Locus 2524

Sequence ID 3R_DroMel_CAF1
Location 6,872,479 – 6,872,583
Length 104
Max. P 0.650290
window4129 window4130

overview

Window 9

Location 6,872,479 – 6,872,583
Length 104
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 75.95
Mean single sequence MFE -24.02
Consensus MFE -3.78
Energy contribution -4.62
Covariance contribution 0.84
Combinations/Pair 1.16
Mean z-score -1.59
Structure conservation index 0.16
SVM decision value 0.24
SVM RNA-class probability 0.650290
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6872479 104 + 27905053
GUU-------GGCAAUGAGGCUUUUUAGCUUACUUCAAGGUGAAGGUUGCUUACUUAAGGAGUUAUCCUA--CUUGUAUUCCUGUAUUUCU-UGGAAUGCCAAAUUGUUUUCUU
((.-------((((((.(((((....))))).((((.....)))))))))).))...((((....)))).--...(((((((.........-.))))))).............. ( -26.30)
>DroSec_CAF1 26734 104 + 1
GUU-------GGCAAUAAGGCUUUUUGGUU-UAUUC-UGGUGAAGGUUGCUCACUUAAGGAGUUAUCUUAUGCUUGUAUUCCUGUAUUUCU-UGGAAAGCCAAAUUGUUUUCUU
(..-------((((((..((((((((((..-(((..-.(((((((((.((((.(....))))).))))).)))).)))..)).........-.))))))))..))))))..).. ( -24.90)
>DroSim_CAF1 27034 89 + 1
GUU-------GGC---------------UU-ACUUC-UGGUGAAGGUUGCUCACUUAAGGAGUUAUCUUAUGCUUGUAUUCCUGUAUUUCU-UGGAAGUCCAAAUUGUUUUCUU
.((-------((.---------------..-(((((-..(..(((((.((((.(....))))).)))))((((..........))))...)-..)))))))))........... ( -17.10)
>DroEre_CAF1 27685 103 + 1
GUU-------GGCAAUGAGGCUUUUGGCCUUAACUC-UGUCGCUAUUUUCUCACUUAAGGAGUAAUCUU--GUUUGUACUUCUGUAUUUCU-UGAAAGCCCAAACUGUUUUUUU
(((-------(((..((((((.....))))))....-.................((((((((((.....--((....)).....)))))))-)))..)))..)))......... ( -20.70)
>DroYak_CAF1 27399 111 + 1
GUUGGCAAUUGGCAAUGAGGCUUUUUGCCUUACCUC-UGGCGCAGGUUGCUCACUUAAGGCGUUAUCUU--GCUGGUAUUCCUGUAUUUCCAAGAAAGCCCAAAUUGUUUUUUU
((.((((((..((..((((((.....))))))((..-.)).))..)))))).))....((.(((.((((--(..(((((....)))))..))))).)))))............. ( -31.10)
>consensus
GUU_______GGCAAUGAGGCUUUUUGCCUUACUUC_UGGUGAAGGUUGCUCACUUAAGGAGUUAUCUUA_GCUUGUAUUCCUGUAUUUCU_UGGAAGCCCAAAUUGUUUUCUU
..........((((((..((.....................................((((((...(........).))))))...((((...))))..))..))))))..... ( -3.78 =  -4.62 +   0.84)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,872,479 – 6,872,583
Length 104
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 75.95
Mean single sequence MFE -17.75
Consensus MFE -2.42
Energy contribution -1.90
Covariance contribution -0.52
Combinations/Pair 1.50
Mean z-score -1.47
Structure conservation index 0.14
SVM decision value 0.07
SVM RNA-class probability 0.566966
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6872479 104 - 27905053
AAGAAAACAAUUUGGCAUUCCA-AGAAAUACAGGAAUACAAG--UAGGAUAACUCCUUAAGUAAGCAACCUUCACCUUGAAGUAAGCUAAAAAGCCUCAUUGCC-------AAC
.......((((..(((.((((.-.........))))(((...--.((((....))))...)))(((...((((.....))))...))).....)))..))))..-------... ( -18.90)
>DroSec_CAF1 26734 104 - 1
AAGAAAACAAUUUGGCUUUCCA-AGAAAUACAGGAAUACAAGCAUAAGAUAACUCCUUAAGUGAGCAACCUUCACCA-GAAUA-AACCAAAAAGCCUUAUUGCC-------AAC
.......((((..((((((...-........((((..................))))...(((((.....)))))..-.....-......))))))..))))..-------... ( -14.57)
>DroSim_CAF1 27034 89 - 1
AAGAAAACAAUUUGGACUUCCA-AGAAAUACAGGAAUACAAGCAUAAGAUAACUCCUUAAGUGAGCAACCUUCACCA-GAAGU-AA---------------GCC-------AAC
..........(((((....)))-)).......((..(((.....((((.......)))).(((((.....)))))..-...))-).---------------.))-------... ( -12.70)
>DroEre_CAF1 27685 103 - 1
AAAAAAACAGUUUGGGCUUUCA-AGAAAUACAGAAGUACAAAC--AAGAUUACUCCUUAAGUGAGAAAAUAGCGACA-GAGUUAAGGCCAAAAGCCUCAUUGCC-------AAC
.........(((((..((((..-(....)...))))..)))))--..............(((((.....((((....-..)))).(((.....))))))))...-------... ( -16.10)
>DroYak_CAF1 27399 111 - 1
AAAAAAACAAUUUGGGCUUUCUUGGAAAUACAGGAAUACCAGC--AAGAUAACGCCUUAAGUGAGCAACCUGCGCCA-GAGGUAAGGCAAAAAGCCUCAUUGCCAAUUGCCAAC
.......((((((((...((((((......))))))..)))((--((......(((((..(((((....)).)))..-))))).((((.....))))..)))).)))))..... ( -26.50)
>consensus
AAGAAAACAAUUUGGCCUUCCA_AGAAAUACAGGAAUACAAGC_UAAGAUAACUCCUUAAGUGAGCAACCUUCACCA_GAAGUAAGCCAAAAAGCCUCAUUGCC_______AAC
..........((((...((((...........))))..))))........................................................................ ( -2.42 =  -1.90 +  -0.52)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:31 2006