Locus 7853

Sequence ID X_DroMel_CAF1
Location 19,564,576 – 19,564,725
Length 149
Max. P 0.999988
window12877 window12878 window12879 window12880

overview

Window 7

Location 19,564,576 – 19,564,685
Length 109
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 69.62
Mean single sequence MFE -21.87
Consensus MFE -9.80
Energy contribution -10.99
Covariance contribution 1.19
Combinations/Pair 1.29
Mean z-score -1.92
Structure conservation index 0.45
SVM decision value 0.06
SVM RNA-class probability 0.562098
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19564576 109 + 22224390
----------AGCCUGUUGCUUUUACGAUCCGUUACUUUUCAGAUGUAAUAUAGCCAUCUCACUCUAAUUCGCUAUAUUGCUCUCUGGUGAGAGCGUCGACUUCGUUUUUCAUUGAGAU
----------(((.....)))....(((..((((.(((.(((((.((((((((((................))))))))))..))))).))))))))))..((((........)))).. ( -23.69)
>DroSec_CAF1 28484 93 + 1
----------AGCCUGUUGCUUUUUCGUUCCGCU-UUUUUCAGAUGUAAUAUAGUCAUCUCACUCUAAUUCGCUAUAUUGCUCUCUAGUGAGAGCGUCGACUUC---------------
----------(((.....)))...(((...((((-(((...(((.((((((((((................))))))))))..)))...))))))).)))....--------------- ( -20.59)
>DroEre_CAF1 28297 117 + 1
AUUUCUUUGAAGUUCGUUGCUUUUACGAUCCGUUACUUUUCAGUUUUCAUAUAGUCAUCUCACUCUAAUUCGCCAAAUUGCUCUAUCGUGAGAGCGUCUACUUAC--UUUCAUUGAGAU
(((((..((((((..((((((((((((((..(..(((....)))...).......................((......))...))))))))))))...))..))--.))))..))))) ( -21.40)
>DroYak_CAF1 27232 90 + 1
---------------------------GUCCGUUACUUUUAAGUUGUAAUAUAGUCAUCUCGCUCUAAUUCAGUAAGUUGCUCUCUUGUGAGAGCGUUAACUUAC--UUUCAUUGAGAU
---------------------------....(((((.........)))))............(((......((((((((((((((....))))))...)))))))--)......))).. ( -21.80)
>consensus
__________AGCCUGUUGCUUUUACGAUCCGUUACUUUUCAGAUGUAAUAUAGUCAUCUCACUCUAAUUCGCUAAAUUGCUCUCUAGUGAGAGCGUCGACUUAC__UUUCAUUGAGAU
..............................((((.(((.((((..((((((((((................))))))))))...)))).)))))))....................... ( -9.80 = -10.99 +   1.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 19,564,576 – 19,564,685
Length 109
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 69.62
Mean single sequence MFE -21.98
Consensus MFE -10.99
Energy contribution -11.05
Covariance contribution 0.06
Combinations/Pair 1.29
Mean z-score -1.97
Structure conservation index 0.50
SVM decision value 0.95
SVM RNA-class probability 0.887802
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19564576 109 - 22224390
AUCUCAAUGAAAAACGAAGUCGACGCUCUCACCAGAGAGCAAUAUAGCGAAUUAGAGUGAGAUGGCUAUAUUACAUCUGAAAAGUAACGGAUCGUAAAAGCAACAGGCU----------
((((((.(((....((....))..((((((....))))))...........)))...)))))).(((...(((((((((........))))).)))).)))........---------- ( -25.80)
>DroSec_CAF1 28484 93 - 1
---------------GAAGUCGACGCUCUCACUAGAGAGCAAUAUAGCGAAUUAGAGUGAGAUGACUAUAUUACAUCUGAAAAA-AGCGGAACGAAAAAGCAACAGGCU----------
---------------....(((..((((((....))))))......((...(((((((((..........)))).)))))....-.))....)))...(((.....)))---------- ( -20.30)
>DroEre_CAF1 28297 117 - 1
AUCUCAAUGAAA--GUAAGUAGACGCUCUCACGAUAGAGCAAUUUGGCGAAUUAGAGUGAGAUGACUAUAUGAAAACUGAAAAGUAACGGAUCGUAAAAGCAACGAACUUCAAAGAAAU
.(((...((((.--((..((((.((.((((((..(((.((......))...)))..)))))))).))))......(((....)))......((((.......)))))))))).)))... ( -20.60)
>DroYak_CAF1 27232 90 - 1
AUCUCAAUGAAA--GUAAGUUAACGCUCUCACAAGAGAGCAACUUACUGAAUUAGAGCGAGAUGACUAUAUUACAACUUAAAAGUAACGGAC---------------------------
(((((..(((.(--(((((((...((((((....))))))))))))))...)))....))))).............................--------------------------- ( -21.20)
>consensus
AUCUCAAUGAAA__GGAAGUCGACGCUCUCACAAGAGAGCAAUAUAGCGAAUUAGAGUGAGAUGACUAUAUUACAACUGAAAAGUAACGGAUCGUAAAAGCAACAGGCU__________
.................(((((.(((((((....))))))......((........))..).))))).................................................... (-10.99 = -11.05 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 19,564,605 – 19,564,725
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 73.11
Mean single sequence MFE -26.67
Consensus MFE -17.93
Energy contribution -20.24
Covariance contribution 2.31
Combinations/Pair 1.11
Mean z-score -3.08
Structure conservation index 0.67
SVM decision value 5.48
SVM RNA-class probability 0.999988
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19564605 120 + 22224390
UCAGAUGUAAUAUAGCCAUCUCACUCUAAUUCGCUAUAUUGCUCUCUGGUGAGAGCGUCGACUUCGUUUUUCAUUGAGAUUUCAGUUUACUUCAUUGGCUGUCCUUUAUUUUAUAUCUGG
.(((((((((.((((((((((((....((..((......(((((((....))))))).......))..))....)))))....((....))....)))))))........))))))))). ( -31.52)
>DroSec_CAF1 28512 97 + 1
UCAGAUGUAAUAUAGUCAUCUCACUCUAAUUCGCUAUAUUGCUCUCUAGUGAGAGCGUCGACUUC-----------------------ACUUCAUCGGCUGUCCUUUAUAUUAUAUCUGG
.((((((((((((((.........................((((((....))))))(((((....-----------------------......)))))......)))))))))))))). ( -29.20)
>DroEre_CAF1 28336 107 + 1
UCAGUUUUCAUAUAGUCAUCUCACUCUAAUUCGCCAAAUUGCUCUAUCGUGAGAGCGUCUACUUAC--UUUCAUUGAGAUAUCAGUU---UUCAUCGGCUGUC-UUUAUGUGA-------
.......((((((((..((((((.................(((((......)))))((......))--......))))))..(((((---......)))))..-.))))))))------- ( -19.30)
>consensus
UCAGAUGUAAUAUAGUCAUCUCACUCUAAUUCGCUAUAUUGCUCUCUAGUGAGAGCGUCGACUUC___UUUCAUUGAGAU_UCAGUU_ACUUCAUCGGCUGUCCUUUAUAUUAUAUCUGG
.((((((((((((((((.......................((((((....))))))................(((((....)))))..........)))))).......)))))))))). (-17.93 = -20.24 +   2.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 19,564,605 – 19,564,725
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 73.11
Mean single sequence MFE -23.20
Consensus MFE -12.52
Energy contribution -13.30
Covariance contribution 0.78
Combinations/Pair 1.05
Mean z-score -1.78
Structure conservation index 0.54
SVM decision value 0.05
SVM RNA-class probability 0.558676
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19564605 120 - 22224390
CCAGAUAUAAAAUAAAGGACAGCCAAUGAAGUAAACUGAAAUCUCAAUGAAAAACGAAGUCGACGCUCUCACCAGAGAGCAAUAUAGCGAAUUAGAGUGAGAUGGCUAUAUUACAUCUGA
.(((((..........((....))......((((...(..((((((.(((....((....))..((((((....))))))...........)))...))))))..)....))))))))). ( -27.10)
>DroSec_CAF1 28512 97 - 1
CCAGAUAUAAUAUAAAGGACAGCCGAUGAAGU-----------------------GAAGUCGACGCUCUCACUAGAGAGCAAUAUAGCGAAUUAGAGUGAGAUGACUAUAUUACAUCUGA
.(((((.(((((((..((....))........-----------------------...((((.(((((((....))))))......((........))..).))))))))))).))))). ( -24.60)
>DroEre_CAF1 28336 107 - 1
-------UCACAUAAA-GACAGCCGAUGAA---AACUGAUAUCUCAAUGAAA--GUAAGUAGACGCUCUCACGAUAGAGCAAUUUGGCGAAUUAGAGUGAGAUGACUAUAUGAAAACUGA
-------...((((.(-(.(((........---..))).(((((((.(((..--((......))(((((......)))))...........)))...))))))).)).))))........ ( -17.90)
>consensus
CCAGAUAUAAAAUAAAGGACAGCCGAUGAAGU_AACUGA_AUCUCAAUGAAA___GAAGUCGACGCUCUCACCAGAGAGCAAUAUAGCGAAUUAGAGUGAGAUGACUAUAUUACAUCUGA
...................(((..........................................((((((....))))))(((((((((..((.....))..)).)))))))....))). (-12.52 = -13.30 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:49:06 2006