Locus 2267

Sequence ID	3L_DroMel_CAF1
Location	6,329,507 – 6,329,633
Length	126
Max. P	0.746960

overview

Window 3

Location	6,329,507 – 6,329,604
Length	97
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	77.82
Mean single sequence MFE	-29.37
Consensus MFE	-16.93
Energy contribution	-17.99
Covariance contribution	1.06
Combinations/Pair	1.04
Mean z-score	-1.77
Structure conservation index	0.58
SVM decision value	0.46
SVM RNA-class probability	0.746960
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6329507 97 + 23771897
------GGUG----AGCUGUUGCUGAA---GCUGCUUCAGCUCCGAUCGUUUUCCGUACAUCAUUUCUAUGCUGUAUUUAUUGCCCGGUCGCAGUGAUCAUCGCGUUCGC
------((((----((((((.((((((---(...)))))))...(((((......(((((.(((....))).)))))........))))))))))..)))))((....)) ( -27.84)
>DroVir_CAF1 106341 92 + 1
------GGAU----GGCUG--GCUAGA---G-AGUUAGAGCUGCGAUCAUUUUCCGUACAUCAUUUCUAUGGUGUAUUUAUUGCCUGGUCGCAAUGAUCAUCGCGGU--C
------....----..(((--(((...---.-)))))).((((((((........(((((((((....)))))))))(((((((......)))))))..))))))))--. ( -28.80)
>DroPse_CAF1 123424 104 + 1
------GAAGCUGAAGCCGAAGCUGAAUCUGCUGCUUCAGCUGCGAUCGUUUUCCGUACAUCAUUUCUAUGCUGUAUUUAUUGCCCGGUCGCAAUGAUCAUCGCGUUCUC
------..(((((((((...(((.......))))))))))))(((((........(((((.(((....))).)))))(((((((......)))))))..)))))...... ( -33.00)
>DroGri_CAF1 96957 98 + 1
GGGAUGAAAU----GGCCG--GCUAGA---G-AGUUAGAGCUGCGAUCAUUUUCCGUACAUCAUUUCUAUGGUGUAUUUAUUGCCUGGUCGCAAUGAUCAUCGCGGU--C
(.(((((...----(((((--(((...---.-)))).).)))(((((((......(((((((((....)))))))))........))))))).....))))).)...--. ( -28.44)
>DroAna_CAF1 94744 91 + 1
------GAUGCUGAUGCUGAAGCUGAA---GCUGCUUCAGCUGCGAUCGUUUUCCGUACAUCAUUUCUAUGGUGUAUUUAUUGCCCCGGCCCA------AUCGCAU----
------.........((((((((....---...))))))))((((((........(((((((((....))))))))).....((....))...------)))))).---- ( -30.30)
>DroPer_CAF1 129380 104 + 1
------GAAGCUGAAGCCGAAGCUGAAUCUGCUGCUUCAUCUGCGAUCGUUUUCCGUACAUCAUUUCUAUGCUGUAUUUAUUGCCCGGUCGCAAUGAUCAUCGCGUUCUC
------(((((((((((...(((.......)))))))))..((((((((......(((((.(((....))).)))))........)))))))).........)).))).. ( -27.84)
>consensus
______GAAG____AGCCGAAGCUGAA___GCUGCUUCAGCUGCGAUCGUUUUCCGUACAUCAUUUCUAUGCUGUAUUUAUUGCCCGGUCGCAAUGAUCAUCGCGUU__C
...............((....((((((........))))))((((((((......(((((.(((....))).)))))........)))))))).........))...... (-16.93 = -17.99 +   1.06)

alignment

secondary structure

dotplot

Window 4

Location	6,329,531 – 6,329,633
Length	102
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	82.35
Mean single sequence MFE	-28.80
Consensus MFE	-16.00
Energy contribution	-17.03
Covariance contribution	1.03
Combinations/Pair	1.11
Mean z-score	-2.40
Structure conservation index	0.56
SVM decision value	0.08
SVM RNA-class probability	0.574468
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6329531 102 + 23771897
CAGCUCCGAUCGUUUUCCGUACAUCAUUUCUAUGCUGUAUUUAUUGCCC-GGUCGCAGUGAUCAUCGCGUUCGC------UGGGCCUCCAUUUCCGUUUCUGCGACUGC
...........((.....(((((.(((....))).))))).....)).(-((((((((.(((....((....))------(((....))).....))).))))))))). ( -22.90)
>DroVir_CAF1 106362 98 + 1
GAGCUGCGAUCAUUUUCCGUACAUCAUUUCUAUGGUGUAUUUAUUGCCU-GGUCGCAAUGAUCAUCGCGGU--C------UGGGCCUCCAUUUCCGUUGCUC--ACUGC
((((((((((((......(((((((((....)))))))))........)-))))))).........((((.--.------(((....)))...)))).))))--..... ( -31.74)
>DroGri_CAF1 96984 98 + 1
GAGCUGCGAUCAUUUUCCGUACAUCAUUUCUAUGGUGUAUUUAUUGCCU-GGUCGCAAUGAUCAUCGCGGU--C------UGGGCCUCCAUUUCCGUUGUUC--ACCUC
((((((((((((......(((((((((....)))))))))........)-))))))).........((((.--.------(((....)))...)))).))))--..... ( -29.34)
>DroWil_CAF1 114771 109 + 1
GAGCUACGAUAAUUUUCCGUACAUCAUUUCUAUGGUGUAUUUAUUGCCCUGGUCGCAAUGAUCAUCGCAUUGCCAGCUUUGGGGCCUCCAUUUCCGUUUUCUUGACUGC
(((..(((..........(((((((((....))))))))).....((((((((.((((((.......))))))..)))..))))).........))).)))........ ( -26.70)
>DroMoj_CAF1 104441 98 + 1
GAGCUGCGAUCAUUUUCCGUACAUCAUUUCUAUGGUGUAUUUAUUGCCU-GGUCGCAAUGAUCAUCGCGCU--C------UGUGCCUCCAUUUCCGCUGUAC--AGUGU
((((.(((((........(((((((((....)))))))))(((((((..-....)))))))..))))))))--)------..............((((....--)))). ( -28.60)
>DroAna_CAF1 94772 92 + 1
CAGCUGCGAUCGUUUUCCGUACAUCAUUUCUAUGGUGUAUUUAUUGCCC-CGGCCCA------AUCGCAU----------UGGGCCUCCAUUUCCGUUUCUGCGGCUGC
((((((((...((.....(((((((((....))))))))).....))..-.((((((------((...))----------))))))..............)))))))). ( -33.50)
>consensus
GAGCUGCGAUCAUUUUCCGUACAUCAUUUCUAUGGUGUAUUUAUUGCCC_GGUCGCAAUGAUCAUCGCGUU__C______UGGGCCUCCAUUUCCGUUGCUC__ACUGC
.(((((((((........(((((((((....)))))))))(((((((.......)))))))..))))))............(((........))))))........... (-16.00 = -17.03 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:14 2006