Locus 4561

Sequence ID X_DroMel_CAF1
Location 11,988,256 – 11,988,438
Length 182
Max. P 0.960804
window7498 window7499 window7500 window7501

overview

Window 8

Location 11,988,256 – 11,988,364
Length 108
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 91.36
Mean single sequence MFE -20.32
Consensus MFE -15.70
Energy contribution -15.38
Covariance contribution -0.32
Combinations/Pair 1.09
Mean z-score -1.79
Structure conservation index 0.77
SVM decision value 0.53
SVM RNA-class probability 0.769639
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11988256 108 + 22224390
AUUUCCAUCACUGCGGCAACAUCUCAACCAACAUUUUCAACGCCG---CC--ACUAAAUUCCUUUGUAGCCAAAUCAAAUUUUUCGCCAACGGGGGCGUUGCAACCGCACUAU
...........(((((..................((.(((((((.---((--((...........)).((.(((.......))).))....)).))))))).))))))).... ( -20.16)
>DroSec_CAF1 27616 110 + 1
AUUUCCAUCACUGUGGAAACAUCUCAACCAACAUUUUCAACGCCACCACC--ACUAAAUUCCUUUGUAGCCAAAUCAAAUUUUUCGCCAAAG-GGGCGUUGCAACCGCACUGU
.(((((((....)))))))..................(((((((......--........((((((..((.(((.......))).)))))))-))))))))............ ( -21.03)
>DroSim_CAF1 28849 110 + 1
AUUUCCAUCACUGCGGCAACAUCUCAACCAACAUUUUCAACGCCACCACC--ACUAAAUUCCUUUGUAGCCAAAUCAAAUUUUUCGCCAAAG-GGGCGUUGCAACCGCACUGU
........((.(((((..................((.(((((((......--........((((((..((.(((.......))).)))))))-)))))))).))))))).)). ( -20.89)
>DroEre_CAF1 26541 112 + 1
AUUUCCAUCACUGCGGCAACAUCUCAACCAACAUUUUCAGCGCCACCACUAACAUAAAUUCCUUUGUAGCCAAAUCAAAUUUUUCGCCAAAG-GGGCGUUGCAACCGCACUGU
........((.(((((..................((.(((((((................((((((..((.(((.......))).)))))))-)))))))).))))))).)). ( -20.75)
>DroYak_CAF1 27682 106 + 1
AUUUCCAUCAUUGCGGUAACAUCUCAACCAACAUUUUCAACGCCACU-----CGUAAAUUCCUUUGUAGCCAAAUCAAAUUUUCCGCCA-AG-GGGCGUUGCAACCGCACAGU
...........((((((....................(((((((...-----..........((((....)))).........((....-.)-))))))))..)))))).... ( -18.75)
>consensus
AUUUCCAUCACUGCGGCAACAUCUCAACCAACAUUUUCAACGCCACCACC__ACUAAAUUCCUUUGUAGCCAAAUCAAAUUUUUCGCCAAAG_GGGCGUUGCAACCGCACUGU
...........(((((..................((.(((((((...........(((((..((((....))))...)))))............))))))).))))))).... (-15.70 = -15.38 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,988,256 – 11,988,364
Length 108
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 91.36
Mean single sequence MFE -31.36
Consensus MFE -23.96
Energy contribution -24.32
Covariance contribution 0.36
Combinations/Pair 1.10
Mean z-score -1.58
Structure conservation index 0.76
SVM decision value 0.09
SVM RNA-class probability 0.577230
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11988256 108 - 22224390
AUAGUGCGGUUGCAACGCCCCCGUUGGCGAAAAAUUUGAUUUGGCUACAAAGGAAUUUAGU--GG---CGGCGUUGAAAAUGUUGGUUGAGAUGUUGCCGCAGUGAUGGAAAU
......(.((..(..((((......))))..((((((..((((....)))).)))))).((--((---(((((((...(((....)))..))))))))))).)..)).).... ( -31.10)
>DroSec_CAF1 27616 110 - 1
ACAGUGCGGUUGCAACGCCC-CUUUGGCGAAAAAUUUGAUUUGGCUACAAAGGAAUUUAGU--GGUGGUGGCGUUGAAAAUGUUGGUUGAGAUGUUUCCACAGUGAUGGAAAU
.(((.(((....((((((((-(..(.((...((((((..((((....)))).)))))).))--.).)).)))))))....)))...)))....(((((((......))))))) ( -28.60)
>DroSim_CAF1 28849 110 - 1
ACAGUGCGGUUGCAACGCCC-CUUUGGCGAAAAAUUUGAUUUGGCUACAAAGGAAUUUAGU--GGUGGUGGCGUUGAAAAUGUUGGUUGAGAUGUUGCCGCAGUGAUGGAAAU
.((.((((((..((((((((-(..(.((...((((((..((((....)))).)))))).))--.).)).)))))))..((((((......)))))))))))).))........ ( -34.10)
>DroEre_CAF1 26541 112 - 1
ACAGUGCGGUUGCAACGCCC-CUUUGGCGAAAAAUUUGAUUUGGCUACAAAGGAAUUUAUGUUAGUGGUGGCGCUGAAAAUGUUGGUUGAGAUGUUGCCGCAGUGAUGGAAAU
.((.((((((.(((.(((((-(.((((((..((((((..((((....)))).)))))).)))))).)).)))((..(.....)..))...).))).)))))).))........ ( -33.50)
>DroYak_CAF1 27682 106 - 1
ACUGUGCGGUUGCAACGCCC-CU-UGGCGGAAAAUUUGAUUUGGCUACAAAGGAAUUUACG-----AGUGGCGUUGAAAAUGUUGGUUGAGAUGUUACCGCAAUGAUGGAAAU
....((((((..(((((((.-((-((.....((((((..((((....)))).)))))).))-----)).)))))))..((((((......))))))))))))........... ( -29.50)
>consensus
ACAGUGCGGUUGCAACGCCC_CUUUGGCGAAAAAUUUGAUUUGGCUACAAAGGAAUUUAGU__GGUGGUGGCGUUGAAAAUGUUGGUUGAGAUGUUGCCGCAGUGAUGGAAAU
.((.((((((.(((.((((......))))..((((((..((((....)))).))))))..........((((((.....)))))).......))).)))))).))........ (-23.96 = -24.32 +   0.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,988,296 – 11,988,404
Length 108
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 91.00
Mean single sequence MFE -25.54
Consensus MFE -21.36
Energy contribution -21.76
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.84
SVM decision value 1.52
SVM RNA-class probability 0.960804
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11988296 108 + 22224390
CGCCG---CC--ACUAAAUUCCUUUGUAGCCAAAUCAAAUUUUUCGCCAACGGGGGCGUUGCAACCGCACUAUGGCCACGCCCACUUUUGGCCAGCACACCGAAAUCCAUUAA
.((.(---(.--((...........)).))...............(((((.((((((((.((............)).)))))).)).)))))..))................. ( -25.10)
>DroSec_CAF1 27656 110 + 1
CGCCACCACC--ACUAAAUUCCUUUGUAGCCAAAUCAAAUUUUUCGCCAAAG-GGGCGUUGCAACCGCACUGUGGCCACGCCCACUAUUGGCCAGCACACCGAAAUCCAUUAA
.((((.....--.........(((((..((.(((.......))).)))))))-((((((.((.((......)).)).)))))).....))))..................... ( -24.70)
>DroSim_CAF1 28889 110 + 1
CGCCACCACC--ACUAAAUUCCUUUGUAGCCAAAUCAAAUUUUUCGCCAAAG-GGGCGUUGCAACCGCACUGUGGCCACGCCCACUUUUGGCCAGCACACCGAAAUCCAUUAA
.((((.....--.........(((((..((.(((.......))).)))))))-((((((.((.((......)).)).)))))).....))))..................... ( -24.70)
>DroEre_CAF1 26581 111 + 1
CGCCACCACUAACAUAAAUUCCUUUGUAGCCAAAUCAAAUUUUUCGCCAAAG-GGGCGUUGCAACCGCACUGUGGCCACGCCCCC-CUUGGCCAGCACACCGAAAUCCAUUAA
.((...................((((....))))...........(((((.(-((((((.((.((......)).)).))))))).-.)))))..))................. ( -26.30)
>DroYak_CAF1 27722 106 + 1
CGCCACU-----CGUAAAUUCCUUUGUAGCCAAAUCAAAUUUUCCGCCA-AG-GGGCGUUGCAACCGCACAGUGGCAACGCCCACUUUUGGCCAGCACACCAAAAUCCAUUAA
.((....-----..........((((....))))...........((((-(.-(((((((((.((......)).)))))))))....)))))..))................. ( -26.90)
>consensus
CGCCACCACC__ACUAAAUUCCUUUGUAGCCAAAUCAAAUUUUUCGCCAAAG_GGGCGUUGCAACCGCACUGUGGCCACGCCCACUUUUGGCCAGCACACCGAAAUCCAUUAA
.((...................((((....))))...........(((((...((((((.((.((......)).)).))))))....)))))..))................. (-21.36 = -21.76 +   0.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,988,327 – 11,988,438
Length 111
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.28
Mean single sequence MFE -30.52
Consensus MFE -15.10
Energy contribution -17.49
Covariance contribution 2.39
Combinations/Pair 1.05
Mean z-score -2.36
Structure conservation index 0.49
SVM decision value 0.57
SVM RNA-class probability 0.786664
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11988327 111 + 22224390
AA---AUUUUUCGCCAACGGGGGCGUUGCAACCGCACUAUGGCCACGCCCACUUUUGGCCAGCACACCGAAAUCCAUUAAGUGCAUUUUGCAAAAGAACUAACACUC------GAAUUCC
..---....((((((((.((((((((.((............)).)))))).)).)))))..((((...............)))).......................------))).... ( -27.46)
>DroSec_CAF1 27690 109 + 1
AA---AUUUUUCGCCAAAG-GGGCGUUGCAACCGCACUGUGGCCACGCCCACUAUUGGCCAGCACACCGAAAUCCAUUAAGUGCAUUUUG-AAAAGAACUCAGACUC------GCAUUCC
..---.(((((((((((((-((((((.((.((......)).)).)))))).)).)))))..((((...............)))).....)-)))))...........------....... ( -30.46)
>DroSim_CAF1 28923 109 + 1
AA---AUUUUUCGCCAAAG-GGGCGUUGCAACCGCACUGUGGCCACGCCCACUUUUGGCCAGCACACCGAAAUCCAUUAAGUGCAUUUUG-AAAAGAACUCACACUC------GCAUUCC
..---.(((((((((((((-((((((.((.((......)).)).)))))).).))))))..((((...............)))).....)-)))))...........------....... ( -30.46)
>DroEre_CAF1 26617 114 + 1
AA---AUUUUUCGCCAAAG-GGGCGUUGCAACCGCACUGUGGCCACGCCCCC-CUUGGCCAGCACACCGAAAUCCAUUAAGUGCAUUGUG-AAAAGAACUCACACUCCUUCCAUGUUUCC
..---.......(((((.(-((((((.((.((......)).)).))))))).-.)))))..((((...............))))..((((-(.......)))))................ ( -32.76)
>DroYak_CAF1 27753 108 + 1
AA---AUUUUCCGCCA-AG-GGGCGUUGCAACCGCACAGUGGCAACGCCCACUUUUGGCCAGCACACCAAAAUCCAUUAAGUGCAUUUUG-AAAAGAACUCACACUC------UCUUUCC
..---.(((((.((((-(.-(((((((((.((......)).)))))))))....)))))..((((...............)))).....)-))))............------....... ( -31.66)
>DroPer_CAF1 129225 90 + 1
AACCAGUUUUGUGGCUGCGGGAG---GGGAAUCGCACUGCGGCCACGCCCACU--UGGC---------------CAUUAAGUGCAUUUCA-AA---CUCUCAGUCUC------UGAUUCC
...(((......(((((..((((---.(((((.(((((..(((((........--))))---------------)....)))))))))).-..---))))))))).)------))..... ( -30.30)
>consensus
AA___AUUUUUCGCCAAAG_GGGCGUUGCAACCGCACUGUGGCCACGCCCACUUUUGGCCAGCACACCGAAAUCCAUUAAGUGCAUUUUG_AAAAGAACUCACACUC______GCAUUCC
............(((((...((((((.((.((......)).)).))))))....)))))..((((...............)))).................................... (-15.10 = -17.49 +   2.39)

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 11:28:11 2006