Locus 6781

Sequence ID	X_DroMel_CAF1
Location	16,862,775 – 16,862,907
Length	132
Max. P	0.958093

overview

Window 6

Location	16,862,775 – 16,862,878
Length	103
Sequences	3
Columns	105
Reading direction	forward
Mean pairwise identity	84.87
Mean single sequence MFE	-32.07
Consensus MFE	-28.54
Energy contribution	-29.43
Covariance contribution	0.89
Combinations/Pair	1.06
Mean z-score	-2.08
Structure conservation index	0.89
SVM decision value	1.21
SVM RNA-class probability	0.931354
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16862775 103 + 22224390
UGAAGA-AGGCCCAGCAAAUGGGGCCGAGCCACCGAUAUCGUUGGCAUCAGAUGCAUCCAUCAUACAUACAUACAUACAUGUAUCAUGCAAGCAAGCAAGGCUG-
......-.(((((........)))))((((((.((....)).)))).))...(((...(((.((((((..........)))))).)))...)))(((...))).- ( -27.80)
>DroSec_CAF1 61404 94 + 1
UGGAGAUGGGCCCAGCAAAUGGGGCCUAGCCACCGACAUUGGUGGCAUCAGAUGCAUCCAUCAUACAU--------ACAUAUAUCAUGCAAGCG---GAGGCUGG
((((..(((((((........)))))))(((((((....)))))))..........))))........--------..............(((.---...))).. ( -31.00)
>DroSim_CAF1 41438 94 + 1
UGGAGAUGGGCCCAGCAAAUGGGGCCUAGCCACCGACAUCGGUGGCAUCAGAUGCAUACAUCAUACAU--------ACAUGUAUCAUGCAAGCG---GAGGCUGG
......(((((((........)))))))(((((((....)))))))..(((.(((...(((.(((((.--------...))))).)))...)))---....))). ( -37.40)
>consensus
UGGAGAUGGGCCCAGCAAAUGGGGCCUAGCCACCGACAUCGGUGGCAUCAGAUGCAUCCAUCAUACAU________ACAUGUAUCAUGCAAGCG___GAGGCUGG
(((...(((((((........)))))))(((((((....))))))).)))..(((((.....((((((..........)))))).)))))(((.......))).. (-28.54 = -29.43 +   0.89)

alignment

secondary structure

dotplot

Window 7

Location	16,862,775 – 16,862,878
Length	103
Sequences	3
Columns	105
Reading direction	reverse
Mean pairwise identity	84.87
Mean single sequence MFE	-34.30
Consensus MFE	-29.12
Energy contribution	-29.57
Covariance contribution	0.45
Combinations/Pair	1.04
Mean z-score	-2.59
Structure conservation index	0.85
SVM decision value	1.49
SVM RNA-class probability	0.958093
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16862775 103 - 22224390
-CAGCCUUGCUUGCUUGCAUGAUACAUGUAUGUAUGUAUGUAUGAUGGAUGCAUCUGAUGCCAACGAUAUCGGUGGCUCGGCCCCAUUUGCUGGGCCU-UCUUCA
-..((((.((.(((.(.(((.(((((((........))))))).))).).))).((((.((((.((....)).))))))))........)).))))..-...... ( -32.90)
>DroSec_CAF1 61404 94 - 1
CCAGCCUC---CGCUUGCAUGAUAUAUGU--------AUGUAUGAUGGAUGCAUCUGAUGCCACCAAUGUCGGUGGCUAGGCCCCAUUUGCUGGGCCCAUCUCCA
...((.((---(((.((((((.......)--------))))).).)))).))....(((((((((......))))))..(((((........))))).))).... ( -32.70)
>DroSim_CAF1 41438 94 - 1
CCAGCCUC---CGCUUGCAUGAUACAUGU--------AUGUAUGAUGUAUGCAUCUGAUGCCACCGAUGUCGGUGGCUAGGCCCCAUUUGCUGGGCCCAUCUCCA
........---.((.(((((.(((((...--------.))))).))))).))....((((((((((....)))))))..(((((........))))).))).... ( -37.30)
>consensus
CCAGCCUC___CGCUUGCAUGAUACAUGU________AUGUAUGAUGGAUGCAUCUGAUGCCACCGAUGUCGGUGGCUAGGCCCCAUUUGCUGGGCCCAUCUCCA
............((.(.(((.((((((..........)))))).))).).)).......(((((((....)))))))..(((((........)))))........ (-29.12 = -29.57 +   0.45)

alignment

secondary structure

dotplot

Window 8

Location	16,862,810 – 16,862,907
Length	97
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	75.90
Mean single sequence MFE	-20.91
Consensus MFE	-12.51
Energy contribution	-12.59
Covariance contribution	0.08
Combinations/Pair	1.12
Mean z-score	-1.56
Structure conservation index	0.60
SVM decision value	-0.05
SVM RNA-class probability	0.509198
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16862810 97 + 22224390
UAUCGUUGGCAUCAGAUGCAUCCAUCAUACAUACAUACAUACAUGUAUCAUGCAAGCAAGCAAGGCUG---GCAAGCUCAAUCAUUCAUGCAACACCGAA
....((((((((..((((....))))....((((((......)))))).))))..((.(((...))).---)).................))))...... ( -16.90)
>DroSec_CAF1 61440 89 + 1
CAUUGGUGGCAUCAGAUGCAUCCAUCAUACAU--------ACAUAUAUCAUGCAAGCG---GAGGCUGGAGGCAAACUCAAUCAUUCAUGCAACACCGAA
..((((((......((((....))))......--------..........(((((((.---...))).(((.....))).........)))).)))))). ( -19.90)
>DroSim_CAF1 41474 89 + 1
CAUCGGUGGCAUCAGAUGCAUACAUCAUACAU--------ACAUGUAUCAUGCAAGCG---GAGGCUGGAGGCAAACUCAAUCAUUCAUGCAACACCGAA
..((((((((((..(((((((...........--------..)))))))))))..(((---(((....(((.....))).....))).)))..)))))). ( -26.82)
>DroEre_CAF1 46518 74 + 1
AAACGGUGCCACCAGAUGCAUCCAUCGAGC--------------------UGCGGGCG---GAGGAAG---GCAAACUCAAUCAUUCAUGCAACACCGAA
...(((((((.((.((((....))))..((--------------------.....)))---).))...---(((..............)))..))))).. ( -17.54)
>DroYak_CAF1 46210 74 + 1
CAACGGUGGCAUCGGAUGCAUCCAUCAUCC--------------------UGCAGGCG---GAGGAUG---GCAAACUCAAUCAUUCAUGCAACACCGAA
...(((((((((.(((((......((((((--------------------(.(....)---.))))))---)..........)))))))))..))))).. ( -23.39)
>consensus
CAUCGGUGGCAUCAGAUGCAUCCAUCAUACAU________ACAU_UAUCAUGCAAGCG___GAGGCUG___GCAAACUCAAUCAUUCAUGCAACACCGAA
...(((((......((((....))))........................((((.......(((............))).........)))).))))).. (-12.51 = -12.59 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:22:49 2006