Locus 9880

Sequence ID 3R_DroMel_CAF1
Location 26,354,659 – 26,354,824
Length 165
Max. P 0.998888
window15762 window15763 window15764

overview

Window 2

Location 26,354,659 – 26,354,773
Length 114
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 92.81
Mean single sequence MFE -40.99
Consensus MFE -36.07
Energy contribution -36.68
Covariance contribution 0.61
Combinations/Pair 1.11
Mean z-score -3.28
Structure conservation index 0.88
SVM decision value 3.27
SVM RNA-class probability 0.998888
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26354659 114 - 27905053
GCGAAUGAGCAAUUUCCCAGCAAUUCUUUGGCCAUUGCCAAUGUUUGCCCUGGCAAGCAUGCUGCGGAAAAUGUUCGCUUAUCGGAAUCCAAGUGGGUCUCAACACUCACCGCA
(((...(((((.((((((((((.....(((((....)))))(((((((....)))))))))))).))))).)))))................((((((......))))))))). ( -44.90)
>DroSec_CAF1 76644 114 - 1
GCGAAUGAGCAAUUUCCCAGCAAUUCUUUGGCCAUUGCCAAUGUUUGCCCUCGCAAGCAUGCUGCGGAAAAUGUUCGCUUAUCGGAAUCCAAGUGGGUCUCAACACUCACCGCA
(((...(((((.((((((((((.....(((((....)))))(((((((....)))))))))))).))))).)))))................((((((......))))))))). ( -42.90)
>DroSim_CAF1 81917 114 - 1
GCGAAUGAGCAAUUUCCCAGCAAUUCUUUGGCCAUUGCCAAUGUUUGCCCUCGCAAGCAUGCUGCGGAAAAUGUUCGCUUAUCGGAAUCCAAGUGGGUCUCAACACUCACCGCA
(((...(((((.((((((((((.....(((((....)))))(((((((....)))))))))))).))))).)))))................((((((......))))))))). ( -42.90)
>DroEre_CAF1 84137 114 - 1
GCGAAUGAGCAAUUUCCCAGCAAUUCUUUGGCCGUUGCCAAUGUUUGCCCUCGCAAGCAUGCUGCGGAAAAUGUUCGCUUAUCGGAAUCCAAGUGGGUCUCAGCCCUCACCGCA
(((...(((((.((((((((((.....(((((....)))))(((((((....)))))))))))).))))).)))))(((....(..((((....))))..))))......))). ( -43.10)
>DroYak_CAF1 80950 114 - 1
GCGAAUGAGCAAUUUCCCAGCAAUUCUUUGGCCGUUGCCAAUGUUUGCCCUCGCAAGCACGCUGCGGAAAAUGUUCGCUUAUCGGAAUCCAAGUGGGUCUCAGCCCUCGCCGCA
(((...(((((.(((((((((......(((((....)))))(((((((....))))))).)))).))))).)))))((.....((...))..(.((((....)))).)))))). ( -43.20)
>DroAna_CAF1 96485 114 - 1
CGGAAUGAGCAUAUUUCCAGCAAUUCUUCGGCCCCUGCCAAUGUUUGCCCUCGGAAGUAUGCUGCGGAAAAUGUACGUUUAUCAGAAUUCAAGUGGGUCCCAGCACUUACCACA
..((((.(((((((((((.((((......(((....))).....))))....)))))))))))(((.........)))........))))..((((.............)))). ( -28.92)
>consensus
GCGAAUGAGCAAUUUCCCAGCAAUUCUUUGGCCAUUGCCAAUGUUUGCCCUCGCAAGCAUGCUGCGGAAAAUGUUCGCUUAUCGGAAUCCAAGUGGGUCUCAACACUCACCGCA
(((..((((((.((((((((((.....(((((....)))))(((((((....)))))))))))).))))).))))))...............(((((........)))))))). (-36.07 = -36.68 +   0.61)

alignment

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secondary structure

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dotplot

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Window 3

Location 26,354,694 – 26,354,793
Length 99
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 83.72
Mean single sequence MFE -39.33
Consensus MFE -29.16
Energy contribution -29.94
Covariance contribution 0.78
Combinations/Pair 1.12
Mean z-score -3.30
Structure conservation index 0.74
SVM decision value 1.02
SVM RNA-class probability 0.901149
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26354694 99 - 27905053
UCUCUGG-------------CCCC-------GCACACCCGGCGAAUGAGCAAUUUCCCAGCAAUUCUUUGGCCAUUGCCAAUGUUUGCCCUGGCAAGCAUGCUGCGGAAAAUGUUCGCU
.....((-------------(..(-------((.......)))...(((((.((((((((((.....(((((....)))))(((((((....)))))))))))).))))).)))))))) ( -39.20)
>DroSec_CAF1 76679 111 - 1
UCUCUGGCCGG-AUUGUCUGCCCC-------GCACACCCGGCGAAUGAGCAAUUUCCCAGCAAUUCUUUGGCCAUUGCCAAUGUUUGCCCUCGCAAGCAUGCUGCGGAAAAUGUUCGCU
......(((((-...((.(((...-------))).)))))))....(((((.((((((((((.....(((((....)))))(((((((....)))))))))))).))))).)))))... ( -44.00)
>DroSim_CAF1 81952 111 - 1
UCUCUGGCCGG-AUUGUCUGCCCC-------GCACACCCGGCGAAUGAGCAAUUUCCCAGCAAUUCUUUGGCCAUUGCCAAUGUUUGCCCUCGCAAGCAUGCUGCGGAAAAUGUUCGCU
......(((((-...((.(((...-------))).)))))))....(((((.((((((((((.....(((((....)))))(((((((....)))))))))))).))))).)))))... ( -44.00)
>DroEre_CAF1 84172 111 - 1
UCUCUGGCCGG-AUUGUCUGCCCU-------GCACACCCGGCGAAUGAGCAAUUUCCCAGCAAUUCUUUGGCCGUUGCCAAUGUUUGCCCUCGCAAGCAUGCUGCGGAAAAUGUUCGCU
......(((((-...((.(((...-------))).)))))))....(((((.((((((((((.....(((((....)))))(((((((....)))))))))))).))))).)))))... ( -44.00)
>DroYak_CAF1 80985 98 - 1
UCUC--------------UGCCCC-------GCACACCCUGCGAAUGAGCAAUUUCCCAGCAAUUCUUUGGCCGUUGCCAAUGUUUGCCCUCGCAAGCACGCUGCGGAAAAUGUUCGCU
....--------------.((..(-------(((.....))))...(((((.(((((((((......(((((....)))))(((((((....))))))).)))).))))).))))))). ( -37.00)
>DroAna_CAF1 96520 119 - 1
UCUCGGAUCGGAAUUGUUUACCCUUCCACCCAUAGACUCCCGGAAUGAGCAUAUUUCCAGCAAUUCUUCGGCCCCUGCCAAUGUUUGCCCUCGGAAGUAUGCUGCGGAAAAUGUACGUU
....(((..((((....)).))..)))............(((.....(((((((((((.((((......(((....))).....))))....))))))))))).)))............ ( -27.80)
>consensus
UCUCUGGCCGG_AUUGUCUGCCCC_______GCACACCCGGCGAAUGAGCAAUUUCCCAGCAAUUCUUUGGCCAUUGCCAAUGUUUGCCCUCGCAAGCAUGCUGCGGAAAAUGUUCGCU
((.((((..............................)))).)).((((((.((((((((((.....(((((....)))))(((((((....)))))))))))).))))).)))))).. (-29.16 = -29.94 +   0.78)

alignment

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secondary structure

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dotplot

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Window 4

Location 26,354,734 – 26,354,824
Length 90
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 80.37
Mean single sequence MFE -36.08
Consensus MFE -21.99
Energy contribution -22.72
Covariance contribution 0.72
Combinations/Pair 1.14
Mean z-score -1.81
Structure conservation index 0.61
SVM decision value 0.31
SVM RNA-class probability 0.683305
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26354734 90 + 27905053
GGCAAUGGCCAAAGAAUUGCUGGGAAAUUGCUCAUUCGCCGGGUGUGC-------GGGG-------------CCAGAGAUUCUUCGCCAUUGCAGAUUUAUGCAUGCCAG---------
(((((((((..((((((..((((....((((.((((.....)))).))-------))..-------------))))..)))))).)))))((((......))))))))..--------- ( -35.20)
>DroSec_CAF1 76719 102 + 1
GGCAAUGGCCAAAGAAUUGCUGGGAAAUUGCUCAUUCGCCGGGUGUGC-------GGGGCAGACAAU-CCGGCCAGAGAUUCUUCGCCACUGCAGAUUUAUGCAUGCCAG---------
((((.((((..((((((..(((.(((........)))(((((((...(-------......)...))-))))))))..)))))).)))).((((......))))))))..--------- ( -37.40)
>DroSim_CAF1 81992 102 + 1
GGCAAUGGCCAAAGAAUUGCUGGGAAAUUGCUCAUUCGCCGGGUGUGC-------GGGGCAGACAAU-CCGGCCAGAGAUUCUUCGCCACUGCAGAUUUAUGCAUGCCAG---------
((((.((((..((((((..(((.(((........)))(((((((...(-------......)...))-))))))))..)))))).)))).((((......))))))))..--------- ( -37.40)
>DroEre_CAF1 84212 102 + 1
GGCAACGGCCAAAGAAUUGCUGGGAAAUUGCUCAUUCGCCGGGUGUGC-------AGGGCAGACAAU-CCGGCCAGAGAUUCUUCGCCACUGCAGAUUUAUGCAUGCCAG---------
((((..(((..((((((..(((.(((........)))(((((((.(((-------...))).))...-))))))))..)))))).)))..((((......))))))))..--------- ( -37.00)
>DroYak_CAF1 81025 98 + 1
GGCAACGGCCAAAGAAUUGCUGGGAAAUUGCUCAUUCGCAGGGUGUGC-------GGGGCA--------------GAGAUUCUUCGCCACUGCAGAUUUAUGCAUGCCAGCUACAGUAG
(((....)))........((((((((........)))(((((((.(((-------(((((.--------------.((...))..))).))))).)))).)))...)))))........ ( -32.00)
>DroAna_CAF1 96560 110 + 1
GGCAGGGGCCGAAGAAUUGCUGGAAAUAUGCUCAUUCCGGGAGUCUAUGGGUGGAAGGGUAAACAAUUCCGAUCCGAGAUUCUUGGCCAGUGCAGAUUUAUUCAUACCAG---------
.(((..((((((.......((((((.........))))))((((((.(((((((((..(....)..)))).)))))))))))))))))..))).................--------- ( -37.50)
>consensus
GGCAAUGGCCAAAGAAUUGCUGGGAAAUUGCUCAUUCGCCGGGUGUGC_______GGGGCAGACAAU_CCGGCCAGAGAUUCUUCGCCACUGCAGAUUUAUGCAUGCCAG_________
((((..(((..((((((..((((......((((.......)))).(((..........)))...........))))..)))))).)))..((((......))))))))........... (-21.99 = -22.72 +   0.72)

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 13:44:07 2006