Locus 1748

Sequence ID	2L_DroMel_CAF1
Location	4,776,851 – 4,777,035
Length	184
Max. P	0.847224

overview

Window 6

Location	4,776,851 – 4,776,962
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	88.55
Mean single sequence MFE	-36.43
Consensus MFE	-31.23
Energy contribution	-32.03
Covariance contribution	0.81
Combinations/Pair	1.10
Mean z-score	-2.00
Structure conservation index	0.86
SVM decision value	0.77
SVM RNA-class probability	0.847224
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4776851 111 + 22407834
AGGGACAGGCCAUUAGCCAUGGAACGAC---------GACGACAACGAAUUGUCAACAACAAGUUGACAAACCGUUGCGCAUACGCCGCGUGUGCGGUGGGCAACUAUUUCCAAGCUGUU
...(((((((.....))).(((((....---------.....(((((..((((((((.....))))))))..)))))((((((((...))))))))((((....)))))))))...)))) ( -39.70)
>DroSec_CAF1 225097 111 + 1
AGGGACAGGCCAUUAGCCAUGGAACGAC---------GACGACAACGAAUUGUCAACAACAAGUUGACAAACCGUUGCGCAUACGCCGCGUGUGCGGUGGGCAACUAUUUCCAAGCUGUU
...(((((((.....))).(((((....---------.....(((((..((((((((.....))))))))..)))))((((((((...))))))))((((....)))))))))...)))) ( -39.70)
>DroSim_CAF1 202078 111 + 1
AGGGACAGGCCAUUAGCCAUGGAACGAC---------GACGACAACGAAUUGUCAACAACAAGUUGACAAACCGUUGCGCAUACGCCGCGUGUGCGGUGGGCAACUAUUUCCAAGCUGUU
...(((((((.....))).(((((....---------.....(((((..((((((((.....))))))))..)))))((((((((...))))))))((((....)))))))))...)))) ( -39.70)
>DroEre_CAF1 213845 114 + 1
AGGGACAGGCCAUUAGCCACGGAACGAC------GACGACGACAACGAAUUGUCAACAACAAGUUGACAAACCGUUGCGCAUACGCCGCGUAUGCGGUGGGCAACUAUUUCCAAGCUGUU
...(((((((.....)))..((((....------........(((((..((((((((.....))))))))..)))))((((((((...))))))))((((....))))))))....)))) ( -39.00)
>DroYak_CAF1 212374 120 + 1
AGGGACAGGCCAUUAGCCACGGAACGACAACAACGACGAGGACAACGAAUUGUCAACAACAAGUUGACAAAGCGUUGCGCAUACGCCGCGUAUGCGGUGGGCAACUAUUUCCAAGCUGUU
...(((((((.....)))..((((..................(((((..((((((((.....))))))))..)))))((((((((...))))))))((((....))))))))....)))) ( -40.10)
>DroAna_CAF1 222754 112 + 1
UGGGACACGCCAUUAGCCACAGAACGACCU--CCGAAGUCGACAAC------UGAACAACAAGUUAACAAAGCGUUGCGCAUACGCCCCGUAUACGCCAAGUAACUAUUUCCAAGCUGUU
(((((.((((..............((((..--.....))))..(((------(........))))......)))).(((.(((((...))))).)))...........)))))....... ( -20.40)
>consensus
AGGGACAGGCCAUUAGCCACGGAACGAC_________GACGACAACGAAUUGUCAACAACAAGUUGACAAACCGUUGCGCAUACGCCGCGUAUGCGGUGGGCAACUAUUUCCAAGCUGUU
.((((...(((....(((......................(.(((((..((((((((.....))))))))..))))))(((((((...)))))))))).)))......))))........ (-31.23 = -32.03 +   0.81)

alignment

secondary structure

dotplot

Window 7

Location	4,776,922 – 4,777,035
Length	113
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	78.25
Mean single sequence MFE	-28.62
Consensus MFE	-21.38
Energy contribution	-22.10
Covariance contribution	0.72
Combinations/Pair	1.09
Mean z-score	-1.21
Structure conservation index	0.75
SVM decision value	0.47
SVM RNA-class probability	0.749727
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4776922 113 + 22407834
AUACGCCGCGUGUGCGGUGGGCAACUAUUUCCAAGCUGUUGCACACUUUCGAGCUCACUAAGCAGCAACUGCUUAUUGGCCCUGCCUCUAUGC-UCGCUCCAUUGUGCUUCAGU
...((((((....))))))(....).........((((..(((((....(((((....(((((((...)))))))..(((...))).....))-)))......)))))..)))) ( -37.80)
>DroSec_CAF1 225168 88 + 1
AUACGCCGCGUGUGCGGUGGGCAACUAUUUCCAAGCUGUUGCACACUUUCGAGCUCACUAAGCAGCAACUGCUUAUUGGCCC--------------------------UUCAGU
...((((((....)))))).(((((............)))))........(.((.((.(((((((...))))))).)))).)--------------------------...... ( -26.60)
>DroSim_CAF1 202149 88 + 1
AUACGCCGCGUGUGCGGUGGGCAACUAUUUCCAAGCUGUUGCACACUUUCGAGCUCACUAAGCAGCAACUGCUUAUUGGCCC--------------------------UUCAGU
...((((((....)))))).(((((............)))))........(.((.((.(((((((...))))))).)))).)--------------------------...... ( -26.60)
>DroEre_CAF1 213919 110 + 1
AUACGCCGCGUAUGCGGUGGGCAACUAUUUCCAAGCUGUUGCACACUUUCGAGCUCACUAAGCAGCUACUGCUUAUUGGCCCUGCCUCUGCG----UACCCUUCGUCCUUCAGC
..(((..(.((((((((.(((((...........((....))........(.((.((.(((((((...))))))).)))).)))))))))))----))).)..)))........ ( -32.70)
>DroYak_CAF1 212454 114 + 1
AUACGCCGCGUAUGCGGUGGGCAACUAUUUCCAAGCUGUUGCACACUUUCGAGCUCACUAAGCAGCUACUGCUUAUUGGCCCUGCCUCUAUGCCUCUAUGCAUCGUCCUGUAGC
...((((((....)))))).(((((............)))))..........((.((.(((((((...))))))).)))).((((..(.((((......)))).)....)))). ( -31.30)
>DroAna_CAF1 222826 107 + 1
AUACGCCCCGUAUACGCCAAGUAACUAUUUCCAAGCUGUUGCACACUUUCGAGCUCACUAAGCAGCGUCACCUUAUUGGCCAUGCCACA-----CCACUGCAUCGAAUUUCG--
(((((...))))).......(((((............))))).....((((((((.....))).((((..((.....))..))))....-----........))))).....-- ( -16.70)
>consensus
AUACGCCGCGUAUGCGGUGGGCAACUAUUUCCAAGCUGUUGCACACUUUCGAGCUCACUAAGCAGCAACUGCUUAUUGGCCCUGCCUCU_________U_CAUCGU_CUUCAGU
...((((((....)))))).(((((............)))))..........((.((.(((((((...))))))).)))).................................. (-21.38 = -22.10 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:09 2006