Locus 1981

Sequence ID	2R_DroMel_CAF1
Location	7,478,393 – 7,478,523
Length	130
Max. P	0.687553

overview

Window 6

Location	7,478,393 – 7,478,513
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.68
Mean single sequence MFE	-34.20
Consensus MFE	-29.68
Energy contribution	-28.02
Covariance contribution	-1.66
Combinations/Pair	1.42
Mean z-score	-0.96
Structure conservation index	0.87
SVM decision value	0.32
SVM RNA-class probability	0.687553
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7478393 120 + 20766785
GUCGGAGAACGACAUCUUGGAGUGCCCCAUCUGGGUGCUCAUCGUUAAUGUGGUGGCCAUGGAUAUGCUGAAGAGCAAACUGCCACCAGGUGGGUUCAUCAAAGCCAUGUCCCAUGCAGA
((((.....))))......(((..(((.....)))..)))........(((((((((...((...((((....))))..))))))))..(((((..(((.......))).)))))))).. ( -40.40)
>DroPse_CAF1 119495 109 + 1
AUCGGAGAGCGAUGUCUUGGAGUGCCCCAUUUGGGUGCUCAUUGUGAAUGUGGUAGCCAUGGAUAUGCUCAAGAGCAAGCUGCCACCAGGUGAGUUAAUG-----CACAGCACA------
.((.((((......)))).))(((((((....))).(((((((......((((((((........((((....)))).))))))))..))))))).....-----....)))).------ ( -34.90)
>DroGri_CAF1 96531 105 + 1
AUCGGAGAAUGACAUUUUGGAGUGCCCCAUUUGGGUGCUCAUUGUGAAUGUGGUAGCCAUGGAUAUGCUAAAGAGCAAACUGCCGCCAGGUGAGUU-AUG-----UGCA---------AG
...((...((.((((((..(((..(((.....)))..))).....)))))).))..)).((.(((((((....))).(((((((....))).))))-)))-----).))---------.. ( -31.90)
>DroWil_CAF1 125933 114 + 1
GUCAGAGAAUGACAUUUUGGAGUGCCCCAUUUGGGUGCUUAUUGUUAAUGUGGUAGCCAUGGAUAUGCUAAAGAGCAAACUGCCACCAGGUGAGACAAUUGGUUGUUUGUCGUU------
((((.....))))..(((((((..(((.....)))..))).........((((((((....)...((((....))))..)))))))))))...(((((........)))))...------ ( -32.20)
>DroAna_CAF1 90861 104 + 1
GUCGGAGAACGAUGUCCUGGAGUGUCCCAUUUGGGUGCUCAUUGUCAAUGUGGUGGCCAUGGAUAUGCUAAAGAGCAAACUGCCACCAGGUAGGCUCUACACA-C---------------
((((.....))))......(((((.(((....))))))))...(((.((.(((((((...((...((((....))))..))))))))).)).)))........-.--------------- ( -33.40)
>DroPer_CAF1 89380 109 + 1
AUCGGAGAGCGAUGUCUUGGAGUGCCCCAUUUGGGUGCUCAUUGUGAAUGUGGUAGCCAUGGAUAUGCUCAAAAGCAAGUUGCCACCAGGUGAGUUAAUG-----CACAGCACA------
......((((.((((((..(((..(((.....)))..))).........((((...))))))))))))))....((((.(..((....))..).)...))-----)........------ ( -32.40)
>consensus
AUCGGAGAACGACAUCUUGGAGUGCCCCAUUUGGGUGCUCAUUGUGAAUGUGGUAGCCAUGGAUAUGCUAAAGAGCAAACUGCCACCAGGUGAGUUAAUG_____CACA_C_CA______
((((.....))))..(((((((..(((.....)))..))).........((((((((....)...((((....))))..))))))))))).............................. (-29.68 = -28.02 +  -1.66)

alignment

secondary structure

dotplot

Window 7

Location	7,478,433 – 7,478,523
Length	90
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	71.11
Mean single sequence MFE	-22.37
Consensus MFE	-15.78
Energy contribution	-15.70
Covariance contribution	-0.08
Combinations/Pair	1.20
Mean z-score	-0.73
Structure conservation index	0.71
SVM decision value	-0.03
SVM RNA-class probability	0.518802
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7478433 90 + 20766785
AUCGUUAAUGUGGUGGCCAUGGAUAUGCUGAAGAGCAAACUGCCACCAGGUGGGUUCAUCAAAGCCAUGUCCCAUGCAGAUUUG----------------AGUCU---U
.(((....(((((((((...((...((((....))))..))))))))..(((((..(((.......))).))))))))....))----------------)....---. ( -23.90)
>DroPse_CAF1 119535 70 + 1
AUUGUGAAUGUGGUAGCCAUGGAUAUGCUCAAGAGCAAGCUGCCACCAGGUGAGUUAAUG-----CACAGCACA----------------------------------C
..((((...((((((((........((((....)))).))))))))...(((........-----)))..))))----------------------------------. ( -19.50)
>DroSec_CAF1 94845 75 + 1
AUCGUCAAUGUGGUGGCCAUGGAUAUGCUGAAGAGCAAGCUGCCACCAGGUGGGUUCAUCGAAGCCAUAUCCCA----------------------------------U
.......(((((((..(.((((((.((((....))))..(..((....))..))))))).)..)))))))....----------------------------------. ( -22.30)
>DroSim_CAF1 87181 75 + 1
AUCGUCAAUGUGGUGGCCAUGGAUAUGCUGAAGAGCAAGCUGCCACCAGGUGGGUUCAUCGAAGCCAUAUCCCA----------------------------------C
.......(((((((..(.((((((.((((....))))..(..((....))..))))))).)..)))))))....----------------------------------. ( -22.30)
>DroYak_CAF1 93241 108 + 1
AUCGUCAACGUGGUGGCCAUGGAUAUGCUGAAGAGCAAGCUGCCGCCAGGUGGGUUCAUCGAAGCCAUAUCACGUGCAGAUUUGGCUGCUAGUCUUUUUUUGUUUUUU-
..........(((..((((......((((....))))..((((((....((((.(((...))).))))....)).))))...))))..))).................- ( -30.10)
>DroPer_CAF1 89420 70 + 1
AUUGUGAAUGUGGUAGCCAUGGAUAUGCUCAAAAGCAAGUUGCCACCAGGUGAGUUAAUG-----CACAGCACA----------------------------------C
..((((...((((((((........((((....)))).))))))))...(((........-----)))..))))----------------------------------. ( -16.10)
>consensus
AUCGUCAAUGUGGUGGCCAUGGAUAUGCUGAAGAGCAAGCUGCCACCAGGUGGGUUCAUCGAAGCCAUAUCACA__________________________________C
.......((.(((((((...((...((((....))))..))))))))).)).......................................................... (-15.78 = -15.70 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:00 2006