Locus 4222

Sequence ID 3L_DroMel_CAF1
Location 12,361,195 – 12,361,299
Length 104
Max. P 0.993385
window6540 window6541

overview

Window 0

Location 12,361,195 – 12,361,299
Length 104
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 80.81
Mean single sequence MFE -27.35
Consensus MFE -17.81
Energy contribution -18.12
Covariance contribution 0.31
Combinations/Pair 1.06
Mean z-score -2.26
Structure conservation index 0.65
SVM decision value 1.25
SVM RNA-class probability 0.936009
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12361195 104 + 23771897
AACCCAAAACCAUUUACCUGGCCAAUUGGCCAUGGCUUUUUGUGUUCUUCACUGUU--CAGUUUGGGCCUGUUCUCUGCCGUUCUGUGCGGUUCUGGCCAAACAAA
..((((((........(((((((....))))).))......(((.....)))....--...))))))..((..(...(((((.....)))))...)..))...... ( -28.10)
>DroSec_CAF1 46172 92 + 1
AACCCAAAACCAUUUACCUGGCCAAUUGGCCAUGGCUUUCU--GUUCUUCACUGUU--CAGUUUGGGCCUGUUCU----------GUGCGGUUCUGGCCAAACAAA
...(((.((((.......(((((....))))).(((((.((--(..(......)..--)))...)))))......----------....)))).)))......... ( -26.50)
>DroSim_CAF1 49405 104 + 1
AACCCAAAACCAUUUACCUGGCCAAUUGGCCAUGGCUUGUG--UUUCUUCACUGUUCUCAGUUUGGGCCUGUUCUGUGCCGUUCUGUGCGGUUCUGGCCAAACAAA
....(((...(((...(((((((....))))).))...)))--.......((((....)))))))((((.(..(((..(......)..)))..).))))....... ( -30.60)
>DroYak_CAF1 46818 90 + 1
AACCCAAAACCAUUUACCUGGCCAAUUGGCCAUGGCUUUUG--GUUCUUCACUCUU--AAUUUCUGGUCAGAUU-----UGUUCUGUUCUGUUCUGGCC-------
.......(((((....(((((((....))))).))....))--)))..........--.......(((((((..-----.(.......)...)))))))------- ( -24.20)
>consensus
AACCCAAAACCAUUUACCUGGCCAAUUGGCCAUGGCUUUUG__GUUCUUCACUGUU__CAGUUUGGGCCUGUUCU____CGUUCUGUGCGGUUCUGGCCAAACAAA
...(((.((((.......(((((....))))).(((((..........................)))))....................)))).)))......... (-17.81 = -18.12 +   0.31)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 1

Location 12,361,195 – 12,361,299
Length 104
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 80.81
Mean single sequence MFE -29.64
Consensus MFE -24.27
Energy contribution -24.40
Covariance contribution 0.13
Combinations/Pair 1.05
Mean z-score -2.55
Structure conservation index 0.82
SVM decision value 2.39
SVM RNA-class probability 0.993385
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12361195 104 - 23771897
UUUGUUUGGCCAGAACCGCACAGAACGGCAGAGAACAGGCCCAAACUG--AACAGUGAAGAACACAAAAAGCCAUGGCCAAUUGGCCAGGUAAAUGGUUUUGGGUU
.((((((.(((...............)))...))))))(((((((((.--....(((.....))).....(((.(((((....))))))))....)).))))))). ( -31.56)
>DroSec_CAF1 46172 92 - 1
UUUGUUUGGCCAGAACCGCAC----------AGAACAGGCCCAAACUG--AACAGUGAAGAAC--AGAAAGCCAUGGCCAAUUGGCCAGGUAAAUGGUUUUGGGUU
.........((((((((((((----------....(((.......)))--....)))......--.....(((.(((((....))))))))...)))))))))... ( -29.20)
>DroSim_CAF1 49405 104 - 1
UUUGUUUGGCCAGAACCGCACAGAACGGCACAGAACAGGCCCAAACUGAGAACAGUGAAGAAA--CACAAGCCAUGGCCAAUUGGCCAGGUAAAUGGUUUUGGGUU
.........(((((((((..(((...(((.(......))))....)))......(((......--)))..(((.(((((....))))))))...)))))))))... ( -32.10)
>DroYak_CAF1 46818 90 - 1
-------GGCCAGAACAGAACAGAACA-----AAUCUGACCAGAAAUU--AAGAGUGAAGAAC--CAAAAGCCAUGGCCAAUUGGCCAGGUAAAUGGUUUUGGGUU
-------.(((.........((((...-----..))))..........--........(((((--((...(((.(((((....))))))))...))))))).))). ( -25.70)
>consensus
UUUGUUUGGCCAGAACCGCACAGAACG____AGAACAGGCCCAAACUG__AACAGUGAAGAAC__AAAAAGCCAUGGCCAAUUGGCCAGGUAAAUGGUUUUGGGUU
.........(((((((((..........................((((....))))..............(((.(((((....))))))))...)))))))))... (-24.27 = -24.40 +   0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:11 2006