Locus 7379

Sequence ID X_DroMel_CAF1
Location 18,376,439 – 18,376,598
Length 159
Max. P 0.981680
window12095 window12096 window12097 window12098

overview

Window 5

Location 18,376,439 – 18,376,558
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 88.61
Mean single sequence MFE -31.93
Consensus MFE -23.99
Energy contribution -23.67
Covariance contribution -0.33
Combinations/Pair 1.09
Mean z-score -2.72
Structure conservation index 0.75
SVM decision value 0.64
SVM RNA-class probability 0.807784
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18376439 119 + 22224390
CCC-AUGCCGGCUGUUCCCGUCGCAUUUUCCCUGAUUAUUAUUAGGCGCAUUAAGUGCGCUUAAAAUGAAACGAAAAUGCAAAUAAAUUGCAUUUAAUUUGCCACUCCAAACAGGGAAAG
...-(((((((......)))..))))((((((((.(((((.((((((((((...))))))))))))))).....((((((((.....))))))))................)))))))). ( -37.20)
>DroAna_CAF1 25018 118 + 1
UGAUUUGUUGACUUU-UCCGCCGUAUUUCCCCUGAUUAUUAUUAGGCGCAUUAAGUGCGCUUAAAAUGAAACGAAAAUGCAAAUAAAUUGCAUUUAAUUUGCCACUCCAAACAGAGCUG-
...((((((......-...((..............(((((.((((((((((...))))))))))))))).....((((((((.....)))))))).....)).......))))))....- ( -23.69)
>DroYak_CAF1 19993 120 + 1
CCGUUUGUCGACUGUUCCCGUCGCAUUUUCCCUGAUUAUUAUUAGGCGCAUUAAGUGCGCUUAAAAUGAAACGAAAAUGCAAAUAAAUUGCAUUUAAUUUGCCACUCCAAACGGAGCUGG
(((((((..(((.......)))((((((((.....(((((.((((((((((...)))))))))))))))...)))))))).........(((.......))).....)))))))...... ( -34.90)
>consensus
CCAUUUGUCGACUGUUCCCGUCGCAUUUUCCCUGAUUAUUAUUAGGCGCAUUAAGUGCGCUUAAAAUGAAACGAAAAUGCAAAUAAAUUGCAUUUAAUUUGCCACUCCAAACAGAGCUGG
......(.((........)).)((((((((.....(((((.((((((((((...)))))))))))))))...)))))))).........(((.......)))..(((......))).... (-23.99 = -23.67 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,376,439 – 18,376,558
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.61
Mean single sequence MFE -33.43
Consensus MFE -27.33
Energy contribution -28.23
Covariance contribution 0.90
Combinations/Pair 1.15
Mean z-score -2.39
Structure conservation index 0.82
SVM decision value 0.67
SVM RNA-class probability 0.817810
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18376439 119 - 22224390
CUUUCCCUGUUUGGAGUGGCAAAUUAAAUGCAAUUUAUUUGCAUUUUCGUUUCAUUUUAAGCGCACUUAAUGCGCCUAAUAAUAAUCAGGGAAAAUGCGACGGGAACAGCCGGCAU-GGG
.((((((((.(((((((((.((...((((((((.....))))))))...)))))))))))(((((.....)))))...........))))))))((((..(((......)))))))-... ( -37.80)
>DroAna_CAF1 25018 118 - 1
-CAGCUCUGUUUGGAGUGGCAAAUUAAAUGCAAUUUAUUUGCAUUUUCGUUUCAUUUUAAGCGCACUUAAUGCGCCUAAUAAUAAUCAGGGGAAAUACGGCGGA-AAAGUCAACAAAUCA
-...(((((.(((((((((.((...((((((((.....))))))))...)))))))))))(((((.....)))))...........))))).......(((...-...)))......... ( -28.50)
>DroYak_CAF1 19993 120 - 1
CCAGCUCCGUUUGGAGUGGCAAAUUAAAUGCAAUUUAUUUGCAUUUUCGUUUCAUUUUAAGCGCACUUAAUGCGCCUAAUAAUAAUCAGGGAAAAUGCGACGGGAACAGUCGACAAACGG
......(((((((...((((........(((((.....)))))((..((((.((((((..(((((.....)))))((.((....)).))..)))))).))))..))..)))).))))))) ( -34.00)
>consensus
CCAGCUCUGUUUGGAGUGGCAAAUUAAAUGCAAUUUAUUUGCAUUUUCGUUUCAUUUUAAGCGCACUUAAUGCGCCUAAUAAUAAUCAGGGAAAAUGCGACGGGAACAGUCGACAAACGG
......(((((((...((((.....((((((((.....))))))))(((((.((((((..(((((.....)))))((.((....)).))..)))))).))))).....)))).))))))) (-27.33 = -28.23 +   0.90)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,376,478 – 18,376,598
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.22
Mean single sequence MFE -37.73
Consensus MFE -26.38
Energy contribution -27.50
Covariance contribution 1.12
Combinations/Pair 1.10
Mean z-score -3.74
Structure conservation index 0.70
SVM decision value 1.19
SVM RNA-class probability 0.928165
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18376478 120 + 22224390
AUUAGGCGCAUUAAGUGCGCUUAAAAUGAAACGAAAAUGCAAAUAAAUUGCAUUUAAUUUGCCACUCCAAACAGGGAAAGGGGAAGGGGGCUGCGCGGAGAGCUGUGCUGCCAUUUUAAU
.((((((((((...))))))))))..........((((((((.....))))))))..(((.((..(((......)))..)).)))...(((.((((((....)))))).)))........ ( -40.00)
>DroAna_CAF1 25057 105 + 1
AUUAGGCGCAUUAAGUGCGCUUAAAAUGAAACGAAAAUGCAAAUAAAUUGCAUUUAAUUUGCCACUCCAAACAGAGCUG---------------GUGGGGAGCUGUGCUGCCAUUUUAAU
.((((((((((...))))))))))..........((((((((.....)))))))).....(((((((......))).))---------------)).((.(((...))).))........ ( -31.20)
>DroYak_CAF1 20033 120 + 1
AUUAGGCGCAUUAAGUGCGCUUAAAAUGAAACGAAAAUGCAAAUAAAUUGCAUUUAAUUUGCCACUCCAAACGGAGCUGGGGAAAGGGGGCUGUGCGGAGAGCUGUGCUGCCAUUUUAAU
.((((((((((...))))))))))..........((((((((.....))))))))..(((.(((((((....)))).))).)))....(((.(..(((....)))..).)))........ ( -42.00)
>consensus
AUUAGGCGCAUUAAGUGCGCUUAAAAUGAAACGAAAAUGCAAAUAAAUUGCAUUUAAUUUGCCACUCCAAACAGAGCUGGGG_AAGGGGGCUG_GCGGAGAGCUGUGCUGCCAUUUUAAU
.((((((((((...))))))))))..........((((((((.....)))))))).........(((......)))............(((.((((((....)))))).)))........ (-26.38 = -27.50 +   1.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,376,478 – 18,376,598
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 87.22
Mean single sequence MFE -32.13
Consensus MFE -27.78
Energy contribution -28.45
Covariance contribution 0.67
Combinations/Pair 1.06
Mean z-score -3.65
Structure conservation index 0.86
SVM decision value 1.89
SVM RNA-class probability 0.981680
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18376478 120 - 22224390
AUUAAAAUGGCAGCACAGCUCUCCGCGCAGCCCCCUUCCCCUUUCCCUGUUUGGAGUGGCAAAUUAAAUGCAAUUUAUUUGCAUUUUCGUUUCAUUUUAAGCGCACUUAAUGCGCCUAAU
.(((((((((.(((...((((((((.((((................)))).))))).))).....((((((((.....))))))))..))))))))))))(((((.....)))))..... ( -34.69)
>DroAna_CAF1 25057 105 - 1
AUUAAAAUGGCAGCACAGCUCCCCAC---------------CAGCUCUGUUUGGAGUGGCAAAUUAAAUGCAAUUUAUUUGCAUUUUCGUUUCAUUUUAAGCGCACUUAAUGCGCCUAAU
.(((((((((..((...(((((..((---------------.......))..))))).)).....((((((((.....)))))))).....)))))))))(((((.....)))))..... ( -28.70)
>DroYak_CAF1 20033 120 - 1
AUUAAAAUGGCAGCACAGCUCUCCGCACAGCCCCCUUUCCCCAGCUCCGUUUGGAGUGGCAAAUUAAAUGCAAUUUAUUUGCAUUUUCGUUUCAUUUUAAGCGCACUUAAUGCGCCUAAU
.(((((((((.(((...((((((((.(((((............)))..)).))))).))).....((((((((.....))))))))..))))))))))))(((((.....)))))..... ( -33.00)
>consensus
AUUAAAAUGGCAGCACAGCUCUCCGC_CAGCCCCCUU_CCCCAGCUCUGUUUGGAGUGGCAAAUUAAAUGCAAUUUAUUUGCAUUUUCGUUUCAUUUUAAGCGCACUUAAUGCGCCUAAU
.(((((((((.(((...((((((((.((....................)).))))).))).....((((((((.....))))))))..))))))))))))(((((.....)))))..... (-27.78 = -28.45 +   0.67)

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 12:37:29 2006