Locus 4065

Sequence ID	2R_DroMel_CAF1
Location	13,428,380 – 13,428,473
Length	93
Max. P	0.978891

overview

Window 7

Location	13,428,380 – 13,428,473
Length	93
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	87.46
Mean single sequence MFE	-20.04
Consensus MFE	-15.80
Energy contribution	-15.80
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.43
Structure conservation index	0.79
SVM decision value	-0.05
SVM RNA-class probability	0.507083
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13428380 93 + 20766785
UGAAUUUUCCGGCUCCCUUGGGCCGCAGUCUGCCAAGGCACACUGCCUGGUCCACCGAAAACCAAACGAACCAACCACCCAGAACAU---------ACAAAC
....(((((.((......(((((((((((.(((....))).)))))..)))))))))))))..........................---------...... ( -23.20)
>DroSec_CAF1 25674 102 + 1
UGAAUUUUCCGGCUCCCUUGGGCCGCAGUCUGCCAAGGCACACCACCUGGUCCACCGAAAACCAAACGAACCAACCACCCAGAACACCGAAGCCACCCAAAC
..........((((.(..(((((((..((.(((....))).))....))))))).((.........))....................).))))........ ( -18.60)
>DroSim_CAF1 26952 102 + 1
UGAAUUUUCCGGCUCCCUUGGGCCGCAGUCUGCCAAGGCACACCACCUGGCCCACCGAAAACCAAACGAACCAACCACCCAGAACACCGAAGCCACCCAAAC
..........((((.(..(((((((..((.(((....))).))....))))))).((.........))....................).))))........ ( -21.30)
>DroEre_CAF1 27272 89 + 1
UGAAUUUUCCGGCUCCCUUGGGCCGCAGUCUGCCAAGGCACACCACCUGGGCCACCGAAAACCAAACGAACCAACCAGCCAGACCACCC-------------
.......((.((((...((((..((..((.(((....))).))....(((....))).........))..))))..)))).))......------------- ( -19.30)
>DroYak_CAF1 26843 102 + 1
UGAAUUUUCCGGCUCCUUUGGGCCGCAGUCUGCCAAGGCACACUACCUGGUCCACCGAAAACCAAACGAACCAACCACCCACACCACCCAAAACACCCAAAA
....(((((.((......(((((((.(((.(((....))).)))...))))))))))))))......................................... ( -17.80)
>consensus
UGAAUUUUCCGGCUCCCUUGGGCCGCAGUCUGCCAAGGCACACCACCUGGUCCACCGAAAACCAAACGAACCAACCACCCAGAACACCCAA__CACCCAAAC
....(((((((((((....))))))..((.(((....))).)).....((....)))))))......................................... (-15.80 = -15.80 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	13,428,380 – 13,428,473
Length	93
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	87.46
Mean single sequence MFE	-37.26
Consensus MFE	-32.36
Energy contribution	-32.00
Covariance contribution	-0.36
Combinations/Pair	1.11
Mean z-score	-2.07
Structure conservation index	0.87
SVM decision value	1.82
SVM RNA-class probability	0.978891
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13428380 93 - 20766785
GUUUGU---------AUGUUCUGGGUGGUUGGUUCGUUUGGUUUUCGGUGGACCAGGCAGUGUGCCUUGGCAGACUGCGGCCCAAGGGAGCCGGAAAAUUCA
......---------.......((((..(((((((.(((((.....((....))..(((((.(((....))).)))))...))))).)))))))...)))). ( -34.80)
>DroSec_CAF1 25674 102 - 1
GUUUGGGUGGCUUCGGUGUUCUGGGUGGUUGGUUCGUUUGGUUUUCGGUGGACCAGGUGGUGUGCCUUGGCAGACUGCGGCCCAAGGGAGCCGGAAAAUUCA
...(((((...((((((.((((((((..((((((((............))))))))(..((.(((....))).))..).)))).)))).))))))..))))) ( -37.50)
>DroSim_CAF1 26952 102 - 1
GUUUGGGUGGCUUCGGUGUUCUGGGUGGUUGGUUCGUUUGGUUUUCGGUGGGCCAGGUGGUGUGCCUUGGCAGACUGCGGCCCAAGGGAGCCGGAAAAUUCA
.((..((..((....))..))..))....(((....(((((((..(..((((((..(..((.(((....))).))..))))))).)..)))))))....))) ( -41.20)
>DroEre_CAF1 27272 89 - 1
-------------GGGUGGUCUGGCUGGUUGGUUCGUUUGGUUUUCGGUGGCCCAGGUGGUGUGCCUUGGCAGACUGCGGCCCAAGGGAGCCGGAAAAUUCA
-------------((((..(((((((..((((..(....((((......))))...(..((.(((....))).))..))..))))...)))))))..)))). ( -34.80)
>DroYak_CAF1 26843 102 - 1
UUUUGGGUGUUUUGGGUGGUGUGGGUGGUUGGUUCGUUUGGUUUUCGGUGGACCAGGUAGUGUGCCUUGGCAGACUGCGGCCCAAAGGAGCCGGAAAAUUCA
((((((.(.((((((((...........((((((((............))))))))(((((.(((....))).))))).)))))))).).))))))...... ( -38.00)
>consensus
GUUUGGGUG__UUCGGUGUUCUGGGUGGUUGGUUCGUUUGGUUUUCGGUGGACCAGGUGGUGUGCCUUGGCAGACUGCGGCCCAAGGGAGCCGGAAAAUUCA
.....................(((((..(((((((.(((((.....((....))..(((((.(((....))).)))))...))))).)))))))...))))) (-32.36 = -32.00 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:55 2006