Locus 4122

Sequence ID 2R_DroMel_CAF1
Location 13,536,517 – 13,536,671
Length 154
Max. P 0.723555
window6637 window6638

overview

Window 7

Location 13,536,517 – 13,536,611
Length 94
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 71.44
Mean single sequence MFE -28.37
Consensus MFE -12.07
Energy contribution -13.02
Covariance contribution 0.95
Combinations/Pair 1.38
Mean z-score -1.84
Structure conservation index 0.43
SVM decision value 0.41
SVM RNA-class probability 0.723555
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13536517 94 + 20766785
-----ACUACUACUCAAGGUCCAUGGUGGGGAAACACUACCACUCAAGGUCCAUGGUGGGGAAACACGACUACUCAAGGUCCAUGGUGGGGAAACACCA
-----....((((.((.((.((.(((((((....).)))))).....)).)).))))))(....)..((((......))))..(((((......))))) ( -31.10)
>DroSim_CAF1 88118 99 + 1
GAAACACUACUACUCAAGGUCCAUGGUGGGGAAACAGCACUACUCAAGGUCCAUGGUGGGGAAACAACUCAACGGAAGGUCCAUGGUGGGGAAACAACU
....(((((((((.((.((.((.(((((((....)....)))).)).)).)).))))))(((..........(....).))).))))).(....).... ( -26.20)
>DroEre_CAF1 85351 94 + 1
-----ACCACUACUCAAGGUCCAUGGUGGGGAAACACCACUACUCAAGGUCCAUGGUGGGGAAACACCACUACUCAAGGCCCAUGGUGGGGAAACUCUA
-----.((.((((.((.((.((.(((((((....).))))))...........(((((((....).)))))).....)).)).))))))))........ ( -34.30)
>DroWil_CAF1 65040 85 + 1
-----UCCACGGCAUAUCCUCCCCAAUGG---AACACCACCACCGAUCGUCCUUGGUGG---AACAAUUCUACCGAAGGUCCUUGGUGGAAU---AACU
-----.....((....(((........))---)...)).(((((((..(.(((((((((---(.....)))))).)))).).)))))))...---.... ( -27.50)
>DroYak_CAF1 88290 94 + 1
-----AACUCUACUCAAGGUCCAUGGUGGGGAAACAACUCAACUGAAGGUCCCUGGUGGGGAAACAACUCGACGGAAGGUCCAUGGUGGGGAAACAACU
-----..((((((.((.((.((.....(((((.....(((....).)).))))).((.(((......))).))....)).)).))))))))........ ( -25.70)
>DroAna_CAF1 86093 88 + 1
-----AAUUCUACCUCUGGACCCAACUGG------AACACCACUGAAGGACCGUGGUGGGGAAAUAACUCGACGGAAGGACCCUGGUGGGGCAACAACU
-----....(((((...((..((..(((.------..((((((.(.....).))))))(((......)))..)))..))..)).)))))(....).... ( -25.40)
>consensus
_____ACCACUACUCAAGGUCCAUGGUGGGGAAACACCACCACUCAAGGUCCAUGGUGGGGAAACAACUCUACGGAAGGUCCAUGGUGGGGAAACAACU
...................(((((.(((((.........(((((..........))))).............(....).))))).)))))......... (-12.07 = -13.02 +   0.95)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,536,579 – 13,536,671
Length 92
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 70.69
Mean single sequence MFE -27.82
Consensus MFE -10.89
Energy contribution -12.03
Covariance contribution 1.14
Combinations/Pair 1.39
Mean z-score -1.81
Structure conservation index 0.39
SVM decision value 0.17
SVM RNA-class probability 0.616562
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13536579 92 + 20766785
GACUACUCAAGGUCCAUGGUGGGGAAACACCACUACUC---AAGGCCCAUGGUGGGGAAACACUACCACUCAAGGUCCAUGGUGGGGAAACACAA
..((((.((.((.((.(((((((....).))))))...---........(((((((....).)))))).....)).)).))))))(....).... ( -34.30)
>DroSim_CAF1 88185 92 + 1
CUCAACGGAAGGUCCAUGGUGGGGAAACAACUCAACGG---AAGGUCCAUGGUGGGGCAAUAACUCUACUCAAGGCCCAUGGUGGGGAAACACCA
..........(((((((.(((((............(..---..)..((.((((((((......)))))).)).))))))).))))(....)))). ( -30.10)
>DroEre_CAF1 85413 92 + 1
CACUACUCAAGGCCCAUGGUGGGGAAACUCUACUACUC---AAGGUCCAUGGUGGGGAAACACUACUACUCAAGGUCCAUGGUGGGGAAACAACU
..((((.((.((.((.(((((((....).))))))...---........(((((((....).)))))).....)).)).))))))(....).... ( -28.60)
>DroWil_CAF1 65096 86 + 1
UUCUACCGAAGGUCCUUGGUGGAAU---AACUCUACGGCAUCUCCUCCACAAUUG---AACACCACCACCGAUCGCCCCUGGUGG---AACAAUU
((((((((..(((..(((((((...---........((........)).....((---.....)))))))))..)))..))))))---))..... ( -23.80)
>DroYak_CAF1 88352 92 + 1
CUCGACGGAAGGUCCAUGGUGGGGAAACAACUCAACCG---AAGGUCCAUGGUGGGGAAACAACUCAACUCAAGGUCCAUGGUGGGGAAACAACU
.....(....)..((((.(((((....)......(((.---..(((....(((..(....).)))..)))...))))))).))))(....).... ( -23.20)
>DroAna_CAF1 86149 86 + 1
CUCGACGGAAGGACCCUGGUGGGGCAACAACUCUACCU---CUGGACCCAACUGG------AACACCACCGAAGGACCAUGGUGGGGAAACAAUU
.....(((..((..((.(((((((......))))))).---..))..))..))).------....((((((........))))))(....).... ( -26.90)
>consensus
CUCUACGGAAGGUCCAUGGUGGGGAAACAACUCUACCG___AAGGUCCAUGGUGGGGAAACAACACCACUCAAGGUCCAUGGUGGGGAAACAACU
............(((((.(((((....).......((......)).)))).))))).........(((((..........)))))(....).... (-10.89 = -12.03 +   1.14)

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 11:12:20 2006