Locus 4086

Sequence ID 2R_DroMel_CAF1
Location 13,462,305 – 13,462,410
Length 105
Max. P 0.890441
window6578 window6579

overview

Window 8

Location 13,462,305 – 13,462,410
Length 105
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 86.50
Mean single sequence MFE -33.32
Consensus MFE -26.84
Energy contribution -27.03
Covariance contribution 0.20
Combinations/Pair 1.03
Mean z-score -2.84
Structure conservation index 0.81
SVM decision value 0.96
SVM RNA-class probability 0.890441
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13462305 105 + 20766785
GGCAAUGUCAAUGUGCUGGA--------AGCAAGUUUGUUCACUUGCAAGUA-AUUGAAAGUCAUUCUUUAUGCAAUAAUAAAUGGCUUUCUC-GCACACUUGGACAAC-AGUUUG----
.....((((..(((((....--------.((((((......)))))).....-...((((((((((..((((...))))..))))))))))..-)))))....))))..-......---- ( -30.20)
>DroPse_CAF1 5983 117 + 1
GGCAGUGUCAAUGUGCUGGAAGGAAAGAAGCAAGUUUGCUCACUUGCAAGUA-AUUGAAAGUCAUUCUUUAUGCAAUAAUAAAUGGCUUUCUC-GCCCACUUGGCCAGC-AGCCCCCCCU
(((.((....)).((((((.(((......((((((......)))))).....-...((((((((((..((((...))))..))))))))))..-.....)))..)))))-))))...... ( -33.30)
>DroSim_CAF1 11253 110 + 1
GGCAAUGUCAAUGUGCUGGA--------AGCAAGUUUGUUCACUUGCAAGUAAAUUGAAAGUCAUUCUUUAUGCAAUAAUAAAUGGCUUUCUC-GCACACUUGGACAAG-AGUUGGGCCA
(((..((((..(((((....--------.((((((......)))))).........((((((((((..((((...))))..))))))))))..-)))))....))))..-......))). ( -32.90)
>DroYak_CAF1 11946 110 + 1
GGCAAUGUCAAUGUGCUGGA--------AGCAAGUUUGUUCACUUGCAAGUA-AUUGAAAGUCAUUCUUUAUGUAAUAAUAAAUGGCUUUCUU-GCACACUUGGACAACCAUUUUUGCCA
(((((((((..(((((....--------.((((((......)))))).....-...((((((((((..((((...))))..))))))))))..-)))))....)))).......))))). ( -35.11)
>DroAna_CAF1 6369 105 + 1
GGCAAUGUCAAUGUGCUGGA--------AGCAAGUUUGUUCACUUGCAAGUA-AUUGAAAGUCAUUCUUUAUGCAAUAAUAAAUGACUUUCUCGGCACACUUGGCCAAG-AGUAG-----
......(((((((((((((.--------.((((((......)))))).....-...((((((((((..((((...))))..)))))))))))))))))).)))))....-.....----- ( -35.10)
>DroPer_CAF1 13622 117 + 1
GGCAGUGUCAAUGUGCUGGAAGGAAAGAAGCAAGUUUGCUCACUUGCAAGUA-AUUGAAAGUCAUUCUUUAUGCAAUAAUAAAUGGCUUUCUC-GCCCACUUGGCCAGC-AGCCCCCCCU
(((.((....)).((((((.(((......((((((......)))))).....-...((((((((((..((((...))))..))))))))))..-.....)))..)))))-))))...... ( -33.30)
>consensus
GGCAAUGUCAAUGUGCUGGA________AGCAAGUUUGUUCACUUGCAAGUA_AUUGAAAGUCAUUCUUUAUGCAAUAAUAAAUGGCUUUCUC_GCACACUUGGACAAC_AGUUCC_CC_
.....(((((((((((.............((((((......)))))).........((((((((((..((((...))))..))))))))))...))))).)))).))............. (-26.84 = -27.03 +   0.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,462,305 – 13,462,410
Length 105
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 86.50
Mean single sequence MFE -31.48
Consensus MFE -22.77
Energy contribution -23.10
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.93
Structure conservation index 0.72
SVM decision value 0.13
SVM RNA-class probability 0.600334
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13462305 105 - 20766785
----CAAACU-GUUGUCCAAGUGUGC-GAGAAAGCCAUUUAUUAUUGCAUAAAGAAUGACUUUCAAU-UACUUGCAAGUGAACAAACUUGCU--------UCCAGCACAUUGACAUUGCC
----......-..((((..(((((((-..(((((.(((((.((((...)))).))))).)))))...-.....((((((......)))))).--------....)))))))))))..... ( -29.30)
>DroPse_CAF1 5983 117 - 1
AGGGGGGGCU-GCUGGCCAAGUGGGC-GAGAAAGCCAUUUAUUAUUGCAUAAAGAAUGACUUUCAAU-UACUUGCAAGUGAGCAAACUUGCUUCUUUCCUUCCAGCACAUUGACACUGCC
.(((((((..-(..(((.((((..((-..(((((.(((((.((((...)))).))))).)))))..(-((((....)))))))..))))))).)..))))))).(((.........))). ( -31.60)
>DroSim_CAF1 11253 110 - 1
UGGCCCAACU-CUUGUCCAAGUGUGC-GAGAAAGCCAUUUAUUAUUGCAUAAAGAAUGACUUUCAAUUUACUUGCAAGUGAACAAACUUGCU--------UCCAGCACAUUGACAUUGCC
.(((......-..((((..(((((((-..(((((.(((((.((((...)))).))))).))))).........((((((......)))))).--------....)))))))))))..))) ( -30.20)
>DroYak_CAF1 11946 110 - 1
UGGCAAAAAUGGUUGUCCAAGUGUGC-AAGAAAGCCAUUUAUUAUUACAUAAAGAAUGACUUUCAAU-UACUUGCAAGUGAACAAACUUGCU--------UCCAGCACAUUGACAUUGCC
.(((((...(((....)))(((((((-..(((((.(((((.((((...)))).))))).)))))...-.....((((((......)))))).--------....)))))))....))))) ( -33.70)
>DroAna_CAF1 6369 105 - 1
-----CUACU-CUUGGCCAAGUGUGCCGAGAAAGUCAUUUAUUAUUGCAUAAAGAAUGACUUUCAAU-UACUUGCAAGUGAACAAACUUGCU--------UCCAGCACAUUGACAUUGCC
-----.....-...(((..(((((((.(.(((((((((((.((((...)))).)))))))))))...-.....((((((......)))))).--------..).)))))))......))) ( -32.50)
>DroPer_CAF1 13622 117 - 1
AGGGGGGGCU-GCUGGCCAAGUGGGC-GAGAAAGCCAUUUAUUAUUGCAUAAAGAAUGACUUUCAAU-UACUUGCAAGUGAGCAAACUUGCUUCUUUCCUUCCAGCACAUUGACACUGCC
.(((((((..-(..(((.((((..((-..(((((.(((((.((((...)))).))))).)))))..(-((((....)))))))..))))))).)..))))))).(((.........))). ( -31.60)
>consensus
_GG_CAAACU_GUUGGCCAAGUGUGC_GAGAAAGCCAUUUAUUAUUGCAUAAAGAAUGACUUUCAAU_UACUUGCAAGUGAACAAACUUGCU________UCCAGCACAUUGACAUUGCC
...................(((((((...(((((.(((((.((((...)))).))))).))))).........((((((......)))))).............)))))))......... (-22.77 = -23.10 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:24 2006