Locus 1089

Sequence ID	2L_DroMel_CAF1
Location	2,999,562 – 2,999,788
Length	226
Max. P	0.670991

overview

Window 7

Location	2,999,562 – 2,999,682
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.75
Mean single sequence MFE	-31.67
Consensus MFE	-29.45
Energy contribution	-29.53
Covariance contribution	0.08
Combinations/Pair	1.03
Mean z-score	-1.27
Structure conservation index	0.93
SVM decision value	0.29
SVM RNA-class probability	0.670991
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2999562 120 + 22407834
AACCGAAAAUAGUUCGCGAAACGCAGCAGGCGACGCGUCUUUUUGGCUCUCGAAAAGGGCAUGAAAACUCGCGAACUGUGGCCAAUAAAAGAUACAUACAGGAAAAAGCGAUUGCGCGAA
........(((((((((((..(((.....)))..((.((((((((.....))))))))))........)))))))))))............................(((....)))... ( -31.80)
>DroSec_CAF1 7042 120 + 1
AACCGAAAAUAGUUCGCGAAACGCAGCAGGCGACGCGUCUUUUGGGCUCUCGAAAAGGGCAUGAAAACUCGCGAACUGGGGCCAAUAAAAGAUACAUACAGGAAAAAGCGAUUGCGCGAA
............((((((((.(((.((.(....)))((((((((((((((.....((..(.(((....))).)..))))))))..))))))))..............))).)).)))))) ( -30.70)
>DroSim_CAF1 6417 120 + 1
AACCGAAAAUAGUUCGCGAAACGCAGCAGGCGACGCGUCUUUUGGGCUCUCGAAAAGGGCAUGAAAACUCGCGAACUGCGGCCAAUAAAAGAUACAUACAGGAAAAAGCGAUUGCGCGAA
............((((((((.(((.((((....((((..((((.((((((.....))))).).))))..))))..))))..((.................)).....))).)).)))))) ( -31.83)
>DroEre_CAF1 7024 120 + 1
AACCGAAAAUAGUUCGCGAAACGCAGCAGGCGACGCGUCUUUUGGGCUCUCGAAAAGGGCAUGAAAACUCGCGAUCUGCGGCCAAUAAAAGAUACAUACAGGAAAAAGCGAUUGCGCGAA
............((((((((.(((.(((((...((((..((((.((((((.....))))).).))))..)))).)))))..((.................)).....))).)).)))))) ( -31.83)
>DroYak_CAF1 6502 120 + 1
AAACGAAAAUAGUUCGCGAAACGCGGCAGGCGACGCGUCUUUUGGGCUCUCAAAAAGGGCAUGAAAACUCGCGAACUGCGGCCAAUAAAAGAUACAUACAGGAAAAAGCGAUUGCGCGAA
............((((((((.((((((..(((.((((..((((.((((((.....))))).).))))..))))...))).)))...........(.....)......))).)).)))))) ( -32.20)
>consensus
AACCGAAAAUAGUUCGCGAAACGCAGCAGGCGACGCGUCUUUUGGGCUCUCGAAAAGGGCAUGAAAACUCGCGAACUGCGGCCAAUAAAAGAUACAUACAGGAAAAAGCGAUUGCGCGAA
............((((((((.(((.((((....((((..((((.((((((.....))))).).))))..))))..))))..((.................)).....))).)).)))))) (-29.45 = -29.53 +   0.08)

alignment

secondary structure

dotplot

Window 8

Location	2,999,682 – 2,999,788
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.52
Mean single sequence MFE	-30.18
Consensus MFE	-21.90
Energy contribution	-21.34
Covariance contribution	-0.56
Combinations/Pair	1.15
Mean z-score	-1.71
Structure conservation index	0.73
SVM decision value	-0.05
SVM RNA-class probability	0.510529
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2999682 106 + 22407834
UUCUCGGCUGCGUGUGCGCUGCAAAUUUGCUCGUGCGGAGC----------AAAAACAAACGAAAAUAGCCGGAUGAAC----AAAUACAUCCAGUGCGAAGAAUAAUCUACGCUGUAUA
.....(((((((....)))......(((((((.....))))----------))).............))))(((((...----.....)))))...(((.(((....))).)))...... ( -30.10)
>DroSec_CAF1 7162 110 + 1
UUCUCGGCUGCGUGUGCGCUGCAAAUUUGCUCGUGCGGAGC----------AAAAACAAACGAAAAUAGCCGGAUGAACAAACAAAUACAUCCAGUGCGAAGAAUAAUCUGCGCUGUAUA
.....(((((((....)))......(((((((.....))))----------))).............))))(((((............)))))(((((..(((....))))))))..... ( -29.70)
>DroSim_CAF1 6537 110 + 1
UUCUCGGCUGCGUGAGCGCUGCAAAUUUGCUCGUGGGGAGC----------AAAAACAAACGAAAAUAGCCGGAUGAACAAACAAAUACAUCCAGUGCGAAGAAUAAUCUGCGCUGUAUA
.....((((((....))........(((((((.....))))----------))).............))))(((((............)))))(((((..(((....))))))))..... ( -30.80)
>DroEre_CAF1 7144 109 + 1
UUCUCGGCUGCGUGUGCGCUGCAAAUUUGCUCGUGCGUAGC----------AAAAACAAACGAAAAUAGCCG-AUGAACAAACAAAUACAGGCAGUGUGAAGAAUAAUCUGCGCUGUUUA
((((((((((((....)))......(((((((....).)))----------))).............)))))-).)))...........(((((((((..(((....)))))))))))). ( -29.70)
>DroYak_CAF1 6622 119 + 1
UUCUCGGCUGCGUGUGCGCUGCAAAUUUGCUCGUGCGGAGCAAAGACAAGCAAAAACAAACGAAAAUAGCCG-AUGAACAAACAAAUACGGCUAGUGUGAAGAAUAAUCUGCGCUGUUUA
((((((((((((....)))(((...(((((((.....))))))).....)))...............)))))-).))).........(((((((((((.....)))..))).)))))... ( -30.60)
>consensus
UUCUCGGCUGCGUGUGCGCUGCAAAUUUGCUCGUGCGGAGC__________AAAAACAAACGAAAAUAGCCGGAUGAACAAACAAAUACAUCCAGUGCGAAGAAUAAUCUGCGCUGUAUA
(((.((((((((....))).........((((.....))))..........................)))))...)))...........((.((((((..(((....))))))))).)). (-21.90 = -21.34 +  -0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:18 2006