Locus 1080

Sequence ID 2R_DroMel_CAF1
Location 4,372,806 – 4,373,062
Length 256
Max. P 0.932093
window1907 window1908 window1909

overview

Window 7

Location 4,372,806 – 4,372,906
Length 100
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 86.78
Mean single sequence MFE -42.32
Consensus MFE -28.74
Energy contribution -29.30
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -1.78
Structure conservation index 0.68
SVM decision value -0.01
SVM RNA-class probability 0.527845
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4372806 100 - 20766785
CGAACCGAGGGACUCGGG-----GACAAGGCGGCCAUCGGUAAUCCAAGGGUCCGAUGGCACG---------CAAUCCC-GUCUCCACCUUCGCCAUUUUGCUGAGCCGGCAGCA
.....((((((....(((-----(((...(((((((((((..(((....))))))))))).))---------)......-)))))).))))))......(((((......))))) ( -42.40)
>DroSec_CAF1 43472 96 - 1
----CCGAUGGACUCGGG-----GACAAGGCGGCCAUCGGUAAUCCAAGGGUCCGAUGGCACG---------CAAUCCC-GCCUCCACCUCCGCCAUUUUGCUGAACCGGCAGCA
----..(.((((..((((-----(.....(((((((((((..(((....))))))))))).))---------)..))))-)..)))).)..........(((((......))))) ( -39.30)
>DroSim_CAF1 43705 100 - 1
CGAACCGAGGGACUCGGG-----GACAAGGCGGCCAUCGGUAAUCCAAGGGUCCGAUGGCACG---------CAAUCCC-GCCUCCACCUCCGCCAUUUUGCUGAACCGGCAGCA
......((((((..((((-----(.....(((((((((((..(((....))))))))))).))---------)..))))-)..))..))))........(((((......))))) ( -39.60)
>DroEre_CAF1 39972 109 - 1
CGAGCCGAGGGACUCGGG-----GACAAGGCGGCCAUCGGUAAUCCAAGGGUCCGAUGGCACACCCCGGGCACAAUCCCGCCCUCCUGCUCCGCCAU-UUGCUGAACCGGCAGCA
.((((.(((((....(((-----(.(.....)((((((((..(((....)))))))))))...))))(((......))).)))))..))))......-.(((((......))))) ( -46.80)
>DroYak_CAF1 41880 104 - 1
UGAAGCGAGGGACUCGGGGCAGGGGUAAGGCGGCCAUCAGUAAUCCAAGGGUCCGAUGGCACG---------CAAUCCC-CCCUCCUCCUCCGCCAU-UUGCUGAACCGGCAGCA
....(((..(((...((((..((((....(((((((((.(..(((....)))).)))))).))---------)...)))-).)))))))..)))...-.(((((......))))) ( -43.50)
>consensus
CGAACCGAGGGACUCGGG_____GACAAGGCGGCCAUCGGUAAUCCAAGGGUCCGAUGGCACG_________CAAUCCC_GCCUCCACCUCCGCCAUUUUGCUGAACCGGCAGCA
....(((((...)))))...........((((((((((((..(((....)))))))))))....................(......)...))))....(((((......))))) (-28.74 = -29.30 +   0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,372,906 – 4,373,026
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.00
Mean single sequence MFE -31.30
Consensus MFE -25.70
Energy contribution -25.38
Covariance contribution -0.32
Combinations/Pair 1.14
Mean z-score -1.38
Structure conservation index 0.82
SVM decision value -0.03
SVM RNA-class probability 0.516618
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4372906 120 + 20766785
CAGACUGACUGCCGCCAGCGAAAUCAGUAAAUUUAUGAGAAAAGUCCUUGCCCAAGGAGAAACACACCCGGCGAACCAGAGAUCAAUUAAUUAGAACUCGUCGCCGGGACUCUCGGGAAA
...(((((.(..((....)).).)))))...(((.(((((....(((((....)))))........((((((((....(((.((.........)).))).))))))))..))))).))). ( -36.70)
>DroSec_CAF1 43568 102 + 1
------------------UGAAAUCAGUAAAGAUAUGAGAAAAGUCCUUGCCCAAGGAGAAACGCACCCGGCGAACCAGAGAGCAAUUAAUUAGAACUCGUCGCCGGGACUCUCGGGAAA
------------------....(((......))).(((((....(((((....)))))........((((((((....(((..(.........)..))).))))))))..)))))..... ( -29.40)
>DroSim_CAF1 43805 120 + 1
CAGACUGACUGCCGCCAGUGAAAUCAGUAAAGAUAUGAGAAAAGUCCUUGCCCAAGGAGAAACGCAACCGGCGAACCAGAGAGCAAUUAAUUAGAACUCGUCGCCGGUACUCUCGGGAAA
...((((((((....))).....))))).......(((((....(((((....)))))........((((((((....(((..(.........)..))).))))))))..)))))..... ( -31.30)
>DroEre_CAF1 40081 120 + 1
CAGACUGACUGCCGCCAGUGAAAUCAGUAAAAAUAUGAGAAAAGUCCUUGCCCAAGGAGAGACCCACCCGGCGAGCCAGAAAGCAAUCAAUUAGAACUCGUCGUCGGGACUCUCGGGAAA
..((((.((((....))))....(((.........)))....))))....(((...(((((.(((...(((((((.....................)))))))..))).))))))))... ( -29.80)
>DroYak_CAF1 41984 120 + 1
CAGACUGACUGCCGCCAGUGAAAUCUGUAAAAAUAUGAGAAUAGUCCUUGCCCAGGGAGAAACCCACCCGGCGAACCAGAAAGCAAUUAAUUAGAACUCGUCGUCGGGACUCUCGGGAAA
..(((((((((....))))....((((((....))).))).)))))....(((.(((.....))).((((((((....((...(.........)...)).))))))))......)))... ( -29.30)
>consensus
CAGACUGACUGCCGCCAGUGAAAUCAGUAAAAAUAUGAGAAAAGUCCUUGCCCAAGGAGAAACCCACCCGGCGAACCAGAGAGCAAUUAAUUAGAACUCGUCGCCGGGACUCUCGGGAAA
...................................(((((....(((((....)))))........((((((((....(((...............))).))))))))..)))))..... (-25.70 = -25.38 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,372,946 – 4,373,062
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.84
Mean single sequence MFE -35.38
Consensus MFE -30.78
Energy contribution -30.66
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -1.61
Structure conservation index 0.87
SVM decision value 1.22
SVM RNA-class probability 0.932093
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4372946 116 + 20766785
AAAGUCCUUGCCCAAGGAGAAACACACCCGGCGAACCAGAGAUCAAUUAAUUAGAACUCGUCGCCGGGACUCUCGGGAAAUCGCAGCAUGUCAGCGGCAACAUGUUGCACAUA----UAG
..........(((...((((......((((((((....(((.((.........)).))).))))))))..))))))).....(((((((((........))))))))).....----... ( -38.90)
>DroSec_CAF1 43590 116 + 1
AAAGUCCUUGCCCAAGGAGAAACGCACCCGGCGAACCAGAGAGCAAUUAAUUAGAACUCGUCGCCGGGACUCUCGGGAAAUCGUAGCAUGCCAGUGGCAACAUGUUGCACAUA----UAG
..........(((...((((......((((((((....(((..(.........)..))).))))))))..))))))).....((((((((((...))))...)))))).....----... ( -34.40)
>DroSim_CAF1 43845 116 + 1
AAAGUCCUUGCCCAAGGAGAAACGCAACCGGCGAACCAGAGAGCAAUUAAUUAGAACUCGUCGCCGGUACUCUCGGGAAAUCGCAGCAUGCCAGUGGCAACAUGUUGCACAUA----UAG
..........(((...((((......((((((((....(((..(.........)..))).))))))))..))))))).....((((((((((...))))...)))))).....----... ( -34.60)
>DroEre_CAF1 40121 116 + 1
AAAGUCCUUGCCCAAGGAGAGACCCACCCGGCGAGCCAGAAAGCAAUCAAUUAGAACUCGUCGUCGGGACUCUCGGGAAAUCGCAUCAUGCGAGUGGCAACAUGUUGCACAUA----UAU
..........(((...(((((.(((...(((((((.....................)))))))..))).))))))))...((((.....))))(((((((....)))).))).----... ( -35.10)
>DroYak_CAF1 42024 120 + 1
AUAGUCCUUGCCCAGGGAGAAACCCACCCGGCGAACCAGAAAGCAAUUAAUUAGAACUCGUCGUCGGGACUCUCGGGAAAUCGCAGCAUGCGAGUGGCAACAUGUUGCACAUAUGUAUAU
...((.....(((.(((.....))).((((((((....((...(.........)...)).))))))))......))).....))...(((((.(((((((....)))).))).))))).. ( -33.90)
>consensus
AAAGUCCUUGCCCAAGGAGAAACCCACCCGGCGAACCAGAGAGCAAUUAAUUAGAACUCGUCGCCGGGACUCUCGGGAAAUCGCAGCAUGCCAGUGGCAACAUGUUGCACAUA____UAG
..........(((...((((......((((((((....(((...............))).))))))))..))))))).....((((((((..........))))))))............ (-30.78 = -30.66 +  -0.12)

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 09:55:57 2006