Locus 4341

Sequence ID 3R_DroMel_CAF1
Location 11,460,209 – 11,460,363
Length 154
Max. P 0.991873
window7095 window7096 window7097 window7098

overview

Window 5

Location 11,460,209 – 11,460,323
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.37
Mean single sequence MFE -39.68
Consensus MFE -33.27
Energy contribution -33.67
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.36
Structure conservation index 0.84
SVM decision value 2.24
SVM RNA-class probability 0.990924
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11460209 114 + 27905053
CAGUUUUAACCUUU-UUUUCUCUGUGUGUUGAC--GGCCAGUAAUUUGUGUUGUUGCUGUUUGUUGGUUGGCUGUCGGCUGAAGGGAAACGCCAGCAGCAAC---AACAAUGGCCACAAA
..(((...(((...-........).))...)))--(((((........(((((((((((((.((...(..((.....))..)..(....))).)))))))))---)))).)))))..... ( -35.40)
>DroSec_CAF1 192736 120 + 1
CAGUUUUAACCUUUUUUUUCUCUGUGUGUUGACGUGGCCAGUAAUUUGUGUUGUUGCUGUUUGUUGGUUGGCUGUCGGCUGAAGGGAAACGCCAGCAGCAACAACAACAAUGGCCACAAA
..(((...(((............).))...)))(((((((.....((((((((((((((((.((...(..((.....))..)..(....))).)))))))))))).)))))))))))... ( -40.60)
>DroSim_CAF1 187850 120 + 1
CAGUUUUAACGUUUUUUUUCUCUGUGUGUUGACGUGGCCAGUAAUUUGUGUUGUUGCUGUUUGUUGGUUGGCUGUCGGCUGAAGGGAAACGCCAGCAGCAACAACAACAAUGGCCACAAA
..(((...(((.............)))...)))(((((((.....((((((((((((((((.((...(..((.....))..)..(....))).)))))))))))).)))))))))))... ( -40.82)
>DroEre_CAF1 181870 115 + 1
CAGUUGUAAC-UUU-UUUUCUCCGUGUGUUGACGUGGCCAGUAAUUUGUGUUGUUGCUGUUUGUUGGUUGGCUGUCGGCUGAAGGGAAACGCCAGCAGCAAC---AACAAUGGCCACGAA
..........-...-.................((((((((........(((((((((((((.((...(..((.....))..)..(....))).)))))))))---)))).)))))))).. ( -40.80)
>DroYak_CAF1 185962 116 + 1
CAGUUGUAACCUUU-UUUUCUCUGUGUGUUGACGUGGCCAGUAAUUUGUGUUGUUGCUGUUUGUUGGUUGGCUGUCGGCUGAAGGGAAACGCCAGCAGCAAC---AACAAUGGCCACGAA
..............-.................((((((((........(((((((((((((.((...(..((.....))..)..(....))).)))))))))---)))).)))))))).. ( -40.80)
>consensus
CAGUUUUAACCUUU_UUUUCUCUGUGUGUUGACGUGGCCAGUAAUUUGUGUUGUUGCUGUUUGUUGGUUGGCUGUCGGCUGAAGGGAAACGCCAGCAGCAAC___AACAAUGGCCACAAA
.................................(((((((.........((((((((((....(..((((.....))))..)..(....)..))))))))))........)))))))... (-33.27 = -33.67 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,460,209 – 11,460,323
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.37
Mean single sequence MFE -31.22
Consensus MFE -25.88
Energy contribution -26.04
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -2.53
Structure conservation index 0.83
SVM decision value 2.29
SVM RNA-class probability 0.991873
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11460209 114 - 27905053
UUUGUGGCCAUUGUU---GUUGCUGCUGGCGUUUCCCUUCAGCCGACAGCCAACCAACAAACAGCAACAACACAAAUUACUGGCC--GUCAACACACAGAGAAAA-AAAGGUUAAAACUG
.(((((((((.((((---(((((((.(((((((...........))).)))).........)))))))))))........)))))--).))).............-.............. ( -26.90)
>DroSec_CAF1 192736 120 - 1
UUUGUGGCCAUUGUUGUUGUUGCUGCUGGCGUUUCCCUUCAGCCGACAGCCAACCAACAAACAGCAACAACACAAAUUACUGGCCACGUCAACACACAGAGAAAAAAAAGGUUAAAACUG
...((((((((((((((((((((((.((((...........)))).)))).........)))))))))))..........)))))))................................. ( -33.60)
>DroSim_CAF1 187850 120 - 1
UUUGUGGCCAUUGUUGUUGUUGCUGCUGGCGUUUCCCUUCAGCCGACAGCCAACCAACAAACAGCAACAACACAAAUUACUGGCCACGUCAACACACAGAGAAAAAAAACGUUAAAACUG
...((((((((((((((((((((((.((((...........)))).)))).........)))))))))))..........)))))))................................. ( -33.60)
>DroEre_CAF1 181870 115 - 1
UUCGUGGCCAUUGUU---GUUGCUGCUGGCGUUUCCCUUCAGCCGACAGCCAACCAACAAACAGCAACAACACAAAUUACUGGCCACGUCAACACACGGAGAAAA-AAA-GUUACAACUG
..((((((((.((((---(((((((.(((((((...........))).)))).........)))))))))))........)))))))).................-...-.......... ( -31.00)
>DroYak_CAF1 185962 116 - 1
UUCGUGGCCAUUGUU---GUUGCUGCUGGCGUUUCCCUUCAGCCGACAGCCAACCAACAAACAGCAACAACACAAAUUACUGGCCACGUCAACACACAGAGAAAA-AAAGGUUACAACUG
..((((((((.((((---(((((((.(((((((...........))).)))).........)))))))))))........)))))))).................-.............. ( -31.00)
>consensus
UUUGUGGCCAUUGUU___GUUGCUGCUGGCGUUUCCCUUCAGCCGACAGCCAACCAACAAACAGCAACAACACAAAUUACUGGCCACGUCAACACACAGAGAAAA_AAAGGUUAAAACUG
..(((((((((((((...(((((((.((((...........)))).))).)))).)))))...(......).........))))))))................................ (-25.88 = -26.04 +   0.16)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,460,246 – 11,460,363
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.31
Mean single sequence MFE -35.00
Consensus MFE -31.76
Energy contribution -31.52
Covariance contribution -0.24
Combinations/Pair 1.02
Mean z-score -1.75
Structure conservation index 0.91
SVM decision value 1.67
SVM RNA-class probability 0.971158
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11460246 117 + 27905053
GUAAUUUGUGUUGUUGCUGUUUGUUGGUUGGCUGUCGGCUGAAGGGAAACGCCAGCAGCAAC---AACAAUGGCCACAAACACACAUGCAAUUUUGUGCAUUAAAAUUUCACACUGCGUU
(((...((((((((.((((((.((((....(((((.(((.....(....)))).)))))..)---))))))))).)).)))))).(((((......))))).............)))... ( -35.30)
>DroSec_CAF1 192776 120 + 1
GUAAUUUGUGUUGUUGCUGUUUGUUGGUUGGCUGUCGGCUGAAGGGAAACGCCAGCAGCAACAACAACAAUGGCCACAAACACACAUGCAAUUUUGUGCAUUAAAAUUUCACACUGCGUU
(((...((((((((.((((((.((((....(((((.(((.....(....)))).))))).....)))))))))).)).)))))).(((((......))))).............)))... ( -35.40)
>DroSim_CAF1 187890 120 + 1
GUAAUUUGUGUUGUUGCUGUUUGUUGGUUGGCUGUCGGCUGAAGGGAAACGCCAGCAGCAACAACAACAAUGGCCACAAACACACAUGCAAUUUUGUGCAUUAAAAUUUCACACUGCGUU
(((...((((((((.((((((.((((....(((((.(((.....(....)))).))))).....)))))))))).)).)))))).(((((......))))).............)))... ( -35.40)
>DroEre_CAF1 181908 117 + 1
GUAAUUUGUGUUGUUGCUGUUUGUUGGUUGGCUGUCGGCUGAAGGGAAACGCCAGCAGCAAC---AACAAUGGCCACGAACACACAUGCAAUUUUGUGCAUUAAAAUUUCACACUGCGUU
(((...((((((((.((((((.((((....(((((.(((.....(....)))).)))))..)---))))))))).)).)))))).(((((......))))).............)))... ( -35.30)
>DroYak_CAF1 186001 117 + 1
GUAAUUUGUGUUGUUGCUGUUUGUUGGUUGGCUGUCGGCUGAAGGGAAACGCCAGCAGCAAC---AACAAUGGCCACGAACACACAUGCAAUUUUGGACAUUAAAAUUUCACACUGCGUU
......((((((((.((((((.((((....(((((.(((.....(....)))).)))))..)---))))))))).)).)))))).(((((....((((.........))))...))))). ( -33.60)
>consensus
GUAAUUUGUGUUGUUGCUGUUUGUUGGUUGGCUGUCGGCUGAAGGGAAACGCCAGCAGCAAC___AACAAUGGCCACAAACACACAUGCAAUUUUGUGCAUUAAAAUUUCACACUGCGUU
(((...((((((((.((((((.(((.((((.((((.(((.....(....)))).))))))))...))))))))).))).)))))..((.(((((((.....))))))).))...)))... (-31.76 = -31.52 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,460,246 – 11,460,363
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.31
Mean single sequence MFE -31.25
Consensus MFE -28.42
Energy contribution -28.46
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.83
Structure conservation index 0.91
SVM decision value 1.93
SVM RNA-class probability 0.982937
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11460246 117 - 27905053
AACGCAGUGUGAAAUUUUAAUGCACAAAAUUGCAUGUGUGUUUGUGGCCAUUGUU---GUUGCUGCUGGCGUUUCCCUUCAGCCGACAGCCAACCAACAAACAGCAACAACACAAAUUAC
...((((((((...........))))...))))...((((((.((.((..(((((---(((((((.((((...........)))).))).))).))))))...)).))))))))...... ( -30.80)
>DroSec_CAF1 192776 120 - 1
AACGCAGUGUGAAAUUUUAAUGCACAAAAUUGCAUGUGUGUUUGUGGCCAUUGUUGUUGUUGCUGCUGGCGUUUCCCUUCAGCCGACAGCCAACCAACAAACAGCAACAACACAAAUUAC
.(((((.(((..((((((.......))))))))))))))(((((((....(((((((((((((((.((((...........)))).)))).........))))))))))))))))))... ( -32.60)
>DroSim_CAF1 187890 120 - 1
AACGCAGUGUGAAAUUUUAAUGCACAAAAUUGCAUGUGUGUUUGUGGCCAUUGUUGUUGUUGCUGCUGGCGUUUCCCUUCAGCCGACAGCCAACCAACAAACAGCAACAACACAAAUUAC
.(((((.(((..((((((.......))))))))))))))(((((((....(((((((((((((((.((((...........)))).)))).........))))))))))))))))))... ( -32.60)
>DroEre_CAF1 181908 117 - 1
AACGCAGUGUGAAAUUUUAAUGCACAAAAUUGCAUGUGUGUUCGUGGCCAUUGUU---GUUGCUGCUGGCGUUUCCCUUCAGCCGACAGCCAACCAACAAACAGCAACAACACAAAUUAC
...((((((((...........))))...))))...((((((.((.((..(((((---(((((((.((((...........)))).))).))).))))))...)).))))))))...... ( -30.80)
>DroYak_CAF1 186001 117 - 1
AACGCAGUGUGAAAUUUUAAUGUCCAAAAUUGCAUGUGUGUUCGUGGCCAUUGUU---GUUGCUGCUGGCGUUUCCCUUCAGCCGACAGCCAACCAACAAACAGCAACAACACAAAUUAC
...(((((....................)))))...((((((.((.((..(((((---(((((((.((((...........)))).))).))).))))))...)).))))))))...... ( -29.45)
>consensus
AACGCAGUGUGAAAUUUUAAUGCACAAAAUUGCAUGUGUGUUUGUGGCCAUUGUU___GUUGCUGCUGGCGUUUCCCUUCAGCCGACAGCCAACCAACAAACAGCAACAACACAAAUUAC
...((((((((...........))))...))))...((((((.((.((..(((((...(((((((.((((...........)))).))).)))).)))))...)).))))))))...... (-28.42 = -28.46 +   0.04)

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 11:26:45 2006