Locus 4800

Sequence ID 3L_DroMel_CAF1
Location 13,430,000 – 13,430,338
Length 338
Max. P 0.986285
window7561 window7562 window7563 window7564 window7565

overview

Window 1

Location 13,430,000 – 13,430,098
Length 98
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.58
Mean single sequence MFE -33.56
Consensus MFE -28.62
Energy contribution -29.52
Covariance contribution 0.90
Combinations/Pair 1.06
Mean z-score -1.74
Structure conservation index 0.85
SVM decision value 1.18
SVM RNA-class probability 0.926691
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13430000 98 - 23771897
GAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUGGGCUCAUUCAUUAUUUUAAAAUCAAUUUAAAAGGUCUUGCCUUCCAAAGUUUUGACGCACGUC----------------------
(.((....)))......((((((((((((((..((((...........(((((((.....)))))))((.....)).))))..).)))))))))))))---------------------- ( -26.60)
>DroSec_CAF1 27148 120 - 1
GAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUGGGCUCAUUCAUUAUUUUGAAAUCAAUUUAAAAGGUCUUGUCUUCCAAAGUUUUGACGCACGUCCUCCGCCUGGCAAGGGAAGCCA
.......(((((.....((((((((((((((..((((..((.......(((((((.....))))))).....))...))))..).))))))))))))).......))))).((....)). ( -34.40)
>DroSim_CAF1 29017 120 - 1
GAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUGGGCUCAUUCAUUAUUUUGAAAUCAAUUUAAAAGGUCUUGCCUUCCAAAGUUUUGACGCACGUCCUCCGCCUGGCAAGGGAAGCCA
.......(((((.....((((((((((((((..(((.....((((......))))..........((((.....)))))))..).))))))))))))).......))))).((....)). ( -37.10)
>DroEre_CAF1 28182 120 - 1
GAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUUGGCUCAUUCAUUAUUUUAAAAUCAAUUUAAAAGGUCUUGCCUUUCAAAGUUUUGACGCACGUCCUCCACUUGGCAAGGGAAGCCA
.......((((((....(((((((((((((.(((((((.....(....(((((((.....))))))).)....))).....)))))))))))))))))......)))))).((....)). ( -35.30)
>DroYak_CAF1 27396 120 - 1
GAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUGGGCUCAUUCAUUAUUUUAAAAUCAAUUUAAAAGGUCUUGCCUUUCAAAGUUUUGACGCACGUCCUUCACUUGGCAAGGAACGCCA
.......((((((....(((((((((((((.(((((((.....(....(((((((.....))))))).)....)))).....))))))))))))))))......)))))).((....)). ( -34.40)
>consensus
GAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUGGGCUCAUUCAUUAUUUUAAAAUCAAUUUAAAAGGUCUUGCCUUCCAAAGUUUUGACGCACGUCCUCCACCUGGCAAGGGAAGCCA
.......(((((.....(((((((((((((.(((((((.....(....(((((((.....))))))).)....)))).....)))))))))))))))).......))))).((....)). (-28.62 = -29.52 +   0.90)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 13,430,018 – 13,430,138
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.42
Mean single sequence MFE -34.72
Consensus MFE -33.72
Energy contribution -33.08
Covariance contribution -0.64
Combinations/Pair 1.09
Mean z-score -1.65
Structure conservation index 0.97
SVM decision value 2.04
SVM RNA-class probability 0.986285
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13430018 120 - 23771897
AUUGCUGCAAUGAUGGUUGAAAGAGGAGGCAUACGGCGAUGAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUGGGCUCAUUCAUUAUUUUAAAAUCAAUUUAAAAGGUCUUGCCUUCC
.......((((....)))).....(((((((...((((((((((.((((((.....((((....))))))))))..))))))).....(((((((.....))))))).))).))))))). ( -35.40)
>DroSec_CAF1 27188 120 - 1
AUUGCUGCAAUGAUGGUUGAAAGAGGAGGCAUACGGCGAUGAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUGGGCUCAUUCAUUAUUUUGAAAUCAAUUUAAAAGGUCUUGUCUUCC
.......((((....)))).....(((((((...((((((((((.((((((.....((((....))))))))))..)))))))..(((..(((....)))..)))...))).))))))). ( -33.30)
>DroSim_CAF1 29057 120 - 1
AUUGCUGCAAUGAUGGUUGAAAGAGGAGGCAUACGGCGAUGAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUGGGCUCAUUCAUUAUUUUGAAAUCAAUUUAAAAGGUCUUGCCUUCC
.......((((....)))).....(((((((...((((((((((.((((((.....((((....))))))))))..)))))))..(((..(((....)))..)))...))).))))))). ( -36.00)
>DroEre_CAF1 28222 120 - 1
AUUGCUGCAAUGAUGGUUCAAAGAGGAGGCAUAAGGCGAUGAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUUGGCUCAUUCAUUAUUUUAAAAUCAAUUUAAAAGGUCUUGCCUUUC
..........(((....)))....(((((((..((((((((((((((((((.....((((....))))))))))).))))))).....(((((((.....))))))).))))))))))). ( -34.90)
>DroYak_CAF1 27436 120 - 1
AUUGCUGCAAUGAUGGUUGAAAGAGGAGGCAUAUGGCGAUGAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUGGGCUCAUUCAUUAUUUUAAAAUCAAUUUAAAAGGUCUUGCCUUUC
.......((((....)))).....(((((((...((((((((((.((((((.....((((....))))))))))..))))))).....(((((((.....))))))).))).))))))). ( -34.00)
>consensus
AUUGCUGCAAUGAUGGUUGAAAGAGGAGGCAUACGGCGAUGAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUGGGCUCAUUCAUUAUUUUAAAAUCAAUUUAAAAGGUCUUGCCUUCC
........................(((((((...((((((((((.((((((.....((((....))))))))))..))))))).....(((((((.....))))))).))).))))))). (-33.72 = -33.08 +  -0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 13,430,058 – 13,430,178
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.42
Mean single sequence MFE -34.18
Consensus MFE -31.68
Energy contribution -31.88
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.88
Structure conservation index 0.93
SVM decision value 1.93
SVM RNA-class probability 0.983141
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13430058 120 - 23771897
AACGAAUAAAGGAAACAAAGGAGCAACUUUGUCAUUAGUCAUUGCUGCAAUGAUGGUUGAAAGAGGAGGCAUACGGCGAUGAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUGGGCUC
..((......(....)......((..((((.(((...(((((((...)))))))...))).))))...))...)).....((((.((((((.....((((....))))))))))..)))) ( -34.00)
>DroSec_CAF1 27228 120 - 1
AACGAAUAAAGGAAACAAAGGAGCAACUUUGUCAUUAGUCAUUGCUGCAAUGAUGGUUGAAAGAGGAGGCAUACGGCGAUGAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUGGGCUC
..((......(....)......((..((((.(((...(((((((...)))))))...))).))))...))...)).....((((.((((((.....((((....))))))))))..)))) ( -34.00)
>DroSim_CAF1 29097 120 - 1
AACGAAUAAAGGAAACAAAGGAGCAACUUUGUCAUUAGUCAUUGCUGCAAUGAUGGUUGAAAGAGGAGGCAUACGGCGAUGAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUGGGCUC
..((......(....)......((..((((.(((...(((((((...)))))))...))).))))...))...)).....((((.((((((.....((((....))))))))))..)))) ( -34.00)
>DroEre_CAF1 28262 120 - 1
AACGAAUGAAGGAAACAAAGGAGCAACUUUGUCAUUAGUCAUUGCUGCAAUGAUGGUUCAAAGAGGAGGCAUAAGGCGAUGAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUUGGCUC
..........(....)....((((..............((((((((......(((.(((......))).)))..)))))))).((((((((.....((((....)))))))))))))))) ( -34.90)
>DroYak_CAF1 27476 120 - 1
AACGAAUAAAGGAAACAAAGGAGCAACUUUGUCAUUAGUCAUUGCUGCAAUGAUGGUUGAAAGAGGAGGCAUAUGGCGAUGAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUGGGCUC
..((.(((..(....)......((..((((.(((...(((((((...)))))))...))).))))...)).)))..))..((((.((((((.....((((....))))))))))..)))) ( -34.00)
>consensus
AACGAAUAAAGGAAACAAAGGAGCAACUUUGUCAUUAGUCAUUGCUGCAAUGAUGGUUGAAAGAGGAGGCAUACGGCGAUGAGCAAGUGCCAAAAUUGAUGUGCGUCAGGCGCUGGGCUC
..((......(....)......((..((((.(((...(((((((...)))))))...))).))))...))......))..((((.((((((.....((((....))))))))))..)))) (-31.68 = -31.88 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,430,098 – 13,430,218
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.42
Mean single sequence MFE -29.21
Consensus MFE -25.20
Energy contribution -25.60
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.60
Structure conservation index 0.86
SVM decision value 0.62
SVM RNA-class probability 0.801977
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13430098 120 - 23771897
CAUAAGCUUCCUGUAAGCUGCGGAUCCAAUAAAAAAGCCAAACGAAUAAAGGAAACAAAGGAGCAACUUUGUCAUUAGUCAUUGCUGCAAUGAUGGUUGAAAGAGGAGGCAUACGGCGAU
.....(((((((.(..(((.(((..............))...........(....)...).))).......(((...(((((((...)))))))...))).).))))))).......... ( -26.94)
>DroSec_CAF1 27268 120 - 1
CAUAAGCUUCCUGUGAGCAGCGGAUCCAAUAAAAAAGCCAAACGAAUAAAGGAAACAAAGGAGCAACUUUGUCAUUAGUCAUUGCUGCAAUGAUGGUUGAAAGAGGAGGCAUACGGCGAU
.....(((((((.(...((((...(((.......................))).((((((......)))))).....(((((((...))))))).))))..).))))))).......... ( -27.60)
>DroSim_CAF1 29137 119 - 1
CAUAAGCUUCCUUUGAGCAGCGGAUCCAAUAAA-AAGCCAAACGAAUAAAGGAAACAAAGGAGCAACUUUGUCAUUAGUCAUUGCUGCAAUGAUGGUUGAAAGAGGAGGCAUACGGCGAU
.....(((((((((...((((...(((......-................))).((((((......)))))).....(((((((...))))))).))))..))))))))).......... ( -29.15)
>DroEre_CAF1 28302 120 - 1
CAUAAGCUUCCUGUGAGCAGCGGAUCCAAUAAAAAAGCCAAACGAAUGAAGGAAACAAAGGAGCAACUUUGUCAUUAGUCAUUGCUGCAAUGAUGGUUCAAAGAGGAGGCAUAAGGCGAU
.....(((((((.(..(((((((..............)).....(((((..((.((((((......))))))..))..))))))))))..(((....))).).))))))).......... ( -31.94)
>DroYak_CAF1 27516 120 - 1
CAUAAGCUUCCUGUGAGCAGCGGAUCCAAUAAAAAAGCCAAACGAAUAAAGGAAACAAAGGAGCAACUUUGUCAUUAGUCAUUGCUGCAAUGAUGGUUGAAAGAGGAGGCAUAUGGCGAU
((((.(((((((.(...((((...(((.......................))).((((((......)))))).....(((((((...))))))).))))..).))))))).))))..... ( -30.40)
>consensus
CAUAAGCUUCCUGUGAGCAGCGGAUCCAAUAAAAAAGCCAAACGAAUAAAGGAAACAAAGGAGCAACUUUGUCAUUAGUCAUUGCUGCAAUGAUGGUUGAAAGAGGAGGCAUACGGCGAU
.....(((((((.(...((((...(((.......................))).((((((......)))))).....(((((((...))))))).))))..).))))))).......... (-25.20 = -25.60 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 13,430,218 – 13,430,338
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.65
Mean single sequence MFE -38.42
Consensus MFE -32.48
Energy contribution -32.08
Covariance contribution -0.40
Combinations/Pair 1.13
Mean z-score -1.71
Structure conservation index 0.85
SVM decision value 1.22
SVM RNA-class probability 0.932564
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13430218 120 - 23771897
CUCCAGCUGCCGCUGGUCCACACACAAAAUGGGCCAAAAACAGGAGGAGGAGCAGCCUGCCUCAGGCAUCUAUUUCCUGGAGACCCGACAGUCCUCACCCUUCUCCCGUGGAGCAUACUU
.....(((.(((((((((((.........)))))))......((((((((....(((((...)))))..........((..(((......)))..)).)))))))).)))))))...... ( -43.80)
>DroSec_CAF1 27388 117 - 1
CUCCAGCUGCCGCUGGUCCACCCACAAAAUGGGCCAAAAAUUGGA---GGAGCAGUCUGCCUCAGGCAUCUAUUUCCUGGAGACCCGACAGUCCUCACCCUUCUCCCGUGGAGCCUACUU
.....(((.(((((((((((.........)))))))......(((---((((..(((((...)))))..........((..(((......)))..))..))))))).)))))))...... ( -36.00)
>DroSim_CAF1 29256 117 - 1
CUCCAGCUGCCGCUGGUCCACCCACAAAAUGGGCCAAAAAUUGGA---GGAGCAGCCUGCCUCAGGCAUCUAUUUCCUGGAGACCCGACAGUCCUCACCCUUUUCCCGUGGAGCCUACUU
.....(((.(((((((((((.........)))))))......(((---((((..(((((...)))))..........((..(((......)))..))..))))))).)))))))...... ( -36.20)
>DroEre_CAF1 28422 117 - 1
CUCCAGCUGCCGCUGGUCCACCCACAAAAUGGGCCAAAAAGAGGA---GGAGCAGCCUGCCACUGGCAUCUAUUUCCUGGAGACUCGACAGUCCUCACCCUUCUCCCGUGGAGCCUACUU
.....(((.(((((((((((.........)))))))....(((((---((....(((.......)))..........((..((((....))))..)).)))))))..)))))))...... ( -38.20)
>DroYak_CAF1 27636 117 - 1
CUCCAGCUGCCGCUGGUCUACCCACAAAAUGGGCCAGAAAGAGGA---GGAGCAGCCUGCCUCGGGCAUCUAUUUCCUGGAGACUCGACAGUCCUCGCCCUACUCCCGUGGAGCCUACUU
.....(((.((((.(((((.((((.....))))..)))..(((((---((.....))).))))((((.((((.....))))((((....))))...))))....)).)))))))...... ( -37.90)
>consensus
CUCCAGCUGCCGCUGGUCCACCCACAAAAUGGGCCAAAAAGAGGA___GGAGCAGCCUGCCUCAGGCAUCUAUUUCCUGGAGACCCGACAGUCCUCACCCUUCUCCCGUGGAGCCUACUU
.....(((.(((((((((((.........)))))))......(((...(((...(((((...))))).)))...)))((..(((......)))..))..........)))))))...... (-32.48 = -32.08 +  -0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:43 2006