Locus 2004

Sequence ID 2R_DroMel_CAF1
Location 7,543,487 – 7,543,664
Length 177
Max. P 0.999134
window3306 window3307 window3308 window3309 window3310

overview

Window 6

Location 7,543,487 – 7,543,592
Length 105
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 95.27
Mean single sequence MFE -31.10
Consensus MFE -29.14
Energy contribution -29.58
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.41
Structure conservation index 0.94
SVM decision value 1.28
SVM RNA-class probability 0.940054
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7543487 105 + 20766785
CUUUUGAACGCGGGCAAUUCCGUUACAGCGUUUGCCGGCUCCAGGUGCCAAUAAUUGUGCAAUUAUCUUUAUCCUAUGUUUGCACUUCUUGCGCCGCGACGGCUA--
.....((((((.(((......)))...))))))((((......(((((........((((((.................)))))).....)))))....))))..-- ( -29.25)
>DroSec_CAF1 1733 105 + 1
UUUUUGAACGCGGGCAAUUCCGUUACAGCGUUUGCCGGCUGCAGGUGCCAAUAAUUGUGCAAUUAUCUUUAUCCUAUGUUUGCACUUCUUGCGCCGAGACGGCUA--
.....((((((.(((......)))...))))))((((.((...(((((........((((((.................)))))).....))))).)).))))..-- ( -29.95)
>DroSim_CAF1 1741 105 + 1
UUUUUGAACGCGGGCAAUUCCGUUACAGCGUUUGCCGGCUGCAGGUGCCAAUAAUUGUGCAAUUAUCUUUAUCCUAUGUUUGCACUUCUUGCGCCGCGACGGCUA--
.....((((((.(((......)))...))))))((((..(((.(((((........((((((.................)))))).....)))))))).))))..-- ( -32.55)
>DroEre_CAF1 4627 107 + 1
CUUUUGAACGCGGGCAAUUCCGUUACGGCUUUUGCCGGCUGCAGGUGCCAAUAAUUGUGCAAUUAUCUUUAUCUUAUGUUUGCACUUCUUGCGCCGCGACGGCAAUU
.........(((((....)))))..((((....))))(((((.(((((........((((((.................)))))).....)))))..).)))).... ( -30.85)
>DroYak_CAF1 1738 105 + 1
CUUUUGAACGCGGGCAAUUCCGUUACGGCGUUUGCCGGCUGCAGGUGCCAAUAAUUGUGCAAUUAUCUUUAUCCUAUGCUUGCACUUCUUGCGCCGCAACGGCAA--
.....((((((.(............).))))))((((..(((.(((((........((((((.(((.........))).)))))).....)))))))).))))..-- ( -32.92)
>consensus
CUUUUGAACGCGGGCAAUUCCGUUACAGCGUUUGCCGGCUGCAGGUGCCAAUAAUUGUGCAAUUAUCUUUAUCCUAUGUUUGCACUUCUUGCGCCGCGACGGCUA__
.....((((((.(((......)))...))))))((((..(((.(((((........((((((.(((.........))).)))))).....)))))))).)))).... (-29.14 = -29.58 +   0.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,543,487 – 7,543,592
Length 105
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 95.27
Mean single sequence MFE -28.54
Consensus MFE -25.81
Energy contribution -25.77
Covariance contribution -0.04
Combinations/Pair 1.05
Mean z-score -1.16
Structure conservation index 0.90
SVM decision value 0.11
SVM RNA-class probability 0.587044
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7543487 105 - 20766785
--UAGCCGUCGCGGCGCAAGAAGUGCAAACAUAGGAUAAAGAUAAUUGCACAAUUAUUGGCACCUGGAGCCGGCAAACGCUGUAACGGAAUUGCCCGCGUUCAAAAG
--.....(.(((((.((((...((((..............(((((((....))))))).))))(((..((.(((....)))))..)))..)))))))))..)..... ( -26.96)
>DroSec_CAF1 1733 105 - 1
--UAGCCGUCUCGGCGCAAGAAGUGCAAACAUAGGAUAAAGAUAAUUGCACAAUUAUUGGCACCUGCAGCCGGCAAACGCUGUAACGGAAUUGCCCGCGUUCAAAAA
--..((((...))))((.....((((((.................)))))).......((((((((((((.(.....)))))))..))...)))).))......... ( -26.33)
>DroSim_CAF1 1741 105 - 1
--UAGCCGUCGCGGCGCAAGAAGUGCAAACAUAGGAUAAAGAUAAUUGCACAAUUAUUGGCACCUGCAGCCGGCAAACGCUGUAACGGAAUUGCCCGCGUUCAAAAA
--.....(.(((((.((((...((((((.................))))))...........((((((((.(.....)))))))..))..)))))))))..)..... ( -28.13)
>DroEre_CAF1 4627 107 - 1
AAUUGCCGUCGCGGCGCAAGAAGUGCAAACAUAAGAUAAAGAUAAUUGCACAAUUAUUGGCACCUGCAGCCGGCAAAAGCCGUAACGGAAUUGCCCGCGUUCAAAAG
..(((....(((((.((((...((((((.................)))))).......(((.......)))(((....))).........)))))))))..)))... ( -28.73)
>DroYak_CAF1 1738 105 - 1
--UUGCCGUUGCGGCGCAAGAAGUGCAAGCAUAGGAUAAAGAUAAUUGCACAAUUAUUGGCACCUGCAGCCGGCAAACGCCGUAACGGAAUUGCCCGCGUUCAAAAG
--...(((((((((((......((((((.................)))))).....(((((.......)))))....)))))))))))................... ( -32.53)
>consensus
__UAGCCGUCGCGGCGCAAGAAGUGCAAACAUAGGAUAAAGAUAAUUGCACAAUUAUUGGCACCUGCAGCCGGCAAACGCUGUAACGGAAUUGCCCGCGUUCAAAAG
.....((((..(((((......((((((.................)))))).....(((((.......)))))....)))))..))))................... (-25.81 = -25.77 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,543,516 – 7,543,627
Length 111
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 94.55
Mean single sequence MFE -38.18
Consensus MFE -33.12
Energy contribution -33.00
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -2.64
Structure conservation index 0.87
SVM decision value 3.39
SVM RNA-class probability 0.999134
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7543516 111 + 20766785
GUUUGCCGGCUCCAGGUGCCAAUAAUUGUGCAAUUAUCUUUAUCCUAUGUUUGCACUUCUUGCGCCGCGACGGCUA-------UGUGGCAACGCUACAGCUGUUUGCCAAGCACAACA
((((((.(((....(((((........((((((.................)))))).....)))))..(((((((.-------.(((....)))...))))))).)))..))).))). ( -35.35)
>DroSec_CAF1 1762 111 + 1
GUUUGCCGGCUGCAGGUGCCAAUAAUUGUGCAAUUAUCUUUAUCCUAUGUUUGCACUUCUUGCGCCGAGACGGCUA-------UGUGGCAACGCCACAGCUGUUUGCCAAGCACAACA
((((((.(((....(((((........((((((.................)))))).....))))).((((((((.-------.(((((...))))))))))))))))..))).))). ( -37.75)
>DroSim_CAF1 1770 111 + 1
GUUUGCCGGCUGCAGGUGCCAAUAAUUGUGCAAUUAUCUUUAUCCUAUGUUUGCACUUCUUGCGCCGCGACGGCUA-------UGUGGCAACGCCACAGCUGUUUGCCAAGCACAACA
((((((.(((.((.(((((........((((((.................)))))).....)))))))(((((((.-------.(((((...)))))))))))).)))..))).))). ( -38.25)
>DroEre_CAF1 4656 118 + 1
UUUUGCCGGCUGCAGGUGCCAAUAAUUGUGCAAUUAUCUUUAUCUUAUGUUUGCACUUCUUGCGCCGCGACGGCAAUUGGCAGUGUGGCAACGCCACAGCUGUUUGCCAAGCACAACA
..((((((..(((.(((((........((((((.................)))))).....)))))))).))))))(((((((((((((...)))))).....)))))))........ ( -41.55)
>DroYak_CAF1 1767 111 + 1
GUUUGCCGGCUGCAGGUGCCAAUAAUUGUGCAAUUAUCUUUAUCCUAUGCUUGCACUUCUUGCGCCGCAACGGCAA-------UGUGGCAACGCCACAGCUGUUUGCCAAGCACAACA
..((((((..(((.(((((........((((((.(((.........))).)))))).....)))))))).))))))-------((((((...))))))(((........)))...... ( -38.02)
>consensus
GUUUGCCGGCUGCAGGUGCCAAUAAUUGUGCAAUUAUCUUUAUCCUAUGUUUGCACUUCUUGCGCCGCGACGGCUA_______UGUGGCAACGCCACAGCUGUUUGCCAAGCACAACA
((((((.(((....(((((........((((((.(((.........))).)))))).....)))))..((((((.........((((((...)))))))))))).)))..))).))). (-33.12 = -33.00 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,543,516 – 7,543,627
Length 111
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 94.55
Mean single sequence MFE -34.61
Consensus MFE -31.21
Energy contribution -31.25
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.34
Structure conservation index 0.90
SVM decision value 0.76
SVM RNA-class probability 0.843688
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7543516 111 - 20766785
UGUUGUGCUUGGCAAACAGCUGUAGCGUUGCCACA-------UAGCCGUCGCGGCGCAAGAAGUGCAAACAUAGGAUAAAGAUAAUUGCACAAUUAUUGGCACCUGGAGCCGGCAAAC
.....((((.(((...(((.(((.(((((((.((.-------.....)).))))))).....((((((.................))))))........))).)))..)))))))... ( -33.43)
>DroSec_CAF1 1762 111 - 1
UGUUGUGCUUGGCAAACAGCUGUGGCGUUGCCACA-------UAGCCGUCUCGGCGCAAGAAGUGCAAACAUAGGAUAAAGAUAAUUGCACAAUUAUUGGCACCUGCAGCCGGCAAAC
((((((((...)))....((((..(.((.((((..-------..((((...)))).......((((((.................))))))......)))))))..)))))))))... ( -31.93)
>DroSim_CAF1 1770 111 - 1
UGUUGUGCUUGGCAAACAGCUGUGGCGUUGCCACA-------UAGCCGUCGCGGCGCAAGAAGUGCAAACAUAGGAUAAAGAUAAUUGCACAAUUAUUGGCACCUGCAGCCGGCAAAC
.....((((.(((.....(((((((((..((....-------..)))))))))))(((....((((..............(((((((....))))))).)))).))).)))))))... ( -33.96)
>DroEre_CAF1 4656 118 - 1
UGUUGUGCUUGGCAAACAGCUGUGGCGUUGCCACACUGCCAAUUGCCGUCGCGGCGCAAGAAGUGCAAACAUAAGAUAAAGAUAAUUGCACAAUUAUUGGCACCUGCAGCCGGCAAAA
.((((((..((((((.(((.((((((...)))))))))....)))))).))))))((.....((((((.................))))))......((((.......)))))).... ( -37.53)
>DroYak_CAF1 1767 111 - 1
UGUUGUGCUUGGCAAACAGCUGUGGCGUUGCCACA-------UUGCCGUUGCGGCGCAAGAAGUGCAAGCAUAGGAUAAAGAUAAUUGCACAAUUAUUGGCACCUGCAGCCGGCAAAC
.(((((.........)))))((((((...))))))-------((((((((((.((((.....))))......(((.....(((((((....)))))))....))))))).)))))).. ( -36.20)
>consensus
UGUUGUGCUUGGCAAACAGCUGUGGCGUUGCCACA_______UAGCCGUCGCGGCGCAAGAAGUGCAAACAUAGGAUAAAGAUAAUUGCACAAUUAUUGGCACCUGCAGCCGGCAAAC
((((((((...)))....(((((((.((.((((...........((((...)))).......((((((.................))))))......))))))))))))))))))... (-31.21 = -31.25 +   0.04)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,543,554 – 7,543,664
Length 110
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 90.06
Mean single sequence MFE -33.66
Consensus MFE -29.70
Energy contribution -29.34
Covariance contribution -0.36
Combinations/Pair 1.10
Mean z-score -1.29
Structure conservation index 0.88
SVM decision value 0.19
SVM RNA-class probability 0.627330
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7543554 110 + 20766785
UUUAUCCUAUGUUUGCACUUCUUGCGCCGCGACGGCUA-------UGUGGCAACGCUACAGCUGUUUGCCAAGCACAACAAACAAAAUUAGAGGUGAGCGCGUGAUUAGCACUAACU
..........((((((...((.(((((((((((((((.-------.(((....)))...)))))))(((...)))..................))).))))).))...)))..))). ( -29.70)
>DroSec_CAF1 1800 110 + 1
UUUAUCCUAUGUUUGCACUUCUUGCGCCGAGACGGCUA-------UGUGGCAACGCCACAGCUGUUUGCCAAGCACAACAAACAAAAUUAGAGGUGGGCGCGUGAUUAGCACUAACU
..........((((((...((.((((((.((((((((.-------.(((((...)))))))))))))......(((..(...........)..))))))))).))...)))..))). ( -32.70)
>DroSim_CAF1 1808 110 + 1
UUUAUCCUAUGUUUGCACUUCUUGCGCCGCGACGGCUA-------UGUGGCAACGCCACAGCUGUUUGCCAAGCACAACAAACAAAAUUAGAGGUGGGCGCGUGAUUAGCACUAACU
..........((((((...((.(((((((((((((((.-------.(((((...)))))))))).))))....(((..(...........)..))))))))).))...)))..))). ( -33.60)
>DroEre_CAF1 4694 116 + 1
UUUAUCUUAUGUUUGCACUUCUUGCGCCGCGACGGCAAUUGGCAGUGUGGCAACGCCACAGCUGUUUGCCAAGCACAACAAACAAAUGUGGAAGUGGGCGCGUGAUUAGGUCUAAC-
......((((((.(.((((((((((((((...))))..(((((((((((((...)))))).....))))))))))..(((......)))))))))).).))))))...........- ( -37.60)
>DroYak_CAF1 1805 109 + 1
UUUAUCCUAUGCUUGCACUUCUUGCGCCGCAACGGCAA-------UGUGGCAACGCCACAGCUGUUUGCCAAGCACAACAAACAAAUGUGGAGGUGGGGUCGUGAUUAGGACUACU-
....(((((......(((.(((..(((((((.......-------))))))..(.(((((..((((((..........))))))..))))).))..)))..)))..))))).....- ( -34.70)
>consensus
UUUAUCCUAUGUUUGCACUUCUUGCGCCGCGACGGCUA_______UGUGGCAACGCCACAGCUGUUUGCCAAGCACAACAAACAAAAUUAGAGGUGGGCGCGUGAUUAGCACUAACU
.......(((((.(.(((((((.((((((...)))).........((((((...))))))))((((((..........)))))).....))))))).).)))))............. (-29.70 = -29.34 +  -0.36)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:32 2006