Locus 3194

Sequence ID	3L_DroMel_CAF1
Location	9,306,618 – 9,306,762
Length	144
Max. P	0.659450

overview

Window 4

Location	9,306,618 – 9,306,722
Length	104
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	67.45
Mean single sequence MFE	-37.73
Consensus MFE	-20.41
Energy contribution	-19.48
Covariance contribution	-0.94
Combinations/Pair	1.17
Mean z-score	-1.46
Structure conservation index	0.54
SVM decision value	0.26
SVM RNA-class probability	0.659450
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9306618 104 - 23771897
GCGAAGUGCUGAGUCAAGUGUCAACUGCAAAUGACAUUUGCAUUUCGCUGGCAGG--GAUCAAGGGGCUGAUGACGGGGGGAGG------GAGGCUCUGGAACCGCUCCGGU--------
(((((((((.((((((..(((.....)))..)))).)).)))))))))(((.(((--(.((.((((.((..(..(....)..).------.)).)))).)).)).)))))..-------- ( -35.20)
>DroPse_CAF1 173013 102 - 1
GCGAAGUGCUGAGUCAAGUGUCAACUGCAAAUGACAUUUGCAUUUCGCUGGCAGCCGGUACAGCGGGUUAC------------------UGGCAAAGGGGAAUGGCCACGGCUACUCCAC
(((((((((.((((((..(((.....)))..)))).)).))))))))).....(((((((........)))------------------)))).....(((.((((....)))).))).. ( -40.20)
>DroAna_CAF1 166718 103 - 1
GCGAAGUGCUGAGUCAAGUGUCAACUGCAAAUGACAUUUGCAUUUUGCUGGCCGG-----CAAGGGAAUGGCGGUAGGGUGUGCCGGGGUGUCGCGGGGGAACCGCUC------------
(((((((((.((((((..(((.....)))..)))).)).)))))))))..((((.-----((......)).))))..((....))........((((.....))))..------------ ( -35.30)
>DroPer_CAF1 174234 102 - 1
GCGAAGUGCUGAGUCAAGUGUCAACUGCAAAUGACAUUUGCAUUUCGCUGGCAGCCGGUACAGCGGGUUAC------------------UGGCAAAGGGGAAUGGCCACGGCUACUCCAC
(((((((((.((((((..(((.....)))..)))).)).))))))))).....(((((((........)))------------------)))).....(((.((((....)))).))).. ( -40.20)
>consensus
GCGAAGUGCUGAGUCAAGUGUCAACUGCAAAUGACAUUUGCAUUUCGCUGGCAGC__GUACAACGGGUUAC__________________UGGCAAAGGGGAACCGCCACGGC________
(((((((((.((((((..(((.....)))..)))).)).))))))))).(((.(......)...............................((........)))))............. (-20.41 = -19.48 +  -0.94)

alignment

secondary structure

dotplot

Window 5

Location	9,306,644 – 9,306,762
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	83.99
Mean single sequence MFE	-37.45
Consensus MFE	-26.56
Energy contribution	-26.38
Covariance contribution	-0.19
Combinations/Pair	1.04
Mean z-score	-1.57
Structure conservation index	0.71
SVM decision value	0.12
SVM RNA-class probability	0.595398
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9306644 118 - 23771897
CAAAGACGCAGGUGAAAACCCCAAAGUGCCCUAGGACAGUGCGAAGUGCUGAGUCAAGUGUCAACUGCAAAUGACAUUUGCAUUUCGCUGGCAGG--GAUCAAGGGGCUGAUGACGGGGG
..................((((.....(((((..(((.(((((((((((.((((((..(((.....)))..)))).)).)))))))))..))...--).))..))))).......)))). ( -37.50)
>DroPse_CAF1 173044 110 - 1
-GAUGACGCAGGUGAAAACCCCAAAGUGCCUUAGGACAGUGCGAAGUGCUGAGUCAAGUGUCAACUGCAAAUGACAUUUGCAUUUCGCUGGCAGCCGGUACAGCGGGUUAC---------
-.....(((.(((....))).....(((((...((.....(((((((((.((((((..(((.....)))..)))).)).)))))))))......))))))).)))......--------- ( -37.70)
>DroAna_CAF1 166746 113 - 1
--AAGACGCAGGUGAAAACCCCAAAGUGCCCUAGGACAGUGCGAAGUGCUGAGUCAAGUGUCAACUGCAAAUGACAUUUGCAUUUUGCUGGCCGG-----CAAGGGAAUGGCGGUAGGGU
--....(((.(((....)))((....((((...((.(...(((((((((.((((((..(((.....)))..)))).)).)))))))))..)))))-----))..))....)))....... ( -36.90)
>DroPer_CAF1 174265 110 - 1
-GAUGACGCAGGUGAAAACCCCAAAGUGCCUUAGGACAGUGCGAAGUGCUGAGUCAAGUGUCAACUGCAAAUGACAUUUGCAUUUCGCUGGCAGCCGGUACAGCGGGUUAC---------
-.....(((.(((....))).....(((((...((.....(((((((((.((((((..(((.....)))..)))).)).)))))))))......))))))).)))......--------- ( -37.70)
>consensus
_GAAGACGCAGGUGAAAACCCCAAAGUGCCCUAGGACAGUGCGAAGUGCUGAGUCAAGUGUCAACUGCAAAUGACAUUUGCAUUUCGCUGGCAGC__GUACAACGGGUUAC_________
..........(((....)))((...((.(....).))...(((((((((.((((((..(((.....)))..)))).)).)))))))))................)).............. (-26.56 = -26.38 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:46 2006