Locus 3956

Sequence ID	2L_DroMel_CAF1
Location	11,525,172 – 11,525,362
Length	190
Max. P	0.844362

overview

Window 9

Location	11,525,172 – 11,525,286
Length	114
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	81.66
Mean single sequence MFE	-44.85
Consensus MFE	-33.20
Energy contribution	-34.02
Covariance contribution	0.81
Combinations/Pair	1.41
Mean z-score	-2.09
Structure conservation index	0.74
SVM decision value	0.76
SVM RNA-class probability	0.844362
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11525172 114 + 22407834
AGAUUCGUGUUGCUGUGCGUUUGGGUGGCAGCCGAAUAGCUAGGUGGAGCUGGCUUGUAUGCCGGGUUGUAGGCUGGCGGACGCUCAUGUAUGUUGGUGUGAGCUCCGCCCACU
..(((((.(((((..(.(....).)..)))))))))).....((((((.(((((......))))).)).......((((((.(((((..(......)..))))))))))))))) ( -49.20)
>DroSim_CAF1 6524 114 + 1
AGGUUCGUGUUGCUGUGCGUUUGGGUGGCAGCCGAAUAACUGGGUGGAGCUGGCUUGUAAGCCGGGUUGUAGGCUGGCGGCCGCUCAUGUAUGUUGGUAUGAGCUCCGCCCACU
..(((((.(((((..(.(....).)..))))))))))...((((((((...((((.((.((((........)))).))))))(((((((........))))))))))))))).. ( -52.30)
>DroEre_CAF1 6310 114 + 1
AGAUUCGUGUUGCCGUGCGUUUGGGUGGCGGCUGAAUAGCUGGGUGGAGCUGGCUUGUACGCCGGGUUGUAGGCUGGUGGUCGCUCAUGUAUGUUGGUGUGAGCUCCGCCCACU
..(((((.((((((((.(....).)))))))))))))((.(((((((((((.((.....((((((.(....).))))))...(((.((....)).))))).))))))))))))) ( -46.40)
>DroWil_CAF1 38478 103 + 1
--AUUACUGUU------GGUAU---UGGCUGCCGAGUAACUCGGUGGCGGCGGUUUAUAUGAUGGAUUGUAUGCUGGAGGGCGUUCAUGUAUAUUGGUAUGAGCUCCACCCACU
--.........------(((((---..((..(((((...)))))..)).(((((((((...))))))))))))))((..((.(((((((........))))))).))..))... ( -34.20)
>DroYak_CAF1 6817 114 + 1
AGAUUCGUGUUGCUGUGCGUUUGUGUGGCGGCCGAGUAGCUGGGUGGAGCUGGCUUGUAUGCCGGAUUGUAGGCUGGCGGGCGCUCAUGUAUGUUGGUGUGAGCUCCGCCCACU
..(((((.(((((((..(....)..))))))))))))((.(((((((((((.(((.....(((........))).))).)))(((((..(......)..))))))))))))))) ( -52.50)
>DroAna_CAF1 2772 111 + 1
AGAUUCGUGUU---GUGCGUCUGGGUGGCAGCAGGAUAACUGGGUGGUGCCGGUCUGUACGAUGGAUUGUAGGCUGGUGGUUUCUCGUGGAUGUUGGUGUGAGCACCUCCCACA
.......((((---.((((((.....))).))).))))...(((.(.(((((((((..((((....))))))))))))).)..)))((((.....((((....))))..)))). ( -34.50)
>consensus
AGAUUCGUGUUGCUGUGCGUUUGGGUGGCAGCCGAAUAACUGGGUGGAGCUGGCUUGUAUGCCGGAUUGUAGGCUGGCGGGCGCUCAUGUAUGUUGGUGUGAGCUCCGCCCACU
..(((((.(((((((..(....)..))))))))))))...(((((((((((((((((((........)))))))))))....(((((((........))))))))))))))).. (-33.20 = -34.02 +   0.81)

alignment

secondary structure

dotplot

Window 0

Location	11,525,246 – 11,525,362
Length	116
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	74.99
Mean single sequence MFE	-40.11
Consensus MFE	-22.07
Energy contribution	-23.21
Covariance contribution	1.14
Combinations/Pair	1.30
Mean z-score	-1.71
Structure conservation index	0.55
SVM decision value	0.52
SVM RNA-class probability	0.767530
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11525246 116 - 22407834
CACCCGCGUCACCAAUUGGCUGGAAUGUCCCAGCAAAGCCCCAAGGACCUCCGCCGGCGUACUCAGCCUCGAAUCCAGUGGGCGGAGCUCACACCAACAUACAUGAGCGUCCGCCA
(((.....((.......(((.(((..((((..............)))).))))))(((.......)))..)).....)))(((((((((((............))))).)))))). ( -37.74)
>DroVir_CAF1 29676 112 - 1
CAA-CGCCUCGCCCAUUGGCUGGAACGUG---CCCAAGGCGCAGGGUCCGCCGCCUGCCUACUCGGCCACUAAUCCGGUUGGUGGUGCUCGCACCAAUGUGCACGAGCCGCCGCCA
...-((.(((((((((..((((((..(((---.((.((..(((((........)))))...)).)).)))...))))))..)))).))..((((....))))..))).))...... ( -46.20)
>DroWil_CAF1 38541 116 - 1
CCACUGCCUCACCCAUUGGCUGGAAUGUACCACCAAAGAAUCAAGGUCCACCGCCGGCCUAUUCGGUCUCAAAUCCAGUGGGUGGAGCUCAUACCAAUAUACAUGAACGCCCUCCA
.....((..((((((((((((((..((.(((.............))).))...)))))).....((........))))))))))..))............................ ( -32.22)
>DroYak_CAF1 6891 116 - 1
CGCCCGCCUCACCAUAUGGCUGGAAUGUCCAAUCCAAGCCCCAAGGACCUCCGCCGGCGUACUCACCCUCGAAUCCAGUGGGCGGAGCUCACACCAACAUACAUGAGCGCCCGCCA
((((.((..........(((((((........))).))))....((....)))).))))....(((...........)))(((((.(((((............)))))..))))). ( -36.20)
>DroMoj_CAF1 31360 113 - 1
CA---GCCUCGCCCAUAGGCUGGAAUGUGCCGCCCAAGGCGCAGGGUCCGCCGCCCUCCUAUACGGCCCACAAUCCGGCUGGCGGUGCUCACACCAACAUACACGAGCCGCCGCCG
.(---(((..(((....))).(((.((((((......))))))(((.(((.............))))))....)))))))((((((((((..............))).))))))). ( -48.16)
>DroAna_CAF1 2843 116 - 1
CCCCAGCUCCCGCAAUCGGAUGGAAUGUUCCAUCCAAGGCGCAAGGACCGCCGCCGGCUUACUCGGCCUCGAAUCCUGUGGGAGGUGCUCACACCAACAUCCACGAGAAACCACCA
...((.((((((((...(((((((....)))))))..((((.......))))(((((.....))))).........)))))))).))(((..............)))......... ( -40.14)
>consensus
CACCCGCCUCACCAAUUGGCUGGAAUGUCCCACCCAAGGCGCAAGGACCGCCGCCGGCCUACUCGGCCUCGAAUCCAGUGGGCGGAGCUCACACCAACAUACACGAGCGCCCGCCA
..................((((((....................((....))(((((.....)))))......)))))).((((((((((..............)))).)))))). (-22.07 = -23.21 +   1.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:44 2006