Locus 4066

Sequence ID X_DroMel_CAF1
Location 10,762,490 – 10,762,674
Length 184
Max. P 0.977280
window6680 window6681 window6682 window6683 window6684

overview

Window 0

Location 10,762,490 – 10,762,598
Length 108
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 93.40
Mean single sequence MFE -44.73
Consensus MFE -36.15
Energy contribution -37.23
Covariance contribution 1.08
Combinations/Pair 1.06
Mean z-score -3.13
Structure conservation index 0.81
SVM decision value 1.34
SVM RNA-class probability 0.943561
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10762490 108 + 22224390
UCCUACUACACAUUGGCCGCUGCAGCUGCGGCUCAUCCGCAUGCCCAUGGCCACGCCCACACGCAUGCGCAUGCCGCCCACUAUGCCGCCGCCGCUGCGGCAGCUGAC
............(..((.((((((((.(((((......((((((....(((...))).....))))))(((((........))))).))))).)))))))).))..). ( -49.20)
>DroSec_CAF1 12181 108 + 1
UCCUACUACACAUUGGCCGCUGCAGCUGCUGCUCAUCCGCAUGCCCAUGGCCACGCCCACACGCAUGCGCAUGCCGCCCACUAUGCCGCCGCCGCUGCGACGGCUGAC
............(..((((.((((((.((.((......((((((....(((...))).....))))))(((((........))))).)).)).)))))).))))..). ( -42.60)
>DroSim_CAF1 9748 108 + 1
UCCUACUACACAUUGGCCGCUGCAGCUGCUGCUCAUCCGCAUGCCCAUGGCCACGCCCACACGCAUGCGCAUGCCGCCCACUAUGCCGCCGCCGCUGCGGCGGCUGAC
............(..(((((((((((.((.((......((((((....(((...))).....))))))(((((........))))).)).)).)))))))))))..). ( -49.20)
>DroEre_CAF1 10688 108 + 1
UCCUACUACACAUUGGCCGCUGCAGCUGCCGCUCAUCCGCAUGCCCAUGGCCACGCCCACACGCAUGCGCAUGCCGCCCACUACGCCGCCGCCGCUGCGGCAGCCGAC
............(((((.((((((((.((.((.(((.(((((((....(((...))).....))))))).)))..((.......)).)).)).)))))))).))))). ( -44.80)
>DroYak_CAF1 12839 108 + 1
UCCUACUACACAUUGGCCGCUGCAGCUGCCGCUCAUCCGCAUGCUCAUGGCCACGCCCACACGCAUGCGCAUGCCGCCCACUAUGCCGCCGCCGCUGCGGCAGCUGAC
............(..((.((((((((.((.((......((((((....(((...))).....))))))(((((........))))).)).)).)))))))).))..). ( -43.10)
>DroAna_CAF1 20504 108 + 1
UCGUACUACACCCUGGCGGCCGCUGCUGCCGGUCAUCCGCAUGCCCAUGGCCACGCCCACGCCCAUGCCCAUGCCGCCCACUAUGCUGCCGCCGCCGCGUCAGCGGAC
............((((((((....))))))))...((((((((..(((((.(........).)))))..)))))..........((((.(((....))).))))))). ( -39.50)
>consensus
UCCUACUACACAUUGGCCGCUGCAGCUGCCGCUCAUCCGCAUGCCCAUGGCCACGCCCACACGCAUGCGCAUGCCGCCCACUAUGCCGCCGCCGCUGCGGCAGCUGAC
............(((((.((((((((.((.((.(((.(((((((....(((...))).....))))))).)))..((.......)).)).)).)))))))).))))). (-36.15 = -37.23 +   1.08)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,762,490 – 10,762,598
Length 108
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 93.40
Mean single sequence MFE -52.72
Consensus MFE -47.11
Energy contribution -47.17
Covariance contribution 0.06
Combinations/Pair 1.13
Mean z-score -1.98
Structure conservation index 0.89
SVM decision value 1.79
SVM RNA-class probability 0.977280
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10762490 108 - 22224390
GUCAGCUGCCGCAGCGGCGGCGGCAUAGUGGGCGGCAUGCGCAUGCGUGUGGGCGUGGCCAUGGGCAUGCGGAUGAGCCGCAGCUGCAGCGGCCAAUGUGUAGUAGGA
....(((((.(((((.(((((.((.......))..(((.(((((((.(((((......))))).))))))).))).))))).))))).)))))............... ( -55.40)
>DroSec_CAF1 12181 108 - 1
GUCAGCCGUCGCAGCGGCGGCGGCAUAGUGGGCGGCAUGCGCAUGCGUGUGGGCGUGGCCAUGGGCAUGCGGAUGAGCAGCAGCUGCAGCGGCCAAUGUGUAGUAGGA
....((((((((....))))))))(((.(((.((.(((.(((((((.(((((......))))).))))))).))).((((...))))..)).))).)))......... ( -51.90)
>DroSim_CAF1 9748 108 - 1
GUCAGCCGCCGCAGCGGCGGCGGCAUAGUGGGCGGCAUGCGCAUGCGUGUGGGCGUGGCCAUGGGCAUGCGGAUGAGCAGCAGCUGCAGCGGCCAAUGUGUAGUAGGA
....((((((((....))))))))(((.(((.((.(((.(((((((.(((((......))))).))))))).))).((((...))))..)).))).)))......... ( -54.60)
>DroEre_CAF1 10688 108 - 1
GUCGGCUGCCGCAGCGGCGGCGGCGUAGUGGGCGGCAUGCGCAUGCGUGUGGGCGUGGCCAUGGGCAUGCGGAUGAGCGGCAGCUGCAGCGGCCAAUGUGUAGUAGGA
...((((((.(((((.((.((..(((.....))).(((.(((((((.(((((......))))).))))))).))).)).)).))))).)))))).............. ( -56.20)
>DroYak_CAF1 12839 108 - 1
GUCAGCUGCCGCAGCGGCGGCGGCAUAGUGGGCGGCAUGCGCAUGCGUGUGGGCGUGGCCAUGAGCAUGCGGAUGAGCGGCAGCUGCAGCGGCCAAUGUGUAGUAGGA
(((.((((((((....)))))))).......((..(((.(((((((..((((......))))..))))))).))).))))).((((((.((.....)))))))).... ( -50.90)
>DroAna_CAF1 20504 108 - 1
GUCCGCUGACGCGGCGGCGGCAGCAUAGUGGGCGGCAUGGGCAUGGGCGUGGGCGUGGCCAUGGGCAUGCGGAUGACCGGCAGCAGCGGCCGCCAGGGUGUAGUACGA
(.((((....)))))((((((.((...((.(.((((((..(((((..(((((......)))))..)))))..))).))).).)).)).)))))).............. ( -47.30)
>consensus
GUCAGCUGCCGCAGCGGCGGCGGCAUAGUGGGCGGCAUGCGCAUGCGUGUGGGCGUGGCCAUGGGCAUGCGGAUGAGCGGCAGCUGCAGCGGCCAAUGUGUAGUAGGA
....((((((((....))))))))......(((..(((.(((((((.(((((......))))).))))))).))).((.((....)).)).))).............. (-47.11 = -47.17 +   0.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,762,530 – 10,762,638
Length 108
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 91.91
Mean single sequence MFE -53.10
Consensus MFE -47.01
Energy contribution -47.07
Covariance contribution 0.06
Combinations/Pair 1.23
Mean z-score -1.49
Structure conservation index 0.89
SVM decision value 0.54
SVM RNA-class probability 0.773815
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10762530 108 - 22224390
CAGCGGCUGCAGCCGCUCCCAGUAGCUGUCCCAUAUUGAAGUCAGCUGCCGCAGCGGCGGCGGCAUAGUGGGCGGCAUGCGCAUGCGUGUGGGCGUGGCCAUGGGCAU
.((((((....))))))((((...((((.(((((..((....))((((((((....))))))))...)))))))))..((.(((((......)))))))..))))... ( -54.60)
>DroSec_CAF1 12221 108 - 1
CAGCGGCUGCAGCCGCACCCAGUAGCUGUCCCAUAUUAAAGUCAGCCGUCGCAGCGGCGGCGGCAUAGUGGGCGGCAUGCGCAUGCGUGUGGGCGUGGCCAUGGGCAU
..(((((....))))).((((...((..((((((((........((((((((....))))))))...((..(((.....)))..))))))))).)..))..))))... ( -51.50)
>DroSim_CAF1 9788 108 - 1
CAGCGGCUGCAGCCGCACCCAGUAGCUGUCCCAUAUUAAAGUCAGCCGCCGCAGCGGCGGCGGCAUAGUGGGCGGCAUGCGCAUGCGUGUGGGCGUGGCCAUGGGCAU
..(((((....))))).((((...((..((((((((........((((((((....))))))))...((..(((.....)))..))))))))).)..))..))))... ( -54.20)
>DroEre_CAF1 10728 108 - 1
CAGCGGCUGCAGCCGCUCCCAGUAGCUGCCCCAUAUUGAAGUCGGCUGCCGCAGCGGCGGCGGCGUAGUGGGCGGCAUGCGCAUGCGUGUGGGCGUGGCCAUGGGCAU
.((((((....))))))((((...((..((((((((........((((((((....))))))))(((.((.((.....)).)))))))))))).)..))..))))... ( -55.40)
>DroYak_CAF1 12879 108 - 1
CAGCGGCUGCAGCCGCUCCCAGUAGCUGCCCCAUAUUGAAGUCAGCUGCCGCAGCGGCGGCGGCAUAGUGGGCGGCAUGCGCAUGCGUGUGGGCGUGGCCAUGAGCAU
.....(((.(((((((.(((....((((((((....((....))((((((((....))))))))...).)))))))(((((....)))))))).)))))..))))).. ( -54.00)
>DroAna_CAF1 20544 108 - 1
CUGCCGCAGCUGCUGCCCCCAAAAGCUGGCUCAUAUUGAAGUCCGCUGACGCGGCGGCGGCAGCAUAGUGGGCGGCAUGGGCAUGGGCGUGGGCGUGGCCAUGGGCAU
(((((.((((((((((((((...(((.(((((.....).)))).)))...).)).)))))))))....)))))))(((((.((((........)))).)))))..... ( -48.90)
>consensus
CAGCGGCUGCAGCCGCUCCCAGUAGCUGUCCCAUAUUGAAGUCAGCUGCCGCAGCGGCGGCGGCAUAGUGGGCGGCAUGCGCAUGCGUGUGGGCGUGGCCAUGGGCAU
.....(((...(((((.(((....((((.(((((..((....))((((((((....))))))))...)))))))))(((((....)))))))).)))))....))).. (-47.01 = -47.07 +   0.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,762,569 – 10,762,674
Length 105
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 83.11
Mean single sequence MFE -51.73
Consensus MFE -34.32
Energy contribution -35.93
Covariance contribution 1.61
Combinations/Pair 1.24
Mean z-score -2.34
Structure conservation index 0.66
SVM decision value 0.31
SVM RNA-class probability 0.683070
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10762569 105 + 22224390
ACUAUGCCGCCGCCGCUGCGGCAGCUGACUUCAAUAUGGGACAGCUACUGGGAGCGGCUGCAGCCGCUGCCGCCUCUGGAGAUCCCGCUGCCCAGCAUGCGGCUG
........(((((.((((.((((((((....))....((((...((.(..(..(((((.((....)).)))))..)..))).))))))))))))))..))))).. ( -55.30)
>DroSec_CAF1 12260 105 + 1
ACUAUGCCGCCGCCGCUGCGACGGCUGACUUUAAUAUGGGACAGCUACUGGGUGCGGCUGCAGCCGCUGCCGCCUCUGGAGAUCCCGCUGCCCAGCAUGCGGCUG
.....(((((.((((......))))...........((((.((((....(((.(((((.((....)).)))))))).((.....))))))))))....))))).. ( -46.20)
>DroEre_CAF1 10767 105 + 1
ACUACGCCGCCGCCGCUGCGGCAGCCGACUUCAAUAUGGGGCAGCUACUGGGAGCGGCUGCAGCCGCUGCCGCCUCUGGAGAUCCGGCUGCACAGCAUGCGGCUG
........(((((.((((..(((((((.(((((....(((((((...))((.((((((....)))))).))))))))))))...))))))).))))..))))).. ( -56.00)
>DroWil_CAF1 7617 102 + 1
AUUAUGCAGCCGCUGCUGCGGCAGCUGACUUCAAUAUGGGACAAUUGCUGGGAGCUGCGGCAGCUGCUGCUGCCACUGGCGACGCAUCGUCGAUGC---CAGCUG
.....(((((.((.(((((.((((((..(..((((........))))..)..)))))).))))).)).)))))..(((((((((...))))...))---)))... ( -49.00)
>DroYak_CAF1 12918 105 + 1
ACUAUGCCGCCGCCGCUGCGGCAGCUGACUUCAAUAUGGGGCAGCUACUGGGAGCGGCUGCAGCCGCUGCCGCUUCUGGAGAUCCGGCUGCACAGCAUGCGGCUG
.....(((((.((.(.(((((((((((.((((.....))))))))).(..((((((((.((....)).))))))))..).......))))))).))..))))).. ( -54.60)
>DroAna_CAF1 20583 105 + 1
ACUAUGCUGCCGCCGCCGCGUCAGCGGACUUCAAUAUGAGCCAGCUUUUGGGGGCAGCAGCUGCGGCAGCCGCCUCCGGGGAUCCGGCGGCCCAACAUGCCGCCG
....(((((((.((.((((....))))..........(((....)))..)).)))))))...((((((...(((.((((....)))).)))......)))))).. ( -49.30)
>consensus
ACUAUGCCGCCGCCGCUGCGGCAGCUGACUUCAAUAUGGGACAGCUACUGGGAGCGGCUGCAGCCGCUGCCGCCUCUGGAGAUCCGGCUGCCCAGCAUGCGGCUG
........((.((((((.(((.(((((.(((......))).))))).))).).))))).))(((((((((.((..((((....))))..))...))).)))))). (-34.32 = -35.93 +   1.61)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,762,569 – 10,762,674
Length 105
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 83.11
Mean single sequence MFE -52.87
Consensus MFE -34.86
Energy contribution -35.42
Covariance contribution 0.56
Combinations/Pair 1.28
Mean z-score -2.74
Structure conservation index 0.66
SVM decision value 0.53
SVM RNA-class probability 0.772394
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10762569 105 - 22224390
CAGCCGCAUGCUGGGCAGCGGGAUCUCCAGAGGCGGCAGCGGCUGCAGCCGCUCCCAGUAGCUGUCCCAUAUUGAAGUCAGCUGCCGCAGCGGCGGCGGCAUAGU
..(((((.(((((((((((((((....(((..((((.((((((....)))))).)).))..)))))))....((....)))))))).)))))...)))))..... ( -57.80)
>DroSec_CAF1 12260 105 - 1
CAGCCGCAUGCUGGGCAGCGGGAUCUCCAGAGGCGGCAGCGGCUGCAGCCGCACCCAGUAGCUGUCCCAUAUUAAAGUCAGCCGUCGCAGCGGCGGCGGCAUAGU
..(((((....(((((((((((.((....)).(((((.((....)).))))).)))....)))).))))...........(((((....))))).)))))..... ( -46.80)
>DroEre_CAF1 10767 105 - 1
CAGCCGCAUGCUGUGCAGCCGGAUCUCCAGAGGCGGCAGCGGCUGCAGCCGCUCCCAGUAGCUGCCCCAUAUUGAAGUCGGCUGCCGCAGCGGCGGCGGCGUAGU
..(((((.((((((((((((((....)).(.((((((((((((....)))))).......)))))).)...........))))).)))))))...)))))..... ( -56.61)
>DroWil_CAF1 7617 102 - 1
CAGCUG---GCAUCGACGAUGCGUCGCCAGUGGCAGCAGCAGCUGCCGCAGCUCCCAGCAAUUGUCCCAUAUUGAAGUCAGCUGCCGCAGCAGCGGCUGCAUAAU
..((((---((..((......))..)))))).(((((.((.(((((.((((((..(..((((........))))..)..)))))).))))).)).)))))..... ( -48.50)
>DroYak_CAF1 12918 105 - 1
CAGCCGCAUGCUGUGCAGCCGGAUCUCCAGAAGCGGCAGCGGCUGCAGCCGCUCCCAGUAGCUGCCCCAUAUUGAAGUCAGCUGCCGCAGCGGCGGCGGCAUAGU
..(((((.((((((......((....))....((((((((((..(((((..(.....)..))))).))....((....)))))))))).)))))))))))..... ( -51.70)
>DroAna_CAF1 20583 105 - 1
CGGCGGCAUGUUGGGCCGCCGGAUCCCCGGAGGCGGCUGCCGCAGCUGCUGCCCCCAAAAGCUGGCUCAUAUUGAAGUCCGCUGACGCGGCGGCGGCAGCAUAGU
..((((((.(((..(((.((((....)))).)))))))))))).((((((((((((...(((.(((((.....).)))).)))...).)).)))))))))..... ( -55.80)
>consensus
CAGCCGCAUGCUGGGCAGCCGGAUCUCCAGAGGCGGCAGCGGCUGCAGCCGCUCCCAGUAGCUGUCCCAUAUUGAAGUCAGCUGCCGCAGCGGCGGCGGCAUAGU
(((((((.((((..((..(.((....)).)..)))))))))))))..(((((.....(((((((.(..........).)))))))(((....))))))))..... (-34.86 = -35.42 +   0.56)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:32 2006