Locus 1796

Sequence ID 2R_DroMel_CAF1
Location 6,718,209 – 6,718,300
Length 91
Max. P 0.794022
window2984 window2985

overview

Window 4

Location 6,718,209 – 6,718,300
Length 91
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 89.33
Mean single sequence MFE -17.52
Consensus MFE -12.80
Energy contribution -12.76
Covariance contribution -0.04
Combinations/Pair 1.05
Mean z-score -1.99
Structure conservation index 0.73
SVM decision value 0.45
SVM RNA-class probability 0.740424
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6718209 91 + 20766785
CCACUUAAGUAGUCAUCUUCUAUCUUCCGUCAAGAGCGAUCGUCACUCUCUCU--CUC--UUUUUUUUCGUUCGAGAGCGCAUGCACUCGCUCUU
..((..((((((.......))).)))..)).((((((((.((((.(((((...--...--.............))))).).)))...)))))))) ( -17.81)
>DroSec_CAF1 66435 93 + 1
CCACUUAAGUAGUCAUCUUCUAUCUUCCGUCAAGAGCGAUCGUCACUCUCUCU--CUCUUUUUAUUUUCGUUCGAGAGCGCAUGCACUCGCUCUU
..((..((((((.......))).)))..)).((((((((.((((.(((((...--..................))))).).)))...)))))))) ( -17.70)
>DroSim_CAF1 74185 95 + 1
CCACUUAAGCAGUCAUCUUCUAUCUUCCGUCAAGAGCGAUCGUCACUCUCUCUCUCUCUCUUUUUUUUCGUUCGAGAGCGCAUGCACUCGCUCUU
...............................((((((((.((((.(((((.......................))))).).)))...)))))))) ( -16.90)
>DroEre_CAF1 68939 82 + 1
CCACUUAAGUAGUCAUCUUCUAUCUUCUGUCAAGAGCGAUC-UC----UUUCU--CUC--UUUU----CGUACGAGAGCGCAUGCACUCGCUCUU
..((..((((((.......))).)))..)).((((((((..-..----...((--(((--....----.....))))).........)))))))) ( -16.39)
>DroYak_CAF1 67416 87 + 1
CCACUUAAGUAGUCAUCUUCUAUCUUCGGUCAAGAGCGAUCGUC----UUUCU--CUC--UUUCCUUGCGUUCGAGAGCGCAUGCACUCGCUCUU
..(((.((((((.......))).))).))).((((((((..((.----...((--(((--.............))))).....))..)))))))) ( -18.82)
>consensus
CCACUUAAGUAGUCAUCUUCUAUCUUCCGUCAAGAGCGAUCGUCACUCUCUCU__CUC__UUUUUUUUCGUUCGAGAGCGCAUGCACUCGCUCUU
..((..((((((.......))).)))..)).((((((((.........((((.....................))))((....))..)))))))) (-12.80 = -12.76 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,718,209 – 6,718,300
Length 91
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 89.33
Mean single sequence MFE -24.06
Consensus MFE -16.52
Energy contribution -17.96
Covariance contribution 1.44
Combinations/Pair 1.04
Mean z-score -2.69
Structure conservation index 0.69
SVM decision value 0.60
SVM RNA-class probability 0.794022
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6718209 91 - 20766785
AAGAGCGAGUGCAUGCGCUCUCGAACGAAAAAAAA--GAG--AGAGAGAGUGACGAUCGCUCUUGACGGAAGAUAGAAGAUGACUACUUAAGUGG
((((((((.(((((...(((((.............--..)--))))...))).)).))))))))..(....)...........((((....)))) ( -25.56)
>DroSec_CAF1 66435 93 - 1
AAGAGCGAGUGCAUGCGCUCUCGAACGAAAAUAAAAAGAG--AGAGAGAGUGACGAUCGCUCUUGACGGAAGAUAGAAGAUGACUACUUAAGUGG
((((((((.(((((...(((((.................)--))))...))).)).))))))))..(....)...........((((....)))) ( -25.43)
>DroSim_CAF1 74185 95 - 1
AAGAGCGAGUGCAUGCGCUCUCGAACGAAAAAAAAGAGAGAGAGAGAGAGUGACGAUCGCUCUUGACGGAAGAUAGAAGAUGACUGCUUAAGUGG
((((((((.(((((...(((((...................)))))...))).)).)))))))).((..(((.(((.......))))))..)).. ( -25.01)
>DroEre_CAF1 68939 82 - 1
AAGAGCGAGUGCAUGCGCUCUCGUACG----AAAA--GAG--AGAAA----GA-GAUCGCUCUUGACAGAAGAUAGAAGAUGACUACUUAAGUGG
((((((((.........(((((.....----....--)))--))...----..-..))))))))...................((((....)))) ( -20.09)
>DroYak_CAF1 67416 87 - 1
AAGAGCGAGUGCAUGCGCUCUCGAACGCAAGGAAA--GAG--AGAAA----GACGAUCGCUCUUGACCGAAGAUAGAAGAUGACUACUUAAGUGG
((((((((.((..(...(((((...(....)....--)))--))..)----..)).)))))))).((..(((.(((.......))))))..)).. ( -24.20)
>consensus
AAGAGCGAGUGCAUGCGCUCUCGAACGAAAAAAAA__GAG__AGAGAGAGUGACGAUCGCUCUUGACGGAAGAUAGAAGAUGACUACUUAAGUGG
((((((((...(((...(((((.....................))))).)))....)))))))).((..(((.(((.......))))))..)).. (-16.52 = -17.96 +   1.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:22 2006