Locus 2425

Sequence ID 3R_DroMel_CAF1
Location 6,764,956 – 6,765,269
Length 313
Max. P 0.999879
window3952 window3953 window3954 window3955 window3956

overview

Window 2

Location 6,764,956 – 6,765,076
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.42
Mean single sequence MFE -33.72
Consensus MFE -28.51
Energy contribution -29.22
Covariance contribution 0.71
Combinations/Pair 1.08
Mean z-score -1.35
Structure conservation index 0.85
SVM decision value 0.27
SVM RNA-class probability 0.660672
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6764956 120 - 27905053
CGUUGGCGCAAAACACAAAGGUGCGAGAAACUCAAAACGCGUCGAAAACAGGGUGCUGAGUGCCGGCAGCAUGCACGUGUAUGCAUUUAAAAAUGUACCGUGUGCGUUUUAAUUUUCCCA
..(((((((....(((....))).(((...))).....))))))).....((((((((.....)))))((((((....)))))).....(((((((((...)))))))))......))). ( -36.00)
>DroSec_CAF1 29068 120 - 1
CGUUGGCGCAAAACACAAAGGUGCGAGAAACUCAAAACGCGUCGAAAACAGGGUGCUGAGUGCCGGCAGCAUGCACGUGUAUGCAUUUAAAAAUGUACCGUGUGCGUUUUAAUUUUCCCA
..(((((((....(((....))).(((...))).....))))))).....((((((((.....)))))((((((....)))))).....(((((((((...)))))))))......))). ( -36.00)
>DroSim_CAF1 33579 120 - 1
CGUUGGUGCAAAACACAAAGGUGCGAGAAACUCAAAACGCGUCAAAAACAGGGUGCUGAGUGCCGGCAGCAUGCACGUGUAUGCAUUUAAAAAUGUACCGUGUGCGUUUUAAUUUUCCCA
..(((..((....(((....))).(((...))).....))..))).....((((((((.....)))))((((((....)))))).....(((((((((...)))))))))......))). ( -32.30)
>DroEre_CAF1 13897 120 - 1
CGUUGGCGCAAAACACAAAGGUGCGAGAAACUCGAAACGCGUCGAAAACAGGGUGCUGAGUGCCGGCACCAUGCACGUGUAUGCAUUUAAAAAUGUACCGUGUGCGUUUUAAUUUUCCCA
...((((((....(((....)))((((...))))....))))))(((((..(((((((.....)))))))..(((((((..((((((....)))))).)))))))))))).......... ( -37.50)
>DroYak_CAF1 25935 106 - 1
CGUUGGCGCAAAACACAAAGGUGCGAGAAACUCAAAACGCCUCGAAAACAGGGUG--------------UAUGCACGUGUAUGCAUUUAAAAAUGUACCGUGUGCGUUUUAAUUUUCCCA
((..((((.....(((....))).(((...)))....)))).))......(((((--------------(((((....)))))))....(((((((((...)))))))))......))). ( -26.80)
>consensus
CGUUGGCGCAAAACACAAAGGUGCGAGAAACUCAAAACGCGUCGAAAACAGGGUGCUGAGUGCCGGCAGCAUGCACGUGUAUGCAUUUAAAAAUGUACCGUGUGCGUUUUAAUUUUCCCA
..(((((((....(((....))).(((...))).....))))))).....((((((((.....)))))((((((....)))))).....(((((((((...)))))))))......))). (-28.51 = -29.22 +   0.71)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,764,996 – 6,765,116
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.08
Mean single sequence MFE -32.50
Consensus MFE -26.01
Energy contribution -26.32
Covariance contribution 0.31
Combinations/Pair 1.09
Mean z-score -1.54
Structure conservation index 0.80
SVM decision value 0.27
SVM RNA-class probability 0.663764
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6764996 120 - 27905053
UGCAAGUCAAGCGUUUGACAAACUUUAUGUUAAAAAUUGACGUUGGCGCAAAACACAAAGGUGCGAGAAACUCAAAACGCGUCGAAAACAGGGUGCUGAGUGCCGGCAGCAUGCACGUGU
((((.(((((...(((((((.......)))))))..)))))((((((((..........(..(((............)))..).....(((....))).))))))))....))))..... ( -34.80)
>DroSec_CAF1 29108 120 - 1
UGCAAGUCAAGCGUUUGACAAACUUUAUGUGAAAAAUUGACGUUGGCGCAAAACACAAAGGUGCGAGAAACUCAAAACGCGUCGAAAACAGGGUGCUGAGUGCCGGCAGCAUGCACGUGU
((((.(((((...(((.(((.......))).)))..)))))((((((((..........(..(((............)))..).....(((....))).))))))))....))))..... ( -32.90)
>DroSim_CAF1 33619 120 - 1
UGCAAGUCAAGCGUUUGACAAACUUUAUGUGAAAAAUUGACGUUGGUGCAAAACACAAAGGUGCGAGAAACUCAAAACGCGUCAAAAACAGGGUGCUGAGUGCCGGCAGCAUGCACGUGU
((((.(((((...(((.(((.......))).)))..)))))(((((..(..........(..(((............)))..).....(((....))).)..)))))....))))..... ( -30.50)
>DroEre_CAF1 13937 120 - 1
UGCAAGUCAAGCGUUUGACAAACUUUAUGUGAAAAAUUGACGUUGGCGCAAAACACAAAGGUGCGAGAAACUCGAAACGCGUCGAAAACAGGGUGCUGAGUGCCGGCACCAUGCACGUGU
((((.(((((...(((.(((.......))).)))..))))).(((((((....(((....)))((((...))))....)))))))......(((((((.....))))))).))))..... ( -38.10)
>DroYak_CAF1 25975 106 - 1
UGCAAGUCAAGCGUUUGACAAACUUUAUGUGAAAAAUUGACGUUGGCGCAAAACACAAAGGUGCGAGAAACUCAAAACGCCUCGAAAACAGGGUG--------------UAUGCACGUGU
.((..(((((...(((.(((.......))).)))..)))))....)).....((((....(((((((...)))...((((((........)))))--------------)..)))))))) ( -26.20)
>consensus
UGCAAGUCAAGCGUUUGACAAACUUUAUGUGAAAAAUUGACGUUGGCGCAAAACACAAAGGUGCGAGAAACUCAAAACGCGUCGAAAACAGGGUGCUGAGUGCCGGCAGCAUGCACGUGU
((((.(((((...(((.(((.......))).)))..))))).(((((((....(((....))).(((...))).....)))))))......(.(((((.....))))).).))))..... (-26.01 = -26.32 +   0.31)

alignment

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secondary structure

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Window 4

Location 6,765,116 – 6,765,229
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.99
Mean single sequence MFE -41.22
Consensus MFE -38.90
Energy contribution -39.54
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -2.46
Structure conservation index 0.94
SVM decision value 4.35
SVM RNA-class probability 0.999879
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6765116 113 + 27905053
UAUAAAUGAGUUGGCCGGAACCGGAAAA-------UGGAAAGCGGAGCCACUGGGAAAGCCCCUCGAAGGUGGCGACCCAGGUGAGGGCUCCCAAAAGCAUUCGAGUUGUCAACUCAUUC
....(((((((((((((....)).....-------..(((.((((((((.(((((...(((((.....)).)))..))))).....)))))).....)).))).....))))))))))). ( -46.40)
>DroSec_CAF1 29228 113 + 1
UAUAAAUGAGUUGGCCGGAACCGGAAAA-------UGGAAAGCGGAGCCACUGGGAAAGCCCCUCGAAGGUGGCGACCCAGGUGAGGGCUCCCAAAAGCAUUCGAGUUGUCAACUCUUUC
.......((((((((((....)).....-------..(((.((((((((.(((((...(((((.....)).)))..))))).....)))))).....)).))).....)))))))).... ( -43.60)
>DroSim_CAF1 33739 113 + 1
UAUAAAUGAGUUGGCCGGAACCGGAAAA-------UGGAAAGCGGAGCCACCGGGAAAGCCCCUCGAAGGUGGCGACCCAGGUGAGGGCUCCCAAAAGCAUUCGAGUUGUCAACUCUUUC
.......((((((((((....)).....-------..(((.((((((((((((((...(((((.....)).)))..))).)))...)))))).....)).))).....)))))))).... ( -41.60)
>DroEre_CAF1 14057 113 + 1
UAUAAAUGAGUUGGCCGGAACCGGAAAA-------UGGAAAGCGGAGCCACUGAGAAAGCCCCUCGAAGGCGGCGACCCAGGUGAGGGCUCCCAAAAGCAUUCGAGUUGUCAACUCUUUC
.......((((((((((....)).....-------..(((.((((((((.(((.(...(((((.....)).)))...)))).....)))))).....)).))).....)))))))).... ( -36.80)
>DroYak_CAF1 26081 120 + 1
UAUAAAUGAGUUGGCCGGAAACGGAAAAUGGAAAAUGGAAAGCGGGGCCACUGAGAAAGCCCCUCGAAAGUGGCGACCCAGGUGAGGGCUCCCAAAAGCAUUCGAGUUGUCAACUCUUUC
.......((((((((((....))..............(((.(((((((..........))))).......(((.(((((......))).)))))...)).))).....)))))))).... ( -37.70)
>consensus
UAUAAAUGAGUUGGCCGGAACCGGAAAA_______UGGAAAGCGGAGCCACUGGGAAAGCCCCUCGAAGGUGGCGACCCAGGUGAGGGCUCCCAAAAGCAUUCGAGUUGUCAACUCUUUC
.......((((((((((....))..............(((.((((((((.(((((...(((((.....)).)))..))))).....)))))).....)).))).....)))))))).... (-38.90 = -39.54 +   0.64)

alignment

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secondary structure

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Window 5

Location 6,765,116 – 6,765,229
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.99
Mean single sequence MFE -39.32
Consensus MFE -37.14
Energy contribution -36.78
Covariance contribution -0.36
Combinations/Pair 1.10
Mean z-score -2.34
Structure conservation index 0.94
SVM decision value 4.13
SVM RNA-class probability 0.999809
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6765116 113 - 27905053
GAAUGAGUUGACAACUCGAAUGCUUUUGGGAGCCCUCACCUGGGUCGCCACCUUCGAGGGGCUUUCCCAGUGGCUCCGCUUUCCA-------UUUUCCGGUUCCGGCCAACUCAUUUAUA
((((((((((.......(((.((.....((((((.....(((((..(((.((.....)))))...))))).)))))))).)))..-------....(((....))).))))))))))... ( -43.60)
>DroSec_CAF1 29228 113 - 1
GAAAGAGUUGACAACUCGAAUGCUUUUGGGAGCCCUCACCUGGGUCGCCACCUUCGAGGGGCUUUCCCAGUGGCUCCGCUUUCCA-------UUUUCCGGUUCCGGCCAACUCAUUUAUA
....((((((.......(((.((.....((((((.....(((((..(((.((.....)))))...))))).)))))))).)))..-------....(((....))).))))))....... ( -39.90)
>DroSim_CAF1 33739 113 - 1
GAAAGAGUUGACAACUCGAAUGCUUUUGGGAGCCCUCACCUGGGUCGCCACCUUCGAGGGGCUUUCCCGGUGGCUCCGCUUUCCA-------UUUUCCGGUUCCGGCCAACUCAUUUAUA
....((((((.......(((.((.....((((((...(((.(((..(((.((.....)))))...)))))))))))))).)))..-------....(((....))).))))))....... ( -40.10)
>DroEre_CAF1 14057 113 - 1
GAAAGAGUUGACAACUCGAAUGCUUUUGGGAGCCCUCACCUGGGUCGCCGCCUUCGAGGGGCUUUCUCAGUGGCUCCGCUUUCCA-------UUUUCCGGUUCCGGCCAACUCAUUUAUA
....((((((.......(((.((.....((((((.....(((((..(((.((.....)))))...))))).)))))))).)))..-------....(((....))).))))))....... ( -36.90)
>DroYak_CAF1 26081 120 - 1
GAAAGAGUUGACAACUCGAAUGCUUUUGGGAGCCCUCACCUGGGUCGCCACUUUCGAGGGGCUUUCUCAGUGGCCCCGCUUUCCAUUUUCCAUUUUCCGUUUCCGGCCAACUCAUUUAUA
....((((((.......(((.((...(((..((((......))))..))).......((((((........)))))))).))).............(((....))).))))))....... ( -36.10)
>consensus
GAAAGAGUUGACAACUCGAAUGCUUUUGGGAGCCCUCACCUGGGUCGCCACCUUCGAGGGGCUUUCCCAGUGGCUCCGCUUUCCA_______UUUUCCGGUUCCGGCCAACUCAUUUAUA
....((((((.......(((.((.....((((((.....(((((..(((.((.....)))))...))))).)))))))).))).............(((....))).))))))....... (-37.14 = -36.78 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,765,149 – 6,765,269
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.00
Mean single sequence MFE -41.46
Consensus MFE -38.88
Energy contribution -38.76
Covariance contribution -0.12
Combinations/Pair 1.11
Mean z-score -1.27
Structure conservation index 0.94
SVM decision value 0.55
SVM RNA-class probability 0.776732
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6765149 120 - 27905053
UCGCCAGUUCGGUUCUCAAGCUCAAAAUGUAAUGCACGUUGAAUGAGUUGACAACUCGAAUGCUUUUGGGAGCCCUCACCUGGGUCGCCACCUUCGAGGGGCUUUCCCAGUGGCUCCGCU
..((..((((((((.((((.((((.(((((.....)))))...)))))))).))).))))).......((((((.....(((((..(((.((.....)))))...))))).)))))))). ( -44.90)
>DroSec_CAF1 29261 120 - 1
UCGCCAGUUUGGUUCUCAAGCUCAAAAUGUAAUGCACGUUGAAAGAGUUGACAACUCGAAUGCUUUUGGGAGCCCUCACCUGGGUCGCCACCUUCGAGGGGCUUUCCCAGUGGCUCCGCU
..((((....(((((((((((((((..((.....))..))))..((((.....))))....)))..)))))))).....(((((..(((.((.....)))))...)))))))))...... ( -42.00)
>DroSim_CAF1 33772 120 - 1
UCGCCAGUUCGGUUCUCAAGCUCAAAAUGUAAUGCACGUUGAAAGAGUUGACAACUCGAAUGCUUUUGGGAGCCCUCACCUGGGUCGCCACCUUCGAGGGGCUUUCCCGGUGGCUCCGCU
..((..((((((((.((((.(((..(((((.....)))))....))))))).))).))))).......((((((...(((.(((..(((.((.....)))))...)))))))))))))). ( -43.40)
>DroEre_CAF1 14090 120 - 1
UCGCCAGUUCGGUUCUCAAGCUGAAAAUGUAAUGCACGUUGAAAGAGUUGACAACUCGAAUGCUUUUGGGAGCCCUCACCUGGGUCGCCGCCUUCGAGGGGCUUUCUCAGUGGCUCCGCU
..((..((((((((.((((.((...(((((.....)))))...))..)))).))).))))).......((((((.....(((((..(((.((.....)))))...))))).)))))))). ( -39.20)
>DroYak_CAF1 26121 120 - 1
UCGCCAGUUCGGUUCUCAAGCUGAAAAUGUAAUGCACGUUGAAAGAGUUGACAACUCGAAUGCUUUUGGGAGCCCUCACCUGGGUCGCCACUUUCGAGGGGCUUUCUCAGUGGCCCCGCU
......((((((((.((((.((...(((((.....)))))...))..)))).))).)))))((...(((..((((......))))..))).......((((((........)))))))). ( -37.80)
>consensus
UCGCCAGUUCGGUUCUCAAGCUCAAAAUGUAAUGCACGUUGAAAGAGUUGACAACUCGAAUGCUUUUGGGAGCCCUCACCUGGGUCGCCACCUUCGAGGGGCUUUCCCAGUGGCUCCGCU
..((..((((((((.((((.(((..(((((.....)))))....))))))).))).))))).......((((((.....(((((..(((.((.....)))))...))))).)))))))). (-38.88 = -38.76 +  -0.12)

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 10:35:42 2006