Locus 6465

Sequence ID	3R_DroMel_CAF1
Location	17,004,765 – 17,004,879
Length	114
Max. P	0.795201

overview

Window 9

Location	17,004,765 – 17,004,879
Length	114
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	80.02
Mean single sequence MFE	-35.42
Consensus MFE	-25.83
Energy contribution	-25.33
Covariance contribution	-0.50
Combinations/Pair	1.29
Mean z-score	-1.18
Structure conservation index	0.73
SVM decision value	0.13
SVM RNA-class probability	0.598903
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17004765 114 + 27905053
GAGC---CGGUGGCCUUAUGAACUCCAUGAAGGUGGCCAUGCAGAACUUUAGCCAUCGCCAGCAUCCCGCCGUGACGAUAACGAGCGCCGACGGCACGCAAUCAACGGCAAAGAGCA
..((---((.((((.(((((.....))))).((((((..............))))))))))((.....(((((.......))).))(((...)))..))......))))........ ( -34.24)
>DroVir_CAF1 38734 111 + 1
GCGC---CGGCGGCCUCAUGAACUCCAUGAAAGUGGCCAUGCAGCAUUUUGGCCAUAAACAACAUCCCGCCGUAACGAUAACCAAUGCCGAUGGCACCGUCUC---CGCCAAGAGCA
.((.---((((((..(((((.....)))))..(((((((..........)))))))..........))))))...))........((((..((((........---.)))).).))) ( -33.50)
>DroGri_CAF1 29631 114 + 1
GUGCUGGUGGCGGUCUCAUGAAUUCCAUGAAAGUGGCCAUGCAACACUUUGGCCAUCGACAGCAUCCCGCCGUAACGAUAACCAAUGCCGAUGGCACCGUCUC---CGCCAAGAGCA
.((((..((((((..(((((.....))))).....((((((((.....((((..((((((.((.....)).))..))))..)))))))..))))).......)---)))))..)))) ( -37.90)
>DroWil_CAF1 37350 111 + 1
CAAC---UGGUGGCAUCAUGAACUCUAUGAAAGUGGCCAUGCAACACUUUGGACACCGGCAACAUCCCGCUGUAACGAUAACCAAUGCCGAUGGCACUGUCU---CGGCCAAAAGCA
....---((((.((.(((((.....)))))..)).))))(((......(((((((.(((.......))).)))........)))).(((((.(((...))))---)))).....))) ( -25.90)
>DroMoj_CAF1 31226 105 + 1
GCAC---UGGCGGCCUCAUGAAUUCCAUGAAAGUGGCCAUGCAGCACUUUGGUCAUAAGCAACAUCCCGCCGUGACGAUAACCAGUGCUGAUGGCACC---------GCCAAGAGCA
((.(---((((((..(((((.....))))).....(((((.(((((((.(.(((((..((........)).))))).).....)))))))))))).))---------))).)).)). ( -42.60)
>DroAna_CAF1 26064 111 + 1
GAGC---CGGUGGCCUUAUGAACUCCAUGAAGGUGGCCAUGCAGAACUUUGGCCACCGCCAGCACCCCGCCGUGACGAUAACUAACGCCGACGGCAC--AGUCUCC-GCCAAGAGCA
(((.---((.((((.(((((.....))))).((((((((..........)))))))))))).).....((((((.((........)).).)))))..--.).))).-((.....)). ( -38.40)
>consensus
GAGC___CGGCGGCCUCAUGAACUCCAUGAAAGUGGCCAUGCAGCACUUUGGCCAUCGACAACAUCCCGCCGUAACGAUAACCAAUGCCGAUGGCACCGUCUC____GCCAAGAGCA
.......((((((..(((((.....)))))..(((((((..........)))))))..........))))))..............((...((((............))))...)). (-25.83 = -25.33 +  -0.50)

alignment

secondary structure

dotplot

Window 0

Location	17,004,765 – 17,004,879
Length	114
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	80.02
Mean single sequence MFE	-43.72
Consensus MFE	-30.75
Energy contribution	-29.82
Covariance contribution	-0.94
Combinations/Pair	1.39
Mean z-score	-1.63
Structure conservation index	0.70
SVM decision value	0.60
SVM RNA-class probability	0.795201
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17004765 114 - 27905053
UGCUCUUUGCCGUUGAUUGCGUGCCGUCGGCGCUCGUUAUCGUCACGGCGGGAUGCUGGCGAUGGCUAAAGUUCUGCAUGGCCACCUUCAUGGAGUUCAUAAGGCCACCG---GCUC
(((.(((((((((((...((((.((((((..((........))..)))))).))))...))))))).))))....))).((((.((((.(((.....))))))).....)---))). ( -41.60)
>DroVir_CAF1 38734 111 - 1
UGCUCUUGGCG---GAGACGGUGCCAUCGGCAUUGGUUAUCGUUACGGCGGGAUGUUGUUUAUGGCCAAAAUGCUGCAUGGCCACUUUCAUGGAGUUCAUGAGGCCGCCG---GCGC
.(((...((((---(....(((((((((((((((((((((....(((((.....)))))..)))))))..)))))).)))).))))((((((.....)))))).))))))---)).. ( -43.20)
>DroGri_CAF1 29631 114 - 1
UGCUCUUGGCG---GAGACGGUGCCAUCGGCAUUGGUUAUCGUUACGGCGGGAUGCUGUCGAUGGCCAAAGUGUUGCAUGGCCACUUUCAUGGAAUUCAUGAGACCGCCACCAGCAC
((((..(((((---(.....((((((((((((((((((((((..(((((.....))))))))))))))..)))))).)))).)))(((((((.....)))))))))))))..)))). ( -52.80)
>DroWil_CAF1 37350 111 - 1
UGCUUUUGGCCG---AGACAGUGCCAUCGGCAUUGGUUAUCGUUACAGCGGGAUGUUGCCGGUGUCCAAAGUGUUGCAUGGCCACUUUCAUAGAGUUCAUGAUGCCACCA---GUUG
.(((..((((..---.((.(((((((((((((((((.(((((...((((.....)))).))))).)))..)))))).)))).)))).))...(....).....))))..)---)).. ( -31.70)
>DroMoj_CAF1 31226 105 - 1
UGCUCUUGGC---------GGUGCCAUCAGCACUGGUUAUCGUCACGGCGGGAUGUUGCUUAUGACCAAAGUGCUGCAUGGCCACUUUCAUGGAAUUCAUGAGGCCGCCA---GUGC
.((.((.(((---------(((((((((((((((((((((.((.(((......))).))..))))))..))))))).)))))....((((((.....)))))))))))))---).)) ( -45.20)
>DroAna_CAF1 26064 111 - 1
UGCUCUUGGC-GGAGACU--GUGCCGUCGGCGUUAGUUAUCGUCACGGCGGGGUGCUGGCGGUGGCCAAAGUUCUGCAUGGCCACCUUCAUGGAGUUCAUAAGGCCACCG---GCUC
.(((...(.(-((..(((--.((((((.((((........)))))))))).))).))).)(((((((...(..((.(((((......))))).))..)....))))))))---)).. ( -47.80)
>consensus
UGCUCUUGGC____GAGACGGUGCCAUCGGCAUUGGUUAUCGUCACGGCGGGAUGCUGCCGAUGGCCAAAGUGCUGCAUGGCCACUUUCAUGGAGUUCAUGAGGCCACCA___GCUC
.((...(((...........((((((((((((((((((((((...((((.....)))).)))))))))..)))))).)))).)))(((((((.....)))))))...)))...)).. (-30.75 = -29.82 +  -0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:22:08 2006