Locus 1951

Sequence ID 3L_DroMel_CAF1
Location 5,404,110 – 5,404,267
Length 157
Max. P 0.980182
window3052 window3053 window3054

overview

Window 2

Location 5,404,110 – 5,404,228
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.15
Mean single sequence MFE -45.78
Consensus MFE -37.11
Energy contribution -39.30
Covariance contribution 2.19
Combinations/Pair 1.15
Mean z-score -1.90
Structure conservation index 0.81
SVM decision value 0.74
SVM RNA-class probability 0.836782
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5404110 118 + 23771897
AGA--GAGCCCAAAACUCCGGACCGAACGCAGGUGAAAGCCGUGAACCGUGAUACAGUUGCAAUGCUCCUGCCUACUGGCCCAAAAGGGGCGUGGCAGGAAGUUUGGGGCGCAGGGGGCC
...--..((((....((.((..((((((((((((....))).......(..((...))..)..)))(((((((.((.(.(((....))).)))))))))).))))))..)).)).)))). ( -50.30)
>DroSec_CAF1 52821 117 + 1
AGA--GAGCCCAAAACUAUGGACCGAACGCAGGUGAAAGCCGUGAACCGUGAUACAGUUGCAAUGCUCCUGCCUUCCGGCC-AAAAGGGGCGUGGCAGGAAGUUUGGGGCGCAGGGGGCC
...--..((((....((.((..((((((((((((....))).......(..((...))..)..)))(((((((...((.((-.....)).)).))))))).))))))..)).)).)))). ( -46.60)
>DroSim_CAF1 49963 117 + 1
AGAGAGAGCCCAAAACUCCGGACCGAACGCA-GUGAAAGCCGUGAACCGUGAUACAGUUGCAAUGCUCCUGCCUACCGGCC-AAAAG-GGCGUGGCAGGAAGUUUGGGGCGCAGGGGGCC
.......((((....((.((..(((((((((-(((...((.(....).))....)).)))).....(((((((...((.((-....)-).)).))))))).))))))..)).)).)))). ( -44.70)
>DroYak_CAF1 53045 117 + 1
AGA--GAGCCUAAAACUACAACCCAAACGCAGGUGAAAGCCGUGAACCGUGAUACAGGUGCAAUGCUGGUGCCUAGCGGCC-AAAAGGGGCGUGGCAGGAAGUUUGGGGCACGGCAGGCU
...--.(((((..........(((((((((((((....))).((.(((........))).)).)))...((((..(((.((-.....)).)))))))....)))))))((...))))))) ( -41.50)
>consensus
AGA__GAGCCCAAAACUACGGACCGAACGCAGGUGAAAGCCGUGAACCGUGAUACAGUUGCAAUGCUCCUGCCUACCGGCC_AAAAGGGGCGUGGCAGGAAGUUUGGGGCGCAGGGGGCC
.......((((....((.((..((((((((((.((...((.(....).))....)).)))).....(((((((...((.((......)).)).))))))).))))))..)).)).)))). (-37.11 = -39.30 +   2.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 5,404,148 – 5,404,267
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.28
Mean single sequence MFE -52.12
Consensus MFE -46.24
Energy contribution -46.68
Covariance contribution 0.44
Combinations/Pair 1.08
Mean z-score -2.57
Structure conservation index 0.89
SVM decision value 1.86
SVM RNA-class probability 0.980182
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5404148 119 + 23771897
CGUGAACCGUGAUACAGUUGCAAUGCUCCUGCCUACUGGCCCAAAAGGGGCGUGGCAGGAAGUUUGGGGCGCAGGGGGCCGUGCCUCGAC-UGCAUGACGCAGAUAACACGGCAACACGG
((((..(((((.((...((((.(((((((((((.((.(.(((....))).))))))))))((((.(((((((.((...))))))))))))-)))))...)))).)).)))))...)))). ( -54.70)
>DroSec_CAF1 52859 118 + 1
CGUGAACCGUGAUACAGUUGCAAUGCUCCUGCCUUCCGGCC-AAAAGGGGCGUGGCAGGAAGUUUGGGGCGCAGGGGGCCGUGCCUCGAC-UGCAUGACGCAGAUAACACGGCAACACGG
((((..(((((.((...((((.(((((((((((...((.((-.....)).)).)))))))((((.(((((((.((...))))))))))))-)))))...)))).)).)))))...)))). ( -52.60)
>DroSim_CAF1 50002 118 + 1
CGUGAACCGUGAUACAGUUGCAAUGCUCCUGCCUACCGGCC-AAAAG-GGCGUGGCAGGAAGUUUGGGGCGCAGGGGGCCGUGCCUCGACAUGCAUGAUGCAGAUAACACGGCAACACGG
((((..(((((.((...((((((((((((((((...((.((-....)-).)).))))))).(((.(((((((.((...))))))))))))..))))..))))).)).)))))...)))). ( -52.60)
>DroYak_CAF1 53083 118 + 1
CGUGAACCGUGAUACAGGUGCAAUGCUGGUGCCUAGCGGCC-AAAAGGGGCGUGGCAGGAAGUUUGGGGCACGGCAGGCUGUGUCUCGAC-UGCAUGACGCAGAUAACACGGCAACACGG
((((..(((((.((...(((..((((...((((..(((.((-.....)).)))))))...((((.(((((((((....))))))))))))-)))))..)))...)).)))))...)))). ( -48.60)
>consensus
CGUGAACCGUGAUACAGUUGCAAUGCUCCUGCCUACCGGCC_AAAAGGGGCGUGGCAGGAAGUUUGGGGCGCAGGGGGCCGUGCCUCGAC_UGCAUGACGCAGAUAACACGGCAACACGG
((((..(((((.((...((((.(((((((((((...((.((......)).)).)))))))...(((((((((........)))))))))...))))...)))).)).)))))...)))). (-46.24 = -46.68 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 5,404,148 – 5,404,267
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.28
Mean single sequence MFE -44.33
Consensus MFE -39.96
Energy contribution -40.77
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -1.77
Structure conservation index 0.90
SVM decision value 0.82
SVM RNA-class probability 0.859079
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5404148 119 - 23771897
CCGUGUUGCCGUGUUAUCUGCGUCAUGCA-GUCGAGGCACGGCCCCCUGCGCCCCAAACUUCCUGCCACGCCCCUUUUGGGCCAGUAGGCAGGAGCAUUGCAACUGUAUCACGGUUCACG
.((((..((((((.(((.((((..((((.-...(.(((.(((....))).))).).....(((((((((((((.....))))..)).)))))))))))))))...))).)))))).)))) ( -49.50)
>DroSec_CAF1 52859 118 - 1
CCGUGUUGCCGUGUUAUCUGCGUCAUGCA-GUCGAGGCACGGCCCCCUGCGCCCCAAACUUCCUGCCACGCCCCUUUU-GGCCGGAAGGCAGGAGCAUUGCAACUGUAUCACGGUUCACG
.((((..((((((.(((.((((..((((.-...(.(((.(((....))).))).).....(((((((.((((......-)).))...)))))))))))))))...))).)))))).)))) ( -45.70)
>DroSim_CAF1 50002 118 - 1
CCGUGUUGCCGUGUUAUCUGCAUCAUGCAUGUCGAGGCACGGCCCCCUGCGCCCCAAACUUCCUGCCACGCC-CUUUU-GGCCGGUAGGCAGGAGCAUUGCAACUGUAUCACGGUUCACG
.((((..((((((.(((.((((..((((.....(.(((.(((....))).))).).....(((((((.((.(-(....-)).))...)))))))))))))))...))).)))))).)))) ( -47.40)
>DroYak_CAF1 53083 118 - 1
CCGUGUUGCCGUGUUAUCUGCGUCAUGCA-GUCGAGACACAGCCUGCCGUGCCCCAAACUUCCUGCCACGCCCCUUUU-GGCCGCUAGGCACCAGCAUUGCACCUGUAUCACGGUUCACG
.((((..((((((.(((..(.((.((((.-((....))...(((((.((.(((.........................-))))).)))))....)))).)).)..))).)))))).)))) ( -34.71)
>consensus
CCGUGUUGCCGUGUUAUCUGCGUCAUGCA_GUCGAGGCACGGCCCCCUGCGCCCCAAACUUCCUGCCACGCCCCUUUU_GGCCGGUAGGCAGGAGCAUUGCAACUGUAUCACGGUUCACG
.((((..((((((.(((.((((..((((.....(.(((.(((....))).))).).....(((((((..(((.......))).....)))))))))))))))...))).)))))).)))) (-39.96 = -40.77 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:55 2006