Locus 1901

Sequence ID	X_DroMel_CAF1
Location	5,275,894 – 5,276,157
Length	263
Max. P	0.935421

overview

Window 1

Location	5,275,894 – 5,276,000
Length	106
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	85.78
Mean single sequence MFE	-33.30
Consensus MFE	-24.19
Energy contribution	-26.12
Covariance contribution	1.94
Combinations/Pair	1.07
Mean z-score	-1.60
Structure conservation index	0.73
SVM decision value	0.20
SVM RNA-class probability	0.632112
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5275894 106 - 22224390
AUCGCAGUCGAUCAGCUCUUGGGAAACACGCUCCCGAUCCUGAUCCUGCUGCUGCUGCUGCUGCAGUCUGGACAACUCGCUCAUGUUGAUA-----GUAUCUUCAAUGCGA
.((((.(((((((((...((((((.......))))))..))))))..(((((.((....)).)))))...)))...........(((((..-----......))))))))) ( -35.20)
>DroSec_CAF1 12796 111 - 1
AUCGCAGUCGAUCAGCUCUUGGGAAACACGCUCCCGAUCCUGAUCCUGCUGCUGCUGCUGCUGCAGUCUGGACAACUCGCUCAUGUUGAUAUGUAUGUAUCUUCAAUGCGA
.((((((((((((((...((((((.......))))))..))))))..(((((.((....)).)))))...)))..........((..(((((....)))))..)).))))) ( -36.90)
>DroSim_CAF1 7461 111 - 1
AUCGCAGUCGAUCAGCUCUUGGGAAACACGCUCCCGAUCCUGAUCCUGCUGCUGCUGCUGCUGCAGUCUGGACAACUCGCUCAUGUUGAUAUGUAAGUAUCUUCUAUGCGA
.((((((((((((((...((((((.......))))))..))))))..(((((.((....)).)))))...)))..............(((((....))))).....))))) ( -36.10)
>DroYak_CAF1 8284 91 - 1
AUCGCAGUCGAUCAGCUCCUGGGGAACUUGCUCCUGAUCCU------------GCUGCUGCUGCAGUCUGGACAACUCGCUCAUGUUGAUC--------UCUUCUUUGGGA
.((.(((..(((((((....((((......))))((.(((.------------(((((....)))))..)))))..........)))))))--------......))).)) ( -25.00)
>consensus
AUCGCAGUCGAUCAGCUCUUGGGAAACACGCUCCCGAUCCUGAUCCUGCUGCUGCUGCUGCUGCAGUCUGGACAACUCGCUCAUGUUGAUA_____GUAUCUUCAAUGCGA
.((((((((((((((...((((((.......))))))..))))))........(((((....)))))...)))..............(((((....))))).....))))) (-24.19 = -26.12 +   1.94)

alignment

secondary structure

dotplot

Window 2

Location	5,275,929 – 5,276,038
Length	109
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	85.15
Mean single sequence MFE	-34.40
Consensus MFE	-26.83
Energy contribution	-29.20
Covariance contribution	2.37
Combinations/Pair	1.07
Mean z-score	-1.55
Structure conservation index	0.78
SVM decision value	0.19
SVM RNA-class probability	0.624737
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5275929 109 - 22224390
--UCCUCCACCUUGGAGGUCGUAUCCUCCACAAAGUCAAUAUCGCAGUCGAUCAGCUCUUGGGAAACACGCUCCCGAUCCUGAUCCUGCUGCUGCUGCUGCUGCAGUCUGG
--....(((...((((((......)))))).............(((((.((((((...((((((.......))))))..))))))..))))).(((((....))))).))) ( -38.40)
>DroSec_CAF1 12836 109 - 1
--UCCCCCACCUUGGAGGCCGCCACCUCCUCAAAGUCAAUAUCGCAGUCGAUCAGCUCUUGGGAAACACGCUCCCGAUCCUGAUCCUGCUGCUGCUGCUGCUGCAGUCUGG
--....(((....(((((......)))))..............(((((.((((((...((((((.......))))))..))))))..))))).(((((....))))).))) ( -37.10)
>DroSim_CAF1 7501 109 - 1
--UCCCCCACCUUGGAGGCCGCCACCUCCUCAAAGUCAAUAUCGCAGUCGAUCAGCUCUUGGGAAACACGCUCCCGAUCCUGAUCCUGCUGCUGCUGCUGCUGCAGUCUGG
--....(((....(((((......)))))..............(((((.((((((...((((((.......))))))..))))))..))))).(((((....))))).))) ( -37.10)
>DroYak_CAF1 8316 99 - 1
CAACCCCCACCUCGGAGGUCGUAUCAUCCAAAGAGGCAAUAUCGCAGUCGAUCAGCUCCUGGGGAACUUGCUCCUGAUCCU------------GCUGCUGCUGCAGUCUGG
..(((.((.....)).))).(((...(((..((..((...((((....))))..))..))..)))...))).......((.------------(((((....)))))..)) ( -25.00)
>consensus
__UCCCCCACCUUGGAGGCCGCAACCUCCACAAAGUCAAUAUCGCAGUCGAUCAGCUCUUGGGAAACACGCUCCCGAUCCUGAUCCUGCUGCUGCUGCUGCUGCAGUCUGG
......(((....(((((......)))))..............(((((.((((((...((((((.......))))))..))))))..))))).(((((....))))).))) (-26.83 = -29.20 +   2.37)

alignment

secondary structure

dotplot

Window 3

Location	5,276,038 – 5,276,157
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.84
Mean single sequence MFE	-44.70
Consensus MFE	-37.48
Energy contribution	-38.40
Covariance contribution	0.92
Combinations/Pair	1.09
Mean z-score	-1.90
Structure conservation index	0.84
SVM decision value	1.24
SVM RNA-class probability	0.935421
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5276038 119 - 22224390
ACCUGGCCUCCUCCUCGGCCAGCAGGAUCAUGGCCUGCUCCAGCAUGCGCUGCACCUUGGUCACCUUCUUCAGGGCUUUGGUGUAUCGCUUGGAACUGGCUGGUGGCAUCCUGGCCUCC-
....((((....((((((((((((((.......)))))(((((...(((.((((((..(((..(((.....))))))..)))))).))))))))..))))))).))......))))...- ( -49.10)
>DroSec_CAF1 12945 116 - 1
ACCUGGCCUCUUCCUCGGCCAGCAGGAUCAUGGCCUGCUCCAGCAUGCGCUGCACCUUGGUCACCAUCUUCAGGGCUUUGGUGUAUCGCUUGGAACUGG---GUGGCAUCCUGGCCUCC-
..((((((........))))))((((((....(((.((.((((((.(((.((((((..((((.(........)))))..)))))).))).))...))))---)))))))))))......- ( -47.20)
>DroSim_CAF1 7610 116 - 1
ACCUGGCCUCUUCCUCGGCCAGCAGGAUCAUGGCCUGCUCCAGCAUGCGCUGCACCUUGGUCACCUUCUUCAGGGCUUUGGUGUAUCGCUUGGAACUGG---GUGGCAUCCUGGCCUCC-
..((((((........))))))((((((....(((.((.((((((.(((.((((((..(((..(((.....))))))..)))))).))).))...))))---)))))))))))......- ( -47.40)
>DroEre_CAF1 12732 112 - 1
ACCUGGCCUCCUCCUCGGCCAGCAGGAUCAGGGCCUGGUCCAGCAUGCGCUGCACCUUGCUUACCUUCUGCAGGGCUUUGGUGUAUCGCUUGGAAGUGG---GUGGCAUCCUGAC-----
..((((((........))))))(((((((...(((((.((((((((((((((..((((((.........))))))...)))))))).)).))))..)))---)).).))))))..----- ( -46.80)
>DroYak_CAF1 8535 117 - 1
ACUUGAACUCCUCCUCGGACAGCAGAAUCAGUGCGUGUCCCAGCAUGCGCUCCACCUUAGUCACCUUAUUCAUGGCUUUGGUGUAUCGCUUGUUACUGG---AUGGCAUCCUGACAUCGC
.........(((((...((((((......(((((((((....))))))))).((((..(((((.........)))))..))))....)).))))...))---).)).............. ( -33.00)
>consensus
ACCUGGCCUCCUCCUCGGCCAGCAGGAUCAUGGCCUGCUCCAGCAUGCGCUGCACCUUGGUCACCUUCUUCAGGGCUUUGGUGUAUCGCUUGGAACUGG___GUGGCAUCCUGGCCUCC_
..((((((........))))))((((((....(((....((((((.(((.((((((..((((...........))))..)))))).))).))...)))).....)))))))))....... (-37.48 = -38.40 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:27 2006