Locus 7941

Sequence ID 3L_DroMel_CAF1
Location 21,072,728 – 21,072,928
Length 200
Max. P 0.999950
window12948 window12949 window12950 window12951 window12952

overview

Window 8

Location 21,072,728 – 21,072,848
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.42
Mean single sequence MFE -42.31
Consensus MFE -30.45
Energy contribution -32.21
Covariance contribution 1.76
Combinations/Pair 1.03
Mean z-score -2.44
Structure conservation index 0.72
SVM decision value 0.70
SVM RNA-class probability 0.827617
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21072728 120 + 23771897
UCUGGAGAGCUCCACCAAACUGAAGCUAUCGCCGGACCCGAACUUCAUCAUGAUCAGCGUGGUGUAGAAUGCCACCAUGGCCAAGGCCAUCAGGGCCUUGACCAGGUAGUACAGCUUCAA
..((((....))))......(((((((.....((....))..((.(((((((.....))))))).))..(((.(((.(((.(((((((.....))))))).)))))).))).))))))). ( -44.10)
>DroSec_CAF1 127994 120 + 1
UCUGGAGAGCUCCACCAAACUGAAGCUAUCGCCGGAGCCGAACUUCAUCAUGAUCAGCGUGGUGUAGAAUGCCACCAUGGACAAGGCCAUCAGGGCCUUGACCAGGUAGUACAGCUUCAA
...((..((((.((......)).))))....))(((((.(..((.(((((((.....))))))).))..(((.(((.(((.(((((((.....))))))).)))))).)))).))))).. ( -44.00)
>DroSim_CAF1 34232 120 + 1
UCUGGAGAGCUCCACCAAGCUGAAGCUAUCGCCGGAGCCGAACUUCAUCAUGAUCAGCGUGGUGUAGAAUGCCACCAUGGACAAGGCCAUCAGGGCCUUGACCAGGUAGUACAGCUUCAA
..(((((..((.(((((.(((((.((....)).((((.....)))).......))))).))))).))..(((.(((.(((.(((((((.....))))))).)))))).)))...))))). ( -45.60)
>DroEre_CAF1 50607 120 + 1
UUUGGAGAGCUCUACCAAGCGGAAAGUGUCGCCGGAGCCGAACUUCAUCAUGAUCAGAGUGGUGUAGAAAGCUACCAUGCUCAAGGCCAUCAGAGCCUUGACCAGGUAGUAGAGCUUCAG
.((((((....)).))))((((......)))).((((((...((.((((((.......)))))).))...((((((.((.((((((((....).))))))).)))))))).).))))).. ( -41.10)
>DroYak_CAF1 22079 120 + 1
UCUGGAGAGCUCUACCAAACUAAAUUCCUCGGUGGAGCUGAACUUCAUCAUGAUCAGAGCGGUGUAAAAUGCCACCAUGCCCAAGGCCAUCAGAGCCUUGACCAGGUAGUACAGCUUCAA
..((((((((((((((..............)))))))))...))))).........((((((((........)))).(((((((((((....).))))))....)))).....))))... ( -36.74)
>consensus
UCUGGAGAGCUCCACCAAACUGAAGCUAUCGCCGGAGCCGAACUUCAUCAUGAUCAGCGUGGUGUAGAAUGCCACCAUGGACAAGGCCAUCAGGGCCUUGACCAGGUAGUACAGCUUCAA
..(((((.(((((....................)))))....((.(((((((.....))))))).))..(((.(((.(((.(((((((.....))))))).)))))).)))...))))). (-30.45 = -32.21 +   1.76)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,072,728 – 21,072,848
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.42
Mean single sequence MFE -45.54
Consensus MFE -38.66
Energy contribution -39.46
Covariance contribution 0.80
Combinations/Pair 1.27
Mean z-score -2.56
Structure conservation index 0.85
SVM decision value 2.97
SVM RNA-class probability 0.997975
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21072728 120 - 23771897
UUGAAGCUGUACUACCUGGUCAAGGCCCUGAUGGCCUUGGCCAUGGUGGCAUUCUACACCACGCUGAUCAUGAUGAAGUUCGGGUCCGGCGAUAGCUUCAGUUUGGUGGAGCUCUCCAGA
((((((((((.((((((((((((((((.....))))))))))).)))))............((((((((.(((......)))))).))))))))))))))).....((((....)))).. ( -53.70)
>DroSec_CAF1 127994 120 - 1
UUGAAGCUGUACUACCUGGUCAAGGCCCUGAUGGCCUUGUCCAUGGUGGCAUUCUACACCACGCUGAUCAUGAUGAAGUUCGGCUCCGGCGAUAGCUUCAGUUUGGUGGAGCUCUCCAGA
((((((((((.((((((((.(((((((.....))))))).))).)))))............(((((....(((......)))....))))))))))))))).....((((....)))).. ( -48.70)
>DroSim_CAF1 34232 120 - 1
UUGAAGCUGUACUACCUGGUCAAGGCCCUGAUGGCCUUGUCCAUGGUGGCAUUCUACACCACGCUGAUCAUGAUGAAGUUCGGCUCCGGCGAUAGCUUCAGCUUGGUGGAGCUCUCCAGA
((((((((((.((((((((.(((((((.....))))))).))).)))))............(((((....(((......)))....))))))))))))))).....((((....)))).. ( -48.60)
>DroEre_CAF1 50607 120 - 1
CUGAAGCUCUACUACCUGGUCAAGGCUCUGAUGGCCUUGAGCAUGGUAGCUUUCUACACCACUCUGAUCAUGAUGAAGUUCGGCUCCGGCGACACUUUCCGCUUGGUAGAGCUCUCCAAA
..((((((((((((..(((((((((((.....))))))))((.(((.((((..((.((.((.........)).)).))...)))))))))........)))..)))))))))).)).... ( -38.80)
>DroYak_CAF1 22079 120 - 1
UUGAAGCUGUACUACCUGGUCAAGGCUCUGAUGGCCUUGGGCAUGGUGGCAUUUUACACCGCUCUGAUCAUGAUGAAGUUCAGCUCCACCGAGGAAUUUAGUUUGGUAGAGCUCUCCAGA
.....(((((((((((((.((((((((.....)))))))).)).))))).....))))..))((((....(((......)))((((.((((((........)))))).))))....)))) ( -37.90)
>consensus
UUGAAGCUGUACUACCUGGUCAAGGCCCUGAUGGCCUUGGCCAUGGUGGCAUUCUACACCACGCUGAUCAUGAUGAAGUUCGGCUCCGGCGAUAGCUUCAGUUUGGUGGAGCUCUCCAGA
((((((((((.((((((((((((((((.....))))))))))).)))))............(((((....(((......)))....))))))))))))))).((((.((....)))))). (-38.66 = -39.46 +   0.80)

alignment

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secondary structure

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Window 0

Location 21,072,768 – 21,072,888
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.58
Mean single sequence MFE -47.06
Consensus MFE -42.64
Energy contribution -43.88
Covariance contribution 1.24
Combinations/Pair 1.03
Mean z-score -3.39
Structure conservation index 0.91
SVM decision value 4.79
SVM RNA-class probability 0.999950
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21072768 120 + 23771897
AACUUCAUCAUGAUCAGCGUGGUGUAGAAUGCCACCAUGGCCAAGGCCAUCAGGGCCUUGACCAGGUAGUACAGCUUCAAUGCGGUGGCCAAGGACACCAGGCAGAGCACCCAGGUGAAC
...((((((.((.((.((.((((((.....((((((.(((.(((((((.....))))))).))).........((......)))))))).....)))))).)).)).))....)))))). ( -51.00)
>DroSec_CAF1 128034 120 + 1
AACUUCAUCAUGAUCAGCGUGGUGUAGAAUGCCACCAUGGACAAGGCCAUCAGGGCCUUGACCAGGUAGUACAGCUUCAAAGCGGUGGCCAAGGACACCAGGCAGAGCACCCAGGUGAAC
...((((((.((.((.((.((((((.....((((((.(((.(((((((.....))))))).))).........(((....))))))))).....)))))).)).)).))....)))))). ( -50.80)
>DroSim_CAF1 34272 120 + 1
AACUUCAUCAUGAUCAGCGUGGUGUAGAAUGCCACCAUGGACAAGGCCAUCAGGGCCUUGACCAGGUAGUACAGCUUCAAAGCGGUGGCCAAGGACACCAGGCAGAGCACCCAGGUGAAC
...((((((.((.((.((.((((((.....((((((.(((.(((((((.....))))))).))).........(((....))))))))).....)))))).)).)).))....)))))). ( -50.80)
>DroEre_CAF1 50647 120 + 1
AACUUCAUCAUGAUCAGAGUGGUGUAGAAAGCUACCAUGCUCAAGGCCAUCAGAGCCUUGACCAGGUAGUAGAGCUUCAGAGCGGUGGCCAAGGACACCAGGCAGAGCACCCAGGUGAAG
..(((((((.((.((.(..((((((.....((((((.((.((((((((....).))))))).)).........(((....))))))))).....))))))..).)).))....))))))) ( -41.90)
>DroYak_CAF1 22119 120 + 1
AACUUCAUCAUGAUCAGAGCGGUGUAAAAUGCCACCAUGCCCAAGGCCAUCAGAGCCUUGACCAGGUAGUACAGCUUCAAGGCGGUGGCCAAUGACACCAGGCAGAGCACCCAGGUGAAC
...((((((...........(((((.....((((((..(((...))).......(((((((...(((......)))))))))))))))).....))))).((........)).)))))). ( -40.80)
>consensus
AACUUCAUCAUGAUCAGCGUGGUGUAGAAUGCCACCAUGGACAAGGCCAUCAGGGCCUUGACCAGGUAGUACAGCUUCAAAGCGGUGGCCAAGGACACCAGGCAGAGCACCCAGGUGAAC
...((((((.((.((.((.((((((.....((((((.(((.(((((((.....))))))).))).........((......)))))))).....)))))).)).)).))....)))))). (-42.64 = -43.88 +   1.24)

alignment

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secondary structure

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dotplot

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Window 1

Location 21,072,768 – 21,072,888
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.58
Mean single sequence MFE -44.50
Consensus MFE -41.40
Energy contribution -42.32
Covariance contribution 0.92
Combinations/Pair 1.08
Mean z-score -2.10
Structure conservation index 0.93
SVM decision value 3.41
SVM RNA-class probability 0.999166
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21072768 120 - 23771897
GUUCACCUGGGUGCUCUGCCUGGUGUCCUUGGCCACCGCAUUGAAGCUGUACUACCUGGUCAAGGCCCUGAUGGCCUUGGCCAUGGUGGCAUUCUACACCACGCUGAUCAUGAUGAAGUU
.((((.(...(((.((.((.((((((.....((((((((......)).........(((((((((((.....))))))))))).)))))).....)))))).)).)).)))).))))... ( -49.90)
>DroSec_CAF1 128034 120 - 1
GUUCACCUGGGUGCUCUGCCUGGUGUCCUUGGCCACCGCUUUGAAGCUGUACUACCUGGUCAAGGCCCUGAUGGCCUUGUCCAUGGUGGCAUUCUACACCACGCUGAUCAUGAUGAAGUU
.((((.(...(((.((.((.((((((.....(((((((((....))).........(((.(((((((.....))))))).))).)))))).....)))))).)).)).)))).))))... ( -47.30)
>DroSim_CAF1 34272 120 - 1
GUUCACCUGGGUGCUCUGCCUGGUGUCCUUGGCCACCGCUUUGAAGCUGUACUACCUGGUCAAGGCCCUGAUGGCCUUGUCCAUGGUGGCAUUCUACACCACGCUGAUCAUGAUGAAGUU
.((((.(...(((.((.((.((((((.....(((((((((....))).........(((.(((((((.....))))))).))).)))))).....)))))).)).)).)))).))))... ( -47.30)
>DroEre_CAF1 50647 120 - 1
CUUCACCUGGGUGCUCUGCCUGGUGUCCUUGGCCACCGCUCUGAAGCUCUACUACCUGGUCAAGGCUCUGAUGGCCUUGAGCAUGGUAGCUUUCUACACCACUCUGAUCAUGAUGAAGUU
(((((...((((.....))))(((((....(((....(((....))).....((((((.((((((((.....)))))))).)).)))))))....))))).............))))).. ( -38.50)
>DroYak_CAF1 22119 120 - 1
GUUCACCUGGGUGCUCUGCCUGGUGUCAUUGGCCACCGCCUUGAAGCUGUACUACCUGGUCAAGGCUCUGAUGGCCUUGGGCAUGGUGGCAUUUUACACCGCUCUGAUCAUGAUGAAGUU
...((((.((((.....))))))))(((((((((((.(((((((....(.....)....)))))))...).)))))..((((..((((........)))))))).......))))).... ( -39.50)
>consensus
GUUCACCUGGGUGCUCUGCCUGGUGUCCUUGGCCACCGCUUUGAAGCUGUACUACCUGGUCAAGGCCCUGAUGGCCUUGGCCAUGGUGGCAUUCUACACCACGCUGAUCAUGAUGAAGUU
.((((.(...(((.((.((.((((((.....((((((((......)).........(((((((((((.....))))))))))).)))))).....)))))).)).)).)))).))))... (-41.40 = -42.32 +   0.92)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,072,808 – 21,072,928
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.00
Mean single sequence MFE -44.63
Consensus MFE -39.24
Energy contribution -40.28
Covariance contribution 1.04
Combinations/Pair 1.03
Mean z-score -2.03
Structure conservation index 0.88
SVM decision value 2.50
SVM RNA-class probability 0.994716
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21072808 120 + 23771897
CCAAGGCCAUCAGGGCCUUGACCAGGUAGUACAGCUUCAAUGCGGUGGCCAAGGACACCAGGCAGAGCACCCAGGUGAACACCAAGUACUCCGGAUGGGCGCACUGCCCCUCAACAUCCG
.(((((((.....)))))))....((.(((((.((......))(((((((..(....)..)))....(((....)))..))))..)))))))((((((((.....))))......)))). ( -46.20)
>DroSec_CAF1 128074 120 + 1
ACAAGGCCAUCAGGGCCUUGACCAGGUAGUACAGCUUCAAAGCGGUGGCCAAGGACACCAGGCAGAGCACCCAGGUGAACACCAAGUACUCCGGAUGGGCACAGUGCCCCUCAACAUCCG
.(((((((.....)))))))....((.(((((.(((....)))(((((((..(....)..)))....(((....)))..))))..)))))))((((((((.....))))......)))). ( -47.30)
>DroSim_CAF1 34312 120 + 1
ACAAGGCCAUCAGGGCCUUGACCAGGUAGUACAGCUUCAAAGCGGUGGCCAAGGACACCAGGCAGAGCACCCAGGUGAACACCAAGUACUCCGGAUGGGCACAGUGCCCCUCAACAUCCG
.(((((((.....)))))))....((.(((((.(((....)))(((((((..(....)..)))....(((....)))..))))..)))))))((((((((.....))))......)))). ( -47.30)
>DroEre_CAF1 50687 120 + 1
UCAAGGCCAUCAGAGCCUUGACCAGGUAGUAGAGCUUCAGAGCGGUGGCCAAGGACACCAGGCAGAGCACCCAGGUGAAGACCAAGUACUCCGGAUGGGCGCACUCCCCCUCCACGUCCG
....(((((((...((((.....))))......(((....))))))))))..((((....((.....(((....)))....)).........(((.(((.......))).)))..)))). ( -39.70)
>DroYak_CAF1 22159 120 + 1
CCAAGGCCAUCAGAGCCUUGACCAGGUAGUACAGCUUCAAGGCGGUGGCCAAUGACACCAGGCAGAGCACCCAGGUGAACACCAAGUACUCCGGAUGGGCGCACAUCCCCUCACCAUCCG
.(((((((....).))))))....((.(((((.(((....)))(((((((..........)))....(((....)))..))))..)))))))((((((...............)))))). ( -42.66)
>consensus
ACAAGGCCAUCAGGGCCUUGACCAGGUAGUACAGCUUCAAAGCGGUGGCCAAGGACACCAGGCAGAGCACCCAGGUGAACACCAAGUACUCCGGAUGGGCGCACUGCCCCUCAACAUCCG
.(((((((.....)))))))....((.(((((.((......))(((((((..........)))....(((....)))..))))..)))))))((((((((.....))))......)))). (-39.24 = -40.28 +   1.04)

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 13:01:32 2006