Locus 880

Sequence ID 2R_DroMel_CAF1
Location 4,033,272 – 4,033,512
Length 240
Max. P 0.872800
window1530 window1531 window1532 window1533

overview

Window 0

Location 4,033,272 – 4,033,392
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.00
Mean single sequence MFE -50.38
Consensus MFE -39.40
Energy contribution -40.16
Covariance contribution 0.76
Combinations/Pair 1.11
Mean z-score -1.92
Structure conservation index 0.78
SVM decision value 0.88
SVM RNA-class probability 0.872800
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4033272 120 + 20766785
CGUGGGCACCGCCUUGCCACCAAUCCUGGUCGCCGUGCUCGUUAUUGCCGGCGAUAUGGUCGGUGCUGCUGGCGCUGCCACAAUAUUGGCAGUUGUCAUUGUUGGCCACGCCUCUGUGGC
....((((.((((..((((((.(((...(((((((.((........)))))))))..))).))))..)).)))).)))).(((((.((((....)))).)))))((((((....)))))) ( -55.30)
>DroSec_CAF1 15923 120 + 1
CGUGGGCACCGCCUUGCCACCAAUCCUGGUCGCCGUGCUCGUUAGUGCCGGCGAUAUGGUCGGUGCGGAUGGACCUGCCACAAUAUUGGCAGUUGUCAUUGUUGGCCACGCCUCUGUGGC
.((((.((((((((.(((((((....)))((((((.((.(....).))))))))..)))).)).))))...(((((((((......))))))..))).....)).))))(((.....))) ( -53.70)
>DroSim_CAF1 18067 120 + 1
CGUGGGCACCGCCUUGCCACCAAUCCUGGUGGCCGUGCUCGCUAGUGCCGGCGAUAUGGUCGGUGCGGCUGGCGCUGCCACAAUAUUGGCAGUUGUCAUUGUUGGCCACGCCUCUGUGGC
.((((((((......(((((((....))))))).))))))))..(..(((((......)))))..)(((..(((((((((......))))))).......))..)))..(((.....))) ( -59.31)
>DroEre_CAF1 15274 120 + 1
CGUGGGCACCGACUUGCCACCAAUCCUGGUCUCCGUGCUCGUUAGUGCCGGCGAUAUGGUCGGUGCGGCUGGCACUGCCACAAUAUUGGCAGUUGUCAUUGUUGGCCACGCCUCUGUGGC
.(((((((((((((((((((((....))))....(..((....))..).))))....)))))))))...(((((((((((......)))))).))))).......))))(((.....))) ( -52.10)
>DroYak_CAF1 19022 105 + 1
CGUGGGCACCGCCUUACCACCGAUCCUGCUCUCCGUGCUCGUUAGUGUUGGCAAUAUGGUCGGU---------------ACAAUAUUGGCAGUUGUCAUUGUUGGCCACGCCUCUGUGGC
.((((((...))).))).(((((((.((((....(..((....))..).))))....)))))))---------------.(((((.((((....)))).)))))((((((....)))))) ( -31.50)
>consensus
CGUGGGCACCGCCUUGCCACCAAUCCUGGUCGCCGUGCUCGUUAGUGCCGGCGAUAUGGUCGGUGCGGCUGGCGCUGCCACAAUAUUGGCAGUUGUCAUUGUUGGCCACGCCUCUGUGGC
.((((((((((....(((((((....)))((((((.((........))))))))..))))))))))..............(((((.((((....)))).))))).))))(((.....))) (-39.40 = -40.16 +   0.76)

alignment

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secondary structure

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Window 1

Location 4,033,272 – 4,033,392
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.00
Mean single sequence MFE -46.10
Consensus MFE -34.24
Energy contribution -35.86
Covariance contribution 1.62
Combinations/Pair 1.06
Mean z-score -1.92
Structure conservation index 0.74
SVM decision value 0.44
SVM RNA-class probability 0.737683
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4033272 120 - 20766785
GCCACAGAGGCGUGGCCAACAAUGACAACUGCCAAUAUUGUGGCAGCGCCAGCAGCACCGACCAUAUCGCCGGCAAUAACGAGCACGGCGACCAGGAUUGGUGGCAAGGCGGUGCCCACG
(((.....)))((((.((..........((((((......))))))((((.((..((((((((...((((((((........)).))))))...)).))))))))..)))).)).)))). ( -51.10)
>DroSec_CAF1 15923 120 - 1
GCCACAGAGGCGUGGCCAACAAUGACAACUGCCAAUAUUGUGGCAGGUCCAUCCGCACCGACCAUAUCGCCGGCACUAACGAGCACGGCGACCAGGAUUGGUGGCAAGGCGGUGCCCACG
(((.....)))((((........(((..((((((......))))))))).....((((((.((....(((((((.(....).)).)))))(((......))).....)))))))))))). ( -50.70)
>DroSim_CAF1 18067 120 - 1
GCCACAGAGGCGUGGCCAACAAUGACAACUGCCAAUAUUGUGGCAGCGCCAGCCGCACCGACCAUAUCGCCGGCACUAGCGAGCACGGCCACCAGGAUUGGUGGCAAGGCGGUGCCCACG
........(((.((((((....))....((((((......)))))).)))))))((((((.((...((((........)))).....((((((......))))))..))))))))..... ( -50.50)
>DroEre_CAF1 15274 120 - 1
GCCACAGAGGCGUGGCCAACAAUGACAACUGCCAAUAUUGUGGCAGUGCCAGCCGCACCGACCAUAUCGCCGGCACUAACGAGCACGGAGACCAGGAUUGGUGGCAAGUCGGUGCCCACG
(((.....)))((((.((....((((.(((((((......)))))))....(((..(((((((...((.(((((.(....).)).))).))...)).))))))))..)))).)).)))). ( -48.00)
>DroYak_CAF1 19022 105 - 1
GCCACAGAGGCGUGGCCAACAAUGACAACUGCCAAUAUUGU---------------ACCGACCAUAUUGCCAACACUAACGAGCACGGAGAGCAGGAUCGGUGGUAAGGCGGUGCCCACG
(((.....)))((((.......((........)).....((---------------((((.((.(((..((....(....).((.......))......))..))).)))))))))))). ( -30.20)
>consensus
GCCACAGAGGCGUGGCCAACAAUGACAACUGCCAAUAUUGUGGCAGCGCCAGCCGCACCGACCAUAUCGCCGGCACUAACGAGCACGGCGACCAGGAUUGGUGGCAAGGCGGUGCCCACG
(((((......)))))......((...((((((.......(((.....)))....((((((((...((((((((.(....).)).))))))...)).))))))....))))))...)).. (-34.24 = -35.86 +   1.62)

alignment

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secondary structure

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Window 2

Location 4,033,312 – 4,033,432
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.17
Mean single sequence MFE -44.34
Consensus MFE -35.62
Energy contribution -36.80
Covariance contribution 1.18
Combinations/Pair 1.13
Mean z-score -1.76
Structure conservation index 0.80
SVM decision value 0.82
SVM RNA-class probability 0.858174
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4033312 120 + 20766785
GUUAUUGCCGGCGAUAUGGUCGGUGCUGCUGGCGCUGCCACAAUAUUGGCAGUUGUCAUUGUUGGCCACGCCUCUGUGGCAUUUGCAUAGCCAUGGGUUAGUUCGGCAUCCGGAUUGAAU
.........((((...(((.((((((.....)))))))))(((((.((((....)))).)))))....))))((((((((.........))))))))(((((((((...))))))))).. ( -44.60)
>DroSec_CAF1 15963 120 + 1
GUUAGUGCCGGCGAUAUGGUCGGUGCGGAUGGACCUGCCACAAUAUUGGCAGUUGUCAUUGUUGGCCACGCCUCUGUGGCAUUUGCAUAGCCAUGGGUUAGUGCGGCAUCCGGAUUGAAU
....(..(((((......)))))..)(((((..(((((((((.....(((.((.((((....)))).)))))..)))))))...((((((((...)))).)))))))))))......... ( -47.20)
>DroSim_CAF1 18107 120 + 1
GCUAGUGCCGGCGAUAUGGUCGGUGCGGCUGGCGCUGCCACAAUAUUGGCAGUUGUCAUUGUUGGCCACGCCUCUGUGGCAUUUGCAUAGCCAUGGGUUAGUGCGGCGUGCUCAUUGAAU
(((.(..(((((......)))))..))))(((((((((((......)))))).)))))....((..((((((.(((((((.........)))))))((....))))))))..))...... ( -50.40)
>DroEre_CAF1 15314 120 + 1
GUUAGUGCCGGCGAUAUGGUCGGUGCGGCUGGCACUGCCACAAUAUUGGCAGUUGUCAUUGUUGGCCACGCCUCUGUGGCAUUUGCAUAGCCAUGGGUUAGUGCGGCAUCCGGAUUCAAU
....(..(((((......)))))..)((((((((.(((((((.....(((.((.((((....)))).)))))..)))))))..))).))))).((((((....(((...))))))))).. ( -47.40)
>DroYak_CAF1 19062 105 + 1
GUUAGUGUUGGCAAUAUGGUCGGU---------------ACAAUAUUGGCAGUUGUCAUUGUUGGCCACGCCUCUGUGGCAUUUGCAUAGCCAUGGGUUAGUGCGGCAUCCGGAUUGAAU
(((.(..(((((..((((((..((---------------((((((.((((....)))).)))))((((((....))))))...)))...)))))).)))))..))))............. ( -32.10)
>consensus
GUUAGUGCCGGCGAUAUGGUCGGUGCGGCUGGCGCUGCCACAAUAUUGGCAGUUGUCAUUGUUGGCCACGCCUCUGUGGCAUUUGCAUAGCCAUGGGUUAGUGCGGCAUCCGGAUUGAAU
....((((((((((..(((.((((((.....)))))))))(((((.((((....)))).)))))((((((....))))))..)))).(((((...)))))...))))))........... (-35.62 = -36.80 +   1.18)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,033,392 – 4,033,512
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.67
Mean single sequence MFE -31.32
Consensus MFE -27.83
Energy contribution -27.91
Covariance contribution 0.08
Combinations/Pair 1.14
Mean z-score -1.27
Structure conservation index 0.89
SVM decision value 0.39
SVM RNA-class probability 0.717260
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4033392 120 + 20766785
AUUUGCAUAGCCAUGGGUUAGUUCGGCAUCCGGAUUGAAUUUUAUAUCGUCCCUCUGAACACUCUGGCCAAUCUUAUUGGUCUUGUCCGACUCGCUGCGCUUUGUUUUUGCUAGUAUUAU
....(((.(((((((((((.((((((.....((((.((........))))))..)))))).....(((((((...)))))))......)))))).)).))).)))............... ( -27.40)
>DroSec_CAF1 16043 120 + 1
AUUUGCAUAGCCAUGGGUUAGUGCGGCAUCCGGAUUGAAUUUUAUAUCGUCCCUCUGAACACUCUGGCCAAUCUUAUUGGUCUUGUCCGACUCGCUGCGCUUUGUUUUUGCUGGCAAUAU
..((((.((((........((((((((...(((((...........(((......))).......(((((((...)))))))..)))))....))))))))........))))))))... ( -32.49)
>DroSim_CAF1 18187 120 + 1
AUUUGCAUAGCCAUGGGUUAGUGCGGCGUGCUCAUUGAAUUUUAUAUCGUACCUCUGAACACUCUGGCCAAUCUUAUUGGUCUUGUCCGACUCGCCGCGCUUUGUUUUUGCUGGCAACAU
..((((.((((........(((((((((((.(((..(...............)..))).)))...(((((((...)))))))...........))))))))........))))))))... ( -33.55)
>DroEre_CAF1 15394 120 + 1
AUUUGCAUAGCCAUGGGUUAGUGCGGCAUCCGGAUUCAAUUUCAUUUCGUCCCUCUGAACACUCAGGCCAAUCUUAUUGGUCUUUUCCGACCCGCUGCGCUUUGUUUUUGCUGGCUUUAU
....((.((((........((((((((...((((...........((((......)))).....((((((((...))))))))..))))....))))))))........))))))..... ( -30.79)
>DroYak_CAF1 19127 120 + 1
AUUUGCAUAGCCAUGGGUUAGUGCGGCAUCCGGAUUGAAUUUUAUUUCGUCCCUCCGAACACUCAGGCCAAUCUUAUUGGUCUUUUCCGACCCGCUGCGCUUUGUUUUUGCUGGUAUUAU
...(((.((((........((((((((...((((.((((......))))....)))).......((((((((...))))))))..........))))))))........))))))).... ( -32.39)
>consensus
AUUUGCAUAGCCAUGGGUUAGUGCGGCAUCCGGAUUGAAUUUUAUAUCGUCCCUCUGAACACUCUGGCCAAUCUUAUUGGUCUUGUCCGACUCGCUGCGCUUUGUUUUUGCUGGCAUUAU
...(((.((((........((((((((...((((............(((......))).......(((((((...)))))))...))))....))))))))........))))))).... (-27.83 = -27.91 +   0.08)

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 09:49:52 2006