Locus 3526

Sequence ID	3R_DroMel_CAF1
Location	9,525,992 – 9,526,083
Length	91
Max. P	0.707152

overview

Window 9

Location	9,525,992 – 9,526,083
Length	91
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	75.32
Mean single sequence MFE	-19.33
Consensus MFE	-13.90
Energy contribution	-13.90
Covariance contribution	0.00
Combinations/Pair	1.17
Mean z-score	-1.01
Structure conservation index	0.72
SVM decision value	0.37
SVM RNA-class probability	0.707152
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9525992 91 + 27905053
-CGUACAGUG---------UACCCAGCCACCACCCACCCACAACCCUCGGAAAAUGUUUGUUUUCCGAAGCGGCAAAAAUGCUGAGCC-----ACUUGUCUUUGCU
-.(.((((((---------...........................(((((((((....)))))))))..(((((....)))))...)-----)).))))...... ( -18.40)
>DroPse_CAF1 2857 87 + 1
-UUUGCAG------------------CCAAUGCACACCUACGCCACUCGCCUCAAGCGAGUCCGACGAAGCGGCAAAAAUGCUGAGCCCCGGCAUUUGCCUUCCCC
-..((((.------------------....))))......((..((((((.....)))))).)).......(((((..((((((.....)))))))))))...... ( -25.30)
>DroSec_CAF1 2999 88 + 1
GUGUACAGUG---------UACCCA-C---CACCCACCCACAACCCUCGGAAAAUGUUUGUUUUCCGAAGCGGCAAAAAUGCUGAGCC-----ACUUGUCUUUGCU
(((.((((((---------......-.---................(((((((((....)))))))))..(((((....)))))...)-----)).)))...))). ( -18.30)
>DroSim_CAF1 3000 91 + 1
GUGUACAGUG---------UACCCA-CCACCACCCACCCACAACCCUCGGAAAAUGUUUGUUUUCCGAAGCGGCAAAAAUGCUGAGCC-----ACUUGUCUUUGCU
(((.((((((---------......-....................(((((((((....)))))))))..(((((....)))))...)-----)).)))...))). ( -18.30)
>DroEre_CAF1 3106 81 + 1
-CAUACAGU-------------------ACCCACCACCCACAAACCUCGGAAAAUGUUUAUUUUCCGAAGCGGCAAAAAUGCUGAGCC-----ACUUGUCUUUGCU
-.....(((-------------------(.................(((((((((....)))))))))..(((((....)))))....-----.........)))) ( -15.30)
>DroYak_CAF1 3144 99 + 1
-CCUACAGUACAUGCCCUCUACGCA-CCACCCACCACCCACAACCCUCGGAAAAUGUUUGUUUUCCGAAGCGGCAAAAAUGCUGAGCC-----ACUUGUAUUUGCU
-.....((((.((((.......((.-....................(((((((((....)))))))))..(((((....))))).)).-----....)))).)))) ( -20.40)
>consensus
_CGUACAGUG_________UACCCA_CCACCACCCACCCACAACCCUCGGAAAAUGUUUGUUUUCCGAAGCGGCAAAAAUGCUGAGCC_____ACUUGUCUUUGCU
....((((......................................(((((((((....)))))))))..(((((....)))))...........))))....... (-13.90 = -13.90 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	9,525,992 – 9,526,083
Length	91
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	75.32
Mean single sequence MFE	-29.75
Consensus MFE	-16.60
Energy contribution	-16.72
Covariance contribution	0.11
Combinations/Pair	1.11
Mean z-score	-1.62
Structure conservation index	0.56
SVM decision value	0.33
SVM RNA-class probability	0.691713
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9525992 91 - 27905053
AGCAAAGACAAGU-----GGCUCAGCAUUUUUGCCGCUUCGGAAAACAAACAUUUUCCGAGGGUUGUGGGUGGGUGGUGGCUGGGUA---------CACUGUACG-
.......(((.((-----((((((((...((..((.((((((((((......))))))))))......))..)).....))))))).---------))))))...- ( -30.30)
>DroPse_CAF1 2857 87 - 1
GGGGAAGGCAAAUGCCGGGGCUCAGCAUUUUUGCCGCUUCGUCGGACUCGCUUGAGGCGAGUGGCGUAGGUGUGCAUUGG------------------CUGCAAA-
.(((..(((....)))....))).(((((..((((((((((((..((((((.....)))))))))).))))).)))..))------------------.)))...- ( -34.10)
>DroSec_CAF1 2999 88 - 1
AGCAAAGACAAGU-----GGCUCAGCAUUUUUGCCGCUUCGGAAAACAAACAUUUUCCGAGGGUUGUGGGUGGGUG---G-UGGGUA---------CACUGUACAC
.......(((.((-----((((((.(((((...(((((((((((((......)))))))))....))))..)))))---.-))))).---------)))))).... ( -28.20)
>DroSim_CAF1 3000 91 - 1
AGCAAAGACAAGU-----GGCUCAGCAUUUUUGCCGCUUCGGAAAACAAACAUUUUCCGAGGGUUGUGGGUGGGUGGUGG-UGGGUA---------CACUGUACAC
.......(((.((-----((((((.((((((..((.((((((((((......))))))))))......))..)).)))).-))))).---------)))))).... ( -28.70)
>DroEre_CAF1 3106 81 - 1
AGCAAAGACAAGU-----GGCUCAGCAUUUUUGCCGCUUCGGAAAAUAAACAUUUUCCGAGGUUUGUGGGUGGUGGGU-------------------ACUGUAUG-
.......(((.((-----(.((((.(((((.....((((((((((((....))))))))))))....))))).)))))-------------------)))))...- ( -26.90)
>DroYak_CAF1 3144 99 - 1
AGCAAAUACAAGU-----GGCUCAGCAUUUUUGCCGCUUCGGAAAACAAACAUUUUCCGAGGGUUGUGGGUGGUGGGUGG-UGCGUAGAGGGCAUGUACUGUAGG-
......((((.((-----((((((.(((((..(((.((.(((((((......))))))))))))...))))).))))).(-(((.......)))).)))))))..- ( -30.30)
>consensus
AGCAAAGACAAGU_____GGCUCAGCAUUUUUGCCGCUUCGGAAAACAAACAUUUUCCGAGGGUUGUGGGUGGGUGGUGG_UGGGUA_________CACUGUACA_
...................((((((((....)))..((((((((((......))))))))))....)))))................................... (-16.60 = -16.72 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:25 2006