Locus 5646

Sequence ID 3R_DroMel_CAF1
Location 14,832,539 – 14,832,809
Length 270
Max. P 0.959602
window9211 window9212 window9213 window9214 window9215 window9216 window9217

overview

Window 1

Location 14,832,539 – 14,832,649
Length 110
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 92.22
Mean single sequence MFE -39.13
Consensus MFE -28.72
Energy contribution -29.63
Covariance contribution 0.92
Combinations/Pair 1.00
Mean z-score -2.75
Structure conservation index 0.73
SVM decision value 0.16
SVM RNA-class probability 0.610723
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14832539 110 + 27905053
GAUUUGUGGCAAUCUCUGUGGGCAACGAUUGCUAUCUGGCCCAGCCUACAUGGCAUGGCUUUGUGUACAUAAGUUUAUGU----------ACACAGACAUUCCUGCGCACAUGACUCACA
((..(((((((.......(((((...(((....)))..)))))(((.....)))..((.((((((((((((....)))))----------)))))))....))))).))))....))... ( -36.00)
>DroSec_CAF1 10713 120 + 1
GAUUUGUGUCAAUCUCUGUGGGCAACGAUUGCUAUCUGUCGCAGCCUACAUGGCAUGGCUUUGUGUACAUAGGUUUAUGUACAGAUGUGUACACAGACAUUCCUGCGCACAUGACUCACA
....((.((((.....(((((((..((((........))))..)))))))(((((.((.((((((((((((.((......))...))))))))))))....))))).))..)))).)).. ( -39.80)
>DroSim_CAF1 10875 120 + 1
GAUUUGUGGCAAUCUCUGUGGGCAACGAUUGCUAUCUGUCGCAGCCUACAUGGCAUGGCUUUGUGUACAUAGGUUUAUGUACAGAUGUGUACACAGACAUUCCUGCGCACAUGACUCACA
((.(..((((......(((((((..((((........))))..)))))))..(((.((.((((((((((((.((......))...))))))))))))....))))))).))..).))... ( -41.60)
>consensus
GAUUUGUGGCAAUCUCUGUGGGCAACGAUUGCUAUCUGUCGCAGCCUACAUGGCAUGGCUUUGUGUACAUAGGUUUAUGUACAGAUGUGUACACAGACAUUCCUGCGCACAUGACUCACA
....((((.....((.(((((((..((((........))))..))))))).))((((....((((((.....((((.((((((....)))))).)))).....))))))))))...)))) (-28.72 = -29.63 +   0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 14,832,539 – 14,832,649
Length 110
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.22
Mean single sequence MFE -38.70
Consensus MFE -30.48
Energy contribution -31.40
Covariance contribution 0.92
Combinations/Pair 1.00
Mean z-score -3.06
Structure conservation index 0.79
SVM decision value 0.75
SVM RNA-class probability 0.840367
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14832539 110 - 27905053
UGUGAGUCAUGUGCGCAGGAAUGUCUGUGU----------ACAUAAACUUAUGUACACAAAGCCAUGCCAUGUAGGCUGGGCCAGAUAGCAAUCGUUGCCCACAGAGAUUGCCACAAAUC
((((((((.((((.((((((.(((((((((----------(((((....)))))))))...(((..(((.....)))..))).)))))....)).)))).))))..))))..)))).... ( -37.80)
>DroSec_CAF1 10713 120 - 1
UGUGAGUCAUGUGCGCAGGAAUGUCUGUGUACACAUCUGUACAUAAACCUAUGUACACAAAGCCAUGCCAUGUAGGCUGCGACAGAUAGCAAUCGUUGCCCACAGAGAUUGACACAAAUC
(((.((((.((((((((((....))))))))))..((((((((((....)))))))....((((.(((...)))))))(((((.(((....))))))))....))))))).)))...... ( -37.70)
>DroSim_CAF1 10875 120 - 1
UGUGAGUCAUGUGCGCAGGAAUGUCUGUGUACACAUCUGUACAUAAACCUAUGUACACAAAGCCAUGCCAUGUAGGCUGCGACAGAUAGCAAUCGUUGCCCACAGAGAUUGCCACAAAUC
((((.(((.((((((((((....))))))))))....((((((((....))))))))....((...(((.....))).))))).....((((((.(((....))).)))))))))).... ( -40.60)
>consensus
UGUGAGUCAUGUGCGCAGGAAUGUCUGUGUACACAUCUGUACAUAAACCUAUGUACACAAAGCCAUGCCAUGUAGGCUGCGACAGAUAGCAAUCGUUGCCCACAGAGAUUGCCACAAAUC
((((.(((.((((..((.....((.((((((((....)))))))).))...))..)))).((((.(((...)))))))..))).....((((((.(((....))).)))))))))).... (-30.48 = -31.40 +   0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 14,832,579 – 14,832,689
Length 110
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.33
Mean single sequence MFE -41.33
Consensus MFE -35.05
Energy contribution -35.30
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -3.96
Structure conservation index 0.85
SVM decision value 1.33
SVM RNA-class probability 0.942972
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14832579 110 + 27905053
CCAGCCUACAUGGCAUGGCUUUGUGUACAUAAGUUUAUGU----------ACACAGACAUUCCUGCGCACAUGACUCACAAAUAAUGUGCAAUGGCAGCCAUGACCAUGGUCGUCACCCA
........(((((((((((((((((((((((....)))))----------)))))))....((...((((((............))))))...))..)))))).)))))........... ( -40.20)
>DroSec_CAF1 10753 120 + 1
GCAGCCUACAUGGCAUGGCUUUGUGUACAUAGGUUUAUGUACAGAUGUGUACACAGACAUUCCUGCGCACAUGACUCACAAAUAAUGUGCAAUGGCAGCCAUGACCAUGGUCGUCACCCA
........(((((((((((((((((((((((.((......))...))))))))))))....((...((((((............))))))...))..)))))).)))))........... ( -41.90)
>DroSim_CAF1 10915 120 + 1
GCAGCCUACAUGGCAUGGCUUUGUGUACAUAGGUUUAUGUACAGAUGUGUACACAGACAUUCCUGCGCACAUGACUCACAAAUAAUGUGCAAUGGCAGCCAUGACCAUGGUCGUCACCCA
........(((((((((((((((((((((((.((......))...))))))))))))....((...((((((............))))))...))..)))))).)))))........... ( -41.90)
>consensus
GCAGCCUACAUGGCAUGGCUUUGUGUACAUAGGUUUAUGUACAGAUGUGUACACAGACAUUCCUGCGCACAUGACUCACAAAUAAUGUGCAAUGGCAGCCAUGACCAUGGUCGUCACCCA
........(((((((((((((..((((.....((((.((((((....)))))).)))).....)))((((((............)))))).)..).))))))).)))))........... (-35.05 = -35.30 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 14,832,579 – 14,832,689
Length 110
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.33
Mean single sequence MFE -42.77
Consensus MFE -37.40
Energy contribution -38.73
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -3.28
Structure conservation index 0.87
SVM decision value 1.50
SVM RNA-class probability 0.959602
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14832579 110 - 27905053
UGGGUGACGACCAUGGUCAUGGCUGCCAUUGCACAUUAUUUGUGAGUCAUGUGCGCAGGAAUGUCUGUGU----------ACAUAAACUUAUGUACACAAAGCCAUGCCAUGUAGGCUGG
..(....)...(((((.(((((((.((..(((((((.(((....))).)))))))..))......(((((----------(((((....)))))))))).))))))))))))........ ( -42.10)
>DroSec_CAF1 10753 120 - 1
UGGGUGACGACCAUGGUCAUGGCUGCCAUUGCACAUUAUUUGUGAGUCAUGUGCGCAGGAAUGUCUGUGUACACAUCUGUACAUAAACCUAUGUACACAAAGCCAUGCCAUGUAGGCUGC
..(....)...(((((.(((((((.......((((.....)))).....((((((((((....))))))))))....((((((((....))))))))...))))))))))))........ ( -43.10)
>DroSim_CAF1 10915 120 - 1
UGGGUGACGACCAUGGUCAUGGCUGCCAUUGCACAUUAUUUGUGAGUCAUGUGCGCAGGAAUGUCUGUGUACACAUCUGUACAUAAACCUAUGUACACAAAGCCAUGCCAUGUAGGCUGC
..(....)...(((((.(((((((.......((((.....)))).....((((((((((....))))))))))....((((((((....))))))))...))))))))))))........ ( -43.10)
>consensus
UGGGUGACGACCAUGGUCAUGGCUGCCAUUGCACAUUAUUUGUGAGUCAUGUGCGCAGGAAUGUCUGUGUACACAUCUGUACAUAAACCUAUGUACACAAAGCCAUGCCAUGUAGGCUGC
..(....)...(((((.(((((((((....))).....((((((.....((((((((((....))))))))))......((((((....)))))))))))))))))))))))........ (-37.40 = -38.73 +   1.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 14,832,619 – 14,832,729
Length 110
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.78
Mean single sequence MFE -47.11
Consensus MFE -46.52
Energy contribution -46.74
Covariance contribution 0.23
Combinations/Pair 1.05
Mean z-score -1.90
Structure conservation index 0.99
SVM decision value 1.20
SVM RNA-class probability 0.929790
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14832619 110 - 27905053
GGCCAAGGAUGCCAAGGGAAACCGGGGGCGUCGUCACGUCUGGGUGACGACCAUGGUCAUGGCUGCCAUUGCACAUUAUUUGUGAGUCAUGUGCGCAGGAAUGUCUGUGU----------
(((((..((((((..((....))...))))))(((((......)))))(((....))).)))))......((((((.(((....))).))))))(((((....)))))..---------- ( -45.50)
>DroSec_CAF1 10793 120 - 1
GGCCAAGGGCGCCAAGGGAAUCCGGGGGCGUCGUCACGUCUGGGUGACGACCAUGGUCAUGGCUGCCAUUGCACAUUAUUUGUGAGUCAUGUGCGCAGGAAUGUCUGUGUACACAUCUGU
(((((.(((((((..((....))...)))))((((((......)))))).)).)))))((((((.......((((.....))))))))))(((((((((....)))))))))........ ( -47.91)
>DroSim_CAF1 10955 120 - 1
GGCCAAGGGCGCCAAGGGAAUCCGGGGGCGUCGUCACGUCUGGGUGACGACCAUGGUCAUGGCUGCCAUUGCACAUUAUUUGUGAGUCAUGUGCGCAGGAAUGUCUGUGUACACAUCUGU
(((((.(((((((..((....))...)))))((((((......)))))).)).)))))((((((.......((((.....))))))))))(((((((((....)))))))))........ ( -47.91)
>consensus
GGCCAAGGGCGCCAAGGGAAUCCGGGGGCGUCGUCACGUCUGGGUGACGACCAUGGUCAUGGCUGCCAUUGCACAUUAUUUGUGAGUCAUGUGCGCAGGAAUGUCUGUGUACACAUCUGU
(((((.(((((((..((....))...)))))((((((......)))))).)).)))))((((((.......((((.....))))))))))(((((((((....)))))))))........ (-46.52 = -46.74 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 14,832,649 – 14,832,769
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.78
Mean single sequence MFE -42.13
Consensus MFE -42.57
Energy contribution -42.13
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -1.76
Structure conservation index 1.01
SVM decision value 0.80
SVM RNA-class probability 0.854074
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14832649 120 - 27905053
CUUGGCAAAAAUUAUUAUUUUCCUCAAAAUACGCUCGGAGGGCCAAGGAUGCCAAGGGAAACCGGGGGCGUCGUCACGUCUGGGUGACGACCAUGGUCAUGGCUGCCAUUGCACAUUAUU
..(((((..............((((............))))((((..((((((..((....))...))))))(((((......)))))(((....))).)))))))))............ ( -44.10)
>DroSec_CAF1 10833 120 - 1
CUUGGCAAAAAUUAUUAUUUUCCUCAAAAUACGCUCAGAGGGCCAAGGGCGCCAAGGGAAUCCGGGGGCGUCGUCACGUCUGGGUGACGACCAUGGUCAUGGCUGCCAUUGCACAUUAUU
..(((((..............((((............))))((((..((((((..((....))...))))))(((((......)))))(((....))).)))))))))............ ( -41.20)
>DroSim_CAF1 10995 120 - 1
CUUGGCAAAAAUUAUUAUUUUCCUCAAAAUACGCUCGGAGGGCCAAGGGCGCCAAGGGAAUCCGGGGGCGUCGUCACGUCUGGGUGACGACCAUGGUCAUGGCUGCCAUUGCACAUUAUU
..(((((..............((((............))))((((..((((((..((....))...))))))(((((......)))))(((....))).)))))))))............ ( -41.10)
>consensus
CUUGGCAAAAAUUAUUAUUUUCCUCAAAAUACGCUCGGAGGGCCAAGGGCGCCAAGGGAAUCCGGGGGCGUCGUCACGUCUGGGUGACGACCAUGGUCAUGGCUGCCAUUGCACAUUAUU
..(((((..............((((............))))((((..((((((..((....))...))))))(((((......)))))(((....))).)))))))))............ (-42.57 = -42.13 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 14,832,689 – 14,832,809
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.78
Mean single sequence MFE -40.43
Consensus MFE -40.87
Energy contribution -40.43
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.55
Structure conservation index 1.01
SVM decision value 0.43
SVM RNA-class probability 0.732864
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14832689 120 - 27905053
CGGAAGCUGACAGCAGCCGUCGCCGGAAAUGGCAAAUUAACUUGGCAAAAAUUAUUAUUUUCCUCAAAAUACGCUCGGAGGGCCAAGGAUGCCAAGGGAAACCGGGGGCGUCGUCACGUC
(((..((((....)))).....)))((..((((.......((((((.(((((....)))))((((............))))))))))((((((..((....))...))))))))))..)) ( -42.40)
>DroSec_CAF1 10873 120 - 1
CGGAAGCUGACAGCAGCCGUCGCCGGAAAUGGCAAAUUAACUUGGCAAAAAUUAUUAUUUUCCUCAAAAUACGCUCAGAGGGCCAAGGGCGCCAAGGGAAUCCGGGGGCGUCGUCACGUC
(((..((((....)))).....)))((..((((.......((((((.(((((....)))))((((............))))))))))((((((..((....))...))))))))))..)) ( -39.50)
>DroSim_CAF1 11035 120 - 1
CGGAAGCUGACAGCAGCCGUCGCCGGAAAUGGCAAAUUAACUUGGCAAAAAUUAUUAUUUUCCUCAAAAUACGCUCGGAGGGCCAAGGGCGCCAAGGGAAUCCGGGGGCGUCGUCACGUC
(((..((((....)))).....)))((..((((.......((((((.(((((....)))))((((............))))))))))((((((..((....))...))))))))))..)) ( -39.40)
>consensus
CGGAAGCUGACAGCAGCCGUCGCCGGAAAUGGCAAAUUAACUUGGCAAAAAUUAUUAUUUUCCUCAAAAUACGCUCGGAGGGCCAAGGGCGCCAAGGGAAUCCGGGGGCGUCGUCACGUC
(((..((((....)))).....)))((..((((.......((((((.(((((....)))))((((............))))))))))((((((..((....))...))))))))))..)) (-40.87 = -40.43 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:29 2006