Locus 5075

Sequence ID 2R_DroMel_CAF1
Location 16,479,871 – 16,479,973
Length 102
Max. P 0.991707
window8113 window8114

overview

Window 3

Location 16,479,871 – 16,479,973
Length 102
Sequences 3
Columns 103
Reading direction forward
Mean pairwise identity 55.70
Mean single sequence MFE -33.97
Consensus MFE -10.93
Energy contribution -13.79
Covariance contribution 2.87
Combinations/Pair 1.19
Mean z-score -2.34
Structure conservation index 0.32
SVM decision value 0.21
SVM RNA-class probability 0.636948
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16479871 102 + 20766785
UCAUUUCCGCAACACACACGCAGUUGCAGUUGCAUACGCACU-UGCCACAGUUGCGGCAGUUGCUGUUGCAGCAGUUGGUGCAGUUGCAGCUGCUGCGAUUGC
........(((((.........)))))(((.((....)))))-.....((((((((((((((((..(((((.(....).)))))..)))))))))))))))). ( -43.10)
>DroSec_CAF1 155123 79 + 1
UCAUUUCCGCAGCACACACGCAGUUGCAGUUGCAGUUGCACUUUGCCACUGUUGCGGCAGUU------------------------GCAGCUGCUGCGGNNNN
......((((((((.....(((..(((.((.(((((.((.....)).))))).)).)))..)------------------------))...)))))))).... ( -33.80)
>DroAna_CAF1 153127 85 + 1
UCAUUUCCGUGGCACACCCGCAACAUCAGUGGCACU-------UUCCACUUCU--GACAGUGGCAGUUGCAGUGGCAC-GGCAGUU--------UGCGGUGGC
..(((.(((((.(((...(((.......)))(((.(-------(.(((((...--...))))).)).))).))).)))-)).))).--------......... ( -25.00)
>consensus
UCAUUUCCGCAGCACACACGCAGUUGCAGUUGCACU_GCACU_UGCCACUGUUGCGGCAGUUGC_GUUGCAG__G_____GCAGUUGCAGCUGCUGCGGU_GC
........(((((...............)))))..................(((((((((((....(((((........)))))....))))))))))).... (-10.93 = -13.79 +   2.87)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 16,479,871 – 16,479,973
Length 102
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 55.70
Mean single sequence MFE -34.47
Consensus MFE -13.23
Energy contribution -15.23
Covariance contribution 2.01
Combinations/Pair 1.21
Mean z-score -2.79
Structure conservation index 0.38
SVM decision value 2.28
SVM RNA-class probability 0.991707
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16479871 102 - 20766785
GCAAUCGCAGCAGCUGCAACUGCACCAACUGCUGCAACAGCAACUGCCGCAACUGUGGCA-AGUGCGUAUGCAACUGCAACUGCGUGUGUGUUGCGGAAAUGA
(((...(((((((.(((....)))....)))))))....(((..((((((....))))))-..)))...)))..(((((((.........)))))))...... ( -42.30)
>DroSec_CAF1 155123 79 - 1
NNNNCCGCAGCAGCUGC------------------------AACUGCCGCAACAGUGGCAAAGUGCAACUGCAACUGCAACUGCGUGUGUGCUGCGGAAAUGA
....(((((((((.(((------------------------(..((((((....))))))...)))).))(((..(((....)))..))))))))))...... ( -33.80)
>DroAna_CAF1 153127 85 - 1
GCCACCGCA--------AACUGCC-GUGCCACUGCAACUGCCACUGUC--AGAAGUGGAA-------AGUGCCACUGAUGUUGCGGGUGUGCCACGGAAAUGA
(((((((((--------(....(.-(((.((((.......(((((...--...)))))..-------)))).))).)...)))).)))).))........... ( -27.30)
>consensus
GC_ACCGCAGCAGCUGCAACUGC_____C__CUGCAAC_GCAACUGCCGCAACAGUGGCA_AGUGC_AAUGCAACUGCAACUGCGUGUGUGCUGCGGAAAUGA
....((((((((................................((((((....))))))..........(((...((....)).))).))))))))...... (-13.23 = -15.23 +   2.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:53 2006