Locus 6639

Sequence ID X_DroMel_CAF1
Location 16,556,946 – 16,557,176
Length 230
Max. P 0.999759
window10843 window10844 window10845 window10846 window10847

overview

Window 3

Location 16,556,946 – 16,557,061
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.60
Mean single sequence MFE -25.48
Consensus MFE -22.52
Energy contribution -22.92
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.79
Structure conservation index 0.88
SVM decision value 4.02
SVM RNA-class probability 0.999759
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16556946 115 - 22224390
UGCUGCCACCUGGGUAGCCAAGCGAAACCGUAGCCAUUAUACCGUUUCAACCGAAAUAACCGAAUCAAUUUUACAACCGUAACUGAAAAGGGUAAAUUCUA-AAACUUCUCUACCA----
.((((((.....)))))).....(((((.(((.......))).)))))....(((.(.(((.........((((....))))((....))))).).)))..-..............---- ( -21.30)
>DroSec_CAF1 12516 119 - 1
UGCUGCCACCUGGGUAGCCAAGCGAAACCGUAACCAUUAUACCGUUUCAACCGAAAUAACCGAAUCAAUUUUACAACCGUAACUGAAAAGGGUAAUUUCGA-AAACUUCCCUACAAUAUU
.((((((.....)))))).....(((((.(((.......))).)))))...((((((.(((.........((((....))))((....))))).)))))).-.................. ( -26.50)
>DroSim_CAF1 9864 119 - 1
UGCUGCCACCUGGGUAGCCAAGCGAAACCGUAACCAUUAAACCGUUUCAACCGAAAUAACCGAAUCAAUUUUACAACCGUAACUGAAAAGGGUAAUUUCGA-AAACUUCUCUACAAUAUU
.((((((.....)))))).....(((((.((.........)).)))))...((((((.(((.........((((....))))((....))))).)))))).-.................. ( -24.90)
>DroEre_CAF1 11039 119 - 1
UGCUGCCACCUGGGUAGCCAACCGAAACCGUAACCAUUAUACCGUUUCAACGGAAAUAACCGAAUCAAUUUUACAACCGUAACUGAAAAAGGUUAUUUCAA-AAACAUCUCUACUAUAAU
.((((((.....)))))).....(((((.(((.......))).)))))....(((((((((...(((...((((....)))).)))....)))))))))..-.................. ( -27.90)
>DroYak_CAF1 12435 113 - 1
UGCUGCCACCUGGGUAGCCAACCGAAACCGUAACCAUUAUACCGUUUCAACCGAAAUAACCGAAUCAAUUUUACAACCGUAACUGAAAAAGGUAAUUUCGAGAAACAUUUCUA-------
.((((((.....)))))).....(((((.(((.......))).)))))...((((((.(((...(((...((((....)))).)))....))).))))))((((....)))).------- ( -26.80)
>consensus
UGCUGCCACCUGGGUAGCCAAGCGAAACCGUAACCAUUAUACCGUUUCAACCGAAAUAACCGAAUCAAUUUUACAACCGUAACUGAAAAGGGUAAUUUCGA_AAACUUCUCUACAAUA_U
.((((((.....)))))).....(((((.(((.......))).)))))....(((((.(((...(((...((((....)))).)))....))).)))))..................... (-22.52 = -22.92 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,556,981 – 16,557,101
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.00
Mean single sequence MFE -23.81
Consensus MFE -22.87
Energy contribution -23.07
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.26
Structure conservation index 0.96
SVM decision value 0.46
SVM RNA-class probability 0.745357
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16556981 120 - 22224390
GCAUCUGGAGGAACAUUAUUUGAUUAUUAUUUUCAAAUAUUGCUGCCACCUGGGUAGCCAAGCGAAACCGUAGCCAUUAUACCGUUUCAACCGAAAUAACCGAAUCAAUUUUACAACCGU
.........((........((((((.....((((.......((((((.....)))))).....(((((.(((.......))).)))))....))))......))))))........)).. ( -24.09)
>DroSec_CAF1 12555 120 - 1
GCAUCUGGAGGAACAUUAUUUGAUUAUUAUUUUCAAAUAUUGCUGCCACCUGGGUAGCCAAGCGAAACCGUAACCAUUAUACCGUUUCAACCGAAAUAACCGAAUCAAUUUUACAACCGU
.........((........((((((.....((((.......((((((.....)))))).....(((((.(((.......))).)))))....))))......))))))........)).. ( -23.29)
>DroSim_CAF1 9903 120 - 1
GCAUCUGGAGGAACAUUAUUUGAUUAUUAUUUUCAAAUAUUGCUGCCACCUGGGUAGCCAAGCGAAACCGUAACCAUUAAACCGUUUCAACCGAAAUAACCGAAUCAAUUUUACAACCGU
.........((........((((((.....((((.......((((((.....)))))).....(((((.((.........)).)))))....))))......))))))........)).. ( -21.69)
>DroEre_CAF1 11078 120 - 1
GCAUCUGGAGGAACACUAUUUGAUUAUUAUUUUCAAAUAUUGCUGCCACCUGGGUAGCCAACCGAAACCGUAACCAUUAUACCGUUUCAACGGAAAUAACCGAAUCAAUUUUACAACCGU
.........((........((((((.((((((((.......((((((.....)))))).....(((((.(((.......))).)))))...))))))))...))))))........)).. ( -26.69)
>DroYak_CAF1 12468 120 - 1
GCAUCUGGAGGAACACUAUUUGAUUAUUAUUUUCAAAUAUUGCUGCCACCUGGGUAGCCAACCGAAACCGUAACCAUUAUACCGUUUCAACCGAAAUAACCGAAUCAAUUUUACAACCGU
.........((........((((((.....((((.......((((((.....)))))).....(((((.(((.......))).)))))....))))......))))))........)).. ( -23.29)
>consensus
GCAUCUGGAGGAACAUUAUUUGAUUAUUAUUUUCAAAUAUUGCUGCCACCUGGGUAGCCAAGCGAAACCGUAACCAUUAUACCGUUUCAACCGAAAUAACCGAAUCAAUUUUACAACCGU
.........((........((((((.....((((.......((((((.....)))))).....(((((.(((.......))).)))))....))))......))))))........)).. (-22.87 = -23.07 +   0.20)

alignment

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secondary structure

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Window 5

Location 16,557,021 – 16,557,137
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.05
Mean single sequence MFE -31.16
Consensus MFE -27.30
Energy contribution -27.74
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.44
Structure conservation index 0.88
SVM decision value 0.85
SVM RNA-class probability 0.865494
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16557021 116 + 22224390
AUAAUGGCUACGGUUUCGCUUGGCUACCCAGGUGGCAGCAAUAUUUGAAAAUAAUAAUCAAAUAAUGUUCCUCCAGAUGCUGUAGGUGCCCCAAAC----AGCUGAGGUACUGAGUAUAG
.......(((((((.((((((((....))))))((.((((.(((((((.........))))))).))))))....)).)))))))(((((.((...----...)).)))))......... ( -33.60)
>DroSec_CAF1 12595 116 + 1
AUAAUGGUUACGGUUUCGCUUGGCUACCCAGGUGGCAGCAAUAUUUGAAAAUAAUAAUCAAAUAAUGUUCCUCCAGAUGCUGUAGGUGCCCCAAAC----AGCUGAGGUACUGAGUAUAG
........((((((.((((((((....))))))((.((((.(((((((.........))))))).))))))....)).))))))((((((.((...----...)).))))))........ ( -31.90)
>DroSim_CAF1 9943 116 + 1
UUAAUGGUUACGGUUUCGCUUGGCUACCCAGGUGGCAGCAAUAUUUGAAAAUAAUAAUCAAAUAAUGUUCCUCCAGAUGCUGUAAGUGCCCCAAAC----AGCUCAGGUACUGAGUAUAG
.....(((((((((.((((((((....))))))((.((((.(((((((.........))))))).))))))....)).))))))...)))......----.((((((...)))))).... ( -31.30)
>DroEre_CAF1 11118 120 + 1
AUAAUGGUUACGGUUUCGGUUGGCUACCCAGGUGGCAGCAAUAUUUGAAAAUAAUAAUCAAAUAGUGUUCCUCCAGAUGCUGAAGGUGCCUCAUACAUAUAGCUGAAGUACUGAGAAUAG
..........(((((((((((((((((....)))))((((.(((((((.........))))))).))))(((.(((...))).))).............))))))))..))))....... ( -27.20)
>DroYak_CAF1 12508 116 + 1
AUAAUGGUUACGGUUUCGGUUGGCUACCCAGGUGGCAGCAAUAUUUGAAAAUAAUAAUCAAAUAGUGUUCCUCCAGAUGCUGUAGGUGCCCCAAAC----AGCUGAGGUACUAAGAAUAG
........((((((.(((((.....)))..((.((.((((.(((((((.........))))))).)))))).)).)).))))))((((((.((...----...)).))))))........ ( -31.80)
>consensus
AUAAUGGUUACGGUUUCGCUUGGCUACCCAGGUGGCAGCAAUAUUUGAAAAUAAUAAUCAAAUAAUGUUCCUCCAGAUGCUGUAGGUGCCCCAAAC____AGCUGAGGUACUGAGUAUAG
........((((((.((...(((....)))((.((.((((.(((((((.........))))))).)))))).)).)).))))))((((((.((..........)).))))))........ (-27.30 = -27.74 +   0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,557,061 – 16,557,176
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.72
Mean single sequence MFE -24.32
Consensus MFE -19.94
Energy contribution -20.46
Covariance contribution 0.52
Combinations/Pair 1.12
Mean z-score -1.84
Structure conservation index 0.82
SVM decision value 1.04
SVM RNA-class probability 0.905600
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16557061 115 + 22224390
AUAUUUGAAAAUAAUAAUCAAAUAAUGUUCCUCCAGAUGCUGUAGGUGCCCCAAAC----AGCUGAGGUACUGAGUAUAGCAUCUAGAAAUAUUUAA-AAACUUUGUAGCUGUCGCAAAU
.(((((((.........)))))))(((((..((.((((((((((((((((.((...----...)).))))))...)))))))))).)))))))....-..........((....)).... ( -26.80)
>DroSec_CAF1 12635 115 + 1
AUAUUUGAAAAUAAUAAUCAAAUAAUGUUCCUCCAGAUGCUGUAGGUGCCCCAAAC----AGCUGAGGUACUGAGUAUAGCAUCUAGAAAUAUUUAA-AAACUUUGUAGCUGUCGCAAAU
.(((((((.........)))))))(((((..((.((((((((((((((((.((...----...)).))))))...)))))))))).)))))))....-..........((....)).... ( -26.80)
>DroSim_CAF1 9983 116 + 1
AUAUUUGAAAAUAAUAAUCAAAUAAUGUUCCUCCAGAUGCUGUAAGUGCCCCAAAC----AGCUCAGGUACUGAGUAUAGCAUCUAGAAACAUUUAAAAAACUUUGUAGCUGUCGCAAAU
.(((((((.........)))))))(((((..((.((((((((((((((((......----......))))))...)))))))))).)))))))...............((....)).... ( -26.10)
>DroEre_CAF1 11158 119 + 1
AUAUUUGAAAAUAAUAAUCAAAUAGUGUUCCUCCAGAUGCUGAAGGUGCCUCAUACAUAUAGCUGAAGUACUGAGAAUAGCGUCUACAAUUAUUUUA-AAACAUUGUACUUAUCGCCAAU
.(((((((.........)))))))(((.......((((((((..(((((.(((..........))).))))).....))))))))(((((.......-....)))))......))).... ( -19.70)
>DroYak_CAF1 12548 115 + 1
AUAUUUGAAAAUAAUAAUCAAAUAGUGUUCCUCCAGAUGCUGUAGGUGCCCCAAAC----AGCUGAGGUACUAAGAAUAGCAUUUACAAUUAUUUAA-AAGCAUUGUUCUUAUCGUAAAG
.(((((((.........)))))))..((.((((.....(((((.((....))..))----))).)))).))((((((((((.((((........)))-).))..))))))))........ ( -22.20)
>consensus
AUAUUUGAAAAUAAUAAUCAAAUAAUGUUCCUCCAGAUGCUGUAGGUGCCCCAAAC____AGCUGAGGUACUGAGUAUAGCAUCUAGAAAUAUUUAA_AAACUUUGUAGCUGUCGCAAAU
.(((((((.........)))))))..........((((((((((((((((.((..........)).))))))...))))))))))................................... (-19.94 = -20.46 +   0.52)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,557,061 – 16,557,176
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.72
Mean single sequence MFE -25.44
Consensus MFE -18.54
Energy contribution -19.42
Covariance contribution 0.88
Combinations/Pair 1.08
Mean z-score -1.67
Structure conservation index 0.73
SVM decision value 0.06
SVM RNA-class probability 0.565502
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16557061 115 - 22224390
AUUUGCGACAGCUACAAAGUUU-UUAAAUAUUUCUAGAUGCUAUACUCAGUACCUCAGCU----GUUUGGGGCACCUACAGCAUCUGGAGGAACAUUAUUUGAUUAUUAUUUUCAAAUAU
....((....))..........-.......((((((((((((.((....((.((((((..----..)))))).)).)).)))))))))))).....(((((((.........))))))). ( -26.20)
>DroSec_CAF1 12635 115 - 1
AUUUGCGACAGCUACAAAGUUU-UUAAAUAUUUCUAGAUGCUAUACUCAGUACCUCAGCU----GUUUGGGGCACCUACAGCAUCUGGAGGAACAUUAUUUGAUUAUUAUUUUCAAAUAU
....((....))..........-.......((((((((((((.((....((.((((((..----..)))))).)).)).)))))))))))).....(((((((.........))))))). ( -26.20)
>DroSim_CAF1 9983 116 - 1
AUUUGCGACAGCUACAAAGUUUUUUAAAUGUUUCUAGAUGCUAUACUCAGUACCUGAGCU----GUUUGGGGCACUUACAGCAUCUGGAGGAACAUUAUUUGAUUAUUAUUUUCAAAUAU
....((....))..............((((((((((((((((...(((((...)))))..----((..(.....)..))))))))))))..))))))((((((.........)))))).. ( -26.50)
>DroEre_CAF1 11158 119 - 1
AUUGGCGAUAAGUACAAUGUUU-UAAAAUAAUUGUAGACGCUAUUCUCAGUACUUCAGCUAUAUGUAUGAGGCACCUUCAGCAUCUGGAGGAACACUAUUUGAUUAUUAUUUUCAAAUAU
..(((((.....((((((....-.......))))))..))))).(((((.(((...........))))))))..(((((((...))))))).....(((((((.........))))))). ( -23.60)
>DroYak_CAF1 12548 115 - 1
CUUUACGAUAAGAACAAUGCUU-UUAAAUAAUUGUAAAUGCUAUUCUUAGUACCUCAGCU----GUUUGGGGCACCUACAGCAUCUGGAGGAACACUAUUUGAUUAUUAUUUUCAAAUAU
........((((((....((.(-(((........)))).))..))))))((.((((.(((----((..((....)).))))).....)))).))..(((((((.........))))))). ( -24.70)
>consensus
AUUUGCGACAGCUACAAAGUUU_UUAAAUAUUUCUAGAUGCUAUACUCAGUACCUCAGCU____GUUUGGGGCACCUACAGCAUCUGGAGGAACAUUAUUUGAUUAUUAUUUUCAAAUAU
...............................(((((((((((.......((.((((((........)))))).))....)))))))))))......(((((((.........))))))). (-18.54 = -19.42 +   0.88)

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 12:18:58 2006