Locus 6532

Sequence ID 2R_DroMel_CAF1
Location 20,417,990 – 20,418,089
Length 99
Max. P 0.840739
window10393 window10394

overview

Window 3

Location 20,417,990 – 20,418,089
Length 99
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 83.53
Mean single sequence MFE -28.02
Consensus MFE -21.04
Energy contribution -21.27
Covariance contribution 0.23
Combinations/Pair 1.19
Mean z-score -2.65
Structure conservation index 0.75
SVM decision value 0.75
SVM RNA-class probability 0.840739
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20417990 99 + 20766785
CACCGACACUGGCGCAAAUUUCAUCGCUAAAAACCACCCCGCCGCUGGCUGCUCUUACCGAGCACCAGCAGCACUUUCAUGCCACAAGCAUUC---------AAGCAG
.........((((((..........)).............((.(((((.(((((.....)))))))))).))........))))...((....---------..)).. ( -27.40)
>DroVir_CAF1 37837 99 + 1
CACCGACACUGGCGCAAAUUUCAUCGCUAAAGGCAACACCGCCGCUGGCUGCCCUCACUGAGCACCAGCAGCACUAUCAUGCCACAAGCAUAC---------AAACCA
..........((.............(((...(((......)))(((((.(((.(.....).)))))))))))......((((.....))))..---------...)). ( -24.80)
>DroGri_CAF1 34645 99 + 1
CACCAACACUGGCGCAAAUUUCAUCGCUAAAGGCAACACCGCCGCUGGCUGCCCUAACGGAGCAUCAGCAGCAUUAUCAUGCCACUAGCAUAC---------AGACCA
........(((..............(((...(((......)))(((((.(((((....)).)))))))))))......((((.....)))).)---------)).... ( -28.40)
>DroWil_CAF1 39662 99 + 1
CACCAACACUGGCGCAAAUUUCAUCGCUAAAGGCCACACCGCCGCUGGCUGCUCUCACCGAGCAUCAGCAGCAUUUUCAUGCAACAAGUAUAC---------AGACAA
........(((..............(((...(((......)))(((((.(((((.....)))))))))))))......((((.....)))).)---------)).... ( -26.00)
>DroMoj_CAF1 39327 102 + 1
CGCCGACACUGGCGCAAAUUUCAUCGCUGAAAGCAACACCGCCGCUGGCUGCUUUGACUGAGCACCAGCAGCACUAUCAUGCGACAAGCAUACAGC------AAACCA
(((((....)))))...........((((...........((.(((((.(((((.....)))))))))).))......((((.....)))).))))------...... ( -34.50)
>DroAna_CAF1 23525 108 + 1
CUCCGACACUGGCGCAAAUUUCAUCGCUCAAGGCCACCCCGCCGCUCGCUGCUCUUACGGAGCACCAGCAGCACUUCCAUGCCACCAGCCUCCAGCAGGCACAAGCAC
.........(((((.................(((......)))(((.(((((((.....))))...)))))).......)))))...((((.....))))........ ( -27.00)
>consensus
CACCGACACUGGCGCAAAUUUCAUCGCUAAAGGCAACACCGCCGCUGGCUGCUCUCACCGAGCACCAGCAGCACUAUCAUGCCACAAGCAUAC_________AAACAA
.........(((((..........)))))...........((.(((((.(((((.....)))))))))).))......((((.....))))................. (-21.04 = -21.27 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 20,417,990 – 20,418,089
Length 99
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 83.53
Mean single sequence MFE -39.83
Consensus MFE -29.36
Energy contribution -30.45
Covariance contribution 1.09
Combinations/Pair 1.11
Mean z-score -2.33
Structure conservation index 0.74
SVM decision value 0.50
SVM RNA-class probability 0.759485
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20417990 99 - 20766785
CUGCUU---------GAAUGCUUGUGGCAUGAAAGUGCUGCUGGUGCUCGGUAAGAGCAGCCAGCGGCGGGGUGGUUUUUAGCGAUGAAAUUUGCGCCAGUGUCGGUG
..((((---------..((((.....))))..))))(((((((((((((.....))))).))))))))((.(..(.(((((....))))).)..).)).......... ( -41.30)
>DroVir_CAF1 37837 99 - 1
UGGUUU---------GUAUGCUUGUGGCAUGAUAGUGCUGCUGGUGCUCAGUGAGGGCAGCCAGCGGCGGUGUUGCCUUUAGCGAUGAAAUUUGCGCCAGUGUCGGUG
...((.---------.(.((((...((((..(((.((((((((((((((.....))))).))))))))).)))))))...)))))..)).....((((......)))) ( -40.90)
>DroGri_CAF1 34645 99 - 1
UGGUCU---------GUAUGCUAGUGGCAUGAUAAUGCUGCUGAUGCUCCGUUAGGGCAGCCAGCGGCGGUGUUGCCUUUAGCGAUGAAAUUUGCGCCAGUGUUGGUG
......---------...((((((.((((..(((.((((((((.(((.((....)))))..)))))))).))))))).))))))..........((((......)))) ( -37.20)
>DroWil_CAF1 39662 99 - 1
UUGUCU---------GUAUACUUGUUGCAUGAAAAUGCUGCUGAUGCUCGGUGAGAGCAGCCAGCGGCGGUGUGGCCUUUAGCGAUGAAAUUUGCGCCAGUGUUGGUG
......---------...((((....((((......(((((((.(((((.....)))))..)))))))((((..(..((((....))))..)..)))).)))).)))) ( -34.60)
>DroMoj_CAF1 39327 102 - 1
UGGUUU------GCUGUAUGCUUGUCGCAUGAUAGUGCUGCUGGUGCUCAGUCAAAGCAGCCAGCGGCGGUGUUGCUUUCAGCGAUGAAAUUUGCGCCAGUGUCGGCG
......------((((.(((((.(.((((.((((.(((((((((((((.......)))).))))))))).))))..(((((....)))))..))))).))))))))). ( -41.00)
>DroAna_CAF1 23525 108 - 1
GUGCUUGUGCCUGCUGGAGGCUGGUGGCAUGGAAGUGCUGCUGGUGCUCCGUAAGAGCAGCGAGCGGCGGGGUGGCCUUGAGCGAUGAAAUUUGCGCCAGUGUCGGAG
..((((((((((..(((((((..(..((((....))))..)..)).)))))..)).))).)))))((((((....)))...((((......))))))).......... ( -44.00)
>consensus
UGGUUU_________GUAUGCUUGUGGCAUGAAAGUGCUGCUGGUGCUCAGUAAGAGCAGCCAGCGGCGGUGUGGCCUUUAGCGAUGAAAUUUGCGCCAGUGUCGGUG
........................((((((......(((((((((((((.....))))).))))))))((((..(..((((....))))..)..)))).))))))... (-29.36 = -30.45 +   1.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:01 2006