Locus 7141

Sequence ID X_DroMel_CAF1
Location 17,926,833 – 17,926,959
Length 126
Max. P 0.997107
window11662 window11663

overview

Window 2

Location 17,926,833 – 17,926,932
Length 99
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 69.85
Mean single sequence MFE -18.39
Consensus MFE -11.90
Energy contribution -12.06
Covariance contribution 0.16
Combinations/Pair 1.27
Mean z-score -2.20
Structure conservation index 0.65
SVM decision value 2.58
SVM RNA-class probability 0.995484
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17926833 99 - 22224390
CACAAAUAG-UAAGUCAGUAAUAAAAUUGACUUACAAAAAAUUAAUCCACCUGUUGCAACGACCUGUGCAGC-CAAUACACCCCAGCUAUCCCUUAUA-----------UAU
........(-(((((((((......)))))))))).................((((((........))))))-.........................-----------... ( -18.40)
>DroSec_CAF1 3548 99 - 1
CACAAAUAG-UAAGUCAGUAAUAACAUUGACUUACGAAAAAUAAAUCCACCUGUUGCAUCGACCUUUGCAGC-AAAUACACCCCAGCUACCCCUUAUA-----------UAU
........(-(((((((((......))))))))))................(((((((........))))))-)........................-----------... ( -20.70)
>DroSim_CAF1 2641 99 - 1
CAUAAAUAG-UAAGUCAGUAAUAACAUUGACUUACGAAAAAUGAAUCCACCUGUUGCAUCGACCUUUGCAGC-CAAUACACCCCAGCUACCCCCUAUA-----------UAU
(((.....(-(((((((((......)))))))))).....))).........((((((........))))))-.........................-----------... ( -19.30)
>DroEre_CAF1 3559 112 - 1
GACAACAAUUUUGGUCAGUAGUAAUACUGGCUUAUCGAACAUGAACCAACCUGUUGCAAUCAGCUUUCCAACCCAAUACACCCCAGUUACCCCAUAAAAGGCCGGCAUGAGG
............((((((((....)))))))).................(((..(((.....(((((..........((......))..........)))))..)))..))) ( -18.75)
>DroYak_CAF1 3398 97 - 1
UACAAAUAU-UAAGUCUGUAAUAAUAUUGACUU--------------CACCUGUUGCAAUGGACACUGCAGCCCAAUACACUCCAGUUACCCACUGACCGGCUGGCAAGAAA
.........-.(((((.(((....))).)))))--------------.....((((((........))))))..........((((((...........))))))....... ( -14.80)
>consensus
CACAAAUAG_UAAGUCAGUAAUAACAUUGACUUACGAAAAAUGAAUCCACCUGUUGCAACGACCUUUGCAGC_CAAUACACCCCAGCUACCCCCUAUA___________UAU
..........(((((((((......)))))))))..................((((((........))))))........................................ (-11.90 = -12.06 +   0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,926,858 – 17,926,959
Length 101
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 68.75
Mean single sequence MFE -21.18
Consensus MFE -11.90
Energy contribution -12.06
Covariance contribution 0.16
Combinations/Pair 1.27
Mean z-score -2.42
Structure conservation index 0.56
SVM decision value 2.80
SVM RNA-class probability 0.997107
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17926858 101 - 22224390
AA-UAC------------AUGGUUGCUUAAGAAUUAAUUGCACAAAUAG-UAAGUCAGUAAUAAAAUUGACUUACAAAAAAUUAAUCCACCUGUUGCAACGACCUGUGCAGC-CAA
..-...------------.(((((((...((......(((((......(-(((((((((......))))))))))............(....).)))))....))..)))))-)). ( -24.70)
>DroSec_CAF1 3573 100 - 1
AC-UA-------------AGAAUUGCUUAAGAAUUAAUGGCACAAAUAG-UAAGUCAGUAAUAACAUUGACUUACGAAAAAUAAAUCCACCUGUUGCAUCGACCUUUGCAGC-AAA
..-..-------------.....((((...........))))......(-(((((((((......))))))))))................(((((((........))))))-).. ( -22.70)
>DroSim_CAF1 2666 100 - 1
AC-UA-------------AGAAUAAGUUAAGAAUGAAUUGCAUAAAUAG-UAAGUCAGUAAUAACAUUGACUUACGAAAAAUGAAUCCACCUGUUGCAUCGACCUUUGCAGC-CAA
..-..-------------...............((.(((.(((.....(-(((((((((......)))))))))).....)))))).))...((((((........))))))-... ( -20.10)
>DroEre_CAF1 3595 116 - 1
AUGUAUUUGGUAUUUGAUAUUGAUACUUUAGAAGCAAUUUGACAACAAUUUUGGUCAGUAGUAAUACUGGCUUAUCGAACAUGAACCAACCUGUUGCAAUCAGCUUUCCAACCCAA
........((((((.......))))))...(((((...(((.(((((.....((((((((....))))))))..((......)).......))))))))...)))))......... ( -23.30)
>DroYak_CAF1 3434 88 - 1
AA-UAC------------AUGUUUGCUUUAGAAUUAAUUCUACAAAUAU-UAAGUCUGUAAUAAUAUUGACUU--------------CACCUGUUGCAAUGGACACUGCAGCCCAA
..-...------------(((((((...(((((....))))))))))))-.(((((.(((....))).)))))--------------.....((((((........)))))).... ( -15.10)
>consensus
AA_UA_____________AUAAUUGCUUAAGAAUUAAUUGCACAAAUAG_UAAGUCAGUAAUAACAUUGACUUACGAAAAAUGAAUCCACCUGUUGCAACGACCUUUGCAGC_CAA
..................................................(((((((((......)))))))))..................((((((........)))))).... (-11.90 = -12.06 +   0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:08 2006