Locus 7113

Sequence ID 3R_DroMel_CAF1
Location 18,748,440 – 18,748,620
Length 180
Max. P 0.999437
window11507 window11508 window11509 window11510 window11511

overview

Window 7

Location 18,748,440 – 18,748,553
Length 113
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 98.24
Mean single sequence MFE -33.28
Consensus MFE -32.58
Energy contribution -32.78
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.98
SVM decision value 3.60
SVM RNA-class probability 0.999437
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18748440 113 + 27905053
UAUAUUGGCAGUUAUGCUGCAAAUUUAUUGGCAUGCUUUGUAAACUGGGUUAGUUGCAUAU--AUCUCGCAGCCGCAAGCUGCGAGCCAAACGAUUAACGUUGAGUAACCCAAAU
.......((((.....))))...(((((.((....))..))))).(((((((.((......--..(((((((.(....))))))))...((((.....)))))).)))))))... ( -33.60)
>DroSec_CAF1 7188 113 + 1
UAUAUUGGCAGUUAUGCUGCAAAUUUAUUGGCAUGCUUUGUAAACUGGGUUAGUUGCAUAU--AUCUCGCAGCCGCAAGCUGCGAGCCAAACGAUUAACGUUGAGUAACCCAAAU
.......((((.....))))...(((((.((....))..))))).(((((((.((......--..(((((((.(....))))))))...((((.....)))))).)))))))... ( -33.60)
>DroEre_CAF1 7250 113 + 1
UAUAUUGGCAGUUAUGCUGAAAAUUUAUUGGCAUGCUUUGUAAACUGGGUUAGUUGCAUAU--AUCUCGCAGCCGCAAGCUGCGAGCCAAACGAUUAACGUUGAGUAACCCAAAU
.......((((.(((((..(.......)..)))))..))))....(((((((.((......--..(((((((.(....))))))))...((((.....)))))).)))))))... ( -35.20)
>DroYak_CAF1 1258 113 + 1
UAUAUUGGCAGUUAUGCUGCAAAUUUAUUGGCAUGCUUUGUAAACUGGGUUAGUUGCAUAU--AUCUCGCAGCCGCAAGCUGCGAGCCAAACGAUUAACGUUGAGUAACCCAAAU
.......((((.....))))...(((((.((....))..))))).(((((((.((......--..(((((((.(....))))))))...((((.....)))))).)))))))... ( -33.60)
>DroAna_CAF1 1423 115 + 1
UAUAUUGGCAGUUAUGCUGCAAAUUUAUUGGCAUGCUUUGUAAACUGGGUUAGUUGCAUAUACAUCUCGCAGCCGCAAGCUGCGCGGCAAACGAUUAACGUUGAGUAACCCAAAU
.......((((.....))))...(((((.((....))..))))).(((((((.((.........((.(((((.(....)))))).))..((((.....)))))).)))))))... ( -30.40)
>consensus
UAUAUUGGCAGUUAUGCUGCAAAUUUAUUGGCAUGCUUUGUAAACUGGGUUAGUUGCAUAU__AUCUCGCAGCCGCAAGCUGCGAGCCAAACGAUUAACGUUGAGUAACCCAAAU
.......((((.((((((...........))))))..))))....(((((((.((..........(((((((.(....))))))))...((((.....)))))).)))))))... (-32.58 = -32.78 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 18,748,440 – 18,748,553
Length 113
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 98.24
Mean single sequence MFE -30.90
Consensus MFE -29.12
Energy contribution -29.72
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.42
Structure conservation index 0.94
SVM decision value 3.36
SVM RNA-class probability 0.999080
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18748440 113 - 27905053
AUUUGGGUUACUCAACGUUAAUCGUUUGGCUCGCAGCUUGCGGCUGCGAGAU--AUAUGCAACUAACCCAGUUUACAAAGCAUGCCAAUAAAUUUGCAGCAUAACUGCCAAUAUA
..((((((((((.((((.....)))).))((((((((.....))))))))..--.........))))))))....................(((.((((.....)))).)))... ( -32.10)
>DroSec_CAF1 7188 113 - 1
AUUUGGGUUACUCAACGUUAAUCGUUUGGCUCGCAGCUUGCGGCUGCGAGAU--AUAUGCAACUAACCCAGUUUACAAAGCAUGCCAAUAAAUUUGCAGCAUAACUGCCAAUAUA
..((((((((((.((((.....)))).))((((((((.....))))))))..--.........))))))))....................(((.((((.....)))).)))... ( -32.10)
>DroEre_CAF1 7250 113 - 1
AUUUGGGUUACUCAACGUUAAUCGUUUGGCUCGCAGCUUGCGGCUGCGAGAU--AUAUGCAACUAACCCAGUUUACAAAGCAUGCCAAUAAAUUUUCAGCAUAACUGCCAAUAUA
..((((((((((.((((.....)))).))((((((((.....))))))))..--.........))))))))........((((((.............)))....)))....... ( -29.22)
>DroYak_CAF1 1258 113 - 1
AUUUGGGUUACUCAACGUUAAUCGUUUGGCUCGCAGCUUGCGGCUGCGAGAU--AUAUGCAACUAACCCAGUUUACAAAGCAUGCCAAUAAAUUUGCAGCAUAACUGCCAAUAUA
..((((((((((.((((.....)))).))((((((((.....))))))))..--.........))))))))....................(((.((((.....)))).)))... ( -32.10)
>DroAna_CAF1 1423 115 - 1
AUUUGGGUUACUCAACGUUAAUCGUUUGCCGCGCAGCUUGCGGCUGCGAGAUGUAUAUGCAACUAACCCAGUUUACAAAGCAUGCCAAUAAAUUUGCAGCAUAACUGCCAAUAUA
..((((((((..(((((((..((((..((((((.....)))))).)))))))))...))....))))))))....................(((.((((.....)))).)))... ( -29.00)
>consensus
AUUUGGGUUACUCAACGUUAAUCGUUUGGCUCGCAGCUUGCGGCUGCGAGAU__AUAUGCAACUAACCCAGUUUACAAAGCAUGCCAAUAAAUUUGCAGCAUAACUGCCAAUAUA
..((((((((((.((((.....)))).))((((((((.....)))))))).............))))))))....................(((.((((.....)))).)))... (-29.12 = -29.72 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 18,748,475 – 18,748,587
Length 112
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 90.54
Mean single sequence MFE -33.42
Consensus MFE -30.77
Energy contribution -30.77
Covariance contribution 0.00
Combinations/Pair 1.03
Mean z-score -2.63
Structure conservation index 0.92
SVM decision value 2.45
SVM RNA-class probability 0.994117
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18748475 112 + 27905053
CUUUGUAAACUGGGUUAGUUGCAUAUAUCUCGCAGCCGCAAGCUGCGAGCCAAACGAUUAACGUUGAGUAACCCAAAUUGAUGUCACCACCCAUCGACCGCAGCUAACAGCC------
.............(((((((((......(((((((.(....))))))))...((((.....))))............((((((........))))))..)))))))))....------ ( -33.50)
>DroSec_CAF1 7223 118 + 1
CUUUGUAAACUGGGUUAGUUGCAUAUAUCUCGCAGCCGCAAGCUGCGAGCCAAACGAUUAACGUUGAGUAACCCAAAUUGAUGUCACCACCCAUCGACCGCAGCUAACAGCCCACCGC
..........((((((((((((......(((((((.(....))))))))...((((.....))))............((((((........))))))..)))))))...))))).... ( -35.80)
>DroEre_CAF1 7285 118 + 1
CUUUGUAAACUGGGUUAGUUGCAUAUAUCUCGCAGCCGCAAGCUGCGAGCCAAACGAUUAACGUUGAGUAACCCAAAUUGAUGUCACCACCCAUCGACCACAGCCCACAACUAACGGC
...(((....(((((((.((........(((((((.(....))))))))...((((.....)))))).)))))))..((((((........))))))..)))(((..........))) ( -32.70)
>DroYak_CAF1 1293 108 + 1
CUUUGUAAACUGGGUUAGUUGCAUAUAUCUCGCAGCCGCAAGCUGCGAGCCAAACGAUUAACGUUGAGUAACCCAAAUUGAUGUCACCACCCAUCGACCAC----------UAACAGC
..((((....(((((((.((........(((((((.(....))))))))...((((.....)))))).)))))))..((((((........))))))....----------..)))). ( -31.70)
>consensus
CUUUGUAAACUGGGUUAGUUGCAUAUAUCUCGCAGCCGCAAGCUGCGAGCCAAACGAUUAACGUUGAGUAACCCAAAUUGAUGUCACCACCCAUCGACCACAGCUAACAGCCAAC_GC
...(((....(((((((.((........(((((((.(....))))))))...((((.....)))))).)))))))..((((((........))))))..)))................ (-30.77 = -30.77 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 18,748,475 – 18,748,587
Length 112
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 90.54
Mean single sequence MFE -40.58
Consensus MFE -34.50
Energy contribution -34.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.23
Structure conservation index 0.85
SVM decision value 1.41
SVM RNA-class probability 0.951100
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18748475 112 - 27905053
------GGCUGUUAGCUGCGGUCGAUGGGUGGUGACAUCAAUUUGGGUUACUCAACGUUAAUCGUUUGGCUCGCAGCUUGCGGCUGCGAGAUAUAUGCAACUAACCCAGUUUACAAAG
------((((((.....))))))....((((....))))...((((((((((.((((.....)))).))((((((((.....))))))))...........))))))))......... ( -41.00)
>DroSec_CAF1 7223 118 - 1
GCGGUGGGCUGUUAGCUGCGGUCGAUGGGUGGUGACAUCAAUUUGGGUUACUCAACGUUAAUCGUUUGGCUCGCAGCUUGCGGCUGCGAGAUAUAUGCAACUAACCCAGUUUACAAAG
...((((((((((((.((((((..(((((((....))))...(((((...))))))))..)))......((((((((.....))))))))......))).)))))..))))))).... ( -43.60)
>DroEre_CAF1 7285 118 - 1
GCCGUUAGUUGUGGGCUGUGGUCGAUGGGUGGUGACAUCAAUUUGGGUUACUCAACGUUAAUCGUUUGGCUCGCAGCUUGCGGCUGCGAGAUAUAUGCAACUAACCCAGUUUACAAAG
........((((((((((.((((((..((((....))))...)))((((.((.((((.....)))).))((((((((.....))))))))........)))).))))))))))))).. ( -42.20)
>DroYak_CAF1 1293 108 - 1
GCUGUUA----------GUGGUCGAUGGGUGGUGACAUCAAUUUGGGUUACUCAACGUUAAUCGUUUGGCUCGCAGCUUGCGGCUGCGAGAUAUAUGCAACUAACCCAGUUUACAAAG
.......----------((((.(....((((....))))....(((((((((.((((.....)))).))((((((((.....))))))))...........)))))))).)))).... ( -35.50)
>consensus
GC_GUUAGCUGUUAGCUGCGGUCGAUGGGUGGUGACAUCAAUUUGGGUUACUCAACGUUAAUCGUUUGGCUCGCAGCUUGCGGCUGCGAGAUAUAUGCAACUAACCCAGUUUACAAAG
....................((.(((.((((....))))....(((((((((.((((.....)))).))((((((((.....))))))))...........)))))))))).)).... (-34.50 = -34.50 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 18,748,513 – 18,748,620
Length 107
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 82.63
Mean single sequence MFE -39.52
Consensus MFE -29.14
Energy contribution -29.32
Covariance contribution 0.19
Combinations/Pair 1.18
Mean z-score -1.89
Structure conservation index 0.74
SVM decision value 0.72
SVM RNA-class probability 0.831827
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18748513 107 - 27905053
AGCGGGCAAAUGUUGGUGGCGGUGGGUGGUGCG------------GGCUGUUAGCUGCGGUCGAUGGGUGGUGACAUCAAUUUGGGUUACUCAACGUUAAUCGUUUGGCUCGCAGCUUG
.(((((((((((....(((((.(((((..(.((------------((((((.....))))))....((((....))))....)).)..))))).)))))..))))).))))))...... ( -41.80)
>DroSec_CAF1 7261 119 - 1
AGCGGGCAGAUGUGGGUGAUGUUGGAUGGUGGGUGGUGGGCGGUGGGCUGUUAGCUGCGGUCGAUGGGUGGUGACAUCAAUUUGGGUUACUCAACGUUAAUCGUUUGGCUCGCAGCUUG
.(((((((((((....(((((((((((.(..(.(((..(.(....).)..))).)..).)))....((((....)))).............))))))))..))))).))))))...... ( -44.00)
>DroEre_CAF1 7323 119 - 1
AGCGGGCAAAUGUGGGUGUUUGUGGGUGGUGGGCGGUGGGCCGUUAGUUGUGGGCUGUGGUCGAUGGGUGGUGACAUCAAUUUGGGUUACUCAACGUUAAUCGUUUGGCUCGCAGCUUG
.((..((((((......))))))..))....(((((....)))))((((((((((((((((..(((((((....))))...(((((...))))))))..))))..)))))))))))).. ( -39.30)
>DroYak_CAF1 1331 109 - 1
AGUGGGCAAAUGUGGGUGGUGCUGGGUGGUGGGCUGUUAGCUGUUA----------GUGGUCGAUGGGUGGUGACAUCAAUUUGGGUUACUCAACGUUAAUCGUUUGGCUCGCAGCUUG
.(((((((((((....(..((.((((((((.(((..((((...)))----------)..))).)).((((....)))).........)))))).))..)..))))).))))))...... ( -33.00)
>consensus
AGCGGGCAAAUGUGGGUGGUGGUGGGUGGUGGGCGGUGGGC_GUUAGCUGUUAGCUGCGGUCGAUGGGUGGUGACAUCAAUUUGGGUUACUCAACGUUAAUCGUUUGGCUCGCAGCUUG
.(((((((((((....(((((.(((((((................(((.....)))....((((..((((....))))...)))).))))))).)))))..))))).))))))...... (-29.14 = -29.32 +   0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:37:46 2006