Locus 1840

Sequence ID	3R_DroMel_CAF1
Location	5,273,350 – 5,273,509
Length	159
Max. P	0.976605

overview

Window 6

Location	5,273,350 – 5,273,469
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	94.08
Mean single sequence MFE	-32.86
Consensus MFE	-28.33
Energy contribution	-28.88
Covariance contribution	0.56
Combinations/Pair	1.06
Mean z-score	-1.69
Structure conservation index	0.86
SVM decision value	0.55
SVM RNA-class probability	0.780035
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5273350 119 - 27905053
CUGACCAGUUAUGGUUACAAUGCGAUUUCUAGUGCCAGGUGCGAAUAUGCCCUUUUUGGAAAUUUGCACAUUUGCGCCAGAAACAUGUUGAAUUUCAACUAA-ACUACGACCGCUCGGAC
((((.(.((..(((((.......(.(((((.((((...((((((((...((......))..))))))))....)))).))))))..((((.....))))..)-))))..)).).)))).. ( -33.50)
>DroVir_CAF1 46290 119 - 1
CUGACCAGUUAUGGUUACAAUGCGAUUUCUAGUGCCAGGUGCGAAUAUGCCCUUUUUGGAAAUUUGCACAUUCGCGCCAGAGACAUGUUGAAUUUCAACUAA-ACUACGACCGUUCGGAC
((((.(.((..(((((.......(.(((((.((((...((((((((...((......))..))))))))....)))).))))))..((((.....))))..)-))))..)).).)))).. ( -33.60)
>DroGri_CAF1 56717 119 - 1
CUGACCAGUAAUGGUAACAAUGCGAUUUCUAGUGCCAGGUGCGAAAAUGCCCUUUUUGGAAAUUUGCACAUUAGCGCCAGAAACAUGUUGAAUUUCAACUAA-ACUACGACCGUUCGGAC
(((((((....))))......(((.(((((.((((...(((((((....((......))...)))))))....)))).)))))...((((.....))))...-........))).))).. ( -29.70)
>DroWil_CAF1 58012 119 - 1
GUGACCAGUUAUGGUUACAAUGCGAUUUCUAGUGCCAGGUGCGAAAAUGCCCUUUUUCGAAAUUUGCACAUUUGCGCCAGAAACAUGUUGAAUUUCAACUAA-ACUACGACCAUUUGGAC
(((((((....)))))))....((.(((((.((((...(((((((.................)))))))....)))).)))))...((((.....))))...-....)).((....)).. ( -29.73)
>DroMoj_CAF1 48024 119 - 1
CUGACCAGUUAUGGUUACAAUGCGAUUUCUAGUGCCAGGUGCGAAUAUGCCUUUUUUGGAAAUUUGCACAUUUGCGCCAGAAGCAUGUUGAAUUUCAACUAA-ACUACGACCGUUCGGAC
((((.(.((..(((((...((((...((((.((((...((((((((...((......))..))))))))....)))).))))))))((((.....))))..)-))))..)).).)))).. ( -36.80)
>DroAna_CAF1 44531 120 - 1
CUGACCAGUUAUGGUUACAAUGCGAUUUCUAGUGCCAGGUGCGAAUAUGCCCUUUUUGGAAAUUUGCACAUUUGCGCCAGAAACAUGUAGAAUUCCAAAAAACACUACGCCCGUUGGGGC
.((((((....))))))......(.(((((.((((...((((((((...((......))..))))))))....)))).))))))..((((..............))))((((....)))) ( -33.84)
>consensus
CUGACCAGUUAUGGUUACAAUGCGAUUUCUAGUGCCAGGUGCGAAUAUGCCCUUUUUGGAAAUUUGCACAUUUGCGCCAGAAACAUGUUGAAUUUCAACUAA_ACUACGACCGUUCGGAC
.((((((....))))))((((..(.(((((.((((...((((((((...((......))..))))))))....)))).))))))..))))....................((....)).. (-28.33 = -28.88 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	5,273,389 – 5,273,509
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	94.67
Mean single sequence MFE	-36.50
Consensus MFE	-33.87
Energy contribution	-34.40
Covariance contribution	0.53
Combinations/Pair	1.03
Mean z-score	-1.59
Structure conservation index	0.93
SVM decision value	1.77
SVM RNA-class probability	0.976605
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5273389 120 - 27905053
UCUGUUCAAUUAGAUAUUGCGCUUUGGCAAUGGCACUCGGCUGACCAGUUAUGGUUACAAUGCGAUUUCUAGUGCCAGGUGCGAAUAUGCCCUUUUUGGAAAUUUGCACAUUUGCGCCAG
........((((((.((((((((..(((....)).)..)))((((((....))))))....))))).))))))....(((((((((.(((((.....))......))).))))))))).. ( -37.40)
>DroPse_CAF1 50136 120 - 1
UCUGCUCAAUUAGAAACUGCGCUUUGGCAAUGGCGUUCGGCUGACCAGUAAUGGUUACAAUGCGAUUUCUAGUGCCAGGUGCGAAUAUGCCCUUUUUGGAAAUUUGCACAUUUGCGCCAG
((((......))))..((((((.((((((.((((((...(.((((((....)))))))...)))....))).))))))((((((((...((......))..))))))))....))).))) ( -37.30)
>DroGri_CAF1 56756 120 - 1
UCUGUUCAAUUAGAAACUGCGCCUUGGCAAUGGCAUUCGGCUGACCAGUAAUGGUAACAAUGCGAUUUCUAGUGCCAGGUGCGAAAAUGCCCUUUUUGGAAAUUUGCACAUUAGCGCCAG
((((......))))..((((((.((((((((.(((((.(....((((....))))..)))))).))......))))))(((((((....((......))...)))))))....))).))) ( -34.90)
>DroWil_CAF1 58051 120 - 1
UCUGUUCAAUUAGACAUUGCGCUUUGGCAAUGGCACUCGGGUGACCAGUUAUGGUUACAAUGCGAUUUCUAGUGCCAGGUGCGAAAAUGCCCUUUUUCGAAAUUUGCACAUUUGCGCCAG
((((......))))....((((..(((((((((((((((.(((((((....)))))))....)))......))))))....((((((......))))))....)))).))...))))... ( -36.80)
>DroMoj_CAF1 48063 120 - 1
UUUGUUCAAUUAGAUACUGCGCUUUGGCAAUGGCACUCGGCUGACCAGUUAUGGUUACAAUGCGAUUUCUAGUGCCAGGUGCGAAUAUGCCUUUUUUGGAAAUUUGCACAUUUGCGCCAG
................((((((.((((((.(((...(((..((((((....)))))).....)))...))).))))))((((((((...((......))..))))))))....))).))) ( -35.30)
>DroPer_CAF1 50679 120 - 1
UCUGCUCAAUUAGAAACUGCGCUUUGGCAAUGGCGUUCGGCUGACCAGUAAUGGUUACAAUGCGAUUUCUAGUGCCAGGUGCGAAUAUGCCCUUUUUGGAAAUUUGCACAUUUGCGCCAG
((((......))))..((((((.((((((.((((((...(.((((((....)))))))...)))....))).))))))((((((((...((......))..))))))))....))).))) ( -37.30)
>consensus
UCUGUUCAAUUAGAAACUGCGCUUUGGCAAUGGCACUCGGCUGACCAGUAAUGGUUACAAUGCGAUUUCUAGUGCCAGGUGCGAAUAUGCCCUUUUUGGAAAUUUGCACAUUUGCGCCAG
((((......))))....((((.((((((.(((...(((..((((((....)))))).....)))...))).))))))((((((((...((......))..))))))))....))))... (-33.87 = -34.40 +   0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:49 2006