))))))). ( -27.00)
>DroEre_CAF1 35576 108 + 1
UUAUUCAAAUGCCCGCCAAUGCCAAUCGAA---GUGUAUUGUUUUUCU--------CCACCCAAGUCUUGGCAUUU-UUAUUUGGUUGCUUUGGCCCGAAAACUGGGUCAUCCAAAUAGC
.................((((((((..((.---.((...((.......--------.))..))..)))))))))).-((((((((......(((((((.....))))))).)))))))). ( -24.50)
>DroYak_CAF1 35999 116 + 1
UUAUUCAAAUGCCCACCAAUGCCAAUCGAA---GUGUAUUGUUUUUUUU-UUUGGUUCACCCAAGUCUUGGCAUUUUUUAUUUGGUUGCUUUGGCCCGAAAACUGGGUCAUCCAAAUAGC
......(((((((...(((((((.......---).))))))........-(((((.....)))))....))))))).((((((((......(((((((.....))))))).)))))))). ( -29.40)
>consensus
UUAUUCAAAUGCCCACCAAUGCCAAUCGAA___GUGUAUGGUUUUUUUU____GCUCCACCCAAGUCUUGGCAUUUUUUAUUUGGUUGCUUUGGCCCGAAAACUGGGUCAUCCAAAUAGC
.................((((((((..((....(((.....................))).....))))))))))..((((((((......(((((((.....))))))).)))))))). (-22.75 = -23.00 +   0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,757,205 – 16,757,325
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.06
Mean single sequence MFE -28.74
Consensus MFE -26.40
Energy contribution -26.21
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -2.23
Structure conservation index 0.92
SVM decision value 1.88
SVM RNA-class probability 0.981305
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16757205 120 - 22224390
GCUAUUUGGAUGACCCAGUUUUCGGGCCAAAGCAACCAAAUAAAAAAUGCCAAGACUUAGGUGGAGCAAAAAAAAAAAACCAUACAUACAUUCGAUUGGCAUUGGUGGGCAUUUGAAUAA
..((((..((((.(((.(((((......))))).((((........(((((((.......((((...............))))............))))))))))))))))))..)))). ( -27.27)
>DroSec_CAF1 44201 113 - 1
GCUAUUUGGAUGACCCAGUUUUCGGGCCAAAGCAACCAAAUAAAAAAUGCCAAGACUUAGGUGGAGA----AAAAAAAACCAUACAC---UUCGAUUGGCAUUGGUGGGCAUUUGAAUAA
..((((..((((.(((.(((((......))))).((((........(((((((.....(((((....----.............)))---))...))))))))))))))))))..)))). ( -29.93)
>DroEre_CAF1 35576 108 - 1
GCUAUUUGGAUGACCCAGUUUUCGGGCCAAAGCAACCAAAUAA-AAAUGCCAAGACUUGGGUGG--------AGAAAAACAAUACAC---UUCGAUUGGCAUUGGCGGGCAUUUGAAUAA
..((((..((((.(((.(((((......)))))..........-.((((((((.....(((((.--------............)))---))...))))))))...)))))))..)))). ( -29.42)
>DroYak_CAF1 35999 116 - 1
GCUAUUUGGAUGACCCAGUUUUCGGGCCAAAGCAACCAAAUAAAAAAUGCCAAGACUUGGGUGAACCAAA-AAAAAAAACAAUACAC---UUCGAUUGGCAUUGGUGGGCAUUUGAAUAA
..((((..((((.(((.(((((......))))).((((........(((((((.....(((((.......-.............)))---))...))))))))))))))))))..)))). ( -28.35)
>consensus
GCUAUUUGGAUGACCCAGUUUUCGGGCCAAAGCAACCAAAUAAAAAAUGCCAAGACUUAGGUGGAGC____AAAAAAAACAAUACAC___UUCGAUUGGCAUUGGUGGGCAUUUGAAUAA
..((((..((((.(((.(((((......)))))............((((((((.......(((.....................)))........))))))))...)))))))..)))). (-26.40 = -26.21 +  -0.19)

alignment

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secondary structure

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Window 4

Location 16,757,245 – 16,757,351
Length 106
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.71
Mean single sequence MFE -28.52
Consensus MFE -20.60
Energy contribution -20.85
Covariance contribution 0.25
Combinations/Pair 1.04
Mean z-score -1.85
Structure conservation index 0.72
SVM decision value 0.63
SVM RNA-class probability 0.805899
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16757245 106 + 22224390
GUUUUUUUUUUUUGCUCCACCUAAGUCUUGGCAUUUUUUAUUUGGUUGCUUUGGCCCGAAAACUGGGUCAUCCAAAUAGCAAAUAUUUUGUGGGGCUCU------UGAUCGU--------
.............(((((((....((....))((((.((((((((......(((((((.....))))))).)))))))).)))).....)))))))...------.......-------- ( -29.40)
>DroSec_CAF1 44238 102 + 1
GUUUUUUUU----UCUCCACCUAAGUCUUGGCAUUUUUUAUUUGGUUGCUUUGGCCCGAAAACUGGGUCAUCCAAAUAGCAAAUAUUUUGUGCGGCUCU------UGAUCGU--------
.........----........((((...(.((((....((((((.(((...(((((((.....)))))))..)))....))))))....)))).)..))------)).....-------- ( -20.80)
>DroEre_CAF1 35613 110 + 1
GUUUUUCU--------CCACCCAAGUCUUGGCAUUU-UUAUUUGGUUGCUUUGGCCCGAAAACUGGGUCAUCCAAAUAGCA-AUGCUUUGUGGGGCUUCAAGUCGCGAUCGCAGCUCUCA
........--------...((((......((((((.-((((((((......(((((((.....))))))).)))))))).)-)))))...))))......(((.((....)).))).... ( -33.30)
>DroYak_CAF1 36036 119 + 1
GUUUUUUUU-UUUGGUUCACCCAAGUCUUGGCAUUUUUUAUUUGGUUGCUUUGGCCCGAAAACUGGGUCAUCCAAAUAGCAAAUAUUUUGUGGGGCUCCAAGUCGCGAUCGCAGCUCUUA
.........-.((((..(.((((.((....))((((.((((((((......(((((((.....))))))).)))))))).))))......)))))..))))((.((....)).))..... ( -30.60)
>consensus
GUUUUUUUU____GCUCCACCCAAGUCUUGGCAUUUUUUAUUUGGUUGCUUUGGCCCGAAAACUGGGUCAUCCAAAUAGCAAAUAUUUUGUGGGGCUCC______CGAUCGC________
...................((((.((....))((((.((((((((......(((((((.....))))))).)))))))).))))......)))).......................... (-20.60 = -20.85 +   0.25)

alignment

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secondary structure

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Window 5

Location 16,757,285 – 16,757,383
Length 98
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 77.42
Mean single sequence MFE -32.88
Consensus MFE -22.35
Energy contribution -22.73
Covariance contribution 0.37
Combinations/Pair 1.08
Mean z-score -1.59
Structure conservation index 0.68
SVM decision value 0.14
SVM RNA-class probability 0.603318
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16757285 98 + 22224390
UUUGGUUGCUUUGGCCCGAAAACUGGGUCAUCCAAAUAGCAAAUAUUUUGUGGGGCUCU------UGAUCGU----------------UCACUCCAGUUGGCUCUUCCCAUCGGGCCAGA
.........((((((((((....((((....((((...((((.....))))((((....------(((....----------------)))))))..)))).....)))))))))))))) ( -31.00)
>DroSec_CAF1 44274 98 + 1
UUUGGUUGCUUUGGCCCGAAAACUGGGUCAUCCAAAUAGCAAAUAUUUUGUGCGGCUCU------UGAUCGU----------------UCCUUCCAGUUGGGUCUUCCCUUCGGGCCAGA
.........((((((((((((((((((...........((((.....))))(((((...------.).))))----------------....)))))))(((....)))))))))))))) ( -32.40)
>DroEre_CAF1 35644 103 + 1
UUUGGUUGCUUUGGCCCGAAAACUGGGUCAUCCAAAUAGCA-AUGCUUUGUGGGGCUUCAAGUCGCGAUCGCAGCUCUCA---------------ACUUGCCUCU-UCCUUCGGGCCAGA
.........(((((((((((.....((((..(((...(((.-..)))...)))(((.....)))..))))((((......---------------..))))....-...))))))))))) ( -31.40)
>DroYak_CAF1 36075 120 + 1
UUUGGUUGCUUUGGCCCGAAAACUGGGUCAUCCAAAUAGCAAAUAUUUUGUGGGGCUCCAAGUCGCGAUCGCAGCUCUUAAACACAACUCCCUCGAGUUGGCUCUUUCCUUCGGGCCAGA
.........(((((((((((..(((((((.........((((.....))))(.(((.....))).))))).)))..........((((((....)))))).........))))))))))) ( -36.70)
>consensus
UUUGGUUGCUUUGGCCCGAAAACUGGGUCAUCCAAAUAGCAAAUAUUUUGUGGGGCUCC______CGAUCGC________________UCCCUCCAGUUGGCUCUUCCCUUCGGGCCAGA
.........(((((((((((....(((((..(.(((((.....))))).)...))))).........................................((......))))))))))))) (-22.35 = -22.73 +   0.37)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,757,285 – 16,757,383
Length 98
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.42
Mean single sequence MFE -32.11
Consensus MFE -20.09
Energy contribution -20.34
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.74
Structure conservation index 0.63
SVM decision value 0.24
SVM RNA-class probability 0.647175
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16757285 98 - 22224390
UCUGGCCCGAUGGGAAGAGCCAACUGGAGUGA----------------ACGAUCA------AGAGCCCCACAAAAUAUUUGCUAUUUGGAUGACCCAGUUUUCGGGCCAAAGCAACCAAA
..(((((((((((......)))(((((.((..----------------.((.(((------(((((..............))).))))).)))))))))..))))))))........... ( -27.64)
>DroSec_CAF1 44274 98 - 1
UCUGGCCCGAAGGGAAGACCCAACUGGAAGGA----------------ACGAUCA------AGAGCCGCACAAAAUAUUUGCUAUUUGGAUGACCCAGUUUUCGGGCCAAAGCAACCAAA
..((((((((((((....)))((((((..((.----------------.(.....------.)..))(((.........)))............)))))))))))))))........... ( -31.40)
>DroEre_CAF1 35644 103 - 1
UCUGGCCCGAAGGA-AGAGGCAAGU---------------UGAGAGCUGCGAUCGCGACUUGAAGCCCCACAAAGCAU-UGCUAUUUGGAUGACCCAGUUUUCGGGCCAAAGCAACCAAA
..(((((((((((.-.(.(((((((---------------((.((.......)).))))))).....(((.(.(((..-.))).).)))....)))..)))))))))))........... ( -33.10)
>DroYak_CAF1 36075 120 - 1
UCUGGCCCGAAGGAAAGAGCCAACUCGAGGGAGUUGUGUUUAAGAGCUGCGAUCGCGACUUGGAGCCCCACAAAAUAUUUGCUAUUUGGAUGACCCAGUUUUCGGGCCAAAGCAACCAAA
..(((((((((((...((((((((((....)))))).))))....(((.(((.......))).))).))................((((.....))))..)))))))))........... ( -36.30)
>consensus
UCUGGCCCGAAGGAAAGAGCCAACUGGAGGGA________________ACGAUCA______AGAGCCCCACAAAAUAUUUGCUAUUUGGAUGACCCAGUUUUCGGGCCAAAGCAACCAAA
..(((((((((((..................................................(((..............)))..((((.....)))))))))))))))........... (-20.09 = -20.34 +   0.25)

alignment

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secondary structure

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Window 7

Location 16,757,325 – 16,757,417
Length 92
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 75.24
Mean single sequence MFE -30.60
Consensus MFE -19.47
Energy contribution -19.81
Covariance contribution 0.34
Combinations/Pair 1.12
Mean z-score -1.64
Structure conservation index 0.64
SVM decision value 0.64
SVM RNA-class probability 0.807595
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16757325 92 + 22224390
AAAUAUUUUGUGGGGCUCU------UGAUCGU----------------UCACUCCAGUUGGCUCUUCCCAUCGGGCCAGAUCCGCAACGAGUCUUGGUGGCUUUAUAGCCACCA
...........(((((((.------(((....----------------)))......(((((((........))))))).........)))))))(((((((....))))))). ( -31.20)
>DroSec_CAF1 44314 91 + 1
AAAUAUUUUGUGCGGCUCU------UGAUCGU----------------UCCUUCCAGUUGGGUCUUCCCUUCGGGCCAGAUCCGCAACGAGUCUUGGUGGCUUUGCAGCU-CCA
..........((.((((..------.......----------------...........((((((..((....))..))))))(((..(((((.....))))))))))))-.)) ( -24.10)
>DroYak_CAF1 36115 113 + 1
AAAUAUUUUGUGGGGCUCCAAGUCGCGAUCGCAGCUCUUAAACACAACUCCCUCGAGUUGGCUCUUUCCUUCGGGCCAGAUCCGCAACGAGUCUCGCCGGCUUUAAAGCU-CCA
..........(((((((..((((((((((((..((..........(((((....)))))((.(((..((....))..))).))))..)))...))).))))))...))))-))) ( -36.50)
>consensus
AAAUAUUUUGUGGGGCUCU______UGAUCGU________________UCCCUCCAGUUGGCUCUUCCCUUCGGGCCAGAUCCGCAACGAGUCUUGGUGGCUUUAAAGCU_CCA
...........(((((((........((((.....................(....).((((((........))))))))))......)))))))((.((((....)))).)). (-19.47 = -19.81 +   0.34)

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 12:21:31 2006