Locus 4843

Sequence ID 2L_DroMel_CAF1
Location 13,766,681 – 13,766,985
Length 304
Max. P 0.993882
window7673 window7674 window7675 window7676 window7677 window7678 window7679

overview

Window 3

Location 13,766,681 – 13,766,800
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.88
Mean single sequence MFE -36.85
Consensus MFE -25.45
Energy contribution -26.85
Covariance contribution 1.40
Combinations/Pair 1.10
Mean z-score -3.16
Structure conservation index 0.69
SVM decision value 1.76
SVM RNA-class probability 0.975739
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13766681 119 + 22407834
UUACAAUAUUGAUUCAUUCAUCUGAGUAAUGCCUUGGCUUUUUUAAGAGAGCGCA-AGCCACUUUUCCAAACGCUCUCUUAAGAGCUGGAAGUUUCCAGUGCUAGCCAAUGAGAGCCAAU
.......((((..((((((....))))......((((((.(((((((((((((..-...............)))))))))))))((((((....))))))...))))))...))..)))) ( -35.43)
>DroSec_CAF1 29312 119 + 1
UUACAGUAUUAAUUCAUUCAUCUGAGUAGUGCUUUGGCUUUUUUAAGAGAGCGCA-AGCCACCUUUCCAGCGGCUCUCUUAAUGCCUGGAAGUUUCCAGUGCGAGCCAAUGAGAGCCAAU
....(((((((.((((......)))))))))))(((((((((((((((((((((.-.............)).))))))))))((((((((....))))).))).......))))))))). ( -40.94)
>DroSim_CAF1 32366 119 + 1
UUACAGUAUUAAUUCAUUCAUCUGAGUAGUGCUUUGGCUUUUUUAAGAGAGCGCA-AGCCACCUUUCCAGCGGCUCUCUUAAUGCCUGGAAGUUUCCAGUGCGAGCCAAUGAGAGCCAAU
....(((((((.((((......)))))))))))(((((((((((((((((((((.-.............)).))))))))))((((((((....))))).))).......))))))))). ( -40.94)
>DroEre_CAF1 31081 120 + 1
UUACAAUAUUAUUUCAUUGUUUUCAAGAGUGCUUUAGAUAUUUUAAGAGAGCGCAAAGCCACUUUCCCAACAGCUCUCUUAAAGCCUGGAAAUUUCCAGUGCGAGCCAAUGAGAGCCGAU
..................(((((((...(.((((.......(((((((((((....................)))))))))))(((((((....))))).)))))))..))))))).... ( -32.25)
>DroYak_CAF1 32327 120 + 1
UUGUAAUAUGAAUUCAUUCACUUGACUAGUGGCUUGUGUAUUUUAAGAGAGCGCAGAACCACUUUCCCAACAGCUCUCUUAAGGCCUGGAAAUUUCCAGAGCGAGCCAAUGAGAGCCAAU
........((((....)))).....((..((((((((...((((((((((((...(((.....)))......)))))))))))).(((((....))))).))))))))...))....... ( -34.70)
>consensus
UUACAAUAUUAAUUCAUUCAUCUGAGUAGUGCUUUGGCUUUUUUAAGAGAGCGCA_AGCCACUUUUCCAACAGCUCUCUUAAGGCCUGGAAGUUUCCAGUGCGAGCCAAUGAGAGCCAAU
...........(((((......)))))......(((((((((((((((((((....................)))))))))).(((((((....))))).))........))))))))). (-25.45 = -26.85 +   1.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,766,681 – 13,766,800
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.88
Mean single sequence MFE -36.38
Consensus MFE -26.40
Energy contribution -26.36
Covariance contribution -0.04
Combinations/Pair 1.13
Mean z-score -2.83
Structure conservation index 0.73
SVM decision value 1.73
SVM RNA-class probability 0.974530
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13766681 119 - 22407834
AUUGGCUCUCAUUGGCUAGCACUGGAAACUUCCAGCUCUUAAGAGAGCGUUUGGAAAAGUGGCU-UGCGCUCUCUUAAAAAAGCCAAGGCAUUACUCAGAUGAAUGAAUCAAUAUUGUAA
((((..((...((((((....(((((....)))))...((((((((((((..((........))-.))))))))))))...))))))..((((.....))))...))..))))....... ( -36.60)
>DroSec_CAF1 29312 119 - 1
AUUGGCUCUCAUUGGCUCGCACUGGAAACUUCCAGGCAUUAAGAGAGCCGCUGGAAAGGUGGCU-UGCGCUCUCUUAAAAAAGCCAAAGCACUACUCAGAUGAAUGAAUUAAUACUGUAA
....(((....((((((.((.(((((....))))))).((((((((((.((.((........))-.))))))))))))...))))))))).....(((......)))............. ( -36.70)
>DroSim_CAF1 32366 119 - 1
AUUGGCUCUCAUUGGCUCGCACUGGAAACUUCCAGGCAUUAAGAGAGCCGCUGGAAAGGUGGCU-UGCGCUCUCUUAAAAAAGCCAAAGCACUACUCAGAUGAAUGAAUUAAUACUGUAA
....(((....((((((.((.(((((....))))))).((((((((((.((.((........))-.))))))))))))...))))))))).....(((......)))............. ( -36.70)
>DroEre_CAF1 31081 120 - 1
AUCGGCUCUCAUUGGCUCGCACUGGAAAUUUCCAGGCUUUAAGAGAGCUGUUGGGAAAGUGGCUUUGCGCUCUCUUAAAAUAUCUAAAGCACUCUUGAAAACAAUGAAAUAAUAUUGUAA
........((((((....((.(((((....)))))))((((((((.(((.((((((.((((......)))).)))))).........))).))))))))..))))))............. ( -33.90)
>DroYak_CAF1 32327 120 - 1
AUUGGCUCUCAUUGGCUCGCUCUGGAAAUUUCCAGGCCUUAAGAGAGCUGUUGGGAAAGUGGUUCUGCGCUCUCUUAAAAUACACAAGCCACUAGUCAAGUGAAUGAAUUCAUAUUACAA
.((((((.....(((((.((.(((((....))))))).((((((((((.((..((((.....))))))))))))))))........)))))..))))))(((((((....))).)))).. ( -38.00)
>consensus
AUUGGCUCUCAUUGGCUCGCACUGGAAACUUCCAGGCAUUAAGAGAGCCGUUGGAAAAGUGGCU_UGCGCUCUCUUAAAAAAGCCAAAGCACUACUCAGAUGAAUGAAUUAAUAUUGUAA
....(((....((((((.((.(((((....))))))).((((((((((..((....))((......))))))))))))...))))))))).............................. (-26.40 = -26.36 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 13,766,721 – 13,766,840
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.40
Mean single sequence MFE -32.72
Consensus MFE -26.69
Energy contribution -27.05
Covariance contribution 0.36
Combinations/Pair 1.06
Mean z-score -2.03
Structure conservation index 0.82
SVM decision value 1.47
SVM RNA-class probability 0.956874
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13766721 119 + 22407834
UUUUAAGAGAGCGCA-AGCCACUUUUCCAAACGCUCUCUUAAGAGCUGGAAGUUUCCAGUGCUAGCCAAUGAGAGCCAAUUCCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGC
(((((((((((((..-...............)))))))))))))((((((....))))))....(..((((((..((......)).))))))..).........((.(((....))))). ( -30.03)
>DroSec_CAF1 29352 119 + 1
UUUUAAGAGAGCGCA-AGCCACCUUUCCAGCGGCUCUCUUAAUGCCUGGAAGUUUCCAGUGCGAGCCAAUGAGAGCCAAUUUCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGC
........(.((...-.)))...........(((((((....((((((((....))))).))).......)))))))...((((((......))))))......((.(((....))))). ( -33.40)
>DroSim_CAF1 32406 119 + 1
UUUUAAGAGAGCGCA-AGCCACCUUUCCAGCGGCUCUCUUAAUGCCUGGAAGUUUCCAGUGCGAGCCAAUGAGAGCCAAUUUCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGC
........(.((...-.)))...........(((((((....((((((((....))))).))).......)))))))...((((((......))))))......((.(((....))))). ( -33.40)
>DroEre_CAF1 31121 120 + 1
UUUUAAGAGAGCGCAAAGCCACUUUCCCAACAGCUCUCUUAAAGCCUGGAAAUUUCCAGUGCGAGCCAAUGAGAGCCGAUUUCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGC
.(((((((((((....................)))))))))))(((((((....))))).))(((..((((((..(((....))).))))))))).........((.(((....))))). ( -33.55)
>DroYak_CAF1 32367 120 + 1
UUUUAAGAGAGCGCAGAACCACUUUCCCAACAGCUCUCUUAAGGCCUGGAAAUUUCCAGAGCGAGCCAAUGAGAGCCAAUUUCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGC
..........(((((((...............((((((....((((((((....))))).....)))...))))))....((((((......))))))...............))))))) ( -33.20)
>consensus
UUUUAAGAGAGCGCA_AGCCACUUUUCCAACAGCUCUCUUAAGGCCUGGAAGUUUCCAGUGCGAGCCAAUGAGAGCCAAUUUCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGC
((((((((((((....................)))))))))))).(((((....)))))..((((..((((((..((......)).))))))))))........((.(((....))))). (-26.69 = -27.05 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 13,766,721 – 13,766,840
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.40
Mean single sequence MFE -34.82
Consensus MFE -30.20
Energy contribution -29.56
Covariance contribution -0.64
Combinations/Pair 1.06
Mean z-score -1.30
Structure conservation index 0.87
SVM decision value 0.34
SVM RNA-class probability 0.693791
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13766721 119 - 22407834
GCACAGAUGUCUGAUGUUUAUGUUCGAAAAUGAAUCCGGAAUUGGCUCUCAUUGGCUAGCACUGGAAACUUCCAGCUCUUAAGAGAGCGUUUGGAAAAGUGGCU-UGCGCUCUCUUAAAA
((.......((((..((((((........)))))).))))..(((((......))))))).(((((....)))))...((((((((((((..((........))-.)))))))))))).. ( -34.50)
>DroSec_CAF1 29352 119 - 1
GCACAGAUGUCUGAUGUUUAUGUUCGAAAAUGAAUCCGAAAUUGGCUCUCAUUGGCUCGCACUGGAAACUUCCAGGCAUUAAGAGAGCCGCUGGAAAGGUGGCU-UGCGCUCUCUUAAAA
((...((((...((.(((....((((..........))))...))))).)))).))..((.(((((....))))))).((((((((((.((.((........))-.)))))))))))).. ( -35.10)
>DroSim_CAF1 32406 119 - 1
GCACAGAUGUCUGAUGUUUAUGUUCGAAAAUGAAUCCGAAAUUGGCUCUCAUUGGCUCGCACUGGAAACUUCCAGGCAUUAAGAGAGCCGCUGGAAAGGUGGCU-UGCGCUCUCUUAAAA
((...((((...((.(((....((((..........))))...))))).)))).))..((.(((((....))))))).((((((((((.((.((........))-.)))))))))))).. ( -35.10)
>DroEre_CAF1 31121 120 - 1
GCACAGAUGUCUGAUGUUUAUGUUCGAAAAUGAAUCCGAAAUCGGCUCUCAUUGGCUCGCACUGGAAAUUUCCAGGCUUUAAGAGAGCUGUUGGGAAAGUGGCUUUGCGCUCUCUUAAAA
((((((....))).)))........(..(((((..(((....)))...)))))..)..((.(((((....)))))))(((((((((((.((..((.......))..))))))))))))). ( -36.40)
>DroYak_CAF1 32367 120 - 1
GCACAGAUGUCUGAUGUUUAUGUUCGAAAAUGAAUCCGAAAUUGGCUCUCAUUGGCUCGCUCUGGAAAUUUCCAGGCCUUAAGAGAGCUGUUGGGAAAGUGGUUCUGCGCUCUCUUAAAA
((.((((...((....(((((........)))))(((.((...(((((((...(((.....(((((....))))))))....))))))).)).))).))....)))).)).......... ( -33.00)
>consensus
GCACAGAUGUCUGAUGUUUAUGUUCGAAAAUGAAUCCGAAAUUGGCUCUCAUUGGCUCGCACUGGAAACUUCCAGGCAUUAAGAGAGCCGUUGGAAAAGUGGCU_UGCGCUCUCUUAAAA
((.(((....)))............(..(((((..(((....)))...)))))..)..)).(((((....)))))...((((((((((..((....))((......)))))))))))).. (-30.20 = -29.56 +  -0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 13,766,760 – 13,766,880
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.50
Mean single sequence MFE -30.38
Consensus MFE -25.96
Energy contribution -26.96
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.08
Structure conservation index 0.85
SVM decision value 2.01
SVM RNA-class probability 0.985619
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13766760 120 + 22407834
AAGAGCUGGAAGUUUCCAGUGCUAGCCAAUGAGAGCCAAUUCCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGCACCAACACCAACAAAGCUCAUGGGGCCAAAAACAUGGCCA
..((((((((....))).((((..(..((((((..((......)).))))))..)............(((....))).))))............)))))....(((((......))))). ( -29.40)
>DroSec_CAF1 29391 120 + 1
AAUGCCUGGAAGUUUCCAGUGCGAGCCAAUGAGAGCCAAUUUCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGCACAAACACCAACAAAGCUCAUGGGGCCAAAAACAUGGCCA
..((((((((....))))).)))..(((.((((.......((((((......))))))......((.(((....))))).................)))))))(((((......))))). ( -32.20)
>DroSim_CAF1 32445 120 + 1
AAUGCCUGGAAGUUUCCAGUGCGAGCCAAUGAGAGCCAAUUUCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGCACAAACACCAACAAAGCUCAUGGGGCCAAAAACAUGUCCA
...(((((((....))))).))(.(((.(((((.......((((((......))))))......((.(((....))))).................)))))..))))............. ( -27.10)
>DroEre_CAF1 31161 120 + 1
AAAGCCUGGAAAUUUCCAGUGCGAGCCAAUGAGAGCCGAUUUCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGCACAAACACCAACAAAGCUCUUGGGGCCAAAAACAUGGCCA
...(((((((....))))).))...(((...(((((....((((((......))))))......((.(((....)))))................))))))))(((((......))))). ( -33.70)
>DroYak_CAF1 32407 120 + 1
AAGGCCUGGAAAUUUCCAGAGCGAGCCAAUGAGAGCCAAUUUCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGCACAAACACCAACAAAGCCCAUGGGGCCAAAAACAUGGCCA
...(((((((....))))).))...(((.((.(.((....((((((......))))))......((.(((....)))))................))))))))(((((......))))). ( -29.50)
>consensus
AAGGCCUGGAAGUUUCCAGUGCGAGCCAAUGAGAGCCAAUUUCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGCACAAACACCAACAAAGCUCAUGGGGCCAAAAACAUGGCCA
...(((((((....))))).))...(((....((((....((((((......))))))......((.(((....)))))................)))).)))(((((......))))). (-25.96 = -26.96 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 13,766,800 – 13,766,918
Length 118
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 97.63
Mean single sequence MFE -25.22
Consensus MFE -22.02
Energy contribution -22.42
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.40
Structure conservation index 0.87
SVM decision value 2.43
SVM RNA-class probability 0.993882
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13766800 118 + 22407834
UCCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGCACCAACACCAACAAAGCUCAUGGGGCCAAAAACAUGGCCAAAAGGUGCAUCCAAAGUGCAUAAAUAACAACAGACGCA
..((((......)))).............(.(.((((((((((....(((..........)))(((((......)))))....))))).......((.........)).))))).)). ( -26.20)
>DroSec_CAF1 29431 118 + 1
UUCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGCACAAACACCAACAAAGCUCAUGGGGCCAAAAACAUGGCCAAAAGGUGCAUCCAAAGUGCAUAAAUAACAACAGACGCA
((((((......))))))...........(.(.(((((((((.....(((..........)))(((((......))))).....)))).......((.........)).))))).)). ( -24.60)
>DroSim_CAF1 32485 118 + 1
UUCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGCACAAACACCAACAAAGCUCAUGGGGCCAAAAACAUGUCCAAAAGGUGCAUCCAAAGUGCAUAAAUAACAACAGACGCA
((((((......)))))).................(((((((.............(((.....))).......((((((....)).)))).....)))))))................ ( -19.20)
>DroEre_CAF1 31201 118 + 1
UUCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGCACAAACACCAACAAAGCUCUUGGGGCCAAAAACAUGGCCAAAAGGUGCAUCCAAAGUGCAUAAAUAACAACAGAUGCA
((((((......))))))...........(.(((((((....................(((..(((((......)))))..)))((((((.....))))))........)))))))). ( -30.60)
>DroYak_CAF1 32447 118 + 1
UUCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGCACAAACACCAACAAAGCCCAUGGGGCCAAAAACAUGGCCAAAAGGUGCAUCCAGAGUGCAUAAAUAACAACAGACGCA
((((((......))))))...........(...(((((((((.....(((..........)))(((((......))))).....)))))..))))...)................... ( -25.50)
>consensus
UUCGGAUUCAUUUUCGAACAUAAACAUCAGACAUCUGUGCACAAACACCAACAAAGCUCAUGGGGCCAAAAACAUGGCCAAAAGGUGCAUCCAAAGUGCAUAAAUAACAACAGACGCA
((((((......))))))...........(.(.(((((((((.....(((..........)))(((((......))))).....)))).......((.........)).))))).)). (-22.02 = -22.42 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 13,766,880 – 13,766,985
Length 105
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 89.39
Mean single sequence MFE -25.38
Consensus MFE -20.32
Energy contribution -20.32
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.80
SVM decision value 0.19
SVM RNA-class probability 0.627253
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13766880 105 + 22407834
AAAGGUGCAUCCAAAGUGCAUAAAUAACAACAGACGCAAGAUGGACUGGCAGGCAGGUGACGAAAGUUGCAAUAUUGUUUCCACGAUGUUGAGGGGGGGGGGGGG
....((((((.....))))))......(((((..(....).((((..(((((....(..((....))..)....)))))))))...))))).............. ( -26.60)
>DroSec_CAF1 29511 105 + 1
AAAGGUGCAUCCAAAGUGCAUAAAUAACAACAGACGCAAGAUGGACUGGCAGGCAGGUGACGAAAGUUGCAAUAUUGUUUCCACGAAGGGGAGCGGUGGGGGGGG
....((((((.....))))))......(..((..(((....((((..(((((....(..((....))..)....)))))))))(....)...))).))..).... ( -27.80)
>DroSim_CAF1 32565 105 + 1
AAAGGUGCAUCCAAAGUGCAUAAAUAACAACAGACGCAAGAUGGACUGGCAGGCAGGUGACGAAAGUUGCAAUAUUGUUUCCACGAAGGGGAGCGGUGGGGGGGG
....((((((.....))))))......(..((..(((....((((..(((((....(..((....))..)....)))))))))(....)...))).))..).... ( -27.80)
>DroEre_CAF1 31281 92 + 1
AAAGGUGCAUCCAAAGUGCAUAAAUAACAACAGAUGCAAGAUGGACUGGCAGGCAGGUGACGAAAGUUGCAAUAUUGU-UCCACGAAG------------GGAGG
...(((.((((.....(((((............))))).)))).))).((((....(..((....))..)....))))-(((......------------))).. ( -22.70)
>DroYak_CAF1 32527 92 + 1
AAAGGUGCAUCCAGAGUGCAUAAAUAACAACAGACGCAGGAUGGACUGGCAGGCAGGUGACGAAAGUUGCAAUAUUGU-UCCAAGAAG------------GGGGG
...(((.(((((....(((................)))))))).))).((((....(..((....))..)....))))-(((......------------))).. ( -21.99)
>consensus
AAAGGUGCAUCCAAAGUGCAUAAAUAACAACAGACGCAAGAUGGACUGGCAGGCAGGUGACGAAAGUUGCAAUAUUGUUUCCACGAAG__GAG_GG_GGGGGGGG
....((((((.....))))))....................((((...((((....(..((....))..)....)))).))))...................... (-20.32 = -20.32 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:03 2006