Locus 5857

Sequence ID	X_DroMel_CAF1
Location	15,118,456 – 15,118,650
Length	194
Max. P	0.682194

overview

Window 6

Location	15,118,456 – 15,118,575
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.45
Mean single sequence MFE	-29.53
Consensus MFE	-21.25
Energy contribution	-21.75
Covariance contribution	0.50
Combinations/Pair	1.07
Mean z-score	-1.73
Structure conservation index	0.72
SVM decision value	0.31
SVM RNA-class probability	0.682194
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15118456 119 + 22224390
GGGGCAGCUUUAGUGAAGAGGAAAGCGGGAUGUAUUAUUUUUAGCGCUUUUCCCUGACUUUUUUGAAUUUUCUUCCCGUUUUUUUUUUU-UUUUUGGCAACUUGAGUUGCAAACAAAUUG
...(((((((.(((((((((((((((((((.(.(((......((((........)).))......)))...).))))))))))))))))-.........))).))))))).......... ( -27.60)
>DroSec_CAF1 30183 120 + 1
GGGGCAGCUUUAGUGAAGAGGAACGCGGGAUGUAUUAUUUUUAGCGCGUUUCCCUGGCUUUUUUGAAUUUUCUUCCCGUUUUUUUCUUUUUUUGUGGCAACUUGAGUUGCAAACAAAUUG
...(((((((.((((((((((((.((((((.(.(((......(((.((......)))))......)))...).)))))).)))))))))..........))).))))))).......... ( -30.50)
>DroEre_CAF1 37314 109 + 1
UGGGUAGCUUUAGUGAAGAGGCAAGCGGGAUGUAUUAUUUUUAGCGCUUUCCCCUGGCUUUUUUGAAUUUUCUUUCC--U--------U-UUUUGGGCAACUUGAGUUGCAAACAAAUUG
((.(((((((.(((((((((((.((.((((.(..(((....)))..)..)))))).))))))))..........(((--.--------.-....)))..))).)))))))...))..... ( -28.80)
>DroYak_CAF1 37541 111 + 1
UGGGUUGCUUUAGUGAAGAGGCGAGCGGGAUGUAUUAUUUUUAGCGCUUUCCCCUGGCUUUUUUGAAUUUUCUUUCCAUU--------U-UUUUGGGAAACUUGAGUUGCAAACAAAUUG
((.((.((((.(((((((((((.((.((((.(..(((....)))..)..)))))).))))))))........((((((..--------.-...))))))))).)))).))...))..... ( -31.20)
>consensus
GGGGCAGCUUUAGUGAAGAGGAAAGCGGGAUGUAUUAUUUUUAGCGCUUUCCCCUGGCUUUUUUGAAUUUUCUUCCCGUU________U_UUUUGGGCAACUUGAGUUGCAAACAAAUUG
...(((((((.(((((((((((.((.((((.(..(((....)))..)..)))))).))))))))((....))...........................))).))))))).......... (-21.25 = -21.75 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	15,118,456 – 15,118,575
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.45
Mean single sequence MFE	-18.65
Consensus MFE	-14.53
Energy contribution	-15.65
Covariance contribution	1.13
Combinations/Pair	1.05
Mean z-score	-1.39
Structure conservation index	0.78
SVM decision value	-0.02
SVM RNA-class probability	0.523048
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15118456 119 - 22224390
CAAUUUGUUUGCAACUCAAGUUGCCAAAAA-AAAAAAAAAAACGGGAAGAAAAUUCAAAAAAGUCAGGGAAAAGCGCUAAAAAUAAUACAUCCCGCUUUCCUCUUCACUAAAGCUGCCCC
...((((...(((((....)))))))))..-............(((..((....)).....(((.((((.((((((.................)))))).))))..))).......))). ( -18.73)
>DroSec_CAF1 30183 120 - 1
CAAUUUGUUUGCAACUCAAGUUGCCACAAAAAAAGAAAAAAACGGGAAGAAAAUUCAAAAAAGCCAGGGAAACGCGCUAAAAAUAAUACAUCCCGCGUUCCUCUUCACUAAAGCUGCCCC
...(((((..(((((....))))).)))))..((((..((..(((((.((....)).....(((...(....)..)))............)))))..))..))))............... ( -21.70)
>DroEre_CAF1 37314 109 - 1
CAAUUUGUUUGCAACUCAAGUUGCCCAAAA-A--------A--GGAAAGAAAAUUCAAAAAAGCCAGGGGAAAGCGCUAAAAAUAAUACAUCCCGCUUGCCUCUUCACUAAAGCUACCCA
...((((...(((((....))))).)))).-.--------.--((...((....)).........(((((.(((((.................))))).))))).............)). ( -17.73)
>DroYak_CAF1 37541 111 - 1
CAAUUUGUUUGCAACUCAAGUUUCCCAAAA-A--------AAUGGAAAGAAAAUUCAAAAAAGCCAGGGGAAAGCGCUAAAAAUAAUACAUCCCGCUCGCCUCUUCACUAAAGCAACCCA
........((((........(((((.....-.--------...))))).................(((((..((((.................))))..)))))........)))).... ( -16.43)
>consensus
CAAUUUGUUUGCAACUCAAGUUGCCAAAAA_A________AACGGAAAGAAAAUUCAAAAAAGCCAGGGAAAAGCGCUAAAAAUAAUACAUCCCGCUUGCCUCUUCACUAAAGCUACCCA
......(((((((((....))))).........................................(((((((((((.................)))))))))))......))))...... (-14.53 = -15.65 +   1.13)

alignment

secondary structure

dotplot

Window 8

Location	15,118,536 – 15,118,650
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.12
Mean single sequence MFE	-23.14
Consensus MFE	-14.74
Energy contribution	-15.62
Covariance contribution	0.88
Combinations/Pair	1.09
Mean z-score	-1.85
Structure conservation index	0.64
SVM decision value	0.06
SVM RNA-class probability	0.562007
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15118536 114 - 22224390
CACAUG-----ACCGCUUCGGGCAAUUUCAUUUGCCGCUCAGCUCUCACACAAUUGAAAUUUUUGUUGCAUACUUUCAAGCAAUUUGUUUGCAACUCAAGUUGCCAAAAA-AAAAAAAAA
....((-----(..(((..((((((......))))).)..)))..))).....(((.(((((..((((((.((.............)).))))))..)))))..)))...-......... ( -22.72)
>DroSec_CAF1 30263 115 - 1
CACAUG-----ACCGCUUCGGGCAAUUUCAUUUGCCGCUCAGCUCUCACACAAUUGAAAUUUUUGUUGCAUACUUUCAAGCAAUUUGUUUGCAACUCAAGUUGCCACAAAAAAAGAAAAA
....((-----(..(((..((((((......))))).)..)))..)))...........(((((((.(((.((((....((((.....)))).....))))))).)))))))........ ( -24.80)
>DroEre_CAF1 37392 106 - 1
CACAUG-----ACCGCUUCGGGCAAUUUCAUUUGCCGCUCAACUCUCAUACAAUUGAAAUUUUUGUUGCAUACUUUCAAGCAAUUUGUUUGCAACUCAAGUUGCCCAAAA-A--------
......-----........(((((((((.................(((......))).......((((((.((.............)).))))))..)))))))))....-.-------- ( -21.62)
>DroYak_CAF1 37621 106 - 1
CACAUG-----ACCGCUUCGGGCAAUUUCAUUUGCCGCUCAGCUCUCACACAAUUGAAAUUUUUGUUGCAUACUUUCAAGCAAUUUGUUUGCAACUCAAGUUUCCCAAAA-A--------
....((-----(..(((..((((((......))))).)..)))..))).......(((((((..((((((.((.............)).))))))..)))))))......-.-------- ( -24.62)
>DroPer_CAF1 84854 102 - 1
CACAGGGAGGGGGGGCCUUGGGCAAUUUCAUUUUCCGCUUAGCUCUUACACAAUUGAAAUUUUUGUUGCAUACUUUCGAGCAAUUUGUUUGCAGCUCAGC----CA--------------
....(((((..(..(((...)))..)..)...))))(((.(((((..(((.(((((........((.....)).......))))))))..).)))).)))----..-------------- ( -21.96)
>consensus
CACAUG_____ACCGCUUCGGGCAAUUUCAUUUGCCGCUCAGCUCUCACACAAUUGAAAUUUUUGUUGCAUACUUUCAAGCAAUUUGUUUGCAACUCAAGUUGCCAAAAA_A________
..............(((..((((((......))))).)..)))..............(((((..((((((.((.............)).))))))..))))).................. (-14.74 = -15.62 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:06 2006