Locus 8532

Sequence ID	3R_DroMel_CAF1
Location	22,769,965 – 22,770,074
Length	109
Max. P	0.878349

overview

Window 1

Location	22,769,965 – 22,770,074
Length	109
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	79.17
Mean single sequence MFE	-25.25
Consensus MFE	-17.02
Energy contribution	-17.22
Covariance contribution	0.19
Combinations/Pair	1.05
Mean z-score	-1.52
Structure conservation index	0.67
SVM decision value	0.49
SVM RNA-class probability	0.758334
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22769965 109 + 27905053
UA------GUUAUGUUCAAUUGCACCAUAGCUAUGGCGAUGGCUUCUCCACGCUGUCCGAGAUGAUCAAAUCGCUGACCAUCUACAUGAACAAGGACUACCAUAAGCACCAGCUU
((------(((.((((((...((......)).((((((.(((.....)))))))))...(((((.(((......))).)))))...))))))..)))))....((((....)))) ( -26.10)
>DroVir_CAF1 10857 95 + 1
------------CC--------AUUUGUAGCUAUGGCGAUGGCUUCUCCACCAUAUCCGAGAUGAUCAAAUCCCUGACCAUCUACAUGAACAAGGACUAUCACAAACAGCAGCUG
------------..--------....((.(((...(.(((((.((((....(((.....(((((.(((......))).)))))..)))....))))))))).)....))).)).. ( -18.50)
>DroPse_CAF1 36164 108 + 1
UA------UCUCCCAUCUAU-CACUCACAGCUAUGGCGAUGGUUUCUCCACCCUCUCCGAGAUGAUCAAAUCCCUGACCAUCUACAUGAACAAGGAGUACCACAAGCAGCAGCUG
..------............-......(((((...((..((((..((((....((....(((((.(((......))).)))))....))....)))).))))...))...))))) ( -27.90)
>DroSim_CAF1 5762 111 + 1
UUUUUUUUGUUAUU-UCAA---AACCAAAGCUAUGGCGAUGGCUUCUCCACGCUGUCCGAGAUGAUCAAGUCGCUGACCAUCUACAUGAACAAGGACUACCACAAGCACCAGCUC
....(((((.....-.)))---))....((((..((((.(((.....)))))))((((.(((((.(((......))).)))))..........)))).............)))). ( -22.70)
>DroEre_CAF1 18145 109 + 1
GA------UUUUUGUUGCUUCGAACCACAGCUAUGGCGACGGCUUCUCCACGCUGUCCGAGAUGAUCAAGUCGCUGACCAUCUACAUGAACAAGGACUACCACAAGCAGCAGCUC
..------...(((((((((.(.........(((((.((((((........))))))).(((((.(((......))).))))).)))).....((....)).))))))))))... ( -27.60)
>DroPer_CAF1 36180 108 + 1
UA------UCUCACACCUAU-UACUCACAGCUACGGCGAUGGUUUCUCCACCCUCUCCGAGAUGAUCAAAUCCUUGACCAUCUACAUGAACAAGGAGUACCACAAGCAGCAGCUG
..------............-......(((((.(.((..((((..((((....((....(((((.((((....)))).)))))....))....)))).))))...)).).))))) ( -28.70)
>consensus
UA______UUUAUC_UCAAU__AACCACAGCUAUGGCGAUGGCUUCUCCACCCUGUCCGAGAUGAUCAAAUCCCUGACCAUCUACAUGAACAAGGACUACCACAAGCAGCAGCUG
............................((((...((..(((.(..(((..........(((((.(((......))).)))))..........)))..))))...))...)))). (-17.02 = -17.22 +   0.19)

alignment

secondary structure

dotplot

Window 2

Location	22,769,965 – 22,770,074
Length	109
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	79.17
Mean single sequence MFE	-34.05
Consensus MFE	-25.69
Energy contribution	-25.33
Covariance contribution	-0.36
Combinations/Pair	1.20
Mean z-score	-1.65
Structure conservation index	0.75
SVM decision value	0.90
SVM RNA-class probability	0.878349
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22769965 109 - 27905053
AAGCUGGUGCUUAUGGUAGUCCUUGUUCAUGUAGAUGGUCAGCGAUUUGAUCAUCUCGGACAGCGUGGAGAAGCCAUCGCCAUAGCUAUGGUGCAAUUGAACAUAAC------UA
..(((.(((((.((((..((.(((.(((((((((((((((((....))))))))))......))))))).)))..))..))))))).)).).)).............------.. ( -31.30)
>DroVir_CAF1 10857 95 - 1
CAGCUGCUGUUUGUGAUAGUCCUUGUUCAUGUAGAUGGUCAGGGAUUUGAUCAUCUCGGAUAUGGUGGAGAAGCCAUCGCCAUAGCUACAAAU--------GG------------
.(((..(((...(((((.(((((((..(((....)))..)))))))...)))))..))).(((((((..(....)..))))))))))......--------..------------ ( -28.70)
>DroPse_CAF1 36164 108 - 1
CAGCUGCUGCUUGUGGUACUCCUUGUUCAUGUAGAUGGUCAGGGAUUUGAUCAUCUCGGAGAGGGUGGAGAAACCAUCGCCAUAGCUGUGAGUG-AUAGAUGGGAGA------UA
((((((..((..(((((.((((.(.(((.((.((((((((((....))))))))))))..))).).))))..))))).))..))))))......-............------.. ( -34.10)
>DroSim_CAF1 5762 111 - 1
GAGCUGGUGCUUGUGGUAGUCCUUGUUCAUGUAGAUGGUCAGCGACUUGAUCAUCUCGGACAGCGUGGAGAAGCCAUCGCCAUAGCUUUGGUU---UUGA-AAUAACAAAAAAAA
((((..(.(((.((((..((.(((.(((((((((((((((((....))))))))))......))))))).)))..))..))))))).)..)))---)...-.............. ( -34.00)
>DroEre_CAF1 18145 109 - 1
GAGCUGCUGCUUGUGGUAGUCCUUGUUCAUGUAGAUGGUCAGCGACUUGAUCAUCUCGGACAGCGUGGAGAAGCCGUCGCCAUAGCUGUGGUUCGAAGCAACAAAAA------UC
((((..(.(((.(((((..(.(((.(((((((((((((((((....))))))))))......))))))).)))..)..)))))))).)..)))).............------.. ( -38.10)
>DroPer_CAF1 36180 108 - 1
CAGCUGCUGCUUGUGGUACUCCUUGUUCAUGUAGAUGGUCAAGGAUUUGAUCAUCUCGGAGAGGGUGGAGAAACCAUCGCCGUAGCUGUGAGUA-AUAGGUGUGAGA------UA
(((((((.((..(((((.((((.(.(((.((.((((((((((....))))))))))))..))).).))))..))))).)).)))))))......-............------.. ( -38.10)
>consensus
CAGCUGCUGCUUGUGGUAGUCCUUGUUCAUGUAGAUGGUCAGCGAUUUGAUCAUCUCGGACAGCGUGGAGAAGCCAUCGCCAUAGCUGUGAUU__AUAGA_GAGAAA______UA
.(((((..((..(((((..(((.(((((....((((((((((....)))))))))).)))))....)))...))))).))..)))))............................ (-25.69 = -25.33 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:13:26 2006