Locus 1263

Sequence ID	2L_DroMel_CAF1
Location	3,351,776 – 3,351,866
Length	90
Max. P	0.967270

overview

Window 6

Location	3,351,776 – 3,351,866
Length	90
Sequences	5
Columns	91
Reading direction	forward
Mean pairwise identity	72.33
Mean single sequence MFE	-26.84
Consensus MFE	-17.22
Energy contribution	-17.54
Covariance contribution	0.32
Combinations/Pair	1.20
Mean z-score	-1.76
Structure conservation index	0.64
SVM decision value	1.29
SVM RNA-class probability	0.938173
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3351776 90 + 22407834
GGUGUCCCCCACUCGGCUUGUGAGAUGUAAUUAAGCAGAUACGGC-UGCCUUUCGGAUUUGCCGAAGGGGAUAUCCCCAACGUGCUGAGUG
.........((((((((.(((.............((((......)-)))..(((((.....)))))((((....)))).))).)))))))) ( -32.00)
>DroSec_CAF1 42591 91 + 1
GGUGUCCCCCACUCAGCUUGCAAGAUGUAAUUAAGCAGAUAUGUCGUGUCUUUCGGAUUCACCGAAGGGGAUAUCCCCAACGAGCUGAGUG
.........(((((((((((................((((((...))))))(((((.....)))))((((....))))..))))))))))) ( -32.70)
>DroSim_CAF1 38547 91 + 1
GGUGUCCCCCACUCAGCCUGCAAGAUGUAAUUAAGCAGAUAUGUCGUGUCUUUCGGAUUUACCGAAGGGGAUAUCCCCAACGAGCUGAGUG
.........((((((((((((.............)))).....((((....(((((.....)))))((((....)))).)))))))))))) ( -33.52)
>DroEre_CAF1 37277 70 + 1
GAUGUCCUUCACUCGGCC--CAAAAUGUAAUUAAGCAGA-----------------UGUU--UUUAGGGGAUAUCCCCAGCGAGCUGAGUG
.........((((((((.--(....(((......)))..-----------------....--....((((....))))...).)))))))) ( -21.50)
>DroYak_CAF1 38202 72 + 1
CAUGUCCUUCAUUCUUUU--UCAGAUGUAAUUGAGCUGG-----------------AUUCACCGAAGGGUAUAUCCCCAACGAGCUGAGUG
..................--.........(((.((((((-----------------((..(((....)))..))))......)))).))). ( -14.50)
>consensus
GGUGUCCCCCACUCAGCUUGCAAGAUGUAAUUAAGCAGAUA_G_C_UG_CUUUCGGAUUUACCGAAGGGGAUAUCCCCAACGAGCUGAGUG
.........((((((((........(((......))).............................((((....)))).....)))))))) (-17.22 = -17.54 +   0.32)

alignment

secondary structure

dotplot

Window 7

Location	3,351,776 – 3,351,866
Length	90
Sequences	5
Columns	91
Reading direction	reverse
Mean pairwise identity	72.33
Mean single sequence MFE	-25.99
Consensus MFE	-12.61
Energy contribution	-15.30
Covariance contribution	2.69
Combinations/Pair	1.16
Mean z-score	-2.12
Structure conservation index	0.49
SVM decision value	1.61
SVM RNA-class probability	0.967270
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3351776 90 - 22407834
CACUCAGCACGUUGGGGAUAUCCCCUUCGGCAAAUCCGAAAGGCA-GCCGUAUCUGCUUAAUUACAUCUCACAAGCCGAGUGGGGGACACC
(((((.((.....((((....))))(((((.....)))))(((((-(......))))))...............)).)))))(....)... ( -29.30)
>DroSec_CAF1 42591 91 - 1
CACUCAGCUCGUUGGGGAUAUCCCCUUCGGUGAAUCCGAAAGACACGACAUAUCUGCUUAAUUACAUCUUGCAAGCUGAGUGGGGGACACC
((((((((((((.((((....))))(((((.....)))))....))))......(((.............))).))))))))(....)... ( -32.42)
>DroSim_CAF1 38547 91 - 1
CACUCAGCUCGUUGGGGAUAUCCCCUUCGGUAAAUCCGAAAGACACGACAUAUCUGCUUAAUUACAUCUUGCAGGCUGAGUGGGGGACACC
((((((((((((.((((....))))(((((.....)))))....)))).....((((.............))))))))))))(....)... ( -35.32)
>DroEre_CAF1 37277 70 - 1
CACUCAGCUCGCUGGGGAUAUCCCCUAAA--AACA-----------------UCUGCUUAAUUACAUUUUG--GGCCGAGUGAAGGACAUC
..((..(((((..((((....))))....--....-----------------...((((((.......)))--))))))))..))...... ( -19.60)
>DroYak_CAF1 38202 72 - 1
CACUCAGCUCGUUGGGGAUAUACCCUUCGGUGAAU-----------------CCAGCUCAAUUACAUCUGA--AAAAGAAUGAAGGACAUG
..(((((....))))).......(((((((.....-----------------))............(((..--...)))..)))))..... ( -13.30)
>consensus
CACUCAGCUCGUUGGGGAUAUCCCCUUCGGUAAAUCCGAAAG_CA_G_C_UAUCUGCUUAAUUACAUCUUGCAAGCCGAGUGGGGGACACC
(((((.(((.((.((((....))))(((((.....)))))..............................)).))).)))))......... (-12.61 = -15.30 +   2.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:05 2006