Locus 7211

Sequence ID 2L_DroMel_CAF1
Location 20,250,583 – 20,250,821
Length 238
Max. P 0.981203
window11526 window11527 window11528 window11529 window11530 window11531 window11532

overview

Window 6

Location 20,250,583 – 20,250,701
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.94
Mean single sequence MFE -33.73
Consensus MFE -32.63
Energy contribution -32.97
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.97
SVM decision value 0.79
SVM RNA-class probability 0.850618
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20250583 118 + 22407834
AGAACGUGGCUAAACACCCAACUUGCGAUGCCCUUUGCUCAUUCGCCUGGCCAUCUAAAGCAAAUUAUCGAAUUAGUUUGUUUUUGUGUGCGGCCAAUUUUUAUUAGCUGUUAUGUGU--
...((((((((((...........((((.((.....))....)))).(((((..(.(((((((((((......)))))))))))...)...))))).......))))))...))))..-- ( -28.80)
>DroSec_CAF1 12169 120 + 1
AGAACGUGGCUAAACACCCAACUCGCGAUGGCCUUUGCUCAUUCGCGUGGCCAUCUAAAGCAAAUUAUCGAAUUAGUUUGUUUUUGUGUGCGGCCAAUUUUUAUUAGCUGUUAUGUGUCG
((((..(((((..((((.........(((((((..(((......))).))))))).(((((((((((......))))))))))).))))..)))))..)))).................. ( -36.20)
>DroSim_CAF1 10578 120 + 1
AGAACGUGGCUAAACACCCAACUUGCGAUGGCCUUUGCUCAUUCGCGUGGCCAUCUAAAGCAAAUUAUCGAAUUAGUUUGUUUUUGUGUGCGGCCAAUUUUUAUUAGCUGUUAUGUGUAG
((((..(((((..((((.........(((((((..(((......))).))))))).(((((((((((......))))))))))).))))..)))))..)))).................. ( -36.20)
>consensus
AGAACGUGGCUAAACACCCAACUUGCGAUGGCCUUUGCUCAUUCGCGUGGCCAUCUAAAGCAAAUUAUCGAAUUAGUUUGUUUUUGUGUGCGGCCAAUUUUUAUUAGCUGUUAUGUGU_G
((((..(((((..((((.........(((((((...((......))..))))))).(((((((((((......))))))))))).))))..)))))..)))).................. (-32.63 = -32.97 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 20,250,583 – 20,250,701
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.94
Mean single sequence MFE -29.03
Consensus MFE -27.00
Energy contribution -27.33
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.61
Structure conservation index 0.93
SVM decision value 0.01
SVM RNA-class probability 0.536999
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20250583 118 - 22407834
--ACACAUAACAGCUAAUAAAAAUUGGCCGCACACAAAAACAAACUAAUUCGAUAAUUUGCUUUAGAUGGCCAGGCGAAUGAGCAAAGGGCAUCGCAAGUUGGGUGUUUAGCCACGUUCU
--((((.((((.((((((....)))))).((..............(((..(((....)))..)))((((.((..((......))...)).))))))..)))).))))............. ( -25.50)
>DroSec_CAF1 12169 120 - 1
CGACACAUAACAGCUAAUAAAAAUUGGCCGCACACAAAAACAAACUAAUUCGAUAAUUUGCUUUAGAUGGCCACGCGAAUGAGCAAAGGCCAUCGCGAGUUGGGUGUUUAGCCACGUUCU
.(((((.((((.((((((....))))))(((..............(((..(((....)))..)))(((((((..((......))...)))))))))).)))).)))))............ ( -32.40)
>DroSim_CAF1 10578 120 - 1
CUACACAUAACAGCUAAUAAAAAUUGGCCGCACACAAAAACAAACUAAUUCGAUAAUUUGCUUUAGAUGGCCACGCGAAUGAGCAAAGGCCAUCGCAAGUUGGGUGUUUAGCCACGUUCU
..((((.((((.((((((....)))))).((..............(((..(((....)))..)))(((((((..((......))...)))))))))..)))).))))............. ( -29.20)
>consensus
C_ACACAUAACAGCUAAUAAAAAUUGGCCGCACACAAAAACAAACUAAUUCGAUAAUUUGCUUUAGAUGGCCACGCGAAUGAGCAAAGGCCAUCGCAAGUUGGGUGUUUAGCCACGUUCU
..((((.((((.((((((....)))))).((..............(((..(((....)))..)))(((((((..((......))...)))))))))..)))).))))............. (-27.00 = -27.33 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 20,250,623 – 20,250,741
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.83
Mean single sequence MFE -38.53
Consensus MFE -35.15
Energy contribution -35.27
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -2.95
Structure conservation index 0.91
SVM decision value 1.55
SVM RNA-class probability 0.962907
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20250623 118 + 22407834
AUUCGCCUGGCCAUCUAAAGCAAAUUAUCGAAUUAGUUUGUUUUUGUGUGCGGCCAAUUUUUAUUAGCUGUUAUGUGU--AGCGCUGCACUUGGCCAGGGAAAUUGAUUUCCGUGCUCAA
.(((.((((((((...(((((((((((......)))))))))))...(((((((.(((....))).((((.......)--)))))))))).))))))))))).................. ( -39.20)
>DroSec_CAF1 12209 120 + 1
AUUCGCGUGGCCAUCUAAAGCAAAUUAUCGAAUUAGUUUGUUUUUGUGUGCGGCCAAUUUUUAUUAGCUGUUAUGUGUCGAGCGUUGCACUUGGCCAGGGAAAUUGAUUUCCCUGCCCAA
...(((.(((((((..(((((((((((......))))))))))).))).(((((.(((....))).))))).....)))).))).......(((.((((((((....)))))))).))). ( -36.90)
>DroSim_CAF1 10618 120 + 1
AUUCGCGUGGCCAUCUAAAGCAAAUUAUCGAAUUAGUUUGUUUUUGUGUGCGGCCAAUUUUUAUUAGCUGUUAUGUGUAGAGCGCUGCACUUGGCCAGGGAAAUUGAUUUCCCUGCCCAG
....((..(((((...(((((((((((......)))))))))))...(((((((.(((....))).(((.(.......).)))))))))).)))))(((((((....))))))))).... ( -39.50)
>consensus
AUUCGCGUGGCCAUCUAAAGCAAAUUAUCGAAUUAGUUUGUUUUUGUGUGCGGCCAAUUUUUAUUAGCUGUUAUGUGU_GAGCGCUGCACUUGGCCAGGGAAAUUGAUUUCCCUGCCCAA
....((..(((((...(((((((((((......)))))))))))...(((((((.(((....))).(((...........)))))))))).)))))(((((((....))))))))).... (-35.15 = -35.27 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 20,250,623 – 20,250,741
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -32.60
Consensus MFE -30.43
Energy contribution -30.77
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.16
Structure conservation index 0.93
SVM decision value 1.88
SVM RNA-class probability 0.981203
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20250623 118 - 22407834
UUGAGCACGGAAAUCAAUUUCCCUGGCCAAGUGCAGCGCU--ACACAUAACAGCUAAUAAAAAUUGGCCGCACACAAAAACAAACUAAUUCGAUAAUUUGCUUUAGAUGGCCAGGCGAAU
....((..(((((....)))))(((((((.((((.(((((--.........)))((((....)))))).))))...........((((..(((....)))..)))).))))))))).... ( -31.80)
>DroSec_CAF1 12209 120 - 1
UUGGGCAGGGAAAUCAAUUUCCCUGGCCAAGUGCAACGCUCGACACAUAACAGCUAAUAAAAAUUGGCCGCACACAAAAACAAACUAAUUCGAUAAUUUGCUUUAGAUGGCCACGCGAAU
....(((((((((....)))))))(((((.((((..(....)..........((((((....)))))).))))...........((((..(((....)))..)))).)))))..)).... ( -33.10)
>DroSim_CAF1 10618 120 - 1
CUGGGCAGGGAAAUCAAUUUCCCUGGCCAAGUGCAGCGCUCUACACAUAACAGCUAAUAAAAAUUGGCCGCACACAAAAACAAACUAAUUCGAUAAUUUGCUUUAGAUGGCCACGCGAAU
....(((((((((....)))))))(((((.((((.(.(.....).)......((((((....)))))).))))...........((((..(((....)))..)))).)))))..)).... ( -32.90)
>consensus
UUGGGCAGGGAAAUCAAUUUCCCUGGCCAAGUGCAGCGCUC_ACACAUAACAGCUAAUAAAAAUUGGCCGCACACAAAAACAAACUAAUUCGAUAAUUUGCUUUAGAUGGCCACGCGAAU
....(((((((((....)))))))(((((.((((...(.....)........((((((....)))))).))))...........((((..(((....)))..)))).)))))..)).... (-30.43 = -30.77 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 20,250,663 – 20,250,781
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.28
Mean single sequence MFE -34.87
Consensus MFE -31.27
Energy contribution -30.50
Covariance contribution -0.77
Combinations/Pair 1.14
Mean z-score -1.83
Structure conservation index 0.90
SVM decision value 0.14
SVM RNA-class probability 0.601127
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20250663 118 + 22407834
UUUUUGUGUGCGGCCAAUUUUUAUUAGCUGUUAUGUGU--AGCGCUGCACUUGGCCAGGGAAAUUGAUUUCCGUGCUCAAAGAAGCUGGCCAAAACAGAAUAAUUCCGGACAGUAAAUUA
.(((((((((((((.(((....))).((((.......)--))))))))))(((((((.(((((....)))))..(((......)))))))))).)))))).................... ( -32.90)
>DroSec_CAF1 12249 120 + 1
UUUUUGUGUGCGGCCAAUUUUUAUUAGCUGUUAUGUGUCGAGCGUUGCACUUGGCCAGGGAAAUUGAUUUCCCUGCCCAAAGAAGCUGGCCAAAACAAGAUAAUUCCGGACAGUAAAUUA
.((((((....(((((.(((((......(((.((((.....)))).))).((((.((((((((....)))))))).))))))))).)))))...)))))).................... ( -34.30)
>DroSim_CAF1 10658 120 + 1
UUUUUGUGUGCGGCCAAUUUUUAUUAGCUGUUAUGUGUAGAGCGCUGCACUUGGCCAGGGAAAUUGAUUUCCCUGCCCAGAGAAGCUGGCCAAAACAAGAUAAUUCCGGACAGUAAAUUA
.((((((....(((((.(((((............((((((....))))))((((.((((((((....)))))))).))))))))).)))))...)))))).................... ( -37.40)
>consensus
UUUUUGUGUGCGGCCAAUUUUUAUUAGCUGUUAUGUGU_GAGCGCUGCACUUGGCCAGGGAAAUUGAUUUCCCUGCCCAAAGAAGCUGGCCAAAACAAGAUAAUUCCGGACAGUAAAUUA
.((((((....(((((.(((((..((((.(((........)))))))...((((.((((((((....)))))))).))))))))).)))))...)))))).................... (-31.27 = -30.50 +  -0.77)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 20,250,663 – 20,250,781
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.28
Mean single sequence MFE -33.83
Consensus MFE -30.83
Energy contribution -31.50
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.01
Structure conservation index 0.91
SVM decision value 1.61
SVM RNA-class probability 0.967682
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20250663 118 - 22407834
UAAUUUACUGUCCGGAAUUAUUCUGUUUUGGCCAGCUUCUUUGAGCACGGAAAUCAAUUUCCCUGGCCAAGUGCAGCGCU--ACACAUAACAGCUAAUAAAAAUUGGCCGCACACAAAAA
........(((.((........((((((((((((((((....))))..(((((....))))).)))))))).))))....--..........((((((....)))))))).)))...... ( -28.90)
>DroSec_CAF1 12249 120 - 1
UAAUUUACUGUCCGGAAUUAUCUUGUUUUGGCCAGCUUCUUUGGGCAGGGAAAUCAAUUUCCCUGGCCAAGUGCAACGCUCGACACAUAACAGCUAAUAAAAAUUGGCCGCACACAAAAA
.......(((.(((((((......))))))).))).....((((.((((((((....)))))))).))))((((..(....)..........((((((....)))))).))))....... ( -36.90)
>DroSim_CAF1 10658 120 - 1
UAAUUUACUGUCCGGAAUUAUCUUGUUUUGGCCAGCUUCUCUGGGCAGGGAAAUCAAUUUCCCUGGCCAAGUGCAGCGCUCUACACAUAACAGCUAAUAAAAAUUGGCCGCACACAAAAA
.......(((.(((((((......))))))).)))......(((.((((((((....)))))))).))).((((.(.(.....).)......((((((....)))))).))))....... ( -35.70)
>consensus
UAAUUUACUGUCCGGAAUUAUCUUGUUUUGGCCAGCUUCUUUGGGCAGGGAAAUCAAUUUCCCUGGCCAAGUGCAGCGCUC_ACACAUAACAGCUAAUAAAAAUUGGCCGCACACAAAAA
.......(((.(((((((......))))))).)))......(((.((((((((....)))))))).))).((((...(.....)........((((((....)))))).))))....... (-30.83 = -31.50 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 20,250,701 – 20,250,821
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -43.64
Consensus MFE -41.26
Energy contribution -40.93
Covariance contribution -0.33
Combinations/Pair 1.08
Mean z-score -2.36
Structure conservation index 0.95
SVM decision value 1.23
SVM RNA-class probability 0.933790
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20250701 120 - 22407834
CAAUUAGGGGGAUAGCCCGCAGCUGUCUGCGGGGCAAACUUAAUUUACUGUCCGGAAUUAUUCUGUUUUGGCCAGCUUCUUUGAGCACGGAAAUCAAUUUCCCUGGCCAAGUGCAGCGCU
.....((.((((((((((((((....)))))))..............)))))).........((((((((((((((((....))))..(((((....))))).)))))))).))))).)) ( -40.33)
>DroSec_CAF1 12289 120 - 1
CAAUUAGGGGGAUAGCCCGCAGCUGUCUGCGGGGCAAACUUAAUUUACUGUCCGGAAUUAUCUUGUUUUGGCCAGCUUCUUUGGGCAGGGAAAUCAAUUUCCCUGGCCAAGUGCAACGCU
.........(((((((.....)))))))(((..(((...........(((.(((((((......))))))).)))....(((((.((((((((....)))))))).))))))))..))). ( -46.20)
>DroSim_CAF1 10698 120 - 1
CAAUUAGGGGGAUAGCCCGCAGCUGUCUGCGGGGCAAACUUAAUUUACUGUCCGGAAUUAUCUUGUUUUGGCCAGCUUCUCUGGGCAGGGAAAUCAAUUUCCCUGGCCAAGUGCAGCGCU
.(((((((..(....(((((((....))))))).)...)))))))...((.(((((((......))))))).))(((.(.((((.((((((((....)))))))).)).)).).)))... ( -44.40)
>consensus
CAAUUAGGGGGAUAGCCCGCAGCUGUCUGCGGGGCAAACUUAAUUUACUGUCCGGAAUUAUCUUGUUUUGGCCAGCUUCUUUGGGCAGGGAAAUCAAUUUCCCUGGCCAAGUGCAGCGCU
.....((.((((((((((((((....)))))))..............)))))).........(((((((((((.(((......)))(((((((....)))))))))))))).))))).)) (-41.26 = -40.93 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:30:25 2006