Locus 1833

Sequence ID X_DroMel_CAF1
Location 5,069,102 – 5,069,232
Length 130
Max. P 0.938072
window2984 window2985 window2986

overview

Window 4

Location 5,069,102 – 5,069,192
Length 90
Sequences 6
Columns 91
Reading direction reverse
Mean pairwise identity 81.23
Mean single sequence MFE -22.82
Consensus MFE -15.44
Energy contribution -15.83
Covariance contribution 0.39
Combinations/Pair 1.08
Mean z-score -1.81
Structure conservation index 0.68
SVM decision value 0.46
SVM RNA-class probability 0.744743
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5069102 90 - 22224390
CAUAGGGCCAUUUGGCCAGUGGCGGCAGUACCAUGGCCUGUACGAAUGUAAAACGGAAACGGAAAUGAGACCGAAAAGCGAUUAAA-AGCA
....((.(((((((((((.(((........))))))))...............((....)).))))).).)).....((.......-.)). ( -22.70)
>DroSec_CAF1 26822 87 - 1
CAUAGGGCCAUUUGGCCAGCGGCGGCAGGACCAUGGCCUGUACGAGCG---AACGAAAACGGAAAUGAGACCGAAAAACGAUUACA-AGCA
.....((((....)))).((.((.(((((.(....))))))....)).---........(((........))).............-.)). ( -23.50)
>DroSim_CAF1 26985 87 - 1
CAUAGGGCCAUUUGGCCAGCGGCGGCAGGACCAUGGCCUGUACGAGCG---AACGAAAACGGAAAUGAGACCGAAAAACGAUUACA-AGCA
.....((((....)))).((.((.(((((.(....))))))....)).---........(((........))).............-.)). ( -23.50)
>DroEre_CAF1 32846 83 - 1
CAUAUGGCCAUUUGGCCAGUGGCGGCAGGACCAUGGCCUGUACG-------AACGAAAACGGAAAUGAUACCGGAAAACGAUUACA-ACCA
....(((((....)))))(((((((((((.(....))))))...-------........(((........))).....)).)))).-.... ( -23.30)
>DroWil_CAF1 7982 82 - 1
CAUAAGGCCAUUUUGCCAACGGUGGCAGGACCAUGGCCUAGAAAAAAA---AACAAUAGAGCAAAA---GCC--AAAGCAAUUAUA-CACA
....((((((((((((((....))))))))...)))))).........---.......(.((....---)))--............-.... ( -19.20)
>DroYak_CAF1 34651 84 - 1
CAUAGGGCCAUUUGGCCAGUGGCGGCAGGACCAUGGCCUGCACG-------AACGAAAACGGAAAUGAAGCCGAAAAACGAUUACAAACUA
..(((((((....)))).(((((((((((.(....))))))...-------........(((........))).....)).))))...))) ( -24.70)
>consensus
CAUAGGGCCAUUUGGCCAGCGGCGGCAGGACCAUGGCCUGUACGA__G___AACGAAAACGGAAAUGAGACCGAAAAACGAUUACA_AGCA
....(((((((...(((......)))......)))))))....................(((........))).................. (-15.44 = -15.83 +   0.39)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,069,130 – 5,069,232
Length 102
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 74.97
Mean single sequence MFE -27.40
Consensus MFE -20.77
Energy contribution -20.63
Covariance contribution -0.14
Combinations/Pair 1.11
Mean z-score -1.40
Structure conservation index 0.76
SVM decision value 1.29
SVM RNA-class probability 0.938072
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5069130 102 + 22224390
CCGUUUCCGUUUUACAUUCGUACAGGCCAUGGUACUGCCGCCACUGGCCAAAUGGCCCUAUGAGAACGGAUUCACCUUUACCACCUGGUUCCGCCUGGAUCC
..(..((((((((.(((..(..(((((((((((......)))).)))))...))..)..)))))))))))..)..........((.((.....)).)).... ( -31.30)
>DroGri_CAF1 9216 90 + 1
CCGCAU---U---------CCACAGGCAAUGGUUUUGCCACCGUUGGCCAAAUGGCCCUACGAAAAUGGAUUUACCUUUACCACCUGGUUUCGAUUGGAUCC
......---.---------.....(((((.....)))))..(((.((((....))))..))).....(((((((.....(((....)))......))))))) ( -24.70)
>DroWil_CAF1 8005 99 + 1
GCUCUAUUGUU---UUUUUUUCUAGGCCAUGGUCCUGCCACCGUUGGCAAAAUGGCCUUAUGAGAAUGGAUUUACCUUUACCACAUGGUUUCGAUUGGAUCC
...........---...(((((.(((((((.....(((((....)))))..)))))))...))))).(((((((.....(((....)))......))))))) ( -27.80)
>DroMoj_CAF1 28286 84 + 1
---------U---------CCACAGGCAAUGGUGCUGCCGCCGCUGGCCAAGUGGCCAUACGAGAAUGGAUUCACCUUCACCACCUGGUUUCGAUUGGAUCC
---------(---------(((..((((.......))))((((((.....))))))....((((((.((.....)))))(((....))).)))..))))... ( -24.20)
>DroAna_CAF1 5477 85 + 1
-----------------UGUUGCAGGCCAUGGUCCUGCCUCCCCUGGCAAAGUGGCCUUACGAGAACGGAUUCACCUUCACCACCUGGUUUCGGCUGGAUCC
-----------------.((...(((((((.....((((......))))..))))))).))......(((((((((...(((....)))...)).))))))) ( -30.20)
>DroPer_CAF1 29828 93 + 1
CCGUAUUUAUU---------UGCAGGCCAUGGUCCUGCCGCCGCUGGCCAAAUGGCCGUAUGAGAAUGGAUUUACCUUUACCACAUGGUUUCGCCUGGAUCC
.(((((.....---------.((((((....).))))).......((((....))))))))).....(((((((.....(((....)))......))))))) ( -26.20)
>consensus
CCG__U___U_________CUACAGGCCAUGGUCCUGCCGCCGCUGGCCAAAUGGCCCUACGAGAAUGGAUUCACCUUUACCACCUGGUUUCGACUGGAUCC
........................((((((......(((......)))...))))))..........(((((((.....(((....)))......))))))) (-20.77 = -20.63 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,069,130 – 5,069,232
Length 102
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 74.97
Mean single sequence MFE -28.87
Consensus MFE -18.91
Energy contribution -19.80
Covariance contribution 0.89
Combinations/Pair 1.15
Mean z-score -1.27
Structure conservation index 0.66
SVM decision value 0.42
SVM RNA-class probability 0.730259
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5069130 102 - 22224390
GGAUCCAGGCGGAACCAGGUGGUAAAGGUGAAUCCGUUCUCAUAGGGCCAUUUGGCCAGUGGCGGCAGUACCAUGGCCUGUACGAAUGUAAAACGGAAACGG
.....(((((...(((....)))...((((...((((...(((..((((....)))).)))))))...))))...))))).............((....)). ( -33.70)
>DroGri_CAF1 9216 90 - 1
GGAUCCAAUCGAAACCAGGUGGUAAAGGUAAAUCCAUUUUCGUAGGGCCAUUUGGCCAACGGUGGCAAAACCAUUGCCUGUGG---------A---AUGCGG
.........((...(((.(.(((((.(((....((((...(((..((((....)))).)))))))....))).)))))).)))---------.---...)). ( -26.90)
>DroWil_CAF1 8005 99 - 1
GGAUCCAAUCGAAACCAUGUGGUAAAGGUAAAUCCAUUCUCAUAAGGCCAUUUUGCCAACGGUGGCAGGACCAUGGCCUAGAAAAAAA---AACAAUAGAGC
((((...(((...(((....)))...)))..)))).((((....((((((((((((((....))))))))...)))))))))).....---........... ( -27.20)
>DroMoj_CAF1 28286 84 - 1
GGAUCCAAUCGAAACCAGGUGGUGAAGGUGAAUCCAUUCUCGUAUGGCCACUUGGCCAGCGGCGGCAGCACCAUUGCCUGUGG---------A---------
..............(((.(.((..(.((((...((....((((.(((((....))))))))).))...)))).)..))).)))---------.--------- ( -29.30)
>DroAna_CAF1 5477 85 - 1
GGAUCCAGCCGAAACCAGGUGGUGAAGGUGAAUCCGUUCUCGUAAGGCCACUUUGCCAGGGGAGGCAGGACCAUGGCCUGCAACA-----------------
((((...(((...(((....)))...)))..))))((((((.(..(((......)))..).)))(((((.(....))))))))).----------------- ( -30.80)
>DroPer_CAF1 29828 93 - 1
GGAUCCAGGCGAAACCAUGUGGUAAAGGUAAAUCCAUUCUCAUACGGCCAUUUGGCCAGCGGCGGCAGGACCAUGGCCUGCA---------AAUAAAUACGG
....((.(.((......((((..((.((.....)).))..)))).((((....))))..)).).(((((.(....)))))).---------.........)) ( -25.30)
>consensus
GGAUCCAAUCGAAACCAGGUGGUAAAGGUAAAUCCAUUCUCAUAAGGCCAUUUGGCCAGCGGCGGCAGGACCAUGGCCUGUAA_________A___A__CGG
((((...(((...(((....)))...)))..)))).........(((((((...(((......)))......)))))))....................... (-18.91 = -19.80 +   0.89)

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 10:19:52 2006