Locus 8337

Sequence ID X_DroMel_CAF1
Location 20,685,258 – 20,685,425
Length 167
Max. P 0.990575
window13695 window13696 window13697

overview

Window 5

Location 20,685,258 – 20,685,348
Length 90
Sequences 3
Columns 90
Reading direction reverse
Mean pairwise identity 91.48
Mean single sequence MFE -31.10
Consensus MFE -29.18
Energy contribution -28.63
Covariance contribution -0.55
Combinations/Pair 1.15
Mean z-score -2.78
Structure conservation index 0.94
SVM decision value 1.91
SVM RNA-class probability 0.982295
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20685258 90 - 22224390
UGACAUUUUUUCCUUUAUACUUUCGCUUCGGCGAAAGAGACGGCAGCCAGGGCCGCAGAAAGAGAAGGAUAGAAGUGUUGUUUGGGCCAU
.(((((((((((((((...(((((((....))))))).(.((((.......))))).......)))))).)))))))))........... ( -32.80)
>DroEre_CAF1 81645 89 - 1
UGACAUUUUUUCCUUUAUACUUUCGCUUCGGCGAAAGAGACGGCAGGCUGGGUCGCAGAAAAAG-GGGGUAGAAGUGUUGUUUGGGCCAU
.(((((((((((((((...(((((((....))))))).(.((((.......)))))......))-)))).)))))))))........... ( -28.50)
>DroYak_CAF1 83220 90 - 1
UGACAUUUUUUCCUUUAUACUUUCGCUUCGGCGAAAGAGACGGCAGCAGGGGUUGUGGAAAGAGAGGGGUAGAAGUGUUGUUUGGGCCAU
.(((((((((((((((...(((((((....)))))))...(.(((((....))))).).....)))))).)))))))))........... ( -32.00)
>consensus
UGACAUUUUUUCCUUUAUACUUUCGCUUCGGCGAAAGAGACGGCAGCCAGGGUCGCAGAAAGAGAGGGGUAGAAGUGUUGUUUGGGCCAU
.(((((((((((((((...(((((((....)))))))...((((.......))))........)))))).)))))))))........... (-29.18 = -28.63 +  -0.55)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 20,685,292 – 20,685,388
Length 96
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 75.77
Mean single sequence MFE -29.03
Consensus MFE -20.75
Energy contribution -20.50
Covariance contribution -0.25
Combinations/Pair 1.13
Mean z-score -2.18
Structure conservation index 0.71
SVM decision value 2.22
SVM RNA-class probability 0.990575
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20685292 96 - 22224390
UCCUUACAAUCAGUUACAGUCUCAGCUGUCAAUAGAUUGUUGACAUUUUUU-CCUUUAUACUUUCGCUUCGGCGAAAG------------AG----------ACGG-CAGCCAGGGCCGC
.....((((((.((((((((....))))).))).))))))...........-........(((((((....)))))))------------..----------.(((-(.......)))). ( -29.10)
>DroEre_CAF1 81678 96 - 1
UCCUUACAAUCAGUUACAGUCUCAGCUGUCAAUAGAUUGUUGACAUUUUUU-CCUUUAUACUUUCGCUUCGGCGAAAG------------AG----------ACGG-CAGGCUGGGUCGC
..................(.(((((((((((((.....)))))).......-........(((((((....)))))))------------..----------....-..))))))).).. ( -30.30)
>DroYak_CAF1 83254 96 - 1
UCCUUACAAUCAGUUACAGUCUCAGCUGUCAAUAGAUUGUUGACAUUUUUU-CCUUUAUACUUUCGCUUCGGCGAAAG------------AG----------ACGG-CAGCAGGGGUUGU
.....((((((.(((.(.(((((...(((((((.....)))))))......-.........((((((....)))))))------------))----------)).)-.)))...)))))) ( -30.00)
>DroAna_CAF1 57358 114 - 1
GCCAUACAAUCAGUUACAGUCUCAGCUGUCAAUAGAUUGUUGACAUUUUUUUUCUCUUUUUUUUUG------CGAGUGUGUGUGUGUGGGAGUCCUCCUUUAAGGACCACCAGGGAGUGU
..((.((((((.((((((((....))))).))).))))))))((((((((...(((..........------.)))..........(((..(((((......)))))..))))))))))) ( -26.70)
>consensus
UCCUUACAAUCAGUUACAGUCUCAGCUGUCAAUAGAUUGUUGACAUUUUUU_CCUUUAUACUUUCGCUUCGGCGAAAG____________AG__________ACGG_CAGCAGGGGUCGC
.((..((((((.((((((((....))))).))).))))))....................(((((((....)))))))...................................))..... (-20.75 = -20.50 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 20,685,311 – 20,685,425
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.06
Mean single sequence MFE -21.74
Consensus MFE -19.30
Energy contribution -19.05
Covariance contribution -0.25
Combinations/Pair 1.14
Mean z-score -2.24
Structure conservation index 0.89
SVM decision value 2.11
SVM RNA-class probability 0.988078
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20685311 114 - 22224390
CGCAUUUACUAGCCCC---GCCCGUUCCGUCUCUGUUUACUCCUUACAAUCAGUUACAGUCUCAGCUGUCAAUAGAUUGUUGACAUUUUUU-CCUUUAUACUUUCGCUUCGGCGAAAG--
.((........))...---.........(((..............((((((.((((((((....))))).))).)))))).))).......-........(((((((....)))))))-- ( -24.46)
>DroEre_CAF1 81697 114 - 1
CGCAUUUCCCAGCCCC---GCCCAUUCCGCCUCUGUUUACUCCUUACAAUCAGUUACAGUCUCAGCUGUCAAUAGAUUGUUGACAUUUUUU-CCUUUAUACUUUCGCUUCGGCGAAAG--
.((........))...---..............((((........((((((.((((((((....))))).))).)))))).))))......-........(((((((....)))))))-- ( -23.50)
>DroYak_CAF1 83273 117 - 1
CGCAUUUCCCAGCCCCUCUGCUUACUGCCCCUCUGUUUACUCCUUACAAUCAGUUACAGUCUCAGCUGUCAAUAGAUUGUUGACAUUUUUU-CCUUUAUACUUUCGCUUCGGCGAAAG--
.(((.....(((.....))).....))).....((((........((((((.((((((((....))))).))).)))))).))))......-........(((((((....)))))))-- ( -25.60)
>DroAna_CAF1 57398 100 - 1
----UUUAUCAUCCCC---ACCC-------CUUUUUUUUCGCCAUACAAUCAGUUACAGUCUCAGCUGUCAAUAGAUUGUUGACAUUUUUUUUCUCUUUUUUUUUG------CGAGUGUG
----............---....-------.......(((((((.((((((.((((((((....))))).))).)))))))).......................)------)))).... ( -13.40)
>consensus
CGCAUUUACCAGCCCC___GCCCAUUCCGCCUCUGUUUACUCCUUACAAUCAGUUACAGUCUCAGCUGUCAAUAGAUUGUUGACAUUUUUU_CCUUUAUACUUUCGCUUCGGCGAAAG__
.............................................((((((.((((((((....))))).))).))))))....................(((((((....))))))).. (-19.30 = -19.05 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:01:34 2006