Locus 7032

Sequence ID	3R_DroMel_CAF1
Location	18,542,710 – 18,542,806
Length	96
Max. P	0.850658

overview

Window 1

Location	18,542,710 – 18,542,806
Length	96
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	78.69
Mean single sequence MFE	-20.65
Consensus MFE	-17.93
Energy contribution	-17.48
Covariance contribution	-0.44
Combinations/Pair	1.14
Mean z-score	-0.92
Structure conservation index	0.87
SVM decision value	0.04
SVM RNA-class probability	0.555559
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18542710 96 + 27905053
CGAGUACUGCAGGCCCACCGUGGCGGGCGACAUGGAAAUCACUGAUUCAAUGGGUAAUGCAUCUACAA-AAC---GCA---ACGGAAAA-----------GAGAGAG-AAC--CAA--A
...(((.((((.((((((((((........))))).((((...))))...)))))..))))..)))..-...---...---........-----------.......-...--...--. ( -18.50)
>DroVir_CAF1 9500 100 + 1
UGAGUAUUGCAAGCCCACCGUGGCGGGCGACAUGGAAAUCACUGAUUCAAUGGGCAAUGCAUCUACAA--AC---GCA---AAAAAAAAA----------ACAACAGAAAUG-CAAUAA
....(((((((.((((((((((........))))).((((...))))...)))))..(((........--..---)))---.........----------..........))-))))). ( -23.40)
>DroGri_CAF1 9915 97 + 1
UGAGUAUUGUAAGCCCACCGUGGCAGGUGACAUGGAAAUCACUGAAUCAAUGGGCAAUGCAUCUACAA--AC---GCA---AAAGGAAAA----------A-AAAG--UACGCCAAUA-
...(((((....(((((...(((..(((((........)))))...))).)))))..(((........--..---)))---.........----------.-..))--))).......- ( -19.70)
>DroWil_CAF1 9898 111 + 1
GGAGUAUUGUAAGCCCACUGUGGCGGGCGACAUGGAAAUCACUGAUUCAAUGGGUAAUGCAUCUACAAGAAC---GCAAAAACGGAAACGGAAACAUAACAUAACAA-AAC--CAA--A
((.(((.((((.(((((.((...(((..((........)).)))...)).)))))..))))..)))......---.......((....)).................-..)--)..--. ( -21.10)
>DroMoj_CAF1 9629 96 + 1
UGAGUAUUGCAAGCCCACCGUGGCGGGCGACAUGGAAAUCACUGAUUCAAUGGGCAAUGCAUCUACAA--AC---GCA---AAUAAAAUA----------A-AACA--GAUG-CAACA-
...(((((((..((((.(....).))))..(((.(((........))).))).)))))))........--..---(((---.........----------.-....--..))-)....- ( -22.29)
>DroAna_CAF1 12728 96 + 1
GGAGUACUGCAGGCCCACCGUGGCGGGCGACAUGGAAAUCACUGAUUCAAUGGGUAAUGCAUCUACAA-AACAAAGCA---ACGGAAAA-------------GAGAG-AAC--CA---A
((.(((.((((.((((((((((........))))).((((...))))...)))))..))))..)))..-.........---.(......-------------)....-..)--).---. ( -18.90)
>consensus
UGAGUAUUGCAAGCCCACCGUGGCGGGCGACAUGGAAAUCACUGAUUCAAUGGGCAAUGCAUCUACAA__AC___GCA___AAGGAAAAA__________A_AACAG_AAC__CAA__A
...(((.((((.((((((((((........))))).((((...))))...)))))..))))..)))..................................................... (-17.93 = -17.48 +  -0.44)

alignment

secondary structure

dotplot

Window 2

Location	18,542,710 – 18,542,806
Length	96
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	78.69
Mean single sequence MFE	-24.67
Consensus MFE	-17.64
Energy contribution	-17.70
Covariance contribution	0.06
Combinations/Pair	1.11
Mean z-score	-1.56
Structure conservation index	0.72
SVM decision value	0.79
SVM RNA-class probability	0.850658
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18542710 96 - 27905053
U--UUG--GUU-CUCUCUC-----------UUUUCCGU---UGC---GUU-UUGUAGAUGCAUUACCCAUUGAAUCAGUGAUUUCCAUGUCGCCCGCCACGGUGGGCCUGCAGUACUCG
.--.((--(..-.((.((.-----------..(((...---((.---((.-.(((....)))..)).))..)))..)).))...)))(((.((((((....))))))..)))....... ( -22.40)
>DroVir_CAF1 9500 100 - 1
UUAUUG-CAUUUCUGUUGU----------UUUUUUUUU---UGC---GU--UUGUAGAUGCAUUGCCCAUUGAAUCAGUGAUUUCCAUGUCGCCCGCCACGGUGGGCUUGCAAUACUCA
.(((((-((..........----------.........---(((---((--(....))))))..((((((((.....(((((......)))))......)))))))).))))))).... ( -28.30)
>DroGri_CAF1 9915 97 - 1
-UAUUGGCGUA--CUUU-U----------UUUUCCUUU---UGC---GU--UUGUAGAUGCAUUGCCCAUUGAUUCAGUGAUUUCCAUGUCACCUGCCACGGUGGGCUUACAAUACUCA
-(((((.....--....-.----------.........---(((---((--(....))))))..((((((((...(((((((......)))).)))...))))))))...))))).... ( -26.00)
>DroWil_CAF1 9898 111 - 1
U--UUG--GUU-UUGUUAUGUUAUGUUUCCGUUUCCGUUUUUGC---GUUCUUGUAGAUGCAUUACCCAUUGAAUCAGUGAUUUCCAUGUCGCCCGCCACAGUGGGCUUACAAUACUCC
.--..(--((.-((((...(.((((...........((...(((---(((......))))))..)).(((((...))))).....)))).)((((((....))))))..)))).))).. ( -22.20)
>DroMoj_CAF1 9629 96 - 1
-UGUUG-CAUC--UGUU-U----------UAUUUUAUU---UGC---GU--UUGUAGAUGCAUUGCCCAUUGAAUCAGUGAUUUCCAUGUCGCCCGCCACGGUGGGCUUGCAAUACUCA
-(((((-((..--....-.----------.........---(((---((--(....))))))..((((((((.....(((((......)))))......)))))))).))))))).... ( -28.10)
>DroAna_CAF1 12728 96 - 1
U---UG--GUU-CUCUC-------------UUUUCCGU---UGCUUUGUU-UUGUAGAUGCAUUACCCAUUGAAUCAGUGAUUUCCAUGUCGCCCGCCACGGUGGGCCUGCAGUACUCC
.---..--...-.....-------------........---......((.-((((((..........(((((...)))))...........((((((....)))))))))))).))... ( -21.00)
>consensus
U__UUG__GUU_CUGUU_U__________UUUUUCCGU___UGC___GU__UUGUAGAUGCAUUACCCAUUGAAUCAGUGAUUUCCAUGUCGCCCGCCACGGUGGGCUUGCAAUACUCA
.....................................................(((..((((...(((((((.....(((((......)))))......)))))))..)))).)))... (-17.64 = -17.70 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:35:55 2006