Locus 5130

Sequence ID	X_DroMel_CAF1
Location	13,405,274 – 13,405,426
Length	152
Max. P	0.994437

overview

Window 6

Location	13,405,274 – 13,405,386
Length	112
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.23
Mean single sequence MFE	-27.74
Consensus MFE	-26.08
Energy contribution	-26.57
Covariance contribution	0.50
Combinations/Pair	1.10
Mean z-score	-2.52
Structure conservation index	0.94
SVM decision value	2.48
SVM RNA-class probability	0.994437
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13405274 112 - 22224390
AAACAUUCUUUCAUUCGCACACUUUGUUUGGCAUU--CGAACU----AUUUGAUAAAUGGCAAACAAAAUGUGUCUGUGAGCAAAUUUCUCUGAUUUCCCGAGACAGUUUUGUUUGAC--
(((((....(((((..(((((.((((((((.((((--(((...----..))))...))).)))))))).)))))..))))).(((((((((.(.....).)))).))))))))))...-- ( -28.10)
>DroSec_CAF1 1166 112 - 1
AAACAUUUUUUCAUUUGCACACUUUGUUUGGCAUU--CGAACU----AUUUGAUAAAUGGCAAACAAAAUGUGUCUGUGAGCAAAUUUCUCUGAUUUCCCGAGGCAGUUUGGUUUGAC--
((((.....(((((..(((((.((((((((.((((--(((...----..))))...))).)))))))).)))))..)))))((((((((((.(.....).)))).))))))))))...-- ( -30.90)
>DroSim_CAF1 1166 112 - 1
AAACAUUCUUUCAUUUGCACACUUUGUUUGGCAUU--CGAACU----AUUUGAUAAAUGGCAAACAAAAUGUGUCUGUGAGCAAAUUUCUCUGAUUUCCCGAGACAGUUUGGUUUGAC--
((((.....(((((..(((((.((((((((.((((--(((...----..))))...))).)))))))).)))))..)))))((((((((((.(.....).)))).))))))))))...-- ( -31.40)
>DroYak_CAF1 8983 120 - 1
AAACAUUCCUUUAUUCACACAUUUUGCUUGGCAUUCUCGAACUACAUAUUUAAUAAAUGGUAAAUAAAAUGUGUCUGUUAGCAAAUUUCUCUGAUUUCCUGAGACAGUUUUGUUUGACAA
................((((((((((.(((.((((....................)))).))).)))))))))).((((((((((..((((.........))))....)))).)))))). ( -20.55)
>consensus
AAACAUUCUUUCAUUCGCACACUUUGUUUGGCAUU__CGAACU____AUUUGAUAAAUGGCAAACAAAAUGUGUCUGUGAGCAAAUUUCUCUGAUUUCCCGAGACAGUUUGGUUUGAC__
((((.....(((((..(((((.((((((((.((((..((((.......))))...)))).)))))))).)))))..)))))((((((((((.(.....).)))).))))))))))..... (-26.08 = -26.57 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	13,405,312 – 13,405,426
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.03
Mean single sequence MFE	-23.68
Consensus MFE	-20.01
Energy contribution	-19.57
Covariance contribution	-0.44
Combinations/Pair	1.15
Mean z-score	-2.58
Structure conservation index	0.84
SVM decision value	1.73
SVM RNA-class probability	0.974372
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13405312 114 + 22224390
UCACAGACACAUUUUGUUUGCCAUUUAUCAAAU----AGUUCG--AAUGCCAAACAAAGUGUGCGAAUGAAAGAAUGUUUGCCAAUGCGAAAGAACUUAAAGCCUUUCAAAUAUUUAUAA
(((..(.(((((((((((((.(((((.......----.....)--)))).))))))))))))))...)))..((((((((((....))(((((..........))))))))))))).... ( -27.00)
>DroSec_CAF1 1204 114 + 1
UCACAGACACAUUUUGUUUGCCAUUUAUCAAAU----AGUUCG--AAUGCCAAACAAAGUGUGCAAAUGAAAAAAUGUUUGCCAAAGCAAAAGAACUUAAAGCCUUUCAAAUAUUUAUAA
(((....(((((((((((((.(((((.......----.....)--)))).)))))))))))))....)))..(((((((((.....((.............))....))))))))).... ( -23.72)
>DroSim_CAF1 1204 114 + 1
UCACAGACACAUUUUGUUUGCCAUUUAUCAAAU----AGUUCG--AAUGCCAAACAAAGUGUGCAAAUGAAAGAAUGUUUGCCAAAGCAAAAGAACUUAAAGCCUUUCAAAUAUUUAUAA
.....(.(((((((((((((.(((((.......----.....)--)))).))))))))))))))...((((((..(.(((((....))))).........)..))))))........... ( -24.90)
>DroYak_CAF1 9023 119 + 1
UAACAGACACAUUUUAUUUACCAUUUAUUAAAUAUGUAGUUCGAGAAUGCCAAGCAAAAUGUGUGAAUAAAGGAAUGUUUGC-AAAGCUAAAGAACUUAAAGCCUUUCAAAUAUUUAUAA
......(((((((((.(((..(((((.(..(((.....)))..))))))..))).)))))))))........(((((((((.-((((((...........)).))))))))))))).... ( -19.10)
>consensus
UCACAGACACAUUUUGUUUGCCAUUUAUCAAAU____AGUUCG__AAUGCCAAACAAAGUGUGCAAAUGAAAGAAUGUUUGCCAAAGCAAAAGAACUUAAAGCCUUUCAAAUAUUUAUAA
.....(.(((((((((((((.((((...(.(((.....))).)..)))).))))))))))))))........(((((((((.....((.............))....))))))))).... (-20.01 = -19.57 +  -0.44)

alignment

secondary structure

dotplot

Window 8

Location	13,405,312 – 13,405,426
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.03
Mean single sequence MFE	-25.19
Consensus MFE	-22.28
Energy contribution	-22.72
Covariance contribution	0.44
Combinations/Pair	1.09
Mean z-score	-2.07
Structure conservation index	0.88
SVM decision value	1.39
SVM RNA-class probability	0.949761
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13405312 114 - 22224390
UUAUAAAUAUUUGAAAGGCUUUAAGUUCUUUCGCAUUGGCAAACAUUCUUUCAUUCGCACACUUUGUUUGGCAUU--CGAACU----AUUUGAUAAAUGGCAAACAAAAUGUGUCUGUGA
............(((((((.....).))))))((....))..........((((..(((((.((((((((.((((--(((...----..))))...))).)))))))).)))))..)))) ( -27.30)
>DroSec_CAF1 1204 114 - 1
UUAUAAAUAUUUGAAAGGCUUUAAGUUCUUUUGCUUUGGCAAACAUUUUUUCAUUUGCACACUUUGUUUGGCAUU--CGAACU----AUUUGAUAAAUGGCAAACAAAAUGUGUCUGUGA
....((((.((((.(((((.............)))))..)))).))))..((((..(((((.((((((((.((((--(((...----..))))...))).)))))))).)))))..)))) ( -28.02)
>DroSim_CAF1 1204 114 - 1
UUAUAAAUAUUUGAAAGGCUUUAAGUUCUUUUGCUUUGGCAAACAUUCUUUCAUUUGCACACUUUGUUUGGCAUU--CGAACU----AUUUGAUAAAUGGCAAACAAAAUGUGUCUGUGA
.................(((..((((......)))).)))..........((((..(((((.((((((((.((((--(((...----..))))...))).)))))))).)))))..)))) ( -27.50)
>DroYak_CAF1 9023 119 - 1
UUAUAAAUAUUUGAAAGGCUUUAAGUUCUUUAGCUUU-GCAAACAUUCCUUUAUUCACACAUUUUGCUUGGCAUUCUCGAACUACAUAUUUAAUAAAUGGUAAAUAAAAUGUGUCUGUUA
.........((((.((((((...........))))))-.)))).............((((((((((.(((.((((....................)))).))).))))))))))...... ( -17.95)
>consensus
UUAUAAAUAUUUGAAAGGCUUUAAGUUCUUUUGCUUUGGCAAACAUUCUUUCAUUCGCACACUUUGUUUGGCAUU__CGAACU____AUUUGAUAAAUGGCAAACAAAAUGUGUCUGUGA
.........((((.(((((.............)))))..)))).......((((..(((((.((((((((.((((..((((.......))))...)))).)))))))).)))))..)))) (-22.28 = -22.72 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:46 2006