Locus 3704

Sequence ID X_DroMel_CAF1
Location 9,868,713 – 9,868,948
Length 235
Max. P 0.933815
window6063 window6064 window6065 window6066 window6067 window6068

overview

Window 3

Location 9,868,713 – 9,868,831
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.28
Mean single sequence MFE -27.40
Consensus MFE -20.50
Energy contribution -22.50
Covariance contribution 2.00
Combinations/Pair 1.03
Mean z-score -2.57
Structure conservation index 0.75
SVM decision value 1.23
SVM RNA-class probability 0.933815
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9868713 118 - 22224390
GUUUGGCGAAAGUCAAAGCGGCUAAACCACGAUGAGGUCUACGAA-AAUGUCAUUA-AAAAAACGGCAACAUUUAAAGUUUUAAUUGAAAGAUAAGAUAGCAAAGUGUUGCUGAUUUUAU
.((((((....))))))(.((.....)).)(((((.((.......-.)).))))).-.((((.(((((((((((...((((((.((....))))))))....))))))))))).)))).. ( -29.30)
>DroSec_CAF1 13435 119 - 1
GUUUGGCGAAAGUCAAAGCGGCUAAACCACGAUGAGGUCCACAAAAAAUUUCAUUA-AAAAAACGGCAACUUUUAAGCUUUUAAUUAAAAGAUAAGAUAGCAACGUGUUGCUGAUUUUAU
.((((((....))))))((((.....))..((((((((.........)))))))).-........))..(((((((........)))))))((((((((((((....))))).))))))) ( -27.10)
>DroSim_CAF1 13598 119 - 1
GUUUGGCGAAAGUCAAAGCGGCUAAACCACGAUGAGGUCCACAAAAAAUUUCAUUA-AAAAAACGGCAACUUUUAAGCUUUUAAUUAAAAGAUAAGAUAGCAAAGUGUUGCUGAUUUUAU
.((((((....))))))((((.....))..((((((((.........)))))))).-........))..(((((((........)))))))((((((((((((....))))).))))))) ( -25.90)
>DroYak_CAF1 13033 107 - 1
GUUUGGCGAAAGUCAAAGCGGCUAAGCCACGA-------------AAAUUGCAUUACAAAAAACGGCAGCUCUUAACUUUUUAAUUGAAAGAUAAGAUAGCAAAGUGUUGCUGAUUUUAU
.((((((....))))))(.(((...))).)..-------------.............((((.(((((((.(((..((.(((.(((....))).))).))..))).))))))).)))).. ( -27.30)
>consensus
GUUUGGCGAAAGUCAAAGCGGCUAAACCACGAUGAGGUCCACAAAAAAUUUCAUUA_AAAAAACGGCAACUUUUAAGCUUUUAAUUAAAAGAUAAGAUAGCAAAGUGUUGCUGAUUUUAU
.((((((....))))))((((.....))..((((((((.........))))))))..........))..(((((((........)))))))((((((((((((....))))).))))))) (-20.50 = -22.50 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 9,868,753 – 9,868,868
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.58
Mean single sequence MFE -27.12
Consensus MFE -19.31
Energy contribution -19.12
Covariance contribution -0.19
Combinations/Pair 1.06
Mean z-score -1.43
Structure conservation index 0.71
SVM decision value -0.02
SVM RNA-class probability 0.523429
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9868753 115 + 22224390
AACUUUAAAUGUUGCCGUUUUUU-UAAUGACAUU-UUCGUAGACCUCAUCGUGGUUUAGCCGCUUUGACUUUCGCCAAACAUCUGGCCAAAAGUGGCAUCCCCC---CUCCACGCUUGCC
......((((((...((((....-.)))))))))-)...((((((.......))))))((((((((.......((((......))))..)))))))).......---............. ( -23.30)
>DroSec_CAF1 13475 116 + 1
AAGCUUAAAAGUUGCCGUUUUUU-UAAUGAAAUUUUUUGUGGACCUCAUCGUGGUUUAGCCGCUUUGACUUUCGCCAAACAUCUGGCCAAAAGUGGCAUCCCCC---UUCCACGCUUGCC
((((..(((((((..((((....-.)))).))))))).(((((((.......))....((((((((.......((((......))))..)))))))).......---.)))))))))... ( -30.00)
>DroSim_CAF1 13638 116 + 1
AAGCUUAAAAGUUGCCGUUUUUU-UAAUGAAAUUUUUUGUGGACCUCAUCGUGGUUUAGCCGCUUUGACUUUCGCCAAACAUCUGGCCAAAAGUGGCAUCCCCC---CACCACGCUUGCC
((((..(((((((..((((....-.)))).))))))).(((((((.......)))...((((((((.......((((......))))..)))))))).......---..))))))))... ( -30.10)
>DroYak_CAF1 13073 107 + 1
AAAGUUAAGAGCUGCCGUUUUUUGUAAUGCAAUUU-------------UCGUGGCUUAGCCGCUUUGACUUUCGCCAAACAUCUGGCCAAAAGUGGCAUCCCCCCCACUCCACACUUGCC
.((((...((((..(.(....(((.....)))...-------------.))..)))).((((((((.......((((......))))..))))))))................))))... ( -25.10)
>consensus
AAGCUUAAAAGUUGCCGUUUUUU_UAAUGAAAUUUUUUGUGGACCUCAUCGUGGUUUAGCCGCUUUGACUUUCGCCAAACAUCUGGCCAAAAGUGGCAUCCCCC___CUCCACGCUUGCC
............((((..................................(((((...)))))....(((((.((((......))))..)))))))))...................... (-19.31 = -19.12 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 9,868,753 – 9,868,868
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.58
Mean single sequence MFE -31.98
Consensus MFE -24.84
Energy contribution -26.40
Covariance contribution 1.56
Combinations/Pair 1.03
Mean z-score -1.46
Structure conservation index 0.78
SVM decision value 0.07
SVM RNA-class probability 0.568353
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9868753 115 - 22224390
GGCAAGCGUGGAG---GGGGGAUGCCACUUUUGGCCAGAUGUUUGGCGAAAGUCAAAGCGGCUAAACCACGAUGAGGUCUACGAA-AAUGUCAUUA-AAAAAACGGCAACAUUUAAAGUU
((((..(((((((---(.((....))...(((((((.(...((((((....)))))).)))))))))).(.....).))))))..-..))))....-.......(....).......... ( -29.70)
>DroSec_CAF1 13475 116 - 1
GGCAAGCGUGGAA---GGGGGAUGCCACUUUUGGCCAGAUGUUUGGCGAAAGUCAAAGCGGCUAAACCACGAUGAGGUCCACAAAAAAUUUCAUUA-AAAAAACGGCAACUUUUAAGCUU
...((((...(((---((....((((...(((((((.(...((((((....)))))).))))))))....((((((((.........)))))))).-.......)))).)))))..)))) ( -32.90)
>DroSim_CAF1 13638 116 - 1
GGCAAGCGUGGUG---GGGGGAUGCCACUUUUGGCCAGAUGUUUGGCGAAAGUCAAAGCGGCUAAACCACGAUGAGGUCCACAAAAAAUUUCAUUA-AAAAAACGGCAACUUUUAAGCUU
...((((....((---((((..((((...(((((((.(...((((((....)))))).))))))))....((((((((.........)))))))).-.......)))).)))))).)))) ( -32.70)
>DroYak_CAF1 13073 107 - 1
GGCAAGUGUGGAGUGGGGGGGAUGCCACUUUUGGCCAGAUGUUUGGCGAAAGUCAAAGCGGCUAAGCCACGA-------------AAAUUGCAUUACAAAAAACGGCAGCUCUUAACUUU
.((((.((((((((((.(....).)))))(((((((.(...((((((....)))))).))))))))))))).-------------...))))............................ ( -32.60)
>consensus
GGCAAGCGUGGAG___GGGGGAUGCCACUUUUGGCCAGAUGUUUGGCGAAAGUCAAAGCGGCUAAACCACGAUGAGGUCCACAAAAAAUUUCAUUA_AAAAAACGGCAACUUUUAAGCUU
.((....((((.....((......))...(((((((.(...((((((....)))))).))))))))))))((((((((.........))))))))..........))............. (-24.84 = -26.40 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 9,868,791 – 9,868,908
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.39
Mean single sequence MFE -35.82
Consensus MFE -30.70
Energy contribution -30.95
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.13
Structure conservation index 0.86
SVM decision value 1.07
SVM RNA-class probability 0.910231
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9868791 117 + 22224390
AGACCUCAUCGUGGUUUAGCCGCUUUGACUUUCGCCAAACAUCUGGCCAAAAGUGGCAUCCCCC---CUCCACGCUUGCCAAUCUCUAUCGCCGGGCAAUUUGCGUUAAUGGGGAAAAUU
(((((.......))))).((((((((.......((((......))))..)))))))).(((((.---....(((((((((...(......)...)))))...))))....)))))..... ( -37.90)
>DroSec_CAF1 13514 117 + 1
GGACCUCAUCGUGGUUUAGCCGCUUUGACUUUCGCCAAACAUCUGGCCAAAAGUGGCAUCCCCC---UUCCACGCUUGCCAAUCUCUAUCGCCGGGCAAUUUGCGUUAAUGGGGAAAAUU
(((((.......))))).((((((((.......((((......))))..)))))))).(((((.---....(((((((((...(......)...)))))...))))....)))))..... ( -37.80)
>DroSim_CAF1 13677 117 + 1
GGACCUCAUCGUGGUUUAGCCGCUUUGACUUUCGCCAAACAUCUGGCCAAAAGUGGCAUCCCCC---CACCACGCUUGCCAAUCUCUAUCGCCGGGCAAUUUGCGUUAAUGGGGAAAAUU
(((((.......))))).((((((((.......((((......))))..))))))))....(((---((..(((((((((...(......)...)))))...))))...)))))...... ( -38.20)
>DroYak_CAF1 13108 112 + 1
--------UCGUGGCUUAGCCGCUUUGACUUUCGCCAAACAUCUGGCCAAAAGUGGCAUCCCCCCCACUCCACACUUGCCAAUCUCUAUCGCCGGGCAAUUUGCGUUAAUGGGGAAAAUU
--------..........((((((((.......((((......))))..)))))))).....(((((...(.((.(((((...(......)...)))))..)).)....)))))...... ( -29.40)
>consensus
GGACCUCAUCGUGGUUUAGCCGCUUUGACUUUCGCCAAACAUCUGGCCAAAAGUGGCAUCCCCC___CUCCACGCUUGCCAAUCUCUAUCGCCGGGCAAUUUGCGUUAAUGGGGAAAAUU
..................((((((((.......((((......))))..)))))))).(((((........(((((((((...(......)...)))))...))))....)))))..... (-30.70 = -30.95 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 9,868,791 – 9,868,908
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.39
Mean single sequence MFE -39.65
Consensus MFE -34.90
Energy contribution -34.52
Covariance contribution -0.38
Combinations/Pair 1.07
Mean z-score -1.70
Structure conservation index 0.88
SVM decision value 0.56
SVM RNA-class probability 0.780502
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9868791 117 - 22224390
AAUUUUCCCCAUUAACGCAAAUUGCCCGGCGAUAGAGAUUGGCAAGCGUGGAG---GGGGGAUGCCACUUUUGGCCAGAUGUUUGGCGAAAGUCAAAGCGGCUAAACCACGAUGAGGUCU
....((((((....((((...(((((...(......)...)))))))))....---)))))).(((...(((((((.(...((((((....)))))).)))))))).(.....).))).. ( -38.20)
>DroSec_CAF1 13514 117 - 1
AAUUUUCCCCAUUAACGCAAAUUGCCCGGCGAUAGAGAUUGGCAAGCGUGGAA---GGGGGAUGCCACUUUUGGCCAGAUGUUUGGCGAAAGUCAAAGCGGCUAAACCACGAUGAGGUCC
....((((((.((.((((...(((((...(......)...))))))))).)).---)))))).(((...(((((((.(...((((((....)))))).)))))))).(.....).))).. ( -37.50)
>DroSim_CAF1 13677 117 - 1
AAUUUUCCCCAUUAACGCAAAUUGCCCGGCGAUAGAGAUUGGCAAGCGUGGUG---GGGGGAUGCCACUUUUGGCCAGAUGUUUGGCGAAAGUCAAAGCGGCUAAACCACGAUGAGGUCC
...(..((((((((.(((...(((((...(......)...)))))))))))))---)))..).(((...(((((((.(...((((((....)))))).)))))))).(.....).))).. ( -40.90)
>DroYak_CAF1 13108 112 - 1
AAUUUUCCCCAUUAACGCAAAUUGCCCGGCGAUAGAGAUUGGCAAGUGUGGAGUGGGGGGGAUGCCACUUUUGGCCAGAUGUUUGGCGAAAGUCAAAGCGGCUAAGCCACGA--------
.(((..(((((((.((((...(((((...(......)...)))))))))..)))))))..)))((((....))))......((((((....))))))(.(((...))).)..-------- ( -42.00)
>consensus
AAUUUUCCCCAUUAACGCAAAUUGCCCGGCGAUAGAGAUUGGCAAGCGUGGAG___GGGGGAUGCCACUUUUGGCCAGAUGUUUGGCGAAAGUCAAAGCGGCUAAACCACGAUGAGGUCC
....((((((....((((...(((((...(......)...))))))))).......)))))).......(((((((.(...((((((....)))))).)))))))).............. (-34.90 = -34.52 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 9,868,831 – 9,868,948
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.64
Mean single sequence MFE -41.50
Consensus MFE -33.87
Energy contribution -34.36
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.84
Structure conservation index 0.82
SVM decision value -0.04
SVM RNA-class probability 0.511286
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9868831 117 - 22224390
GGCCGCUUAUCACACUGCAUUUGUCGCCGUUUAAUGGUGCAAUUUUCCCCAUUAACGCAAAUUGCCCGGCGAUAGAGAUUGGCAAGCGUGGAG---GGGGGAUGCCACUUUUGGCCAGAU
((((......(((.((((.((((((((((.(((((((.(........)))))))).((.....)).)))))))))).....)).)).)))(((---((((....)).))))))))).... ( -39.50)
>DroSec_CAF1 13554 117 - 1
AGCCGCUUAUCACUUUGCAUUUGUCGCCGUUUAAUGGUGCAAUUUUCCCCAUUAACGCAAAUUGCCCGGCGAUAGAGAUUGGCAAGCGUGGAA---GGGGGAUGCCACUUUUGGCCAGAU
..((.(((.(((((((((.((((((((((.(((((((.(........)))))))).((.....)).)))))))))).....))))).)))).)---)).))..((((....))))..... ( -39.70)
>DroSim_CAF1 13717 117 - 1
AGCCGCUUAUCACUUUGCAUUUGUCGCCGUUUAAUGGUGCAAUUUUCCCCAUUAACGCAAAUUGCCCGGCGAUAGAGAUUGGCAAGCGUGGUG---GGGGGAUGCCACUUUUGGCCAGAU
..((.(((((((((((((.((((((((((.(((((((.(........)))))))).((.....)).)))))))))).....))))).))))))---)).))..((((....))))..... ( -43.70)
>DroYak_CAF1 13140 120 - 1
GGCCGCUUAUCACUUUGCAUUUGUCGCCGUUUAAUGCUGCAAUUUUCCCCAUUAACGCAAAUUGCCCGGCGAUAGAGAUUGGCAAGUGUGGAGUGGGGGGGAUGCCACUUUUGGCCAGAU
((((......((((((((.((((((((((..((((..(((................))).))))..)))))))))).....))))).)))((((((.(....).))))))..)))).... ( -43.09)
>consensus
AGCCGCUUAUCACUUUGCAUUUGUCGCCGUUUAAUGGUGCAAUUUUCCCCAUUAACGCAAAUUGCCCGGCGAUAGAGAUUGGCAAGCGUGGAG___GGGGGAUGCCACUUUUGGCCAGAU
..((.((..(((((((((.((((((((((..((((..(((................))).))))..)))))))))).....))))).)))).....)).))..((((....))))..... (-33.87 = -34.36 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:07 2006