Locus 7122

Sequence ID X_DroMel_CAF1
Location 17,872,122 – 17,872,298
Length 176
Max. P 0.999766
window11629 window11630 window11631 window11632 window11633

overview

Window 9

Location 17,872,122 – 17,872,234
Length 112
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 69.26
Mean single sequence MFE -39.78
Consensus MFE -7.61
Energy contribution -9.45
Covariance contribution 1.84
Combinations/Pair 1.39
Mean z-score -2.25
Structure conservation index 0.19
SVM decision value -0.02
SVM RNA-class probability 0.521364
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17872122 112 + 22224390
AUUUAUAGCCAAUU-UAAAAGCCCAAAGAGCUGCACUUUCCGAGACCGUCGGCGCAUAGUGGUGGCCACUGGUGGCCACUGUUGGCUACUGGUAUCUACUGGUGGC-----CACUGGU
.......((((...-....(((.......))).((((..((((.....)))).....))))(((((((....)))))))...(((((((..((....))..)))))-----)).)))) ( -39.80)
>DroVir_CAF1 187014 106 + 1
AUUUAUAACCAAUUUUAAAAGCCCAAAGAGCCGCACCGACAGACGUCCGCUGC---CAGAAGCAGUGGGUGGUG-CCAUAG-----UGCAGUGGUGCAGUGCUG-CGCUGUAGCGG--
........((...................(((((.(((((....))).(((((---.....))))))))))))(-(.((((-----((((((........))))-)))))).))))-- ( -36.50)
>DroSec_CAF1 135623 92 + 1
AUUUAUAGCCAAUU-UAAAAGCCCAAAGAGCUGCACUUUCCGAGACCGUCGGCGCGUAGUGGCGGCCACUGGUGGCC--------------------ACUGGUGGC-----UACUGGU
.......((((...-.....(((......(((((.(...((((.....)))).).))))))))((((((..((....--------------------))..)))))-----)..)))) ( -31.30)
>DroSim_CAF1 106601 112 + 1
AUUUAUAGCCAAUU-UAAAAGCCCAAAGAGCUGCACUUUCCGAGACCGUCGGCGCAUAGUGGCGGCCACUGGUGGCCACUGUUGGCUACUGGUGGCCACUGGUGGC-----UACUGCU
.....((((((...-..............((..(.....((((.....))))......)..))((((((..(((((((....)))))))..)))))).....))))-----))..... ( -46.90)
>DroEre_CAF1 132629 109 + 1
AUUUAUAGCCAAUU-UAAAAGCCCAGAGGGCUGCACUUUCCGAAACUGGUGGUC---ACUAGUCGCUACUGCUGGCCACUGCUGGCCACUGCUGGCCACUGCUGGC-----CACUGGU
..............-....(((((...)))))............((..((((((---(.((((.((((..((((((((....))))))..)))))).)))).))))-----)))..)) ( -41.40)
>DroYak_CAF1 131539 99 + 1
AUUUAUAGCCAAUU-UAAAAGCCCAAAGAGCUGCACUUUCCGAGACUGGCGGCC---ACU----------GAUGGCCACUGGUGGCCACUGGUGGCUACUGGUCUC-----CUCUGGU
.......((((...-....(((.......))).........(((((..(..(((---(((----------..((((((....))))))..))))))..)..)))))-----...)))) ( -42.80)
>consensus
AUUUAUAGCCAAUU_UAAAAGCCCAAAGAGCUGCACUUUCCGAGACCGGCGGCG__UAGUGGCGGCCACUGGUGGCCACUG_UGGCUACUGGUGGCCACUGGUGGC_____CACUGGU
.......((((..................(((((.....(((.......)))......))))).........((((((....))))))...........))))............... ( -7.61 =  -9.45 +   1.84)

alignment

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secondary structure

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Window 0

Location 17,872,122 – 17,872,234
Length 112
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 69.26
Mean single sequence MFE -37.43
Consensus MFE -13.51
Energy contribution -13.57
Covariance contribution 0.06
Combinations/Pair 1.33
Mean z-score -1.99
Structure conservation index 0.36
SVM decision value 0.66
SVM RNA-class probability 0.815610
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17872122 112 - 22224390
ACCAGUG-----GCCACCAGUAGAUACCAGUAGCCAACAGUGGCCACCAGUGGCCACCACUAUGCGCCGACGGUCUCGGAAAGUGCAGCUCUUUGGGCUUUUA-AAUUGGCUAUAAAU
....(((-----((((....((((..((((.(((.....(((((((....)))))))((((.....((((.....))))..))))..)))..))))...))))-...))))))).... ( -37.70)
>DroVir_CAF1 187014 106 - 1
--CCGCUACAGCG-CAGCACUGCACCACUGCA-----CUAUGG-CACCACCCACUGCUUCUG---GCAGCGGACGUCUGUCGGUGCGGCUCUUUGGGCUUUUAAAAUUGGUUAUAAAU
--..((((.((.(-(((..........)))).-----)).)))-)((((((((((((..(((---(((((....).))))))).)))).....))))..........))))....... ( -31.20)
>DroSec_CAF1 135623 92 - 1
ACCAGUA-----GCCACCAGU--------------------GGCCACCAGUGGCCGCCACUACGCGCCGACGGUCUCGGAAAGUGCAGCUCUUUGGGCUUUUA-AAUUGGCUAUAAAU
....(((-----((((...((--------------------(((((....))))))).....(((.((((.....))))...))).((((.....))))....-...))))))).... ( -32.80)
>DroSim_CAF1 106601 112 - 1
AGCAGUA-----GCCACCAGUGGCCACCAGUAGCCAACAGUGGCCACCAGUGGCCGCCACUAUGCGCCGACGGUCUCGGAAAGUGCAGCUCUUUGGGCUUUUA-AAUUGGCUAUAAAU
....(((-----((((...((((((((..((.((((....)))).))..))))))))((((.....((((.....))))..)))).((((.....))))....-...))))))).... ( -42.10)
>DroEre_CAF1 132629 109 - 1
ACCAGUG-----GCCAGCAGUGGCCAGCAGUGGCCAGCAGUGGCCAGCAGUAGCGACUAGU---GACCACCAGUUUCGGAAAGUGCAGCCCUCUGGGCUUUUA-AAUUGGCUAUAAAU
....(((-----(((((((.(..((.((..((((((....))))))))....(.((((.((---....)).)))).)))..).)))(((((...)))))....-...))))))).... ( -38.70)
>DroYak_CAF1 131539 99 - 1
ACCAGAG-----GAGACCAGUAGCCACCAGUGGCCACCAGUGGCCAUC----------AGU---GGCCGCCAGUCUCGGAAAGUGCAGCUCUUUGGGCUUUUA-AAUUGGCUAUAAAU
.((((..-----(((((..(..(((((..(((((((....))))))).----------.))---)))..)..))))).((((((.(((....))).)))))).-..))))........ ( -42.10)
>consensus
ACCAGUG_____GCCACCAGUGGCCACCAGUAGCCA_CAGUGGCCACCAGUGGCCGCCACUA__CGCCGACGGUCUCGGAAAGUGCAGCUCUUUGGGCUUUUA_AAUUGGCUAUAAAU
.......................................(((((((....................(((.......)))(((((.(((....))).)))))......))))))).... (-13.51 = -13.57 +   0.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,872,161 – 17,872,264
Length 103
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 72.86
Mean single sequence MFE -47.40
Consensus MFE -32.09
Energy contribution -35.78
Covariance contribution 3.69
Combinations/Pair 1.29
Mean z-score -3.19
Structure conservation index 0.68
SVM decision value 4.03
SVM RNA-class probability 0.999766
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17872161 103 + 22224390
CGAGACCGUCGGCGCAUAGUGGUGGCCACUGGUGGCCACUGUUGGCUACUGGUAUCUACUGGUGGCCACUGGUGGCCACUG---GUGGGCGGAUAAUGAUAGUUGG
.....((((((((.(((....))))))((..(((((((((..(((((((..((....))..)))))))..)))))))))..---)).))))).............. ( -56.20)
>DroSec_CAF1 135662 83 + 1
CGAGACCGUCGGCGCGUAGUGGCGGCCACUGGUGGCC--------------------ACUGGUGGCUACUGGUAGUCACUG---GUGGGCGGGUAAAGAUAGUUGG
.....(((((.((....((((((.(((...))).)))--------------------)))((((((((....)))))))).---)).))))).............. ( -36.80)
>DroSim_CAF1 106640 103 + 1
CGAGACCGUCGGCGCAUAGUGGCGGCCACUGGUGGCCACUGUUGGCUACUGGUGGCCACUGGUGGCUACUGCUGGUCACUG---GUGGGCGGGUAAUGAUAGUUGG
.....((((((.(((...))).)((((((..(((((((....)))))))..))))))((..(((((((....)))))))..---)).))))).............. ( -52.60)
>DroEre_CAF1 132668 100 + 1
CGAAACUGGUGGUC---ACUAGUCGCUACUGCUGGCCACUGCUGGCCACUGCUGGCCACUGCUGGCCACUGGUGGCCACUG---AUGGGCGGGUAAUGAUAGCUGG
....((((((....---)))))).((((.((((.(((.....((((((((..((((((....))))))..))))))))...---...))).))))....))))... ( -44.70)
>DroYak_CAF1 131578 93 + 1
CGAGACUGGCGGCC---ACU----------GAUGGCCACUGGUGGCCACUGGUGGCUACUGGUCUCCUCUGGUGGCCACUGGCGGUGGGCGGGUAAUGAUAGUUGG
.(((((..(..(((---(((----------..((((((....))))))..))))))..)..))))).((((.(.(((......))).).))))............. ( -46.70)
>consensus
CGAGACCGUCGGCGC_UAGUGGCGGCCACUGGUGGCCACUGUUGGCCACUGGUGGCCACUGGUGGCCACUGGUGGCCACUG___GUGGGCGGGUAAUGAUAGUUGG
.....(((((.((......(((.((((((((((((((((((.((((((....)))))).)))))))))))))))))).)))...)).))))).............. (-32.09 = -35.78 +   3.69)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,872,161 – 17,872,264
Length 103
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 72.86
Mean single sequence MFE -32.36
Consensus MFE -11.28
Energy contribution -13.98
Covariance contribution 2.70
Combinations/Pair 1.27
Mean z-score -1.80
Structure conservation index 0.35
SVM decision value 0.34
SVM RNA-class probability 0.697563
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17872161 103 - 22224390
CCAACUAUCAUUAUCCGCCCAC---CAGUGGCCACCAGUGGCCACCAGUAGAUACCAGUAGCCAACAGUGGCCACCAGUGGCCACCACUAUGCGCCGACGGUCUCG
.........((..((.((.((.---..((((((((..((((((((..((.(.((....))..).)).))))))))..)))))))).....)).)).))..)).... ( -35.50)
>DroSec_CAF1 135662 83 - 1
CCAACUAUCUUUACCCGCCCAC---CAGUGACUACCAGUAGCCACCAGU--------------------GGCCACCAGUGGCCGCCACUACGCGCCGACGGUCUCG
................(.((((---..(((.(((....))).)))..))--------------------)).)(((..((((((......)).))))..))).... ( -21.30)
>DroSim_CAF1 106640 103 - 1
CCAACUAUCAUUACCCGCCCAC---CAGUGACCAGCAGUAGCCACCAGUGGCCACCAGUAGCCAACAGUGGCCACCAGUGGCCGCCACUAUGCGCCGACGGUCUCG
......................---..(.((((.......(((((..((((((((..((.....)).))))))))..)))))(((......))).....)))).). ( -33.90)
>DroEre_CAF1 132668 100 - 1
CCAGCUAUCAUUACCCGCCCAU---CAGUGGCCACCAGUGGCCAGCAGUGGCCAGCAGUGGCCAGCAGUGGCCAGCAGUAGCGACUAGU---GACCACCAGUUUCG
...(((((..((..((((....---...((((((....))))))((..((((((....)))))))).))))..))..)))))((((.((---....)).))))... ( -33.90)
>DroYak_CAF1 131578 93 - 1
CCAACUAUCAUUACCCGCCCACCGCCAGUGGCCACCAGAGGAGACCAGUAGCCACCAGUGGCCACCAGUGGCCAUC----------AGU---GGCCGCCAGUCUCG
................(.((((.....)))).).......(((((..(..(((((..(((((((....))))))).----------.))---)))..)..))))). ( -37.20)
>consensus
CCAACUAUCAUUACCCGCCCAC___CAGUGGCCACCAGUGGCCACCAGUAGCCACCAGUAGCCAACAGUGGCCACCAGUGGCCACCACUA_GCGCCGACGGUCUCG
...........................(.((((....((((((((.....((((....)))).....)))))))).(((((...)))))..........)))).). (-11.28 = -13.98 +   2.70)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,872,199 – 17,872,298
Length 99
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 81.94
Mean single sequence MFE -38.77
Consensus MFE -23.30
Energy contribution -27.30
Covariance contribution 4.00
Combinations/Pair 1.17
Mean z-score -2.31
Structure conservation index 0.60
SVM decision value 0.87
SVM RNA-class probability 0.870226
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17872199 99 + 22224390
CUGUUGGCUACUGGUAUCUACUGGUGGCCACUGGUGGCCACUG---GUGGGCGGAUAAUGAUAGUUGGCCACUGGCCGUUUGGAUAUAUCAUUUACAGGGCG
......(((.(((...(((((..(((((((....)))))))..---)))))..((((....(((.(((((...))))).)))....)))).....)))))). ( -39.40)
>DroSec_CAF1 135699 80 + 1
-------------------ACUGGUGGCUACUGGUAGUCACUG---GUGGGCGGGUAAAGAUAGUUGGCCACUGGCCGUUUGGAUAUAUCAUUUACAGGGCG
-------------------((..(((((((....)))))))..---))..((..(((((((((..(((((...)))))........)))).)))))...)). ( -27.10)
>DroSim_CAF1 106678 99 + 1
CUGUUGGCUACUGGUGGCCACUGGUGGCUACUGCUGGUCACUG---GUGGGCGGGUAAUGAUAGUUGGCCACUGGCCGUUUGGAUAUAUCAUUUACAGGGCG
......(((.(((.((.((((..(((((((....)))))))..---)))).))...(((((((..(((((...)))))........)))))))..)))))). ( -37.40)
>DroEre_CAF1 132703 99 + 1
CUGCUGGCCACUGCUGGCCACUGCUGGCCACUGGUGGCCACUG---AUGGGCGGGUAAUGAUAGCUGGCCACCGCCCGUUUGGAUAUAUCAUUUACAGAGCG
..((((((((((..((((((....))))))..))))))).(.(---((((((((.................))))))))).)................))). ( -44.03)
>DroYak_CAF1 131603 102 + 1
CUGGUGGCCACUGGUGGCUACUGGUCUCCUCUGGUGGCCACUGGCGGUGGGCGGGUAAUGAUAGUUGGCCACUGACCGGUUGGAUAUAUCAUUUACAGGGCG
(((.(.(((.(..((((((((..(......)..))))))))..).))).).)))(((((((((.(..(((.......)))..)...))))).))))...... ( -45.90)
>consensus
CUGUUGGCCACUGGUGGCCACUGGUGGCCACUGGUGGCCACUG___GUGGGCGGGUAAUGAUAGUUGGCCACUGGCCGUUUGGAUAUAUCAUUUACAGGGCG
....((((((((((((((((....))))))))))))))))(((...((((.(((.((....)).))).))))...((....))............))).... (-23.30 = -27.30 +   4.00)

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 12:30:42 2006