Locus 2263

Sequence ID	3L_DroMel_CAF1
Location	6,305,911 – 6,306,094
Length	183
Max. P	0.775500

overview

Window 7

Location	6,305,911 – 6,306,014
Length	103
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	79.92
Mean single sequence MFE	-27.68
Consensus MFE	-19.10
Energy contribution	-19.30
Covariance contribution	0.20
Combinations/Pair	1.20
Mean z-score	-1.37
Structure conservation index	0.69
SVM decision value	0.26
SVM RNA-class probability	0.658364
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6305911 103 - 23771897
AACGGUGAGUGCUAAUACUCGACA---UAGCCACAUGGCCAACUUGGCCAAAAUAGAAAACAGUGGGCGUAGGA-CAAGCACAGUGGGCGUAGUGGAUAAUCAAUCA
...((((((((....)))))..((---(.(((...(((((.....)))))..........((.((.((......-...)).)).)))))...)))....)))..... ( -25.60)
>DroSec_CAF1 71577 99 - 1
AACGGUGAGUGCUAGUACUCGACA---UAGCCACAUGGCCAACUUGGCCAAAAUAGAAAACAGUGGGCGUAGGC-CAAGCACAGUGGGCGUAGUGGAUAAU----CA
...((((((((....)))))....---...(((((((.(((.(((((((......................)))-)))).....))).))).))))...))----). ( -29.25)
>DroSim_CAF1 76808 99 - 1
AACGGUGAGUGCUAAUACUCGACA---UAGCCACAUGGCCAACUUGGCCAAAAUAGAAAACAGUGGGCGUAGGC-CAAGCACAGUGGGCGUAGUGGAUAAU----CA
...((((((((....)))))....---...(((((((.(((.(((((((......................)))-)))).....))).))).))))...))----). ( -27.85)
>DroEre_CAF1 73222 98 - 1
AACGGUGAGUGCUAAUACUCCACA---UAGCCACAUGGCCAAGUUGGCCGAAAAAGA-AACAGUGGGCGUAGGC-CAAGCACGGUGGGCACAGUGGCUACU----AA
....(((((((....)))).))).---(((((((.(((((.....))))).....(.-.((.((((((....))-)...))).))...)...)))))))..----.. ( -31.30)
>DroYak_CAF1 79940 99 - 1
AACGGUGAGUGCUAAUACUCGACA---UAGCCACAUGGCCAACUUGGCCAAAUAGGAAAACAGUGGGCGUAGGC-CAGGCACAGUGGGCACAGUGGAUAAU----CA
...((((((((....)))))....---...((((.(((((.(((..(((.....(.....)....(((....))-).)))..))).))).))))))...))----). ( -28.50)
>DroAna_CAF1 70704 90 - 1
AACGGUGAGUACACACACGUCCAAUACUUGCAACAUGGCCAACAUGGCCA---------ACAGUGGGCGGAUGAGUAAACAUGGCGAAGACAGUGGGAA--------
..(.(((..(((.((..((((((............(((((.....)))))---------....))))))..)).)))..))).)...............-------- ( -23.59)
>consensus
AACGGUGAGUGCUAAUACUCGACA___UAGCCACAUGGCCAACUUGGCCAAAAUAGAAAACAGUGGGCGUAGGC_CAAGCACAGUGGGCACAGUGGAUAAU____CA
......(((((....)))))..........((((.(((((.....)))))..........((.((.((..........)).)).))......))))........... (-19.10 = -19.30 +   0.20)

alignment

secondary structure

dotplot

Window 8

Location	6,305,980 – 6,306,094
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.94
Mean single sequence MFE	-37.02
Consensus MFE	-25.24
Energy contribution	-25.10
Covariance contribution	-0.14
Combinations/Pair	1.19
Mean z-score	-1.27
Structure conservation index	0.68
SVM decision value	0.54
SVM RNA-class probability	0.775500
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6305980 114 - 23771897
CCGUGUUGUCGGCGCUGCUAGGCGCCAUCAUCAUGAUUGCCGUGGUGCGCUGCCGGCGCAAAAAGUCCUCCAACAAUCGCAACGGUGAGUGCU--AAUACUCGACA---UAGCCACAUG-
.((((.((..((((((....))))))..)).))))......(((((((((.....)))).....(((........((((...))))(((((..--..)))))))).---..)))))...- ( -39.30)
>DroVir_CAF1 81862 100 - 1
CCGUGCUGUCGGCGCUGCUCGGCGCCAUCAUCAUGAUUGCCGUGGUGCGUUGUCGGCGCAAAAAGUCGUCUAACAAUCGCAAUGGUAAGUACU--AAGCAC--U----------------
..(((((...((((((....))))))..........(((((((..((((((((((((.......))))....)))).))))))))))).....--.)))))--.---------------- ( -36.80)
>DroGri_CAF1 71667 102 - 1
CCGUGCUGUCGGCGCUUCUCGGCGCCAUCAUCAUGAUUGCUGUGGUGCGUUGCCGUCGCAAAAAGUCCUCGAACAAUCGUAAUGGUGAGUAUU--UUGCAGCCU----------------
..(.(((((.((((((....))))))(((((.(((((((.((.((.((.((((....))))...)))).))..))))))).))))).......--..)))))).---------------- ( -34.20)
>DroWil_CAF1 88169 117 - 1
CGGUGUUGUCGGCGCUGCUAGGCGCCAUCAUCAUGAUUGCCGUUGUGCGCUGUCGGCGCAAAAAGUCCUCCAACAAUCGAAAUGGUGAGUACAUGAAAACAAGAAC---UAACCAAGCAU
.(((....((((((((....))))))....(((((.(..(((((.(((((.....)))))....((......))......)))))..)...)))))......))..---..)))...... ( -37.20)
>DroMoj_CAF1 79439 102 - 1
CGGUUCUAUCGGCGCUAUUGGGCGCCAUCAUCAUGAUUGCCGUGGUGCGUUGCCGGCGCAAAAAGUCGUCCAAUAAUCGCAAUGGUGAGUAUU--GAGCCAGCC----------------
.(((((....((((((....))))))....((((.(((((...(((..((((.((((.......))))..)))).)))))))).)))).....--)))))....---------------- ( -36.20)
>DroAna_CAF1 70757 117 - 1
CCGUGUUGUCGGCGCUGCUAGGCGCCAUCAUCAUGAUUGCUGUGGUGCGCUGCCGGCGCAAAAAGUCCUCAAAUAAUCGCAACGGUGAGUACA--CACACGUCCAAUACUUGCAACAUG-
.((((((((.((((((....)))))).........((((.(((((((..((((((..((...................))..)))).))..))--).))))..))))....))))))))- ( -38.41)
>consensus
CCGUGCUGUCGGCGCUGCUAGGCGCCAUCAUCAUGAUUGCCGUGGUGCGCUGCCGGCGCAAAAAGUCCUCCAACAAUCGCAAUGGUGAGUACU__AAGACACCA________________
.((((.((..((((((....))))))..)).)))).(((((((..(((((.....)))))....((......)).......)))))))................................ (-25.24 = -25.10 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:08 2006