Locus 1998

Sequence ID 2R_DroMel_CAF1
Location 7,525,442 – 7,525,558
Length 116
Max. P 1.000000
window3297 window3298 window3299 window3300

overview

Window 7

Location 7,525,442 – 7,525,538
Length 96
Sequences 3
Columns 96
Reading direction forward
Mean pairwise identity 67.36
Mean single sequence MFE -31.30
Consensus MFE -12.69
Energy contribution -14.47
Covariance contribution 1.78
Combinations/Pair 1.05
Mean z-score -3.42
Structure conservation index 0.41
SVM decision value 2.06
SVM RNA-class probability 0.986935
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7525442 96 + 20766785
UGGACUUAUGCAGCCCUUCUGCGCUUCCAUCUAUCCAGUUGUCCAACUGGAAAACUGGACACUGGCCAGUGGCUAGCGGCUAGUGGCCACUCCACU
((((....(((((.....)))))..))))....(((((((.(((....))).)))))))...((((((.((((.....)))).))))))....... ( -38.30)
>DroSec_CAF1 7311 84 + 1
UGGACUUACGCAGCCCUU------------CUAUCCAGUUGUGCAAGUGGAAAACUGGACACUGUCCAGUGGCCAGUGGCUAGUGGCCACUCCACU
(((((((.((((((....------------.......)))))).))))((...(((((((...)))))))..))((((((.....))))))))).. ( -31.80)
>DroYak_CAF1 7437 74 + 1
UGGACUUACGCAGCCCUUCCCUGCUUCCAUCUAUCCAGUUGUCCAA--------CUGGACACUGGCCAGUGGCCACU----CCACU----------
((((.....((((.......))))..(((.((..(((((.((((..--------..)))))))))..)))))....)----)))..---------- ( -23.80)
>consensus
UGGACUUACGCAGCCCUUC___GCUUCCAUCUAUCCAGUUGUCCAA_UGGAAAACUGGACACUGGCCAGUGGCCAGUGGCUAGUGGCCACUCCACU
.((.((.....)).)).................(((((((............)))))))((((((((...)))))))).................. (-12.69 = -14.47 +   1.78)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,525,442 – 7,525,538
Length 96
Sequences 3
Columns 96
Reading direction reverse
Mean pairwise identity 67.36
Mean single sequence MFE -34.57
Consensus MFE -22.21
Energy contribution -24.27
Covariance contribution 2.06
Combinations/Pair 1.04
Mean z-score -3.28
Structure conservation index 0.64
SVM decision value 7.23
SVM RNA-class probability 1.000000
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7525442 96 - 20766785
AGUGGAGUGGCCACUAGCCGCUAGCCACUGGCCAGUGUCCAGUUUUCCAGUUGGACAACUGGAUAGAUGGAAGCGCAGAAGGGCUGCAUAAGUCCA
(((((((((((.....))))))..)))))..(((.(((((((((.(((....))).)))))))))..)))..........(((((.....))))). ( -41.80)
>DroSec_CAF1 7311 84 - 1
AGUGGAGUGGCCACUAGCCACUGGCCACUGGACAGUGUCCAGUUUUCCACUUGCACAACUGGAUAG------------AAGGGCUGCGUAAGUCCA
.((..((((((((........))))))))..))..(((((((((...(....)...))))))))).------------..(((((.....))))). ( -32.20)
>DroYak_CAF1 7437 74 - 1
----------AGUGG----AGUGGCCACUGGCCAGUGUCCAG--------UUGGACAACUGGAUAGAUGGAAGCAGGGAAGGGCUGCGUAAGUCCA
----------.....----.((..((((((.(((((((((..--------..)))).))))).))).)))..))......(((((.....))))). ( -29.70)
>consensus
AGUGGAGUGGCCACUAGCCACUGGCCACUGGCCAGUGUCCAGUUUUCCA_UUGGACAACUGGAUAGAUGGAAGC___GAAGGGCUGCGUAAGUCCA
.....((((((.....)))))).....(((.(((((((((((........)))))).))))).)))..............(((((.....))))). (-22.21 = -24.27 +   2.06)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,525,467 – 7,525,558
Length 91
Sequences 3
Columns 91
Reading direction forward
Mean pairwise identity 82.84
Mean single sequence MFE -29.17
Consensus MFE -25.14
Energy contribution -25.81
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.69
Structure conservation index 0.86
SVM decision value 2.54
SVM RNA-class probability 0.995086
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7525467 91 + 20766785
UCCAUCUAUCCAGUUGUCCAACUGGAAAACUGGACACUGGCCAGUGGCUAGCGGCUAGUGGCCACUCCACUCCAUUUCACUUCAAUUGGCU
.(((....(((((((.(((....))).)))))))...((((((.((((.....)))).))))))......................))).. ( -32.50)
>DroSec_CAF1 7329 86 + 1
-----CUAUCCAGUUGUGCAAGUGGAAAACUGGACACUGUCCAGUGGCCAGUGGCUAGUGGCCACUCCACUCCAUUUCACUUCAAUUGGCU
-----....(((((((((.(((((((..(((((((...)))))))((..((((((.....))))))))..))))))))))...)))))).. ( -34.60)
>DroSim_CAF1 7290 72 + 1
-----CUAUCCAGUUGUGCAACUGGAAAACUGGACACUGGCCA--------------GUGGCCACUCCACUCCAUUUCACUUCAAUUGGCU
-----....(((((((((.((.((((....((((...(((((.--------------..))))).)))).)))).)))))...)))))).. ( -20.40)
>consensus
_____CUAUCCAGUUGUGCAACUGGAAAACUGGACACUGGCCAGUGGC_AG_GGCUAGUGGCCACUCCACUCCAUUUCACUUCAAUUGGCU
.........(((((((......((((....((((...((((((.((((.....)))).)))))).)))).))))........))))))).. (-25.14 = -25.81 +   0.67)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,525,467 – 7,525,558
Length 91
Sequences 3
Columns 91
Reading direction reverse
Mean pairwise identity 82.84
Mean single sequence MFE -29.03
Consensus MFE -19.50
Energy contribution -20.33
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -2.35
Structure conservation index 0.67
SVM decision value 0.81
SVM RNA-class probability 0.855616
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7525467 91 - 20766785
AGCCAAUUGAAGUGAAAUGGAGUGGAGUGGCCACUAGCCGCUAGCCACUGGCCAGUGUCCAGUUUUCCAGUUGGACAACUGGAUAGAUGGA
..(((.((......)).)))(((((((((((.....))))))..)))))..(((.(((((((((.(((....))).)))))))))..))). ( -36.30)
>DroSec_CAF1 7329 86 - 1
AGCCAAUUGAAGUGAAAUGGAGUGGAGUGGCCACUAGCCACUGGCCACUGGACAGUGUCCAGUUUUCCACUUGCACAACUGGAUAG-----
..(((...(..(((.....((((((((.(((((........)))))(((((((...))))))).)))))))).)))..))))....----- ( -29.80)
>DroSim_CAF1 7290 72 - 1
AGCCAAUUGAAGUGAAAUGGAGUGGAGUGGCCAC--------------UGGCCAGUGUCCAGUUUUCCAGUUGCACAACUGGAUAG-----
..................(((.((((.(((((..--------------.)))))...)))).)))(((((((....)))))))...----- ( -21.00)
>consensus
AGCCAAUUGAAGUGAAAUGGAGUGGAGUGGCCACUAGCC_CU_GCCACUGGCCAGUGUCCAGUUUUCCAGUUGCACAACUGGAUAG_____
..................(((.((((.((((((...((.....))...))))))...)))).)))(((((((....)))))))........ (-19.50 = -20.33 +   0.83)

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 10:18:22 2006