Locus 5253

Sequence ID 3R_DroMel_CAF1
Location 13,701,468 – 13,701,585
Length 117
Max. P 0.992404
window8576 window8577

overview

Window 6

Location 13,701,468 – 13,701,558
Length 90
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 88.51
Mean single sequence MFE -10.92
Consensus MFE -10.42
Energy contribution -10.45
Covariance contribution 0.03
Combinations/Pair 1.08
Mean z-score -1.99
Structure conservation index 0.95
SVM decision value 2.33
SVM RNA-class probability 0.992404
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13701468 90 - 27905053
UAAGCACCCAAGCACAAUUCA-AUUCAAGCGAACC-UUAAACUGAACUGAAUUCAGUAAGUGCACCCAA-----AUCAAUAACAAAUUUAAAUCAAU
...........((((......-.(((....)))..-....((((((.....))))))..))))......-----....................... ( -11.10)
>DroSec_CAF1 11294 89 - 1
UAAGCACCCAAGCACAAUUCA-AUUCAAGCGAACC-UUAAACUGAACUGAAUUCAGUAAGUGCACCCAA-----AUCAAUAACA-AUUUAAAUCAAU
...........((((......-.(((....)))..-....((((((.....))))))..))))......-----..........-............ ( -11.10)
>DroSim_CAF1 11372 89 - 1
UAAGCACCCAAGCACAAUUCA-AUUCAAGCGAACC-UUAAACUGAACUGAAUUCAGUAAGUGCACCCAA-----AUCAAUAACA-AUUUAAAUCAAU
...........((((......-.(((....)))..-....((((((.....))))))..))))......-----..........-............ ( -11.10)
>DroEre_CAF1 11711 94 - 1
UAAGCACCCAAGCACAAUUCA-AUUCAAGCGAACU-UAAAACUGAACUGAAUUCAGUAAGUGCACCAAAUCAAUACCAAUAUCA-AUUUAAGUCAAU
...........((((......-.(((....)))..-....((((((.....))))))..)))).....................-............ ( -11.10)
>DroYak_CAF1 19984 89 - 1
UAAGCACCCAAGCACAAUUCA-AUUCAAGCGAACU-UUAAACUGAACUGAAUUUAGUAAGUGCACCCAA-----AUCAAUAUCA-AUUUAAAUCAAU
...((((....((..((((((-.((((........-......)))).))))))..))..))))......-----..........-............ ( -10.54)
>DroAna_CAF1 677 88 - 1
UAAGCACCUAAGCACAAAUCAAAAUCAAGCGAACUCUAAAACUGAACUGGAUUCAGUAAGUGCACCACA-----ACUAAU---U-AUUAAAUUUAUU
...((((....((...............))..........((((((.....))))))..))))......-----......---.-............ ( -10.56)
>consensus
UAAGCACCCAAGCACAAUUCA_AUUCAAGCGAACC_UUAAACUGAACUGAAUUCAGUAAGUGCACCCAA_____AUCAAUAACA_AUUUAAAUCAAU
...........((((........(((....))).......((((((.....))))))..)))).................................. (-10.42 = -10.45 +   0.03)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,701,494 – 13,701,585
Length 91
Sequences 6
Columns 92
Reading direction reverse
Mean pairwise identity 85.77
Mean single sequence MFE -10.82
Consensus MFE -9.19
Energy contribution -9.13
Covariance contribution -0.05
Combinations/Pair 1.15
Mean z-score -1.55
Structure conservation index 0.85
SVM decision value 0.08
SVM RNA-class probability 0.571933
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13701494 91 - 27905053
CAAACAGCCAACACAACGAAAACACUUUAAGCACCCAAGCACAAUUCAAUUCAAGCGAACCUU-AAACUGAACUGAAUUCAGUAAGUGCACC
......................................((((.......(((....)))....-..((((((.....))))))..))))... ( -11.10)
>DroSec_CAF1 11319 91 - 1
CAAACAGCCACCAAAACGAAAACACUUUAAGCACCCAAGCACAAUUCAAUUCAAGCGAACCUU-AAACUGAACUGAAUUCAGUAAGUGCACC
......................................((((.......(((....)))....-..((((((.....))))))..))))... ( -11.10)
>DroSim_CAF1 11397 91 - 1
CAAACAGCCACCACAACGAAAACACUUUAAGCACCCAAGCACAAUUCAAUUCAAGCGAACCUU-AAACUGAACUGAAUUCAGUAAGUGCACC
......................................((((.......(((....)))....-..((((((.....))))))..))))... ( -11.10)
>DroEre_CAF1 11741 91 - 1
CAAACAGCCACCUCAACGAAAACACUUUAAGCACCCAAGCACAAUUCAAUUCAAGCGAACUUA-AAACUGAACUGAAUUCAGUAAGUGCACC
......................................((((.......(((....)))....-..((((((.....))))))..))))... ( -11.10)
>DroYak_CAF1 20009 91 - 1
CAAACAGCCUCCACAACGAAAACAUUUUAAGCACCCAAGCACAAUUCAAUUCAAGCGAACUUU-AAACUGAACUGAAUUUAGUAAGUGCACC
..............................((((....((..((((((.((((..........-....)))).))))))..))..))))... ( -10.54)
>DroMoj_CAF1 503 76 - 1
------------ACAGUGAAAACACUUUAAAGCACCAAGCACAAACAAAUUU--CCAAACUUGCAAACUGAACUGAAUU--GUAAGUGCACA
------------...(((.............((.....))............--....((((((((...........))--)))))).))). ( -10.00)
>consensus
CAAACAGCCACCACAACGAAAACACUUUAAGCACCCAAGCACAAUUCAAUUCAAGCGAACCUU_AAACUGAACUGAAUUCAGUAAGUGCACC
......................................((((.......(((....))).......((((((.....))))))..))))... ( -9.19 =  -9.13 +  -0.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:21 2006