Locus 60

Sequence ID 2R_DroMel_CAF1
Location 1,315,185 – 1,315,345
Length 160
Max. P 0.946711
window112 window113 window114 window115

overview

Window 2

Location 1,315,185 – 1,315,305
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.97
Mean single sequence MFE -28.60
Consensus MFE -23.83
Energy contribution -24.95
Covariance contribution 1.12
Combinations/Pair 1.06
Mean z-score -1.41
Structure conservation index 0.83
SVM decision value 0.01
SVM RNA-class probability 0.537608
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1315185 120 + 20766785
AAUAAAGUCAAUCAAAUAGUGUCUUAAUUGUUAAAGGGCCGUGAAGGGUUUUAUGCCGGAGAAUUGGAUUUAUUCCCAAUGCAAACAUAAACAAUGGGCUGCAAGAUGUCGAGCAGCCAA
....(((.((.........)).))).((((((..((((((......)))))).(((.((.((((.......))))))...)))......)))))).((((((..(....)..)))))).. ( -25.60)
>DroSec_CAF1 33580 120 + 1
AACAAAGUCAAUCAAAUAGUGGCUUAAUUGUUAAAGGGCCGUGAAGGGUUUUAUGUCUGCGAAUUGGAUUUAUUCCCAAUACAAACAUAAACAAUGGGCUGCAAGAUGUCGAGCAGCCAA
....((((((.........)))))).((((((...(((((......)))))(((((.((...(((((........))))).)).))))))))))).((((((..(....)..)))))).. ( -29.70)
>DroSim_CAF1 12530 120 + 1
AACAAAGUCAAUCAAAUAGUGGCUUAAUCGUUGAAGGGCCGUGAAGGGUUUUAUGUCUGCGAAUUGGAUUUAUUCCCAAUACAAACAUAAACAAUGGGCUGCAAGAUGUCGAGCAGCCAA
....((((((.........))))))...(((((....(((......)))(((((((.((...(((((........))))).)).))))))))))))((((((..(....)..)))))).. ( -30.90)
>DroEre_CAF1 16021 120 + 1
AGUAAAGUCAAUCGAAUAGUGGCUAAAUUGUUAAAAAGCCAUAAAGGGUUUUAUGUCUGAAAAUUGGAUUUACUCCCAAUACAAACAUUAACAAUGGGCUGGAAGUCGUCGAGCAGCCAA
...................(((((..((((((((((((((......)))))).(((.((...(((((........))))).)).)))))))))))..(((.((.....)).)))))))). ( -28.20)
>consensus
AACAAAGUCAAUCAAAUAGUGGCUUAAUUGUUAAAGGGCCGUGAAGGGUUUUAUGUCUGAGAAUUGGAUUUAUUCCCAAUACAAACAUAAACAAUGGGCUGCAAGAUGUCGAGCAGCCAA
....((((((.........)))))).((((((..((((((......))))))((((.((...(((((........))))).)).)))).)))))).((((((..(....)..)))))).. (-23.83 = -24.95 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 1,315,185 – 1,315,305
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.97
Mean single sequence MFE -27.57
Consensus MFE -24.48
Energy contribution -25.10
Covariance contribution 0.62
Combinations/Pair 1.06
Mean z-score -2.04
Structure conservation index 0.89
SVM decision value 1.37
SVM RNA-class probability 0.946711
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1315185 120 - 20766785
UUGGCUGCUCGACAUCUUGCAGCCCAUUGUUUAUGUUUGCAUUGGGAAUAAAUCCAAUUCUCCGGCAUAAAACCCUUCACGGCCCUUUAACAAUUAAGACACUAUUUGAUUGACUUUAUU
..((((((..(....)..)))))).....((((((((.(.((((((......)))))).)...))))))))...................((((((((......))))))))........ ( -24.30)
>DroSec_CAF1 33580 120 - 1
UUGGCUGCUCGACAUCUUGCAGCCCAUUGUUUAUGUUUGUAUUGGGAAUAAAUCCAAUUCGCAGACAUAAAACCCUUCACGGCCCUUUAACAAUUAAGCCACUAUUUGAUUGACUUUGUU
..((((((..(....)..)))))).....(((((((((((((((((......))))))..)))))))))))...................((((((((......))))))))........ ( -30.30)
>DroSim_CAF1 12530 120 - 1
UUGGCUGCUCGACAUCUUGCAGCCCAUUGUUUAUGUUUGUAUUGGGAAUAAAUCCAAUUCGCAGACAUAAAACCCUUCACGGCCCUUCAACGAUUAAGCCACUAUUUGAUUGACUUUGUU
..((((((..(....)..)))))).....(((((((((((((((((......))))))..)))))))))))...................((((((((......))))))))........ ( -30.00)
>DroEre_CAF1 16021 120 - 1
UUGGCUGCUCGACGACUUCCAGCCCAUUGUUAAUGUUUGUAUUGGGAGUAAAUCCAAUUUUCAGACAUAAAACCCUUUAUGGCUUUUUAACAAUUUAGCCACUAUUCGAUUGACUUUACU
.((((((((.((.....)).)))..((((((((((((((.((((((......))))))...)))))))((((.((.....)).)))))))))))..)))))................... ( -25.70)
>consensus
UUGGCUGCUCGACAUCUUGCAGCCCAUUGUUUAUGUUUGUAUUGGGAAUAAAUCCAAUUCGCAGACAUAAAACCCUUCACGGCCCUUUAACAAUUAAGCCACUAUUUGAUUGACUUUAUU
..((((((..(....)..)))))).....((((((((((.((((((......))))))...))))))))))...................((((((((......))))))))........ (-24.48 = -25.10 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 1,315,225 – 1,315,345
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.89
Mean single sequence MFE -29.18
Consensus MFE -23.34
Energy contribution -24.27
Covariance contribution 0.94
Combinations/Pair 1.10
Mean z-score -1.36
Structure conservation index 0.80
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1315225 120 + 20766785
GUGAAGGGUUUUAUGCCGGAGAAUUGGAUUUAUUCCCAAUGCAAACAUAAACAAUGGGCUGCAAGAUGUCGAGCAGCCAAUUCAAAUUAGAUCCCCUGCCUAAAGCUUCACAAAUUAAGC
((((..(((((((.((.((.(((((((........)))))................((((((..(....)..)))))).............)).)).)).)))))))))))......... ( -32.20)
>DroSec_CAF1 33620 120 + 1
GUGAAGGGUUUUAUGUCUGCGAAUUGGAUUUAUUCCCAAUACAAACAUAAACAAUGGGCUGCAAGAUGUCGAGCAGCCAAUUCAAAUUAAAUCCCCUGCCGGAGGCUUUACAAAUUAAGC
((((((((.(((((((.((...(((((........))))).)).))))))).....((((((..(....)..))))))...............))))(((...))).))))......... ( -31.00)
>DroSim_CAF1 12570 120 + 1
GUGAAGGGUUUUAUGUCUGCGAAUUGGAUUUAUUCCCAAUACAAACAUAAACAAUGGGCUGCAAGAUGUCGAGCAGCCAAUUCAAAUUAGAUCCCCUGCCGGAGGCUUUACAAAUUAAGC
((((((((.(((((((.((...(((((........))))).)).))))))).....((((((..(....)..))))))...............))))(((...))).))))......... ( -31.00)
>DroEre_CAF1 16061 120 + 1
AUAAAGGGUUUUAUGUCUGAAAAUUGGAUUUACUCCCAAUACAAACAUUAACAAUGGGCUGGAAGUCGUCGAGCAGCCAAUUCAAAUUACAACUCCUUCCUGGAGCUUUACAAACGGAUC
.(((((.(((..((((.((...(((((........))))).)).)))).)))....(((((...(....)...)))))..............((((.....))))))))).......... ( -22.50)
>consensus
GUGAAGGGUUUUAUGUCUGAGAAUUGGAUUUAUUCCCAAUACAAACAUAAACAAUGGGCUGCAAGAUGUCGAGCAGCCAAUUCAAAUUAGAUCCCCUGCCGGAAGCUUUACAAAUUAAGC
((((((((.(((((((.((...(((((........))))).)).))))))).....((((((..(....)..))))))...............))))((.....)).))))......... (-23.34 = -24.27 +   0.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 1,315,225 – 1,315,345
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.89
Mean single sequence MFE -32.30
Consensus MFE -27.34
Energy contribution -27.27
Covariance contribution -0.06
Combinations/Pair 1.19
Mean z-score -1.91
Structure conservation index 0.85
SVM decision value 0.96
SVM RNA-class probability 0.889912
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1315225 120 - 20766785
GCUUAAUUUGUGAAGCUUUAGGCAGGGGAUCUAAUUUGAAUUGGCUGCUCGACAUCUUGCAGCCCAUUGUUUAUGUUUGCAUUGGGAAUAAAUCCAAUUCUCCGGCAUAAAACCCUUCAC
((((((...(.....).))))))(((((..........(((.((((((..(....)..)))))).))).((((((((.(.((((((......)))))).)...)))))))).)))))... ( -31.90)
>DroSec_CAF1 33620 120 - 1
GCUUAAUUUGUAAAGCCUCCGGCAGGGGAUUUAAUUUGAAUUGGCUGCUCGACAUCUUGCAGCCCAUUGUUUAUGUUUGUAUUGGGAAUAAAUCCAAUUCGCAGACAUAAAACCCUUCAC
..............(((...)))(((((..........(((.((((((..(....)..)))))).))).(((((((((((((((((......))))))..))))))))))).)))))... ( -35.90)
>DroSim_CAF1 12570 120 - 1
GCUUAAUUUGUAAAGCCUCCGGCAGGGGAUCUAAUUUGAAUUGGCUGCUCGACAUCUUGCAGCCCAUUGUUUAUGUUUGUAUUGGGAAUAAAUCCAAUUCGCAGACAUAAAACCCUUCAC
..............(((...)))(((((..........(((.((((((..(....)..)))))).))).(((((((((((((((((......))))))..))))))))))).)))))... ( -35.90)
>DroEre_CAF1 16061 120 - 1
GAUCCGUUUGUAAAGCUCCAGGAAGGAGUUGUAAUUUGAAUUGGCUGCUCGACGACUUCCAGCCCAUUGUUAAUGUUUGUAUUGGGAGUAAAUCCAAUUUUCAGACAUAAAACCCUUUAU
.....((((....((((((.....))))))........(((.(((((............))))).)))....(((((((.((((((......))))))...))))))).))))....... ( -25.50)
>consensus
GCUUAAUUUGUAAAGCCUCAGGCAGGGGAUCUAAUUUGAAUUGGCUGCUCGACAUCUUGCAGCCCAUUGUUUAUGUUUGUAUUGGGAAUAAAUCCAAUUCGCAGACAUAAAACCCUUCAC
.........((((((((((.....))))..........(((.((((((..(....)..)))))).))).((((((((((.((((((......))))))...))))))))))...)))))) (-27.34 = -27.27 +  -0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:25:09 2006