Locus 4705

Sequence ID X_DroMel_CAF1
Location 12,243,999 – 12,244,121
Length 122
Max. P 0.994369
window7717 window7718 window7719 window7720

overview

Window 7

Location 12,243,999 – 12,244,092
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 74.89
Mean single sequence MFE -34.47
Consensus MFE -15.87
Energy contribution -16.40
Covariance contribution 0.53
Combinations/Pair 1.07
Mean z-score -2.60
Structure conservation index 0.46
SVM decision value 1.98
SVM RNA-class probability 0.984468
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12243999 93 + 22224390
--------AAAUGCUGACUGUGUCAGAUAGGCCAACGCGGUCCUUU-GGCCGCUCAUGUCUAUGAAUAUUCAUGAGAUGCCAAAAAAUGAAC------------------GUUGGAAAAA
--------.....(((((...))))).....((((((..((..(((-(((..((((((..((....))..))))))..))))))..))...)------------------)))))..... ( -27.40)
>DroPse_CAF1 43338 109 + 1
--------CGGGUCUGACUCGCUCAGAUAGCC--ACGCGGUCCUUU-GGCCGCUCAUGUCUAUGAAUAUUCAUGAGCUGCCAAAAAAUGAACCCCGCCAGAGGCGUCGGCGUCGGUAAAA
--------...((((((.....)))))).(((--(((((((.((((-(((.(((((((..((....))..))))))).))))))....).))).((((...))))...)))).))).... ( -39.60)
>DroGri_CAF1 13076 115 + 1
GGCUGAGGGGCUGCUGACGUCGCCAGAUAGCU--AGCCGGGCCUUUAGUGCGUUCAUGUCCAUGAAUAUUCAUGAGCUGCCAAAAAAUGAACCGUGCAUAAGGCGAC---GGUACCAAAA
(((((...(((.((....)).)))...)))))--.((((.(((((..(..((((((((..(((((....)))))..).........))))).))..)..)))))..)---)))....... ( -37.80)
>DroEre_CAF1 8932 93 + 1
--------AAAUGCUGACUGUGUCAGAUAGUCAAACGCGGUCCUUU-GGCCGCUCAUGUCUAUGAAUAUUCAUGAGCUGCCAAAAAAUGAAC------------------GUUGGAAAAA
--------.((((..((((((((..(.....)..)))))))).(((-(((.(((((((..((....))..))))))).)))))).......)------------------)))....... ( -29.40)
>DroYak_CAF1 1301 93 + 1
--------AAAUGCUGACUGUGUCAGAUAGUCCAACGCGGUCCUUU-GGCCGCUCAUGUCUAUGAAUAUUCAUGAGCUGCCAAAAAAUGAAC------------------GUUGGAAAAA
--------.....(((((...)))))....(((((((..((..(((-(((.(((((((..((....))..))))))).))))))..))...)------------------)))))).... ( -33.00)
>DroPer_CAF1 40478 109 + 1
--------CAGGUCUGACUCGCUCAGAUAGCC--ACGCGGUCCUUU-GGCCGCUCAUGUCUAUGAAUAUUCAUGAGCUGCCAAAAAAUGAACCCCGCCAGAGGCGUCGGCGUCGGUAAAA
--------...((((((.....)))))).(((--(((((((.((((-(((.(((((((..((....))..))))))).))))))....).))).((((...))))...)))).))).... ( -39.60)
>consensus
________AAAUGCUGACUGUGUCAGAUAGCC__ACGCGGUCCUUU_GGCCGCUCAUGUCUAUGAAUAUUCAUGAGCUGCCAAAAAAUGAAC__________________GUUGGAAAAA
.............((((.....)))).....................(((.(((((((............))))))).)))....................................... (-15.87 = -16.40 +   0.53)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,243,999 – 12,244,092
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.89
Mean single sequence MFE -34.65
Consensus MFE -16.54
Energy contribution -17.10
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -2.84
Structure conservation index 0.48
SVM decision value 2.47
SVM RNA-class probability 0.994369
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12243999 93 - 22224390
UUUUUCCAAC------------------GUUCAUUUUUUGGCAUCUCAUGAAUAUUCAUAGACAUGAGCGGCC-AAAGGACCGCGUUGGCCUAUCUGACACAGUCAGCAUUU--------
.....(((((------------------((...(((((((((..((((((..((....))..))))))..)))-))))))..))))))).....(((((...))))).....-------- ( -30.50)
>DroPse_CAF1 43338 109 - 1
UUUUACCGACGCCGACGCCUCUGGCGGGGUUCAUUUUUUGGCAGCUCAUGAAUAUUCAUAGACAUGAGCGGCC-AAAGGACCGCGU--GGCUAUCUGAGCGAGUCAGACCCG--------
.........(((((.......)))))(((((....(((((((.(((((((..((....))..))))))).)))-))))((((((..--((....))..))).))).))))).-------- ( -40.90)
>DroGri_CAF1 13076 115 - 1
UUUUGGUACC---GUCGCCUUAUGCACGGUUCAUUUUUUGGCAGCUCAUGAAUAUUCAUGGACAUGAACGCACUAAAGGCCCGGCU--AGCUAUCUGGCGACGUCAGCAGCCCCUCAGCC
..(((.(..(---((((((((.(((...((((((.........(..(((((....)))))..))))))))))...)))))...(((--((....)))))))))..).))).......... ( -28.90)
>DroEre_CAF1 8932 93 - 1
UUUUUCCAAC------------------GUUCAUUUUUUGGCAGCUCAUGAAUAUUCAUAGACAUGAGCGGCC-AAAGGACCGCGUUUGACUAUCUGACACAGUCAGCAUUU--------
....((.(((------------------((...(((((((((.(((((((..((....))..))))))).)))-))))))..))))).))....(((((...))))).....-------- ( -30.30)
>DroYak_CAF1 1301 93 - 1
UUUUUCCAAC------------------GUUCAUUUUUUGGCAGCUCAUGAAUAUUCAUAGACAUGAGCGGCC-AAAGGACCGCGUUGGACUAUCUGACACAGUCAGCAUUU--------
....((((((------------------((...(((((((((.(((((((..((....))..))))))).)))-))))))..))))))))....(((((...))))).....-------- ( -36.80)
>DroPer_CAF1 40478 109 - 1
UUUUACCGACGCCGACGCCUCUGGCGGGGUUCAUUUUUUGGCAGCUCAUGAAUAUUCAUAGACAUGAGCGGCC-AAAGGACCGCGU--GGCUAUCUGAGCGAGUCAGACCUG--------
.....((.((((...((((...)))).(((((....((((((.(((((((..((....))..))))))).)))-))))))))))))--))...(((((.....)))))....-------- ( -40.50)
>consensus
UUUUUCCAAC__________________GUUCAUUUUUUGGCAGCUCAUGAAUAUUCAUAGACAUGAGCGGCC_AAAGGACCGCGU__GGCUAUCUGACACAGUCAGCAUUU________
............................((((.(((...(((.(((((((..((....))..))))))).))).))))))).............((((.....))))............. (-16.54 = -17.10 +   0.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,244,031 – 12,244,121
Length 90
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 79.51
Mean single sequence MFE -33.95
Consensus MFE -27.00
Energy contribution -26.64
Covariance contribution -0.36
Combinations/Pair 1.13
Mean z-score -2.87
Structure conservation index 0.80
SVM decision value 1.63
SVM RNA-class probability 0.968584
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12244031 90 + 22224390
UCCUUUGGCCGCUCAUGUCUAUGAAUAUUCAUGAGAUGCCAAAAAAUGAAC------------------GUUGGAAAAACAUCCACGGCCCAAUGGA-------AACGUGGGUGG
...((((((..((((((..((....))..))))))..)))))).......(------------------((.(((......))))))(((((.((..-------..))))))).. ( -30.90)
>DroPse_CAF1 43368 108 + 1
UCCUUUGGCCGCUCAUGUCUAUGAAUAUUCAUGAGCUGCCAAAAAAUGAACCCCGCCAGAGGCGUCGGCGUCGGUAAAACAUCAGAGAAGGAGAGAA-------GACUCGGGUGG
...((((((.(((((((..((....))..))))))).))))))......((((.(((.((.((....)).))))).................(((..-------..))))))).. ( -34.40)
>DroSim_CAF1 1190 90 + 1
UCCUUUGGCCGCUCAUGUCUAUGAAUAUUCAUGAGAUGCCAAAAAAUGAAC------------------GUUGGAAAAACAUCCACGGCCCAAUGGA-------AGCGUGGGUGG
(((((((((..((((((..((....))..))))))..)))))).(((....------------------))))))....((((((((.((....)).-------..)))))))). ( -29.70)
>DroEre_CAF1 8964 90 + 1
UCCUUUGGCCGCUCAUGUCUAUGAAUAUUCAUGAGCUGCCAAAAAAUGAAC------------------GUUGGAAAAACAUCCACGGCCCAAUGGA-------AACGUGGGUGG
...((((((.(((((((..((....))..))))))).)))))).......(------------------((.(((......))))))(((((.((..-------..))))))).. ( -34.90)
>DroYak_CAF1 1333 97 + 1
UCCUUUGGCCGCUCAUGUCUAUGAAUAUUCAUGAGCUGCCAAAAAAUGAAC------------------GUUGGAAAAACAUCCACGGCCCAAUGGACGUGGGGAACGUGGGUGG
(((((((((.(((((((..((....))..))))))).)))))).(((....------------------))))))....((((((((.((((.......))))...)))))))). ( -38.30)
>DroPer_CAF1 40508 108 + 1
UCCUUUGGCCGCUCAUGUCUAUGAAUAUUCAUGAGCUGCCAAAAAAUGAACCCCGCCAGAGGCGUCGGCGUCGGUAAAACGUCAGAGAAGGAGAGAA-------GACUCGGGUGG
...((((((.(((((((..((....))..))))))).))))))......((((((((...))))..(((((.......))))).........(((..-------..))))))).. ( -35.50)
>consensus
UCCUUUGGCCGCUCAUGUCUAUGAAUAUUCAUGAGCUGCCAAAAAAUGAAC__________________GUUGGAAAAACAUCCACGGCCCAAUGGA_______AACGUGGGUGG
...((((((.(((((((..((....))..))))))).))))))....................................((((((((...................)))))))). (-27.00 = -26.64 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,244,031 – 12,244,121
Length 90
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 79.51
Mean single sequence MFE -31.30
Consensus MFE -23.05
Energy contribution -22.83
Covariance contribution -0.22
Combinations/Pair 1.09
Mean z-score -2.64
Structure conservation index 0.74
SVM decision value 1.55
SVM RNA-class probability 0.963291
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12244031 90 - 22224390
CCACCCACGUU-------UCCAUUGGGCCGUGGAUGUUUUUCCAAC------------------GUUCAUUUUUUGGCAUCUCAUGAAUAUUCAUAGACAUGAGCGGCCAAAGGA
...((((....-------.....))))(((((((((((.....)))------------------))))))..((((((..((((((..((....))..))))))..)))))))). ( -26.70)
>DroPse_CAF1 43368 108 - 1
CCACCCGAGUC-------UUCUCUCCUUCUCUGAUGUUUUACCGACGCCGACGCCUCUGGCGGGGUUCAUUUUUUGGCAGCUCAUGAAUAUUCAUAGACAUGAGCGGCCAAAGGA
(((((((((..-------..)))......................(((((.......)))))))))......((((((.(((((((..((....))..))))))).)))))))). ( -35.30)
>DroSim_CAF1 1190 90 - 1
CCACCCACGCU-------UCCAUUGGGCCGUGGAUGUUUUUCCAAC------------------GUUCAUUUUUUGGCAUCUCAUGAAUAUUCAUAGACAUGAGCGGCCAAAGGA
...((((....-------.....))))(((((((((((.....)))------------------))))))..((((((..((((((..((....))..))))))..)))))))). ( -26.70)
>DroEre_CAF1 8964 90 - 1
CCACCCACGUU-------UCCAUUGGGCCGUGGAUGUUUUUCCAAC------------------GUUCAUUUUUUGGCAGCUCAUGAAUAUUCAUAGACAUGAGCGGCCAAAGGA
...((((....-------.....))))(((((((((((.....)))------------------))))))..((((((.(((((((..((....))..))))))).)))))))). ( -30.90)
>DroYak_CAF1 1333 97 - 1
CCACCCACGUUCCCCACGUCCAUUGGGCCGUGGAUGUUUUUCCAAC------------------GUUCAUUUUUUGGCAGCUCAUGAAUAUUCAUAGACAUGAGCGGCCAAAGGA
.((.(((((...((((.......)))).))))).))..........------------------.....(((((((((.(((((((..((....))..))))))).))))))))) ( -32.90)
>DroPer_CAF1 40508 108 - 1
CCACCCGAGUC-------UUCUCUCCUUCUCUGACGUUUUACCGACGCCGACGCCUCUGGCGGGGUUCAUUUUUUGGCAGCUCAUGAAUAUUCAUAGACAUGAGCGGCCAAAGGA
(((((((((..-------..)))......................(((((.......)))))))))......((((((.(((((((..((....))..))))))).)))))))). ( -35.30)
>consensus
CCACCCACGUU_______UCCAUUGGGCCGUGGAUGUUUUUCCAAC__________________GUUCAUUUUUUGGCAGCUCAUGAAUAUUCAUAGACAUGAGCGGCCAAAGGA
((..(((((...................))))).......................................((((((.(((((((..((....))..))))))).)))))))). (-23.05 = -22.83 +  -0.22)

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 11:31:26 2006