Locus 4381

Sequence ID 3L_DroMel_CAF1
Location 12,855,866 – 12,856,060
Length 194
Max. P 0.992108
window6780 window6781 window6782 window6783

overview

Window 0

Location 12,855,866 – 12,855,984
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.45
Mean single sequence MFE -30.52
Consensus MFE -21.94
Energy contribution -22.66
Covariance contribution 0.72
Combinations/Pair 1.10
Mean z-score -2.16
Structure conservation index 0.72
SVM decision value 0.50
SVM RNA-class probability 0.760919
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12855866 118 + 23771897
CUUUCUUAGGUUGCACAUAAAAGCGACAACUUCUGCGGCAAAACUCGCUUAAUUUGCAUGAAAUAAGUUUUAGGCCAGGAAACUA--UCUCUUGGCCCAGAGACUUGAAGUCUGUGGAUA
.........(((((........))))).......((((......))))...(((..((.((..((((((((.((((((((.....--..))))))))..))))))))...))))..))). ( -34.50)
>DroSec_CAF1 94166 120 + 1
CUUCCUAAGUUUGCAUAUAAAAGCGACAACUUCUGCGGCAAAACUCGCUUAAUUUGCAUGAAAAAAGUUUUAGGCCAGGAAACUAUAUCUCUUGGCCCAGAGACUUGAAGUCUGUGUACU
......((((((((........))))..))))..((((......))))......(((((((...(((((((.((((((((.........))))))))..)))))))....)).))))).. ( -28.60)
>DroSim_CAF1 95671 120 + 1
CUUCCUAAGUUUGCACAUAAAAGCGAAAACUUCUGCGGCAAAACUCGCUUAAUUUGCAUGAAAUAAGUUUUAGGCCAGGAAACUAUAUAUCUUGGCCCAGAGACUUGAAGUCUGUGGACU
.......((((..((.......(((((.......((((......))))....)))))..((..((((((((.((((((((.........))))))))..))))))))...))))..)))) ( -32.40)
>DroEre_CAF1 99576 117 + 1
CUUUCUUAGUUUGCACAUAAAAGCCACAACUUCUCCGGCA-AACUCUCUUUAUUUGCAUAAAAUAAGUUUUAGGCCAGGAAACUA--UCUCUUGGCCCAGAGACAUGAAGUCUGUGGACU
.....................((((((((((((....(((-((.........))))).........(((((.((((((((.....--..))))))))..)))))..))))).))))).)) ( -31.40)
>DroYak_CAF1 105709 118 + 1
CUUUCUUAGCUUGCACAUAAAUGCCGCAACUUCUGCUGCAAAACUCUCUUCAUUUGCAUAAAAUAAGUUUUAGGCACGGAAACUA--UCUCUUGGUCCAAAGACAUGAAGUCUGUGGACU
.....................(((((((.....)))((((((..........))))))..............)))).(....)..--......((((((.((((.....)))).)))))) ( -25.70)
>consensus
CUUUCUUAGUUUGCACAUAAAAGCGACAACUUCUGCGGCAAAACUCGCUUAAUUUGCAUGAAAUAAGUUUUAGGCCAGGAAACUA__UCUCUUGGCCCAGAGACUUGAAGUCUGUGGACU
............((........)).((((((((....(((((..........))))).......(((((((.((((((((.........))))))))..)))))))))))).)))..... (-21.94 = -22.66 +   0.72)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,855,906 – 12,856,020
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.93
Mean single sequence MFE -30.69
Consensus MFE -26.29
Energy contribution -26.45
Covariance contribution 0.16
Combinations/Pair 1.15
Mean z-score -2.09
Structure conservation index 0.86
SVM decision value 2.10
SVM RNA-class probability 0.988066
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12855906 114 + 23771897
AAACUCGCUUAAUUUGCAUGAAAUAAGUUUUAGGCCAGGAAACUA--UCUCUUGGCCCAGAGACUUGAAGUCUGUGGAUAUCACUUCCGCGUUGCCCAUAGAGUAUA----UGUUCAAAU
..((((((.......))(((...((((((((.((((((((.....--..))))))))..))))))))......(((((.......)))))......))).))))...----......... ( -31.90)
>DroSec_CAF1 94206 120 + 1
AAACUCGCUUAAUUUGCAUGAAAAAAGUUUUAGGCCAGGAAACUAUAUCUCUUGGCCCAGAGACUUGAAGUCUGUGUACUUCACUUCCGCGUUGCCCAUAGAGUAUAUGUAUGUUCAAAU
.....(((................(((((((.((((((((.........))))))))..)))))))(((((......)))))......)))(((..((((.(.....).))))..))).. ( -28.50)
>DroSim_CAF1 95711 120 + 1
AAACUCGCUUAAUUUGCAUGAAAUAAGUUUUAGGCCAGGAAACUAUAUAUCUUGGCCCAGAGACUUGAAGUCUGUGGACUUCACUUCCGCGUUGCCCACAGAGUAUAUGUAUGUUCAAAU
..........(((.((((((...((((((((.((((((((.........))))))))..)))))))).(.(((((((.(..(.(....).)..).))))))).).)))))).)))..... ( -32.60)
>DroEre_CAF1 99616 113 + 1
-AACUCUCUUUAUUUGCAUAAAAUAAGUUUUAGGCCAGGAAACUA--UCUCUUGGCCCAGAGACAUGAAGUCUGUGGACUUCACUUCCGCGUUGCCCAUAGAGUAUG----UGUUCAGAU
-.((...((((((..(((........(((((.((((((((.....--..))))))))..))))).(((((((....))))))).........)))..))))))...)----)........ ( -32.40)
>DroYak_CAF1 105749 114 + 1
AAACUCUCUUCAUUUGCAUAAAAUAAGUUUUAGGCACGGAAACUA--UCUCUUGGUCCAAAGACAUGAAGUCUGUGGACUUCACUUCCGUGUUGCCCAUAGAGUAUA----UGUUCAGAU
....(((...(((.(((.(((((....)))))(((((((((....--......((((((.((((.....)))).))))))....))))))))).........))).)----))...))). ( -28.04)
>consensus
AAACUCGCUUAAUUUGCAUGAAAUAAGUUUUAGGCCAGGAAACUA__UCUCUUGGCCCAGAGACUUGAAGUCUGUGGACUUCACUUCCGCGUUGCCCAUAGAGUAUA____UGUUCAAAU
..((((........(((.........(((((.((((((((.........))))))))..))))).(((((((....))))))).....))).........))))................ (-26.29 = -26.45 +   0.16)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,855,906 – 12,856,020
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.93
Mean single sequence MFE -32.74
Consensus MFE -26.12
Energy contribution -27.16
Covariance contribution 1.04
Combinations/Pair 1.04
Mean z-score -2.69
Structure conservation index 0.80
SVM decision value 2.31
SVM RNA-class probability 0.992108
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12855906 114 - 23771897
AUUUGAACA----UAUACUCUAUGGGCAACGCGGAAGUGAUAUCCACAGACUUCAAGUCUCUGGGCCAAGAGA--UAGUUUCCUGGCCUAAAACUUAUUUCAUGCAAAUUAAGCGAGUUU
.........----...((((....(....)((((((((((.......((((.....)))).(((((((.((((--...)))).)))))))....))))))).))).........)))).. ( -28.00)
>DroSec_CAF1 94206 120 - 1
AUUUGAACAUACAUAUACUCUAUGGGCAACGCGGAAGUGAAGUACACAGACUUCAAGUCUCUGGGCCAAGAGAUAUAGUUUCCUGGCCUAAAACUUUUUUCAUGCAAAUUAAGCGAGUUU
..(((..((((.........))))..)))((((((..((((((......))))))..))).(((((((.(((((...))))).)))))))......................)))..... ( -31.10)
>DroSim_CAF1 95711 120 - 1
AUUUGAACAUACAUAUACUCUGUGGGCAACGCGGAAGUGAAGUCCACAGACUUCAAGUCUCUGGGCCAAGAUAUAUAGUUUCCUGGCCUAAAACUUAUUUCAUGCAAAUUAAGCGAGUUU
....((((..........(((((((((..(((....)))..)))))))))..((((((...(((((((.((.........)).)))))))..)))).......((.......)))))))) ( -36.90)
>DroEre_CAF1 99616 113 - 1
AUCUGAACA----CAUACUCUAUGGGCAACGCGGAAGUGAAGUCCACAGACUUCAUGUCUCUGGGCCAAGAGA--UAGUUUCCUGGCCUAAAACUUAUUUUAUGCAAAUAAAGAGAGUU-
....(((((----.....(((.(((((..(((....)))..))))).))).....))).))(((((((.((((--...)))).))))))).(((((.((((((....)))))).)))))- ( -34.10)
>DroYak_CAF1 105749 114 - 1
AUCUGAACA----UAUACUCUAUGGGCAACACGGAAGUGAAGUCCACAGACUUCAUGUCUUUGGACCAAGAGA--UAGUUUCCGUGCCUAAAACUUAUUUUAUGCAAAUGAAGAGAGUUU
.........----.........(((((...((((((((((((((....)))))))(((((((......)))))--)).))))))))))))((((((.((((((....)))))).)))))) ( -33.60)
>consensus
AUUUGAACA____UAUACUCUAUGGGCAACGCGGAAGUGAAGUCCACAGACUUCAAGUCUCUGGGCCAAGAGA__UAGUUUCCUGGCCUAAAACUUAUUUCAUGCAAAUUAAGCGAGUUU
................((((..(((((..(((....)))..))))).((((.....)))).(((((((.((((.....)))).)))))))........................)))).. (-26.12 = -27.16 +   1.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,855,946 – 12,856,060
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.89
Mean single sequence MFE -34.48
Consensus MFE -29.66
Energy contribution -29.86
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -1.38
Structure conservation index 0.86
SVM decision value 0.51
SVM RNA-class probability 0.764903
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12855946 114 - 23771897
GAGGAUAUGAGGUUGUCUCAUGUGUCGCGCUGUCAGUCAAAUUUGAACA----UAUACUCUAUGGGCAACGCGGAAGUGAUAUCCACAGACUUCAAGUCUCUGGGCCAAGAGA--UAGUU
..(((((((((.....))))))).))..((((((.............((----((.....))))(((..(((....)))....(((.((((.....)))).))))))....))--)))). ( -32.70)
>DroSec_CAF1 94246 120 - 1
GAGGAUAUGAGGUUGUCUCAUGUGUCGCGCUGUCAGUCAAAUUUGAACAUACAUAUACUCUAUGGGCAACGCGGAAGUGAAGUACACAGACUUCAAGUCUCUGGGCCAAGAGAUAUAGUU
....(((((((.....))))))).(((((.((((..(((....))).....((((.....)))))))).)))))...((((((......)))))).((((((......))))))...... ( -31.60)
>DroSim_CAF1 95751 120 - 1
GAGGAUAUGAGGUUGUCUCAUGUGUCGCGCUGUCAGUCAAAUUUGAACAUACAUAUACUCUGUGGGCAACGCGGAAGUGAAGUCCACAGACUUCAAGUCUCUGGGCCAAGAUAUAUAGUU
(((.(((......))))))(((((((..(((..(((....(((((((...........(((((((((..(((....)))..))))))))).)))))))..))))))...))))))).... ( -36.30)
>DroEre_CAF1 99655 114 - 1
GAGGAUAUGAGGUUGUCUCAUGUGUCGCGCUGUCAGUCAAAUCUGAACA----CAUACUCUAUGGGCAACGCGGAAGUGAAGUCCACAGACUUCAUGUCUCUGGGCCAAGAGA--UAGUU
(((((((((((.....))))))).....(.((((((......))).)))----)....(((.(((((..(((....)))..))))).))))))).(((((((......)))))--))... ( -36.60)
>DroYak_CAF1 105789 114 - 1
GAGGAUAUGAGGUUGUCUCAUGUGUCGCGCUGUCAGUCAAAUCUGAACA----UAUACUCUAUGGGCAACACGGAAGUGAAGUCCACAGACUUCAUGUCUUUGGACCAAGAGA--UAGUU
((((((((((((((.....((((((.......((((......)))))))----)))......(((((..(((....)))..)))))..))))))))))))))...........--..... ( -35.21)
>consensus
GAGGAUAUGAGGUUGUCUCAUGUGUCGCGCUGUCAGUCAAAUUUGAACA____UAUACUCUAUGGGCAACGCGGAAGUGAAGUCCACAGACUUCAAGUCUCUGGGCCAAGAGA__UAGUU
..(((((((((.....))))))).))..((((((((......))))...........((((...(((..(((....)))....(((.((((.....)))).)))))).))))...)))). (-29.66 = -29.86 +   0.20)

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 11:21:05 2006