Locus 1338

Sequence ID X_DroMel_CAF1
Location 4,016,219 – 4,016,348
Length 129
Max. P 0.950420
window2133 window2134 window2135 window2136

overview

Window 3

Location 4,016,219 – 4,016,321
Length 102
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 87.56
Mean single sequence MFE -33.90
Consensus MFE -25.94
Energy contribution -27.82
Covariance contribution 1.88
Combinations/Pair 1.04
Mean z-score -2.21
Structure conservation index 0.77
SVM decision value 1.17
SVM RNA-class probability 0.925274
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4016219 102 + 22224390
-CUAGCCACCGCCUGUUCGUUCCACUGGACUCUCCCGGGGGAGUGGAUUUCGUCUCUCUAGCUGCAAAUUAUGCAGCCCGACGGGGCCAUCGAUCAAAAAUCC
-...(((.(((...(((((((((.((((......)))).)))))))))........((..((((((.....))))))..))))))))................ ( -31.20)
>DroSec_CAF1 30469 99 + 1
AUUUGCCACCGCCUGU----UCCCCUGGACACUCCCGGGGGAGUGGAUUUCGUCUCUCUAGCUGCAAAUUAUGCAGCCCGACGGGGCCAUCGAUCAAAAAUCC
....(((.(((.(..(----((((((((......)))))))))..)..........((..((((((.....))))))..))))))))................ ( -38.40)
>DroSim_CAF1 29331 99 + 1
GUUUGCCACCGCCUGU----UCCCCUGGACACUCCCGGGGGAGUGGAUUUCGUCUCUCUAGCUGCAAAUUAUGCAGCCCGACGGGGCCAUCGAUCAAAAAUCC
....(((.(((.(..(----((((((((......)))))))))..)..........((..((((((.....))))))..))))))))................ ( -38.40)
>DroEre_CAF1 28928 86 + 1
GUUUUCCACCGCCUUU-----------------CCCGGGGGAGUGGAUUUCGUCUCUGUAGCUGCAAAUUAUGCAGCCCGACGGGGCCAUCGAUCAAAAAUCC
....((((((.(((..-----------------...))).).)))))..(((.((((((.((((((.....))))))...))))))....))).......... ( -28.70)
>DroYak_CAF1 28713 98 + 1
GUUUUCCACCGCCUUU----UUCCCU-GACUUACCCGGGGGAGUGGAUUUCGUCCCUCUAGCUGCAAAUUAUGCAGCCCGACGGGGCCAUCGAUCAAAAAUUC
(...(((((.......----((((((-(.......))))))))))))...)(((((((..((((((.....))))))..)).)))))................ ( -32.81)
>consensus
GUUUGCCACCGCCUGU____UCCCCUGGACACUCCCGGGGGAGUGGAUUUCGUCUCUCUAGCUGCAAAUUAUGCAGCCCGACGGGGCCAUCGAUCAAAAAUCC
....................((((((((......))))))))((((.(..((((......((((((.....))))))..))))..)))))............. (-25.94 = -27.82 +   1.88)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,016,219 – 4,016,321
Length 102
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 87.56
Mean single sequence MFE -35.50
Consensus MFE -27.74
Energy contribution -28.08
Covariance contribution 0.34
Combinations/Pair 1.04
Mean z-score -1.70
Structure conservation index 0.78
SVM decision value 0.43
SVM RNA-class probability 0.732776
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4016219 102 - 22224390
GGAUUUUUGAUCGAUGGCCCCGUCGGGCUGCAUAAUUUGCAGCUAGAGAGACGAAAUCCACUCCCCCGGGAGAGUCCAGUGGAACGAACAGGCGGUGGCUAG-
.((((...))))..((((((((((.(((((((.....)))))))............((((((((....)))(....).))))).......))))).))))).- ( -37.10)
>DroSec_CAF1 30469 99 - 1
GGAUUUUUGAUCGAUGGCCCCGUCGGGCUGCAUAAUUUGCAGCUAGAGAGACGAAAUCCACUCCCCCGGGAGUGUCCAGGGGA----ACAGGCGGUGGCAAAU
.((((...))))....((((((((.(((((((.....))))))).................(((((.(((....))).)))))----...))))).))).... ( -38.30)
>DroSim_CAF1 29331 99 - 1
GGAUUUUUGAUCGAUGGCCCCGUCGGGCUGCAUAAUUUGCAGCUAGAGAGACGAAAUCCACUCCCCCGGGAGUGUCCAGGGGA----ACAGGCGGUGGCAAAC
.((((...))))....((((((((.(((((((.....))))))).................(((((.(((....))).)))))----...))))).))).... ( -38.30)
>DroEre_CAF1 28928 86 - 1
GGAUUUUUGAUCGAUGGCCCCGUCGGGCUGCAUAAUUUGCAGCUACAGAGACGAAAUCCACUCCCCCGGG-----------------AAAGGCGGUGGAAAAC
(((((((...((((((....)))).(((((((.....)))))))...))...)))))))..(((.(((..-----------------.....))).))).... ( -31.60)
>DroYak_CAF1 28713 98 - 1
GAAUUUUUGAUCGAUGGCCCCGUCGGGCUGCAUAAUUUGCAGCUAGAGGGACGAAAUCCACUCCCCCGGGUAAGUC-AGGGAA----AAAGGCGGUGGAAAAC
...(((((.((((....((((.((.(((((((.....))))))).)).)(((...((((........))))..)))-.)))..----.....)))).))))). ( -32.20)
>consensus
GGAUUUUUGAUCGAUGGCCCCGUCGGGCUGCAUAAUUUGCAGCUAGAGAGACGAAAUCCACUCCCCCGGGAGAGUCCAGGGGA____ACAGGCGGUGGCAAAC
(((((((...((((((....)))).(((((((.....)))))))...))...))))))).(..((((.......((.....)).......)).))..)..... (-27.74 = -28.08 +   0.34)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,016,258 – 4,016,348
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 96.64
Mean single sequence MFE -30.52
Consensus MFE -26.96
Energy contribution -27.08
Covariance contribution 0.12
Combinations/Pair 1.07
Mean z-score -1.53
Structure conservation index 0.88
SVM decision value 0.89
SVM RNA-class probability 0.874757
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4016258 90 + 22224390
GAGUGGAUUUCGUCUCUCUAGCUGCAAAUUAUGCAGCCCGACGGGGCCAUCGAUCAAAAAUCCGUAUGCAGGGAGCAGCUGGGUCGGAUU
((.(((.(..((((......((((((.....))))))..))))..)))))).......((((((.((.(((.......))).)))))))) ( -30.10)
>DroSec_CAF1 30505 89 + 1
GAGUGGAUUUCGUCUCUCUAGCUGCAAAUUAUGCAGCCCGACGGGGCCAUCGAUCAAAAAUCCGUAUGCAG-GAGCAGCUGGGUCGGAUU
((.(((.(..((((......((((((.....))))))..))))..)))))).......((((((.((.(((-......))).)))))))) ( -30.60)
>DroSim_CAF1 29367 89 + 1
GAGUGGAUUUCGUCUCUCUAGCUGCAAAUUAUGCAGCCCGACGGGGCCAUCGAUCAAAAAUCCGUAUGCAG-GAGCAGCUGGGUCGGAUU
((.(((.(..((((......((((((.....))))))..))))..)))))).......((((((.((.(((-......))).)))))))) ( -30.60)
>DroEre_CAF1 28951 89 + 1
GAGUGGAUUUCGUCUCUGUAGCUGCAAAUUAUGCAGCCCGACGGGGCCAUCGAUCAAAAAUCCGUACGCAG-GAGCAGCUGGGACGGAUU
((.(((.(..((((......((((((.....))))))..))))..)))))).......(((((((.(.(((-......))).)))))))) ( -32.10)
>DroYak_CAF1 28748 89 + 1
GAGUGGAUUUCGUCCCUCUAGCUGCAAAUUAUGCAGCCCGACGGGGCCAUCGAUCAAAAAUUCGUACGCAG-GAGCAGCUGGUUCGGAUU
(((.....)))((((..((((((((......(((.((((....))))...(((........)))...))).-..))))))))...)))). ( -29.20)
>consensus
GAGUGGAUUUCGUCUCUCUAGCUGCAAAUUAUGCAGCCCGACGGGGCCAUCGAUCAAAAAUCCGUAUGCAG_GAGCAGCUGGGUCGGAUU
((.(((.(..((((......((((((.....))))))..))))..)))))).......((((((.((.(((.......))).)))))))) (-26.96 = -27.08 +   0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,016,258 – 4,016,348
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 96.64
Mean single sequence MFE -27.38
Consensus MFE -25.80
Energy contribution -25.60
Covariance contribution -0.20
Combinations/Pair 1.09
Mean z-score -1.48
Structure conservation index 0.94
SVM decision value 1.40
SVM RNA-class probability 0.950420
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4016258 90 - 22224390
AAUCCGACCCAGCUGCUCCCUGCAUACGGAUUUUUGAUCGAUGGCCCCGUCGGGCUGCAUAAUUUGCAGCUAGAGAGACGAAAUCCACUC
.............(((.....)))...(((((((...((((((....)))).(((((((.....)))))))...))...))))))).... ( -27.20)
>DroSec_CAF1 30505 89 - 1
AAUCCGACCCAGCUGCUC-CUGCAUACGGAUUUUUGAUCGAUGGCCCCGUCGGGCUGCAUAAUUUGCAGCUAGAGAGACGAAAUCCACUC
.............(((..-..)))...(((((((...((((((....)))).(((((((.....)))))))...))...))))))).... ( -27.20)
>DroSim_CAF1 29367 89 - 1
AAUCCGACCCAGCUGCUC-CUGCAUACGGAUUUUUGAUCGAUGGCCCCGUCGGGCUGCAUAAUUUGCAGCUAGAGAGACGAAAUCCACUC
.............(((..-..)))...(((((((...((((((....)))).(((((((.....)))))))...))...))))))).... ( -27.20)
>DroEre_CAF1 28951 89 - 1
AAUCCGUCCCAGCUGCUC-CUGCGUACGGAUUUUUGAUCGAUGGCCCCGUCGGGCUGCAUAAUUUGCAGCUACAGAGACGAAAUCCACUC
..(((((.((((......-))).).)))))((((((..(((((....)))))(((((((.....))))))).))))))............ ( -29.40)
>DroYak_CAF1 28748 89 - 1
AAUCCGAACCAGCUGCUC-CUGCGUACGAAUUUUUGAUCGAUGGCCCCGUCGGGCUGCAUAAUUUGCAGCUAGAGGGACGAAAUCCACUC
....((.(((((......-))).)).))..........(((((....)))))(((((((.....))))))).((((((.....))).))) ( -25.90)
>consensus
AAUCCGACCCAGCUGCUC_CUGCAUACGGAUUUUUGAUCGAUGGCCCCGUCGGGCUGCAUAAUUUGCAGCUAGAGAGACGAAAUCCACUC
.............(((.....)))...(((((((...((((((....)))).(((((((.....)))))))...))...))))))).... (-25.80 = -25.60 +  -0.20)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:54 2006