Locus 2549

Sequence ID 3R_DroMel_CAF1
Location 6,921,135 – 6,921,278
Length 143
Max. P 0.959534
window4159 window4160 window4161 window4162

overview

Window 9

Location 6,921,135 – 6,921,252
Length 117
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -29.92
Consensus MFE -27.68
Energy contribution -27.74
Covariance contribution 0.06
Combinations/Pair 1.06
Mean z-score -1.49
Structure conservation index 0.93
SVM decision value 1.50
SVM RNA-class probability 0.959534
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6921135 117 + 27905053
UUGCAGUCGUUCGUUUAUGUUUGU-CCUGGUCAGGCCAUAAAUAUUUUAUGCAUUGACACUUUUUUGGCACUAAGCCAAUAAUACGCACACGACAAUGAGUCAUUGUUGUUGCCGUGG
.....((((..(((..((((((((-(((....)))..))))))))...)))...))))......(((((.....)))))...((((((.(((((((((...))))))))))).)))). ( -30.00)
>DroSec_CAF1 69776 117 + 1
UUGCAAUCGUUCGUUUAUGUUUGU-CCUGGUCAGGCCAUAAAUAUUUUAUGCAUUGACACUUUUUUGGCACUAAGCCAAUAAUACGCACACGACAAUGAGUCAUUGUUGUUGCCGUGG
...((((.((......((((((((-(((....)))..)))))))).....)))))).(((....(((((.....)))))......(((.(((((((((...)))))))))))).))). ( -28.70)
>DroSim_CAF1 70028 117 + 1
UUGCAAUCGUUCGUUUAUGUUUGU-CCUGGUCAGGCCAUAAAUAUUUUAUGCAUUGACACUUUUUUGGCACUAAGCCAAUAAUACGCACACGACAAUGAGUCAUUGUUGUUGCCGUGG
...((((.((......((((((((-(((....)))..)))))))).....)))))).(((....(((((.....)))))......(((.(((((((((...)))))))))))).))). ( -28.70)
>DroEre_CAF1 71648 117 + 1
UUGCAAUCGUUCGUUUAUGUUUGU-CCUGGUCAGGCCAUAAAUAUUUUAUGCAUUGACACUUUUUUGGCACUAAGCCAAUAAUACGCACACGACAAUGAGUCAUUGUUGUUGCCGUGG
...((((.((......((((((((-(((....)))..)))))))).....)))))).(((....(((((.....)))))......(((.(((((((((...)))))))))))).))). ( -28.70)
>DroYak_CAF1 71635 117 + 1
UUGCAAUCGUUCGUUUAUGUUUGU-CCUGGUCAGGCUAUAAAUAUUUUAUGCAUUGACACUUUUUUGGCACUAAGCCAAUAAUACGCACACGACAAUGAGUCAUUGUUGUUGCCGUGG
...((((.((......((((((((-(((....)))..)))))))).....)))))).(((....(((((.....)))))......(((.(((((((((...)))))))))))).))). ( -28.70)
>DroAna_CAF1 67712 118 + 1
UUACAAUGGUUCGUUUAUGUUUGUGCCUGGUCAGGCAAUAAAUAUUUUAUGCAUUGACACUUUUUCGGCACUAAGCCAAUAAUACGCACACAACAGUGACUCAUUGUUGUUGCCGUGG
...(((((...(((..((((((((((((....)))).))))))))...)))))))).(((......(((.....)))........(((.(((((((((...)))))))))))).))). ( -34.70)
>consensus
UUGCAAUCGUUCGUUUAUGUUUGU_CCUGGUCAGGCCAUAAAUAUUUUAUGCAUUGACACUUUUUUGGCACUAAGCCAAUAAUACGCACACGACAAUGAGUCAUUGUUGUUGCCGUGG
.((((.......(((((((((((........))))).))))))......))))....(((....(((((.....)))))......(((.(((((((((...)))))))))))).))). (-27.68 = -27.74 +   0.06)

alignment

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secondary structure

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Window 0

Location 6,921,135 – 6,921,252
Length 117
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -26.41
Consensus MFE -23.00
Energy contribution -23.23
Covariance contribution 0.22
Combinations/Pair 1.06
Mean z-score -1.42
Structure conservation index 0.87
SVM decision value 0.18
SVM RNA-class probability 0.620731
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6921135 117 - 27905053
CCACGGCAACAACAAUGACUCAUUGUCGUGUGCGUAUUAUUGGCUUAGUGCCAAAAAAGUGUCAAUGCAUAAAAUAUUUAUGGCCUGACCAGG-ACAAACAUAAACGAACGACUGCAA
.(((.(((((.((((((...)))))).)).)))......(((((.....)))))....)))....((((.......((((((.(((....)))-.....))))))........)))). ( -26.16)
>DroSec_CAF1 69776 117 - 1
CCACGGCAACAACAAUGACUCAUUGUCGUGUGCGUAUUAUUGGCUUAGUGCCAAAAAAGUGUCAAUGCAUAAAAUAUUUAUGGCCUGACCAGG-ACAAACAUAAACGAACGAUUGCAA
.(((.(((((.((((((...)))))).)).)))......(((((.....)))))....)))....((((.......((((((.(((....)))-.....))))))........)))). ( -26.86)
>DroSim_CAF1 70028 117 - 1
CCACGGCAACAACAAUGACUCAUUGUCGUGUGCGUAUUAUUGGCUUAGUGCCAAAAAAGUGUCAAUGCAUAAAAUAUUUAUGGCCUGACCAGG-ACAAACAUAAACGAACGAUUGCAA
.(((.(((((.((((((...)))))).)).)))......(((((.....)))))....)))....((((.......((((((.(((....)))-.....))))))........)))). ( -26.86)
>DroEre_CAF1 71648 117 - 1
CCACGGCAACAACAAUGACUCAUUGUCGUGUGCGUAUUAUUGGCUUAGUGCCAAAAAAGUGUCAAUGCAUAAAAUAUUUAUGGCCUGACCAGG-ACAAACAUAAACGAACGAUUGCAA
.(((.(((((.((((((...)))))).)).)))......(((((.....)))))....)))....((((.......((((((.(((....)))-.....))))))........)))). ( -26.86)
>DroYak_CAF1 71635 117 - 1
CCACGGCAACAACAAUGACUCAUUGUCGUGUGCGUAUUAUUGGCUUAGUGCCAAAAAAGUGUCAAUGCAUAAAAUAUUUAUAGCCUGACCAGG-ACAAACAUAAACGAACGAUUGCAA
.....((((...(((((...)))))((((...(((....(((((.....)))))....(.((((..((((((.....)))).)).)))))...-..........))).)))))))).. ( -23.50)
>DroAna_CAF1 67712 118 - 1
CCACGGCAACAACAAUGAGUCACUGUUGUGUGCGUAUUAUUGGCUUAGUGCCGAAAAAGUGUCAAUGCAUAAAAUAUUUAUUGCCUGACCAGGCACAAACAUAAACGAACCAUUGUAA
....(....).((((((..((..((((.(((((......(((((.....)))))....(.((((..(((............))).)))))..))))))))).....))..)))))).. ( -28.20)
>consensus
CCACGGCAACAACAAUGACUCAUUGUCGUGUGCGUAUUAUUGGCUUAGUGCCAAAAAAGUGUCAAUGCAUAAAAUAUUUAUGGCCUGACCAGG_ACAAACAUAAACGAACGAUUGCAA
.(((.(((((.((((((...)))))).)).)))......(((((.....)))))....)))....((((.......((((((.(((....)))......))))))........)))). (-23.00 = -23.23 +   0.22)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,921,174 – 6,921,278
Length 104
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 92.56
Mean single sequence MFE -26.05
Consensus MFE -24.76
Energy contribution -24.52
Covariance contribution -0.25
Combinations/Pair 1.11
Mean z-score -1.06
Structure conservation index 0.95
SVM decision value 0.56
SVM RNA-class probability 0.782928
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6921174 104 + 27905053
AAUAUUUUAUGCAUUGACACUUUUUUGGCACUAAGCCAAUAAUACGCACACGACAAUGAGUCAUUGUUGUUGCCGUGGUGUUGCGAUU-------G--UACU----UCUGCCUGUGU
.........((((...((((....(((((.....)))))...((((((.(((((((((...))))))))))).))))))))))))...-------.--....----........... ( -24.90)
>DroSec_CAF1 69815 106 + 1
AAUAUUUUAUGCAUUGACACUUUUUUGGCACUAAGCCAAUAAUACGCACACGACAAUGAGUCAUUGUUGUUGCCGUGGUGUUGCGAUU-------GUGUACU----UCUGCCUGUGU
..........(((...((((....(((((.....)))))((((((.(((.((((((..(....)..))))))..))))))))).....-------))))...----..)))...... ( -26.50)
>DroSim_CAF1 70067 106 + 1
AAUAUUUUAUGCAUUGACACUUUUUUGGCACUAAGCCAAUAAUACGCACACGACAAUGAGUCAUUGUUGUUGCCGUGGUGUUGCGAUU-------GUGUACU----UCUGCCUGUGU
..........(((...((((....(((((.....)))))((((((.(((.((((((..(....)..))))))..))))))))).....-------))))...----..)))...... ( -26.50)
>DroEre_CAF1 71687 104 + 1
AAUAUUUUAUGCAUUGACACUUUUUUGGCACUAAGCCAAUAAUACGCACACGACAAUGAGUCAUUGUUGUUGCCGUGGUGUUGCGAUU-------G--UACU----UCAGCCUGUGU
.........((((...((((....(((((.....)))))...((((((.(((((((((...))))))))))).))))))))))))...-------.--....----........... ( -24.90)
>DroYak_CAF1 71674 104 + 1
AAUAUUUUAUGCAUUGACACUUUUUUGGCACUAAGCCAAUAAUACGCACACGACAAUGAGUCAUUGUUGUUGCCGUGGUGUUGCGAUU-------G--UACU----UCAGCCUGUGU
.........((((...((((....(((((.....)))))...((((((.(((((((((...))))))))))).))))))))))))...-------.--....----........... ( -24.90)
>DroAna_CAF1 67752 117 + 1
AAUAUUUUAUGCAUUGACACUUUUUCGGCACUAAGCCAAUAAUACGCACACAACAGUGACUCAUUGUUGUUGCCGUGGUGUUGCACUUGCUGUUUGUGUACUUGUUUCAGCCGCUGU
..........(((...((((.....(((((....((.((((.((((((.(((((((((...))))))))))).)))).))))))...)))))...))))...)))............ ( -28.60)
>consensus
AAUAUUUUAUGCAUUGACACUUUUUUGGCACUAAGCCAAUAAUACGCACACGACAAUGAGUCAUUGUUGUUGCCGUGGUGUUGCGAUU_______G__UACU____UCAGCCUGUGU
.........((((...((((....(((((.....)))))...((((((.(((((((((...))))))))))).))))))))))))................................ (-24.76 = -24.52 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,921,174 – 6,921,278
Length 104
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 92.56
Mean single sequence MFE -25.38
Consensus MFE -20.61
Energy contribution -20.50
Covariance contribution -0.11
Combinations/Pair 1.09
Mean z-score -1.97
Structure conservation index 0.81
SVM decision value -0.04
SVM RNA-class probability 0.513073
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6921174 104 - 27905053
ACACAGGCAGA----AGUA--C-------AAUCGCAACACCACGGCAACAACAAUGACUCAUUGUCGUGUGCGUAUUAUUGGCUUAGUGCCAAAAAAGUGUCAAUGCAUAAAAUAUU
......(((..----..((--(-------(((((((.(((...(....)......(((.....)))))))))).))).(((((.....)))))....)))....))).......... ( -24.00)
>DroSec_CAF1 69815 106 - 1
ACACAGGCAGA----AGUACAC-------AAUCGCAACACCACGGCAACAACAAUGACUCAUUGUCGUGUGCGUAUUAUUGGCUUAGUGCCAAAAAAGUGUCAAUGCAUAAAAUAUU
......(((..----.(.((((-------(((((((.(((...(....)......(((.....)))))))))).))).(((((.....)))))....)))))..))).......... ( -26.60)
>DroSim_CAF1 70067 106 - 1
ACACAGGCAGA----AGUACAC-------AAUCGCAACACCACGGCAACAACAAUGACUCAUUGUCGUGUGCGUAUUAUUGGCUUAGUGCCAAAAAAGUGUCAAUGCAUAAAAUAUU
......(((..----.(.((((-------(((((((.(((...(....)......(((.....)))))))))).))).(((((.....)))))....)))))..))).......... ( -26.60)
>DroEre_CAF1 71687 104 - 1
ACACAGGCUGA----AGUA--C-------AAUCGCAACACCACGGCAACAACAAUGACUCAUUGUCGUGUGCGUAUUAUUGGCUUAGUGCCAAAAAAGUGUCAAUGCAUAAAAUAUU
.....(((..(----(((.--(-------(((((((.(((...(....)......(((.....))))))))))....))))))))...)))......((((....))))........ ( -22.60)
>DroYak_CAF1 71674 104 - 1
ACACAGGCUGA----AGUA--C-------AAUCGCAACACCACGGCAACAACAAUGACUCAUUGUCGUGUGCGUAUUAUUGGCUUAGUGCCAAAAAAGUGUCAAUGCAUAAAAUAUU
.....(((..(----(((.--(-------(((((((.(((...(....)......(((.....))))))))))....))))))))...)))......((((....))))........ ( -22.60)
>DroAna_CAF1 67752 117 - 1
ACAGCGGCUGAAACAAGUACACAAACAGCAAGUGCAACACCACGGCAACAACAAUGAGUCACUGUUGUGUGCGUAUUAUUGGCUUAGUGCCGAAAAAGUGUCAAUGCAUAAAAUAUU
...(((..(((.((..((((((((.(((...(((......)))(....)............)))))))))))......(((((.....)))))....)).))).))).......... ( -29.90)
>consensus
ACACAGGCAGA____AGUA__C_______AAUCGCAACACCACGGCAACAACAAUGACUCAUUGUCGUGUGCGUAUUAUUGGCUUAGUGCCAAAAAAGUGUCAAUGCAUAAAAUAUU
.....(((........................((((.(((...(....).((((((...)))))).))))))).....(((((.....)))))......)))............... (-20.61 = -20.50 +  -0.11)

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 10:39:03 2006