Locus 6780

Sequence ID 3L_DroMel_CAF1
Location 18,214,355 – 18,214,509
Length 154
Max. P 0.985043
window11014 window11015 window11016 window11017

overview

Window 4

Location 18,214,355 – 18,214,469
Length 114
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 93.27
Mean single sequence MFE -38.77
Consensus MFE -35.91
Energy contribution -37.47
Covariance contribution 1.56
Combinations/Pair 1.07
Mean z-score -3.24
Structure conservation index 0.93
SVM decision value 1.99
SVM RNA-class probability 0.985043
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18214355 114 + 23771897
UAUUUUGUUCUCUGUAUUCAAAAUAGGCAGCAAGAUAAAAGCCGUAACAGGCCUUGUGGCGAGCCUUUAACAUUUGUUAAAGCCACGAGUGCCAUUCGGCCUCUUUGGGCUCUG
(((((((((.(((((.......))))).)))))))))..((((..((.(((((..((((((..((((((((....)))))))....)..))))))..))))).))..))))... ( -39.50)
>DroSec_CAF1 115826 114 + 1
UAUUUUCCUCUCUGUAGUCAAAAUAGGCAAAAAGAUAAAAGCCCAUGCAGGCCUUGUGGCGAGCCUUUAACAUUUGUUAAAGCCACGAGUGCCAUUCGGCCUCUUUGGGCUCUG
..........(((...(((......)))....)))....((((((...(((((..((((((..((((((((....)))))))....)..))))))..)))))...))))))... ( -37.80)
>DroEre_CAF1 118007 114 + 1
CAUUUUGUUCUCUGUAGUCAAAAUAGGCAAUAAGAAAAAAGCCGAAGCAGGCCUUGUGGCGAGCCUUUAACAUUUGUUAAAGCCACGAGUGCCAUUCGGCCUCUUUGGGCUCUG
..(((((((.(((((.......))))).)))))))....((((.(((.(((((..((((((..((((((((....)))))))....)..))))))..))))).))).))))... ( -39.00)
>consensus
UAUUUUGUUCUCUGUAGUCAAAAUAGGCAAAAAGAUAAAAGCCGAAGCAGGCCUUGUGGCGAGCCUUUAACAUUUGUUAAAGCCACGAGUGCCAUUCGGCCUCUUUGGGCUCUG
(((((((((.(((((.......))))).)))))))))..((((.(((.(((((..((((((..((((((((....)))))))....)..))))))..))))).))).))))... (-35.91 = -37.47 +   1.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,214,355 – 18,214,469
Length 114
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 93.27
Mean single sequence MFE -35.50
Consensus MFE -30.70
Energy contribution -30.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.57
Structure conservation index 0.86
SVM decision value 0.91
SVM RNA-class probability 0.880403
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18214355 114 - 23771897
CAGAGCCCAAAGAGGCCGAAUGGCACUCGUGGCUUUAACAAAUGUUAAAGGCUCGCCACAAGGCCUGUUACGGCUUUUAUCUUGCUGCCUAUUUUGAAUACAGAGAACAAAAUA
.((((((..((.(((((...((((....(.(.(((((((....))))))).).)))))...))))).))..))))))............(((((((...........))))))) ( -33.00)
>DroSec_CAF1 115826 114 - 1
CAGAGCCCAAAGAGGCCGAAUGGCACUCGUGGCUUUAACAAAUGUUAAAGGCUCGCCACAAGGCCUGCAUGGGCUUUUAUCUUUUUGCCUAUUUUGACUACAGAGAGGAAAAUA
.((((((((...(((((...((((....(.(.(((((((....))))))).).)))))...)))))...)))))))).....((((.(((.(((((....)))))))))))).. ( -39.80)
>DroEre_CAF1 118007 114 - 1
CAGAGCCCAAAGAGGCCGAAUGGCACUCGUGGCUUUAACAAAUGUUAAAGGCUCGCCACAAGGCCUGCUUCGGCUUUUUUCUUAUUGCCUAUUUUGACUACAGAGAACAAAAUG
.((.((..((((((((((((.(((.((.(((((((((((....)))))).....))))).)))))...))))))))))))......))))((((((.((....))..)))))). ( -33.70)
>consensus
CAGAGCCCAAAGAGGCCGAAUGGCACUCGUGGCUUUAACAAAUGUUAAAGGCUCGCCACAAGGCCUGCUUCGGCUUUUAUCUUAUUGCCUAUUUUGACUACAGAGAACAAAAUA
.((((((.....(((((...((((....(.(.(((((((....))))))).).)))))...))))).....))))))..............(((((....)))))......... (-30.70 = -30.70 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,214,395 – 18,214,509
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.76
Mean single sequence MFE -36.78
Consensus MFE -24.62
Energy contribution -24.10
Covariance contribution -0.52
Combinations/Pair 1.07
Mean z-score -1.82
Structure conservation index 0.67
SVM decision value 0.13
SVM RNA-class probability 0.596955
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18214395 114 + 23771897
GCCGUAACAGGCCUUGUGGCGAGCCU-UUAACAUUUGUUAAAGCCACGAGUGCCAUUCGGCCUCUUUGGGCU-----CUGUGCAUACUGCAGGUAAUUUUCGCAACGACGCAAUUGAGUU
((((.....(((((((((((.....(-(((((....)))))))))))))).)))...)))).......((((-----(..(((....(((..(.....)..))).....)))...))))) ( -36.70)
>DroPse_CAF1 146282 106 + 1
----------GCCUUGUGGCGAGCCUUUUAACAUUUGU----GCCACAAGUGGCUCUCGGCCUCUUUGGGCUCUGCUCUGUGCAUAUUGCAGUUAAUUUUCGCAACGACGCAAUAGAGUU
----------(((....)))((((((..........(.----((((....)))).)...........)))))).(((((((((...((((...........))))....)).))))))). ( -32.40)
>DroSec_CAF1 115866 114 + 1
GCCCAUGCAGGCCUUGUGGCGAGCCU-UUAACAUUUGUUAAAGCCACGAGUGCCAUUCGGCCUCUUUGGGCU-----CUGUGCAUACUGCAGGUAAUUUUCGCAACGACGCAAUUGAGUU
(((((...(((((..((((((..(((-(((((....)))))))....)..))))))..)))))...)))))(-----(..(((....(((..(.....)..))).....)))...))... ( -39.40)
>DroEre_CAF1 118047 114 + 1
GCCGAAGCAGGCCUUGUGGCGAGCCU-UUAACAUUUGUUAAAGCCACGAGUGCCAUUCGGCCUCUUUGGGCU-----CUGUGCAUGCUGCAGGUAAUUUUCGCAACUACGCAAUUGAGUU
.((((((.(((((..((((((..(((-(((((....)))))))....)..))))))..)))))))))))(((-----(..(((..(.(((..(.....)..))).)...)))...)))). ( -43.00)
>DroPer_CAF1 135413 106 + 1
----------GCCUUGUGGCGAGCCUUUUAACAUUUGU----GCCACAAGUGGCUCUCGGCCUCUUUGGGCUCUGCUCUGUGCAUAUUGCAGUUAAUUUUCGCAACGACGCAAUAGAGUU
----------(((....)))((((((..........(.----((((....)))).)...........)))))).(((((((((...((((...........))))....)).))))))). ( -32.40)
>consensus
GCC____CAGGCCUUGUGGCGAGCCU_UUAACAUUUGUUAAAGCCACGAGUGCCAUUCGGCCUCUUUGGGCU_____CUGUGCAUACUGCAGGUAAUUUUCGCAACGACGCAAUUGAGUU
..........((.((((.(((((........(((((((.......)))))))((....(((((....)))))........(((.....))))).....))))).)))).))......... (-24.62 = -24.10 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,214,395 – 18,214,509
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.76
Mean single sequence MFE -35.06
Consensus MFE -24.23
Energy contribution -23.99
Covariance contribution -0.24
Combinations/Pair 1.12
Mean z-score -2.11
Structure conservation index 0.69
SVM decision value 0.62
SVM RNA-class probability 0.802981
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18214395 114 - 23771897
AACUCAAUUGCGUCGUUGCGAAAAUUACCUGCAGUAUGCACAG-----AGCCCAAAGAGGCCGAAUGGCACUCGUGGCUUUAACAAAUGUUAA-AGGCUCGCCACAAGGCCUGUUACGGC
........(((((.((((((.........)))))))))))...-----.(((..((.(((((...((((....(.(.(((((((....)))))-)).).)))))...))))).))..))) ( -34.00)
>DroPse_CAF1 146282 106 - 1
AACUCUAUUGCGUCGUUGCGAAAAUUAACUGCAAUAUGCACAGAGCAGAGCCCAAAGAGGCCGAGAGCCACUUGUGGC----ACAAAUGUUAAAAGGCUCGCCACAAGGC----------
..((((..(((((.((((((.........))))))))))).))))..(((((..(((.(((.....))).))).((((----(....)))))...)))))(((....)))---------- ( -31.30)
>DroSec_CAF1 115866 114 - 1
AACUCAAUUGCGUCGUUGCGAAAAUUACCUGCAGUAUGCACAG-----AGCCCAAAGAGGCCGAAUGGCACUCGUGGCUUUAACAAAUGUUAA-AGGCUCGCCACAAGGCCUGCAUGGGC
.......(((((....)))))......(((((((........(-----((((((..((((((....))).))).)))(((((((....)))))-))))))(((....)))))))).)).. ( -38.50)
>DroEre_CAF1 118047 114 - 1
AACUCAAUUGCGUAGUUGCGAAAAUUACCUGCAGCAUGCACAG-----AGCCCAAAGAGGCCGAAUGGCACUCGUGGCUUUAACAAAUGUUAA-AGGCUCGCCACAAGGCCUGCUUCGGC
..(((...(((((.((((((.........)))))))))))..)-----)).((.((((((((...((((....(.(.(((((((....)))))-)).).)))))...))))).))).)). ( -40.20)
>DroPer_CAF1 135413 106 - 1
AACUCUAUUGCGUCGUUGCGAAAAUUAACUGCAAUAUGCACAGAGCAGAGCCCAAAGAGGCCGAGAGCCACUUGUGGC----ACAAAUGUUAAAAGGCUCGCCACAAGGC----------
..((((..(((((.((((((.........))))))))))).))))..(((((..(((.(((.....))).))).((((----(....)))))...)))))(((....)))---------- ( -31.30)
>consensus
AACUCAAUUGCGUCGUUGCGAAAAUUACCUGCAGUAUGCACAG_____AGCCCAAAGAGGCCGAAUGGCACUCGUGGCUUUAACAAAUGUUAA_AGGCUCGCCACAAGGCCUG____GGC
........(((((.((((((.........))))))))))).........(((....((((((....))).)))(((((......................)))))..))).......... (-24.23 = -23.99 +  -0.24)

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 12:29:47 2006