Locus 2827

Sequence ID 3L_DroMel_CAF1
Location 8,046,555 – 8,046,771
Length 216
Max. P 0.981404
window4418 window4419 window4420 window4421 window4422

overview

Window 8

Location 8,046,555 – 8,046,675
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.17
Mean single sequence MFE -25.12
Consensus MFE -22.28
Energy contribution -23.08
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.43
Structure conservation index 0.89
SVM decision value 0.92
SVM RNA-class probability 0.882950
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8046555 120 + 23771897
UUAUAAACAUUCUGAGGGAGCAAAGGUCAUGACUCACUUGGAGCUGUUCUCUGGUUUUAUGGUGUCCAUAAACUCUCACUCAAGCUUUUGUUAUCCCUCAUUCGUUACCUUUAACAACCC
............(((((((((((((((..(((.....(..(((.....)))..).(((((((...))))))).......))).))))))))..)))))))...((((....))))..... ( -28.20)
>DroSec_CAF1 17678 118 + 1
UUAUAAACAUUCUCAGGGAGCAAAGGUCAUGACUCACUUGGAGCUGUUCUCUGGUUUUAUGG--ACAAUAAACUCUCACUCAAGCUUUUGUUAUCCCUCAUUCGUUAUCUUUAACAACCC
..............(((((((((((((..((((((.....))).(((((...........))--)))............))).))))))))..))))).....((((....))))..... ( -21.20)
>DroSim_CAF1 17714 118 + 1
UUAUAAACAUUCUGAGGGAGCAAAGGUCAUGACUCACUUGGAGU--CUCUCUGGUUUUAUGGUGUCCAUAAACUCUCACUCAAGCUUUUGUUAUCCCUCAUUCGUUACCUUUAACAACCC
............(((((((((((((((...(((((.....))))--).....(..(((((((...)))))))..)........))))))))..)))))))...((((....))))..... ( -31.00)
>DroEre_CAF1 17484 120 + 1
UUAUAAACAUUCAGUGGGAGCAAAGGUCAUGACUCACUUGGAGCUGUUCUCUGGUUUUAUGGUGUCCAUAAACUCUCACUCAAGCUUUUGUUAUCCCUCAUUCGUUACCUUUUACAACCC
.............(.((((((((((((..(((.....(..(((.....)))..).(((((((...))))))).......))).))))))))..)))).)..................... ( -22.60)
>DroYak_CAF1 18046 120 + 1
UUAUAAACACACAGUGGGAGCAAAGGUCAUGACUCACUUGGAGCUGUUCUCUGGUUUUAUGGUGUCCAUAAACUCUUACUCAAGCUUUUGUUAUCCCUCAUUCGUUACCUUUUACAACCC
.............(.((((((((((((..(((.....(..(((.....)))..).(((((((...))))))).......))).))))))))..)))).)..................... ( -22.60)
>consensus
UUAUAAACAUUCUGAGGGAGCAAAGGUCAUGACUCACUUGGAGCUGUUCUCUGGUUUUAUGGUGUCCAUAAACUCUCACUCAAGCUUUUGUUAUCCCUCAUUCGUUACCUUUAACAACCC
.............((((((((((((((..(((.....(..(((.....)))..).(((((((...))))))).......))).))))))))..))))))..................... (-22.28 = -23.08 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 8,046,595 – 8,046,715
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.50
Mean single sequence MFE -21.98
Consensus MFE -18.33
Energy contribution -18.97
Covariance contribution 0.64
Combinations/Pair 1.04
Mean z-score -1.58
Structure conservation index 0.83
SVM decision value 0.68
SVM RNA-class probability 0.821697
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8046595 120 + 23771897
GAGCUGUUCUCUGGUUUUAUGGUGUCCAUAAACUCUCACUCAAGCUUUUGUUAUCCCUCAUUCGUUACCUUUAACAACCCCUGAGCCACUUUUUAGGCUCAUUUUCAUUAUAGUUUUGCA
(((((.......(..(((((((...)))))))..).......)))))((((((..................))))))....((((((........))))))................... ( -21.51)
>DroSec_CAF1 17718 118 + 1
GAGCUGUUCUCUGGUUUUAUGG--ACAAUAAACUCUCACUCAAGCUUUUGUUAUCCCUCAUUCGUUAUCUUUAACAACCCCUGAGCCACUUUUUAGGCUCAUUUUGAUUAUAGUUUUGCA
(((((((..((.((((....((--(.((((((..((......))..)))))).))).......((((....))))))))..((((((........))))))....))..))))))).... ( -24.90)
>DroSim_CAF1 17754 118 + 1
GAGU--CUCUCUGGUUUUAUGGUGUCCAUAAACUCUCACUCAAGCUUUUGUUAUCCCUCAUUCGUUACCUUUAACAACCCCUGAGCCAGUUUUUAGGCUCAUUUUGAUUAUAGUUUUGCA
((((--......(..(((((((...)))))))..)..))))..((..((((.(((........((((....))))......((((((........))))))....))).))))....)). ( -22.20)
>DroEre_CAF1 17524 120 + 1
GAGCUGUUCUCUGGUUUUAUGGUGUCCAUAAACUCUCACUCAAGCUUUUGUUAUCCCUCAUUCGUUACCUUUUACAACCCCUGAGCCGCUUUUUAGGCUCAUUUUGAUUAUUGUUUUGCA
(((((.......(..(((((((...)))))))..).......)))))..................................((((((........))))))................... ( -20.64)
>DroYak_CAF1 18086 120 + 1
GAGCUGUUCUCUGGUUUUAUGGUGUCCAUAAACUCUUACUCAAGCUUUUGUUAUCCCUCAUUCGUUACCUUUUACAACCCCUGAGCCGCUUUUUAGGCUCAUUUUGAUUAUUGUUUUGCA
(((((.......(..(((((((...)))))))..).......)))))..................................((((((........))))))................... ( -20.64)
>consensus
GAGCUGUUCUCUGGUUUUAUGGUGUCCAUAAACUCUCACUCAAGCUUUUGUUAUCCCUCAUUCGUUACCUUUAACAACCCCUGAGCCACUUUUUAGGCUCAUUUUGAUUAUAGUUUUGCA
(((((.......(..(((((((...)))))))..).......)))))((((((..................))))))....((((((........))))))................... (-18.33 = -18.97 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 8,046,595 – 8,046,715
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.50
Mean single sequence MFE -25.56
Consensus MFE -22.10
Energy contribution -22.98
Covariance contribution 0.88
Combinations/Pair 1.07
Mean z-score -1.89
Structure conservation index 0.86
SVM decision value 1.89
SVM RNA-class probability 0.981404
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8046595 120 - 23771897
UGCAAAACUAUAAUGAAAAUGAGCCUAAAAAGUGGCUCAGGGGUUGUUAAAGGUAACGAAUGAGGGAUAACAAAAGCUUGAGUGAGAGUUUAUGGACACCAUAAAACCAGAGAACAGCUC
...................((((((........)))))).((((((((...(((..(......)((....((.((((((......)))))).))....)).....)))....)))))))) ( -26.90)
>DroSec_CAF1 17718 118 - 1
UGCAAAACUAUAAUCAAAAUGAGCCUAAAAAGUGGCUCAGGGGUUGUUAAAGAUAACGAAUGAGGGAUAACAAAAGCUUGAGUGAGAGUUUAUUGU--CCAUAAAACCAGAGAACAGCUC
.((................((((((........))))))..((((((((....)))).......((((((.(((..(((....)))..))).))))--))....))))........)).. ( -26.80)
>DroSim_CAF1 17754 118 - 1
UGCAAAACUAUAAUCAAAAUGAGCCUAAAAACUGGCUCAGGGGUUGUUAAAGGUAACGAAUGAGGGAUAACAAAAGCUUGAGUGAGAGUUUAUGGACACCAUAAAACCAGAGAG--ACUC
(((......((((((....((((((........))))))..)))))).....)))........((.....((.((((((......)))))).))....))..............--.... ( -23.90)
>DroEre_CAF1 17524 120 - 1
UGCAAAACAAUAAUCAAAAUGAGCCUAAAAAGCGGCUCAGGGGUUGUAAAAGGUAACGAAUGAGGGAUAACAAAAGCUUGAGUGAGAGUUUAUGGACACCAUAAAACCAGAGAACAGCUC
.((......((((((....((((((........))))))..))))))....(((..(......)((....((.((((((......)))))).))....)).....)))........)).. ( -25.10)
>DroYak_CAF1 18086 120 - 1
UGCAAAACAAUAAUCAAAAUGAGCCUAAAAAGCGGCUCAGGGGUUGUAAAAGGUAACGAAUGAGGGAUAACAAAAGCUUGAGUAAGAGUUUAUGGACACCAUAAAACCAGAGAACAGCUC
.((......((((((....((((((........))))))..))))))....(((..(......)((....((.((((((......)))))).))....)).....)))........)).. ( -25.10)
>consensus
UGCAAAACUAUAAUCAAAAUGAGCCUAAAAAGUGGCUCAGGGGUUGUUAAAGGUAACGAAUGAGGGAUAACAAAAGCUUGAGUGAGAGUUUAUGGACACCAUAAAACCAGAGAACAGCUC
...................((((((........)))))).((((((((...(((..(......)((....((.((((((......)))))).))....)).....)))....)))))))) (-22.10 = -22.98 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 8,046,635 – 8,046,754
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.11
Mean single sequence MFE -28.57
Consensus MFE -19.56
Energy contribution -19.08
Covariance contribution -0.48
Combinations/Pair 1.17
Mean z-score -2.15
Structure conservation index 0.68
SVM decision value 0.13
SVM RNA-class probability 0.598214
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8046635 119 - 23771897
AUUUUCUUAGUGCAGAACGCCAC-UUUUUCUUUAAGUGUAUGCAAAACUAUAAUGAAAAUGAGCCUAAAAAGUGGCUCAGGGGUUGUUAAAGGUAACGAAUGAGGGAUAACAAAAGCUUG
..(..((((.((((......(((-((.......)))))..))))...((.(((..(...((((((........))))))....)..))).))........))))..)............. ( -25.30)
>DroSec_CAF1 17756 119 - 1
AUAUCCCAAGUGCAGAACACCAU-UUUUUUUCUAAGUGUAUGCAAAACUAUAAUCAAAAUGAGCCUAAAAAGUGGCUCAGGGGUUGUUAAAGAUAACGAAUGAGGGAUAACAAAAGCUUG
.((((((...((((..((((...-...........)))).)))).....((((((....((((((........))))))..))))))................))))))........... ( -29.74)
>DroSim_CAF1 17792 120 - 1
AUUUCCCAAGUGCAGAACACCACUUUUUUUUCUAAGUGUAUGCAAAACUAUAAUCAAAAUGAGCCUAAAAACUGGCUCAGGGGUUGUUAAAGGUAACGAAUGAGGGAUAACAAAAGCUUG
...((((...((((......(((((........)))))..))))..(((((((((....((((((........))))))..))))))....))).........))))............. ( -27.90)
>DroEre_CAF1 17564 119 - 1
AUUUCUCAGGCACAAGGCAGCAC-UUUUGUUUCAAGUGUAUGCAAAACAAUAAUCAAAAUGAGCCUAAAAAGCGGCUCAGGGGUUGUAAAAGGUAACGAAUGAGGGAUAACAAAAGCUUG
((..((((..(.....(((((((-((.......)))))).)))......((((((....((((((........))))))..))))))..........)..))))..))............ ( -31.60)
>DroYak_CAF1 18126 118 - 1
AUUUCUCAGGUAGAAGACAGCAC-UUUUCUUU-AAGUGUAUGCAAAACAAUAAUCAAAAUGAGCCUAAAAAGCGGCUCAGGGGUUGUAAAAGGUAACGAAUGAGGGAUAACAAAAGCUUG
((..((((...........((((-((......-)))))).(((......((((((....((((((........))))))..)))))).....))).....))))..))............ ( -28.30)
>consensus
AUUUCCCAAGUGCAGAACACCAC_UUUUUUUUUAAGUGUAUGCAAAACUAUAAUCAAAAUGAGCCUAAAAAGUGGCUCAGGGGUUGUUAAAGGUAACGAAUGAGGGAUAACAAAAGCUUG
...((((..((.....))..................(((.(((......((((((....((((((........))))))..)))))).....)))))).....))))............. (-19.56 = -19.08 +  -0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 8,046,675 – 8,046,771
Length 96
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.99
Mean single sequence MFE -21.22
Consensus MFE -10.98
Energy contribution -11.86
Covariance contribution 0.88
Combinations/Pair 1.14
Mean z-score -1.81
Structure conservation index 0.52
SVM decision value 0.27
SVM RNA-class probability 0.660270
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8046675 96 - 23771897
----AUUU----CUAGCUACUU-------U--------GUAUUUUCUUAGUGCAGAACGCCAC-UUUUUCUUUAAGUGUAUGCAAAACUAUAAUGAAAAUGAGCCUAAAAAGUGGCUCAG
----.(((----(.......((-------(--------(((((.....))))))))..(((((-((.......)))))...))...........)))).((((((........)))))). ( -21.20)
>DroSec_CAF1 17796 104 - 1
----AUUU----CUAAUUACUU-------UUCAGUACUAUAUAUCCCAAGUGCAGAACACCAU-UUUUUUUCUAAGUGUAUGCAAAACUAUAAUCAAAAUGAGCCUAAAAAGUGGCUCAG
----....----.....((((.-------...))))..............((((..((((...-...........)))).))))...............((((((........)))))). ( -16.84)
>DroSim_CAF1 17832 105 - 1
----AUUU----CUAAUUACCU-------UUCAGUACUAUAUUUCCCAAGUGCAGAACACCACUUUUUUUUCUAAGUGUAUGCAAAACUAUAAUCAAAAUGAGCCUAAAAACUGGCUCAG
----....----..........-------(((.(((((..........))))).)))...(((((........))))).....................((((((........)))))). ( -17.90)
>DroEre_CAF1 17604 119 - 1
GCACAUUUACGUCAAAUUACUGCUAAUACUGCAGUAUUGUAUUUCUCAGGCACAAGGCAGCAC-UUUUGUUUCAAGUGUAUGCAAAACAAUAAUCAAAAUGAGCCUAAAAAGCGGCUCAG
((..........(((..((((((.......)))))))))..........)).....(((((((-((.......)))))).)))................((((((........)))))). ( -27.75)
>DroYak_CAF1 18166 107 - 1
----AAUUACGGCUUAUUACUG-------UGCACUAUUAUAUUUCUCAGGUAGAAGACAGCAC-UUUUCUUU-AAGUGUAUGCAAAACAAUAAUCAAAAUGAGCCUAAAAAGCGGCUCAG
----......((.(((((....-------((((........(((((.....)))))...((((-((......-)))))).))))....)))))))....((((((........)))))). ( -22.40)
>consensus
____AUUU____CUAAUUACUU_______UGCAGUACUAUAUUUCCCAAGUGCAGAACACCAC_UUUUUUUUUAAGUGUAUGCAAAACUAUAAUCAAAAUGAGCCUAAAAAGUGGCUCAG
..................................................((((..((((...............)))).))))...............((((((........)))))). (-10.98 = -11.86 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:48 2006