Locus 4334

Sequence ID X_DroMel_CAF1
Location 11,403,176 – 11,403,311
Length 135
Max. P 0.999491
window7117 window7118 window7119

overview

Window 7

Location 11,403,176 – 11,403,271
Length 95
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 74.37
Mean single sequence MFE -28.07
Consensus MFE -18.30
Energy contribution -18.67
Covariance contribution 0.38
Combinations/Pair 1.23
Mean z-score -2.71
Structure conservation index 0.65
SVM decision value 3.65
SVM RNA-class probability 0.999491
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11403176 95 + 22224390
UCGGAAUUAAACAAAAUACAUUCCGAAUAUUGAUUAGAUGGCGGAUUUCCGCCGAAAAGCGGUAUGAUAUCAUGC---------CUAUGAUG----------------UACGAUAGUUUA
(((((((............))))))).(((((......((((((....))))))......((((((....)))))---------).......----------------..)))))..... ( -27.80)
>DroSec_CAF1 4485 104 + 1
UCGGAAUUAAACAAAAUACAGUCCGAAUAUUGAUUAGACGGCGGAUUUCCGCCGAAGAGCGGAAUGAUAUCAUAGGCAUGAAUGAUAUGAUA----------------UACGAUAGUUUA
(((((................)))))............((((((....))))))..((((......((((((((..((....)).)))))))----------------)......)))). ( -26.69)
>DroEre_CAF1 2999 118 + 1
UCAAAAUAAGGCUGAAUACAAUCCGAAUAUUGAUUAGGCGGCGGAUUUCCGCCGAAGUG-GGUAUGAUAUCAUGUCUAUAG-UAUUAUGGUAUUAUGGUAAAUGUAUGUACGAAAGUGUA
...............(((((..(((((((((.......((((((....))))))..(((-(..(((....)))..))))..-......)))))).)))....))))).(((....))).. ( -30.00)
>DroYak_CAF1 1940 103 + 1
UCAAAAUAAAACAAAAUACAUUCCGAAUAUUGAUUAGGCGGCGGAUUUCCGCUGAAAAGCGGUAUGAUAUCAUGCCUAUGG-UAUUAUGGUAU----------------GCGAAAGUGUA
......................(((((((((...((((((....(((.(((((....)))))...)))....)))))).))-)))).)))(((----------------((....))))) ( -27.80)
>consensus
UCAAAAUAAAACAAAAUACAUUCCGAAUAUUGAUUAGACGGCGGAUUUCCGCCGAAAAGCGGUAUGAUAUCAUGCCUAUGG_UAUUAUGAUA________________UACGAAAGUGUA
...............((((.(((...((((((......((((((....)))))).....))))))..(((((((...........)))))))...................))).)))). (-18.30 = -18.67 +   0.38)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,403,176 – 11,403,271
Length 95
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 74.37
Mean single sequence MFE -19.89
Consensus MFE -12.07
Energy contribution -12.32
Covariance contribution 0.25
Combinations/Pair 1.13
Mean z-score -1.78
Structure conservation index 0.61
SVM decision value 0.60
SVM RNA-class probability 0.795198
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11403176 95 - 22224390
UAAACUAUCGUA----------------CAUCAUAG---------GCAUGAUAUCAUACCGCUUUUCGGCGGAAAUCCGCCAUCUAAUCAAUAUUCGGAAUGUAUUUUGUUUAAUUCCGA
............----------------.......(---------(.(((....))).)).......(((((....))))).............(((((((............))))))) ( -21.60)
>DroSec_CAF1 4485 104 - 1
UAAACUAUCGUA----------------UAUCAUAUCAUUCAUGCCUAUGAUAUCAUUCCGCUCUUCGGCGGAAAUCCGCCGUCUAAUCAAUAUUCGGACUGUAUUUUGUUUAAUUCCGA
(((((....(((----------------((..(((((((........)))))))...((((.....((((((....)))))).............)))).)))))...)))))....... ( -21.97)
>DroEre_CAF1 2999 118 - 1
UACACUUUCGUACAUACAUUUACCAUAAUACCAUAAUA-CUAUAGACAUGAUAUCAUACC-CACUUCGGCGGAAAUCCGCCGCCUAAUCAAUAUUCGGAUUGUAUUCAGCCUUAUUUUGA
......................................-...(((..(((....)))...-.....((((((....)))))).))).((((.((..((.(((....)))))..)).)))) ( -17.00)
>DroYak_CAF1 1940 103 - 1
UACACUUUCGC----------------AUACCAUAAUA-CCAUAGGCAUGAUAUCAUACCGCUUUUCAGCGGAAAUCCGCCGCCUAAUCAAUAUUCGGAAUGUAUUUUGUUUUAUUUUGA
.........((----------------((.((......-...((((((((....))).(((((....))))).........)))))..........)).))))................. ( -19.01)
>consensus
UAAACUAUCGUA________________UACCAUAAUA_CCAUAGGCAUGAUAUCAUACCGCUCUUCGGCGGAAAUCCGCCGCCUAAUCAAUAUUCGGAAUGUAUUUUGUUUAAUUCCGA
...............................................(((....)))..........(((((....))))).............(((((((............))))))) (-12.07 = -12.32 +   0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,403,216 – 11,403,311
Length 95
Sequences 3
Columns 105
Reading direction forward
Mean pairwise identity 78.91
Mean single sequence MFE -31.43
Consensus MFE -23.51
Energy contribution -22.97
Covariance contribution -0.55
Combinations/Pair 1.15
Mean z-score -2.57
Structure conservation index 0.75
SVM decision value 2.55
SVM RNA-class probability 0.995199
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11403216 95 + 22224390
GCGGAUUUCCGCCGAAAAGCGGUAUGAUAUCAUGC---------CUAUGAUG-UACGAUAGUUUAAUUCGCAUGCCAAGCAACUUGGCCCAAGCAACAGGUUGUU
((((....))))........(((((((((((((..---------..))))))-).(((.........))))))))).(((((((((((....))..))))))))) ( -28.70)
>DroSec_CAF1 4525 104 + 1
GCGGAUUUCCGCCGAAGAGCGGAAUGAUAUCAUAGGCAUGAAUGAUAUGAUA-UACGAUAGUUUAAUUCGUAUGCUAAGCAACUUGGGCCAAGCAACAGGUUGUU
((((....)))).....(((...((.(((((((........))))))).))(-(((((.........))))))))).(((((((((.((...))..))))))))) ( -29.00)
>DroYak_CAF1 1980 98 + 1
GCGGAUUUCCGCUGAAAAGCGGUAUGAUAUCAUGCCUAUGG-UAUUAUGGUAU-GCGAAAGUGUAAUUCGCAUGCUAACCAACUUGG-----GCAACAGGUUGUU
........(((((....)))))..(((((((((....))))-)))))((((((-(((((.......)))))))))))..(((((((.-----....))))))).. ( -36.60)
>consensus
GCGGAUUUCCGCCGAAAAGCGGUAUGAUAUCAUGC__AUG__U_AUAUGAUA_UACGAUAGUUUAAUUCGCAUGCUAAGCAACUUGG_CCAAGCAACAGGUUGUU
(((((((.((((......)))).....(((((((...........)))))))............)))))))......(((((((((..........))))))))) (-23.51 = -22.97 +  -0.55)

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 11:22:22 2006