Locus 2009

Sequence ID 2L_DroMel_CAF1
Location 5,448,128 – 5,448,255
Length 127
Max. P 0.934480
window3234 window3235 window3236

overview

Window 4

Location 5,448,128 – 5,448,220
Length 92
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 81.73
Mean single sequence MFE -18.05
Consensus MFE -11.36
Energy contribution -11.42
Covariance contribution 0.06
Combinations/Pair 1.17
Mean z-score -2.09
Structure conservation index 0.63
SVM decision value 0.38
SVM RNA-class probability 0.714152
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5448128 92 + 22407834
UAAAAAAAGAC-CGCGUCCUUCUUGGGUUUAUUUUAUU-----UUUUUUUUGUGUUCGCUUUCGCUUAUCUUUAACUGCCAUCAACAAGAUGGCAACU
.....(((((.-.((((((.....)))...........-----........((....))...)))...)))))...(((((((.....)))))))... ( -17.20)
>DroPse_CAF1 79902 87 + 1
UAAAAAAAAACUCGCGUCCUGCUUGGGUUUUU---GUU-----UUGUUUU---UUUCGCUUUCGCUUAUCUUUAACUGCCAUCAACAAGAUGGCAACU
((((((((((((((.(.....).)))))))))---.))-----)))....---....((....))...........(((((((.....)))))))... ( -18.60)
>DroSec_CAF1 67686 93 + 1
UAAAAAAAGAC-CGCGUCCUUCUUGGGUUUAUUU-A---UUUUUUUUUUUCGUGUUCGCUUUCGCUUAUCUUUAACUGCCAUCAACAAGAUGGCAACU
.....(((((.-.((((((.....))).......-.---............((....))...)))...)))))...(((((((.....)))))))... ( -17.50)
>DroEre_CAF1 68597 89 + 1
UAAA-AAAGUC-CGCGUCCUUCUUGGGUUUAUUUUAUUUU-------UUUUGUGUUCGCUUUCGCUUAUCUUUAACUGCCAUCAACAAGAUGGCAACU
....-((((..-.((((((.....))).............-------....((....))...)))....))))...(((((((.....)))))))... ( -15.80)
>DroWil_CAF1 98883 88 + 1
UACG-AAAACU-CGGAUACUGCUUACAUUUUUUUCC-------CCGUUUUCGU-UUCGUUUUCGCUUAUCUUUAACUGCCAUCAACAAGAUGGCAACU
.(((-(((((.-.(((.................)))-------..))))))))-......................(((((((.....)))))))... ( -20.63)
>DroPer_CAF1 79484 87 + 1
UAAAAAAAAACUCGCGUCCUGCUUGGGUUUUU---GUU-----UUGUUUU---UUUCGCUUUCGCUUAUCUUUAACUGCCAUCAACAAGAUGGCAACU
((((((((((((((.(.....).)))))))))---.))-----)))....---....((....))...........(((((((.....)))))))... ( -18.60)
>consensus
UAAAAAAAAAC_CGCGUCCUGCUUGGGUUUAUUU_AUU_____UUGUUUU_GUGUUCGCUUUCGCUUAUCUUUAACUGCCAUCAACAAGAUGGCAACU
................(((.....)))..............................((....))...........(((((((.....)))))))... (-11.36 = -11.42 +   0.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,448,128 – 5,448,220
Length 92
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 81.73
Mean single sequence MFE -21.60
Consensus MFE -15.78
Energy contribution -16.00
Covariance contribution 0.22
Combinations/Pair 1.13
Mean z-score -3.04
Structure conservation index 0.73
SVM decision value 1.24
SVM RNA-class probability 0.934480
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5448128 92 - 22407834
AGUUGCCAUCUUGUUGAUGGCAGUUAAAGAUAAGCGAAAGCGAACACAAAAAAAA-----AAUAAAAUAAACCCAAGAAGGACGCG-GUCUUUUUUUA
..((((((((.....))))))))..........((....))..............-----..............(((((((((...-))))))))).. ( -21.80)
>DroPse_CAF1 79902 87 - 1
AGUUGCCAUCUUGUUGAUGGCAGUUAAAGAUAAGCGAAAGCGAAA---AAAACAA-----AAC---AAAAACCCAAGCAGGACGCGAGUUUUUUUUUA
..((((((((.....))))))))..........((....))((((---((((...-----...---......((.....))((....)))))))))). ( -21.30)
>DroSec_CAF1 67686 93 - 1
AGUUGCCAUCUUGUUGAUGGCAGUUAAAGAUAAGCGAAAGCGAACACGAAAAAAAAAAA---U-AAAUAAACCCAAGAAGGACGCG-GUCUUUUUUUA
..((((((((.....))))))))..........((....))..................---.-..........(((((((((...-))))))))).. ( -21.80)
>DroEre_CAF1 68597 89 - 1
AGUUGCCAUCUUGUUGAUGGCAGUUAAAGAUAAGCGAAAGCGAACACAAAA-------AAAAUAAAAUAAACCCAAGAAGGACGCG-GACUUU-UUUA
..((((((((.....))))))))..........((....))..........-------................((((((......-..))))-)).. ( -19.10)
>DroWil_CAF1 98883 88 - 1
AGUUGCCAUCUUGUUGAUGGCAGUUAAAGAUAAGCGAAAACGAA-ACGAAAACGG-------GGAAAAAAAUGUAAGCAGUAUCCG-AGUUUU-CGUA
..((((((((.....)))))))).....................-((((((((..-------(((.(....((....)).).))).-.)))))-))). ( -24.30)
>DroPer_CAF1 79484 87 - 1
AGUUGCCAUCUUGUUGAUGGCAGUUAAAGAUAAGCGAAAGCGAAA---AAAACAA-----AAC---AAAAACCCAAGCAGGACGCGAGUUUUUUUUUA
..((((((((.....))))))))..........((....))((((---((((...-----...---......((.....))((....)))))))))). ( -21.30)
>consensus
AGUUGCCAUCUUGUUGAUGGCAGUUAAAGAUAAGCGAAAGCGAACAC_AAAACAA_____AAU_AAAAAAACCCAAGAAGGACGCG_GUCUUUUUUUA
..((((((((.....))))))))..........((....)).....................................(((((....)))))...... (-15.78 = -16.00 +   0.22)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,448,151 – 5,448,255
Length 104
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 81.45
Mean single sequence MFE -22.67
Consensus MFE -17.70
Energy contribution -18.20
Covariance contribution 0.50
Combinations/Pair 1.06
Mean z-score -2.32
Structure conservation index 0.78
SVM decision value 1.07
SVM RNA-class probability 0.909673
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5448151 104 - 22407834
GCUGUGUAGGGAAAACAUUAUGGCGCGCGAACGGAAGUUGCCAUCUUGUUGAUGGCAGUUAAAGAUAAGCGAAAGCGAACACAAAAAAAA-----AAUAAAAUAAACCC
..(((((.............((((.....(((....)))((((((.....)))))).)))).......((....))..))))).......-----.............. ( -25.40)
>DroGri_CAF1 105513 95 - 1
UCUAUGUAGAGAAAACAUUAUGGCGCGCGAACGGAAGUUGCCAUCUUGUUGAUGGCAGUUAAAGAUAAGCACAAAAAAAGCUAAAAACAAA--AAAA------------
....................((((.....(((....)))((((((.....)))))).......................))))........--....------------ ( -18.10)
>DroSec_CAF1 67709 105 - 1
GCUGUGUAGGGAAAACAUUAUGGCGCGCGAACGGAAGUUGCCAUCUUGUUGAUGGCAGUUAAAGAUAAGCGAAAGCGAACACGAAAAAAAAAAA---U-AAAUAAACCC
..(((((.............((((.....(((....)))((((((.....)))))).)))).......((....))..)))))...........---.-.......... ( -24.70)
>DroEre_CAF1 68619 102 - 1
GCUGUGUAGGGAAAACAUUAUGGCGCGCGAACGGAAGUUGCCAUCUUGUUGAUGGCAGUUAAAGAUAAGCGAAAGCGAACACAAAA-------AAAAUAAAAUAAACCC
..(((((.............((((.....(((....)))((((((.....)))))).)))).......((....))..)))))...-------................ ( -25.40)
>DroMoj_CAF1 110432 103 - 1
UCUAUGUAGAGAAAACAUUAUGGCGCGCGAACGGAAGUUGCCAUCUUGUUGAUGGCAGUUAAAGAUAAGCACACAAAA---UAAAAACAAC--AAAA-AAAGUAAAUAC
.................((((.(.(.((.(((....)))((((((.....))))))............)).).)...)---))).......--....-........... ( -17.90)
>DroPer_CAF1 79508 96 - 1
GCU--GCAGAGAAAACAUUAUGGCGCGCGAACGGAAGUUGCCAUCUUGUUGAUGGCAGUUAAAGAUAAGCGAAAGCGAAA---AAAACAA-----AAC---AAAAACCC
(((--((......((((..((((((.....((....))))))))..))))....))))).........((....))....---.......-----...---........ ( -24.50)
>consensus
GCUGUGUAGAGAAAACAUUAUGGCGCGCGAACGGAAGUUGCCAUCUUGUUGAUGGCAGUUAAAGAUAAGCGAAAGCGAACACAAAAACAA___A_AAU_AAAUAAACCC
((((((..(......)..))))))..((.(((....)))((((((.....))))))............))....................................... (-17.70 = -18.20 +   0.50)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:03 2006