Locus 3977

Sequence ID X_DroMel_CAF1
Location 10,538,291 – 10,538,489
Length 198
Max. P 0.999446
window6539 window6540 window6541 window6542

overview

Window 9

Location 10,538,291 – 10,538,411
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.09
Mean single sequence MFE -21.54
Consensus MFE -14.36
Energy contribution -14.84
Covariance contribution 0.48
Combinations/Pair 1.09
Mean z-score -3.26
Structure conservation index 0.67
SVM decision value 2.56
SVM RNA-class probability 0.995300
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10538291 120 + 22224390
CCAGAAAAAAACCCAAUACUCCCACUCCACCGACCCAUUUUGAACAGAGAGAAAAAAAUGUAGUUAUGGCUUAAAGCAAUACAAGCCAUAUUUACAUUUUAUUGACCACGUUUUUUGCCA
.(((((((.....((((.......(((...(((......)))....))).....(((((((((.((((((((..(....)..)))))))).)))))))))))))......)))))))... ( -22.70)
>DroSec_CAF1 64730 110 + 1
CCAGAAAAAAACCCAAUACCCCCACUCCACCA---------UAACAGAGAGAAA-AAAUGUAGUUAUGGCUUAAAGCAAUACAAGCCAUAUUUACAUUUUAUUGACCACGUUUUUUGCCA
.(((((((.....((((.......((((....---------.....).)))..(-((((((((.((((((((..(....)..)))))))).)))))))))))))......)))))))... ( -22.50)
>DroSim_CAF1 68548 110 + 1
GCAGAAAAAAACCCAAUACCCCCACUCCACCA---------UAACAGAGAGAAA-AAAUGUAGUUAUGGCUUAAAGCAAUACAAGCCAUAUUUACAUUUUAUUGACCACGUUUUUUGCCA
((((((((.....((((.......((((....---------.....).)))..(-((((((((.((((((((..(....)..)))))))).)))))))))))))......)))))))).. ( -26.00)
>DroEre_CAF1 66150 94 + 1
CCAAAAAAAAAAAAAAGAG-------------------------CAGGGAGAAA-AAAUGUAGCUAUGGCUUAAAGCAAUACAAGCCAUAUUUAACUUUUAUUGACCAUGUUUUUUGCCA
.............((((((-------------------------((((..((.(-(((..(((.((((((((..(....)..)))))))).)))..)))).))..)).)))))))).... ( -20.60)
>DroYak_CAF1 67140 105 + 1
GCAGAAAAAAACCAAAUACCCCCC------AGA---------CACAGAGAAAAAAAUAUGUAGUUUUGGCUUAAAGCAAUACAAGCCAUAUUUACAUUUUAUUGACCACGUUUUUUGCCA
((((((((......((((......------...---------(.....)........((((((...((((((..(....)..))))))...))))))..)))).......)))))))).. ( -15.92)
>consensus
CCAGAAAAAAACCCAAUACCCCCACUCCACCA__________AACAGAGAGAAA_AAAUGUAGUUAUGGCUUAAAGCAAUACAAGCCAUAUUUACAUUUUAUUGACCACGUUUUUUGCCA
............................................(((((((....((((((((.((((((((..........)))))))).))))))))...........)))))))... (-14.36 = -14.84 +   0.48)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,538,331 – 10,538,449
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.44
Mean single sequence MFE -29.60
Consensus MFE -25.94
Energy contribution -26.10
Covariance contribution 0.16
Combinations/Pair 1.11
Mean z-score -2.59
Structure conservation index 0.88
SVM decision value 3.61
SVM RNA-class probability 0.999446
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10538331 118 + 22224390
UGAACAGAGAGAAAAAAAUGUAGUUAUGGCUUAAAGCAAUACAAGCCAUAUUUACAUUUUAUUGACCACGUUUUUUGCCAAUCUGCCUUGUAU--GUCAAUACACAAUGCGGUUGGAAAU
....(((((((...(((((((((.((((((((..(....)..)))))))).)))))))))..........)))))))((((.((((..(((((--....)))))....)))))))).... ( -29.72)
>DroSec_CAF1 64762 116 + 1
-UAACAGAGAGAAA-AAAUGUAGUUAUGGCUUAAAGCAAUACAAGCCAUAUUUACAUUUUAUUGACCACGUUUUUUGCCAGUCUGCCUUGUAU--GUCAAUACACAAUGCGGUUGGAAAU
-...(((((((..(-((((((((.((((((((..(....)..)))))))).)))))))))..........)))))))((((.((((..(((((--....)))))....)))))))).... ( -29.80)
>DroSim_CAF1 68580 116 + 1
-UAACAGAGAGAAA-AAAUGUAGUUAUGGCUUAAAGCAAUACAAGCCAUAUUUACAUUUUAUUGACCACGUUUUUUGCCAGUCUGCCUUGUAU--GUCAAUACACAAUGCGGUUGGAAAU
-...(((((((..(-((((((((.((((((((..(....)..)))))))).)))))))))..........)))))))((((.((((..(((((--....)))))....)))))))).... ( -29.80)
>DroEre_CAF1 66169 113 + 1
----CAGGGAGAAA-AAAUGUAGCUAUGGCUUAAAGCAAUACAAGCCAUAUUUAACUUUUAUUGACCAUGUUUUUUGCCAGUCUGCCUUGUAU--GUCAAUACACAAUGCGGCUGGAAAU
----..((..((.(-(((..(((.((((((((..(....)..)))))))).)))..)))).))..))..........((((.((((..(((((--....)))))....)))))))).... ( -28.90)
>DroYak_CAF1 67167 118 + 1
--CACAGAGAAAAAAAUAUGUAGUUUUGGCUUAAAGCAAUACAAGCCAUAUUUACAUUUUAUUGACCACGUUUUUUGCCAGUCUGCCUUGUGUUGGCAAAUACACAAUGCGGUUGGAAAU
--..(((((((...(((((((((...((((((..(....)..))))))...)))))...)))).......)))))))((((.((((.((((((........)))))).)))))))).... ( -29.80)
>consensus
__AACAGAGAGAAA_AAAUGUAGUUAUGGCUUAAAGCAAUACAAGCCAUAUUUACAUUUUAUUGACCACGUUUUUUGCCAGUCUGCCUUGUAU__GUCAAUACACAAUGCGGUUGGAAAU
....(((((((....((((((((.((((((((..........)))))))).))))))))...........)))))))((((.((((.((((............)))).)))))))).... (-25.94 = -26.10 +   0.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,538,331 – 10,538,449
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.44
Mean single sequence MFE -28.46
Consensus MFE -24.26
Energy contribution -25.18
Covariance contribution 0.92
Combinations/Pair 1.08
Mean z-score -2.61
Structure conservation index 0.85
SVM decision value 3.20
SVM RNA-class probability 0.998709
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10538331 118 - 22224390
AUUUCCAACCGCAUUGUGUAUUGAC--AUACAAGGCAGAUUGGCAAAAAACGUGGUCAAUAAAAUGUAAAUAUGGCUUGUAUUGCUUUAAGCCAUAACUACAUUUUUUUCUCUCUGUUCA
.((((((((.((.((((((......--)))))).)).).)))).))).((((.((..((.((((((((..(((((((((........)))))))))..)))))))).))..)).)))).. ( -30.70)
>DroSec_CAF1 64762 116 - 1
AUUUCCAACCGCAUUGUGUAUUGAC--AUACAAGGCAGACUGGCAAAAAACGUGGUCAAUAAAAUGUAAAUAUGGCUUGUAUUGCUUUAAGCCAUAACUACAUUU-UUUCUCUCUGUUA-
.((((((..(((.((((((......--)))))).)).)..))).))).((((.((.....((((((((..(((((((((........)))))))))..)))))))-)....)).)))).- ( -28.80)
>DroSim_CAF1 68580 116 - 1
AUUUCCAACCGCAUUGUGUAUUGAC--AUACAAGGCAGACUGGCAAAAAACGUGGUCAAUAAAAUGUAAAUAUGGCUUGUAUUGCUUUAAGCCAUAACUACAUUU-UUUCUCUCUGUUA-
.((((((..(((.((((((......--)))))).)).)..))).))).((((.((.....((((((((..(((((((((........)))))))))..)))))))-)....)).)))).- ( -28.80)
>DroEre_CAF1 66169 113 - 1
AUUUCCAGCCGCAUUGUGUAUUGAC--AUACAAGGCAGACUGGCAAAAAACAUGGUCAAUAAAAGUUAAAUAUGGCUUGUAUUGCUUUAAGCCAUAGCUACAUUU-UUUCUCCCUG----
.((((((((.((.((((((......--)))))).)).).)))).)))...((.((.....((((((((..(((((((((........)))))))))..)).))))-))...)).))---- ( -27.10)
>DroYak_CAF1 67167 118 - 1
AUUUCCAACCGCAUUGUGUAUUUGCCAACACAAGGCAGACUGGCAAAAAACGUGGUCAAUAAAAUGUAAAUAUGGCUUGUAUUGCUUUAAGCCAAAACUACAUAUUUUUUUCUCUGUG--
.......(((((.((.(((.((((((.......))))))...)))...)).))))).......(((((....(((((((........)))))))....)))))...............-- ( -26.90)
>consensus
AUUUCCAACCGCAUUGUGUAUUGAC__AUACAAGGCAGACUGGCAAAAAACGUGGUCAAUAAAAUGUAAAUAUGGCUUGUAUUGCUUUAAGCCAUAACUACAUUU_UUUCUCUCUGUU__
.((((((..(((.((((((........)))))).)).)..))).))).((((.((......(((((((..(((((((((........)))))))))..)))))))......)).)))).. (-24.26 = -25.18 +   0.92)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,538,371 – 10,538,489
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.61
Mean single sequence MFE -22.66
Consensus MFE -20.26
Energy contribution -20.18
Covariance contribution -0.08
Combinations/Pair 1.11
Mean z-score -1.29
Structure conservation index 0.89
SVM decision value 0.51
SVM RNA-class probability 0.765789
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10538371 118 + 22224390
ACAAGCCAUAUUUACAUUUUAUUGACCACGUUUUUUGCCAAUCUGCCUUGUAU--GUCAAUACACAAUGCGGUUGGAAAUAAGUAAUCAAGCUGAUGUGAUAAAUUAAAAUUAAACAAUC
...........(((((((...((((..((....(((.((((.((((..(((((--....)))))....)))))))))))...))..))))...))))))).................... ( -22.00)
>DroSec_CAF1 64800 118 + 1
ACAAGCCAUAUUUACAUUUUAUUGACCACGUUUUUUGCCAGUCUGCCUUGUAU--GUCAAUACACAAUGCGGUUGGAAAUAAGUAAUCAAGCUGAUGUGAUAAAUUAAAAAUAAACAAAC
...........(((((((...((((..((....(((.((((.((((..(((((--....)))))....)))))))))))...))..))))...))))))).................... ( -22.00)
>DroSim_CAF1 68618 118 + 1
ACAAGCCAUAUUUACAUUUUAUUGACCACGUUUUUUGCCAGUCUGCCUUGUAU--GUCAAUACACAAUGCGGUUGGAAAUAAGUAAUCAAGCUGAUGUGAUAAAUUAAAAACAAACAAAC
...........(((((((...((((..((....(((.((((.((((..(((((--....)))))....)))))))))))...))..))))...))))))).................... ( -22.00)
>DroEre_CAF1 66204 118 + 1
ACAAGCCAUAUUUAACUUUUAUUGACCAUGUUUUUUGCCAGUCUGCCUUGUAU--GUCAAUACACAAUGCGGCUGGAAAUAAGUAAUCAAGUUGAUGUGAUAAAUUAAAAUUAACCAAAC
......((((((.(((((..((((....(((((....((((.((((..(((((--....)))))....)))))))))))))..)))).)))))))))))..................... ( -20.50)
>DroYak_CAF1 67205 120 + 1
ACAAGCCAUAUUUACAUUUUAUUGACCACGUUUUUUGCCAGUCUGCCUUGUGUUGGCAAAUACACAAUGCGGUUGGAAAUAAGUAAUCAAGUUGAUGUGAUAAAUUAAAAUUAAACAAAC
...........(((((((...((((..((....(((.((((.((((.((((((........)))))).)))))))))))...))..))))...))))))).................... ( -26.80)
>consensus
ACAAGCCAUAUUUACAUUUUAUUGACCACGUUUUUUGCCAGUCUGCCUUGUAU__GUCAAUACACAAUGCGGUUGGAAAUAAGUAAUCAAGCUGAUGUGAUAAAUUAAAAUUAAACAAAC
...........(((((((...((((..((....(((.((((.((((.((((............)))).)))))))))))...))..))))...))))))).................... (-20.26 = -20.18 +  -0.08)

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 11:13:24 2006