Locus 4584

Sequence ID	3R_DroMel_CAF1
Location	12,079,652 – 12,079,794
Length	142
Max. P	0.925625

overview

Window 6

Location	12,079,652 – 12,079,754
Length	102
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	92.69
Mean single sequence MFE	-34.42
Consensus MFE	-27.12
Energy contribution	-28.62
Covariance contribution	1.50
Combinations/Pair	1.03
Mean z-score	-1.95
Structure conservation index	0.79
SVM decision value	0.38
SVM RNA-class probability	0.711682
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12079652 102 + 27905053
UUCGCUGGCUGCUUGGUUGGCUCAUAACCUGAAACUUGAAUAUUGUGGAAUUUGAAGGUAGCGACGAUGUUGUUUUUGUUACUGCAGC---------AGCAACAACUGCAG
.(((.(.((((((((((((.....)))))......(..(((........)))..)))))))).))))(((((((.((((....)))).---------)))))))....... ( -25.90)
>DroSec_CAF1 16391 108 + 1
UUCGCUGGCUGCUUGGUUGGCUCAUAACCUGAAACUUGAAUAUUGUGGAAUUUGAAGGUAGCGACGAUGUUGUUGUUGUUACUGCAGCGGCA---GCAACAACAACUGCAG
.(((.(.((((((((((((.....)))))......(..(((........)))..)))))))).))))(((.(((((((((.((((....)))---).))))))))).))). ( -36.10)
>DroSim_CAF1 16578 108 + 1
UUCGCUGGCUGCUUGGUUGGCUCAUAACCUGAAACUUGAAUAUUGUGGAAUUUGAAGGUAGCGACGAUGUUGUUGUUGUUACUGCAGCGGCA---GCAACAACAACUGCAG
.(((.(.((((((((((((.....)))))......(..(((........)))..)))))))).))))(((.(((((((((.((((....)))---).))))))))).))). ( -36.10)
>DroEre_CAF1 18425 111 + 1
UUCGCUGGCUGCUUGUUUGGCUCAUAACCUGAAACUUGAAUAUGUUGGAAUUUGAAGGUAGCGACGAUGUUGUUGUUGUUGCUGCAGCAGCAACAGCAGCAACAACUGCAG
.((((((.((.(..((((.(..((((..(........)..)))).).))))..).)).))))))...(((((((((((((((((...)))))))))))))))))....... ( -39.60)
>consensus
UUCGCUGGCUGCUUGGUUGGCUCAUAACCUGAAACUUGAAUAUUGUGGAAUUUGAAGGUAGCGACGAUGUUGUUGUUGUUACUGCAGCGGCA___GCAACAACAACUGCAG
.(((.(.((((((((((((.....)))))......(..(((........)))..)))))))).)))).(((((((((((...(((....)))...)))))))))))..... (-27.12 = -28.62 +   1.50)

alignment

secondary structure

dotplot

Window 7

Location	12,079,692 – 12,079,794
Length	102
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	93.15
Mean single sequence MFE	-39.75
Consensus MFE	-32.95
Energy contribution	-34.20
Covariance contribution	1.25
Combinations/Pair	1.03
Mean z-score	-2.43
Structure conservation index	0.83
SVM decision value	1.17
SVM RNA-class probability	0.925625
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12079692 102 + 27905053
UAUUGUGGAAUUUGAAGGUAGCGACGAUGUUGUUUUUGUUACUGCAGC---------AGCAACAACUGCAGCGACGCUGCGUGCGAGCUUUAGACUCGGGCCGUCAAUUUG
......................((((.(((((((.((((....)))).---------)))))))...(((((...)))))((.(((((....).)))).))))))...... ( -29.30)
>DroSec_CAF1 16431 108 + 1
UAUUGUGGAAUUUGAAGGUAGCGACGAUGUUGUUGUUGUUACUGCAGCGGCA---GCAACAACAACUGCAGCGACGCUGCGUGCGAGCUUUAGACUCGGGCCGUCAAUUUG
...........((((.(((((((.((.(((.(((((((((.((((....)))---).))))))))).))).)).))))))((.(((((....).)))).))).)))).... ( -41.70)
>DroSim_CAF1 16618 108 + 1
UAUUGUGGAAUUUGAAGGUAGCGACGAUGUUGUUGUUGUUACUGCAGCGGCA---GCAACAACAACUGCAGCGACGCUGCGUGCGAGCUUUAGACUCGGGCCGUCAAUUUG
...........((((.(((((((.((.(((.(((((((((.((((....)))---).))))))))).))).)).))))))((.(((((....).)))).))).)))).... ( -41.70)
>DroEre_CAF1 18465 111 + 1
UAUGUUGGAAUUUGAAGGUAGCGACGAUGUUGUUGUUGUUGCUGCAGCAGCAACAGCAGCAACAACUGCAGCGACGCUGCGUGCGAGCUUUAGACUCGGGCCGUCAAUUUG
...(((.((.(((((((.(.((.((..(((((((((((((((((...)))))))))))))))))...(((((...))))))))).).))))))).)).))).......... ( -46.30)
>consensus
UAUUGUGGAAUUUGAAGGUAGCGACGAUGUUGUUGUUGUUACUGCAGCGGCA___GCAACAACAACUGCAGCGACGCUGCGUGCGAGCUUUAGACUCGGGCCGUCAAUUUG
...........((((.(((((((.((..(((((((((((...(((....)))...))))))))))).....)).))))))((.(((((....).)))).))).)))).... (-32.95 = -34.20 +   1.25)

alignment

secondary structure

dotplot

Window 8

Location	12,079,692 – 12,079,794
Length	102
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	93.15
Mean single sequence MFE	-36.60
Consensus MFE	-28.51
Energy contribution	-28.82
Covariance contribution	0.31
Combinations/Pair	1.07
Mean z-score	-3.92
Structure conservation index	0.78
SVM decision value	0.73
SVM RNA-class probability	0.835880
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12079692 102 - 27905053
CAAAUUGACGGCCCGAGUCUAAAGCUCGCACGCAGCGUCGCUGCAGUUGUUGCU---------GCUGCAGUAACAAAAACAACAUCGUCGCUACCUUCAAAUUCCACAAUA
......((((((.(((((.....)))))...))...((..(((((((.......---------)))))))..))...........))))...................... ( -26.80)
>DroSec_CAF1 16431 108 - 1
CAAAUUGACGGCCCGAGUCUAAAGCUCGCACGCAGCGUCGCUGCAGUUGUUGUUGC---UGCCGCUGCAGUAACAACAACAACAUCGUCGCUACCUUCAAAUUCCACAAUA
....((((.((..(((((.....))))).....((((.((.((..(((((((((((---(((....))))))))))))))..)).)).)))).)).))))........... ( -40.40)
>DroSim_CAF1 16618 108 - 1
CAAAUUGACGGCCCGAGUCUAAAGCUCGCACGCAGCGUCGCUGCAGUUGUUGUUGC---UGCCGCUGCAGUAACAACAACAACAUCGUCGCUACCUUCAAAUUCCACAAUA
....((((.((..(((((.....))))).....((((.((.((..(((((((((((---(((....))))))))))))))..)).)).)))).)).))))........... ( -40.40)
>DroEre_CAF1 18465 111 - 1
CAAAUUGACGGCCCGAGUCUAAAGCUCGCACGCAGCGUCGCUGCAGUUGUUGCUGCUGUUGCUGCUGCAGCAACAACAACAACAUCGUCGCUACCUUCAAAUUCCAACAUA
....((((.((...((((.....))))(((((((((...))))).(((((((((((.((....)).))))))))))).........)).))..)).))))........... ( -38.80)
>consensus
CAAAUUGACGGCCCGAGUCUAAAGCUCGCACGCAGCGUCGCUGCAGUUGUUGCUGC___UGCCGCUGCAGUAACAACAACAACAUCGUCGCUACCUUCAAAUUCCACAAUA
....((((.((...((((.....))))(((((((((...))))).(((((((((((..........))))))))))).........)).))..)).))))........... (-28.51 = -28.82 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:40 2006